Changelog¶

0.8.001 (2023-01-30)¶

[APERO] update README.md (move developer and main to v0.7.275) [Neil Cook]
[APERO] fix typo apero.science.telluric.gen_tellu.py - image.shape[0] –> range(image.shape[0]) [njcuk9999]
[APERO] update date / version / documentation. [Neil Cook]

0.7.290 (2024-04-05)¶

Update run.ini files. [Neil Cook]
[NIRPS] update pp_ref to give error when there are no LED files + mini_data to use engineering. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.290-live’ into v0.7.290-live. [Neil Cook]
[APERO] apero_ri - finder - allow connection problems (try again 10 times) [Neil Cook]
[APERO] fix problem with finder charts (sorted alphabetically for name not for table) - leads to wrong finder charts. [Neil Cook]
[APERO] apero_remove.py - allow multiple obsdir to be defined. [Neil Cook]
[APERO] apero_remove.py - allow multiple obsdir to be defined. [Neil Cook]
[APERO] apero_ri.py - fix problems with finding charts. [Neil Cook]
[APERO] tapas_all_sp.fits.gz - fix column name (duplicate ch_4 –> o_3) [Neil Cook]
[APERO] background fixes (both at the badpix calibration level and in the extraction code [from EA] [Neil Cook]
[APERO] apero_astrometrics.py - add a check for objects in database that all files match DRSOBJN to that expected by database. (Issue #756) [Neil Cook]
[APERO] apero_astrometrics.py - add a check for objects in database that all files match DRSOBJN to that expected by database. (Issue #756) [Neil Cook]
[APERO] apero_astrometrics.py - add a check for objects in database that all files match DRSOBJN to that expected by database. (Issue #756) [Neil Cook]
[APERO] apero_astrometrics.py - add a check for objects in database that all files match DRSOBJN to that expected by database. [Neil Cook]
[APERO] apero_remove add a –block and –objnames argument. [Neil Cook]
[APERO] Try to catch ARI errors in object page creation. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.289-live’ into v0.7.289-live. [Neil Cook]
[ARI] update forgot.html and index.html. [Neil Cook]
[NIRPS] Correct that preprocessing missing KW_PPVERSION key. [Neil Cook]
[ARI] add ari-home to resources/ari. [Neil Cook]
[ARI] add ari-home to resources/ari. [Neil Cook]
[ARI] add ari-home to resources/ari. [Neil Cook]
[ARI] must update the ari home page. [Neil Cook]
[ARI] fix page header. [Neil Cook]
[ARI] fix page header. [Neil Cook]
[ARI] fix page header. [Neil Cook]
[APERO] Fix apero_remove (boolean args should use switch) [Neil Cook]
[APERO] Fix apero_remove (boolean args should use switch) [Neil Cook]
[APERO] Fix the column names in tapas_all_sp.fits.gz (Issue #742) [Neil Cook]
[APERO] Make runstring work better implicit arguments like –nosave only present if used (previous had –nosave=False or –nosave=True) which makes runstring unusable without removing them manually. [Neil Cook]
[APERO] Add a header key CRUNFILE that gives the config run file used (if given) [Neil Cook]
[ARI] Edit html of recipe and finder pages. [Neil Cook]
[ARI] Edit html of recipe and finder pages. [Neil Cook]
[ARI] Edit html of recipe and finder pages. [Neil Cook]
[ARI] Edit html of recipe and finder pages. [Neil Cook]
[ARI] Add css to recipe and finder pages. [Neil Cook]
[APERO CHECKS] PREV_REDUC - need to not flag rejected files. [Neil Cook]
[ARI] Fix font css in ARI. [Neil Cook]
[ARI] Remove ARI sidebar. [Neil Cook]
[ARI] Add BERV to extracted 2D header file. [Neil Cook]
[APERO] update date/changelog. [Neil Cook]

0.7.289 (2024-03-12)¶

[APERO] correct typo. [Neil Cook]
[APERO] Add –objname to reject code (Issue https://github.com/users/n jcuk9999/projects/7/views/5?pane=issue&itemId=54972211) [Neil Cook]
[APERO] Add –identifier to reject code (Issue https://github.com/user s/njcuk9999/projects/7/views/5?pane=issue&itemId=54972211) [TODO: objname] [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.289-live’ into v0.7.289-live. [Neil Cook]
[APERO] update neesd ASK_CREATE. [Neil Cook]
[APERO] add ari-home content. [Neil Cook]
[APERO] add ari-home content. [Neil Cook]
[APERO] update ARI with new login procedure. [Neil Cook]
[APERO] update offline and minidata paths. [Neil Cook]
[APERO] Remove sys.exit and replace with WLOG(params, ‘error’, …) + raise SystemExit() [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.289-live’ into v0.7.289-live. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.289-live’ into v0.7.289-live. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.289-live’ into v0.7.289-live. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.289-live’ into v0.7.289-live. [Neil Cook]
[APERO] add extra object to tellu whitelist. [Neil Cook]
[APERO] bug fix - deal with recalculating templates when qc fails. [Neil Cook]
[APERO] astrometric check - write bad objects to file. [Neil Cook]
[APERO] add extra object to tellu whitelist. [Neil Cook]
[APERO] astrometric check - write bad objects to file. [Neil Cook]
[APERO] bug fix - deal with recalculating templates when qc fails (Issue https://github.com/njcuk9999/apero-utils/issues/218) [Neil Cook]
[APERO] fix typo. [Neil Cook]
[APERO] astrometric check - write bad objects to file. [Neil Cook]
[APERO] astrometric check - write bad objects to file. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.289-live’ into v0.7.289-live. [Neil Cook]
[APERO] fix teff source limit (Issue https://github.com/njcuk9999/apero-utils/issues/215) [Neil Cook]
[APERO] fix for having datadir defined and not LBL_PATH or DRS_DATA_OTHER - we didn’t create directories (Issue #748), also fixed dev mode for installation not working. [Neil Cook]
[APERO] bug fix - deal with no rows in table for astrometric pending table. [Neil Cook]
[APERO] upgrade requirements on mysql-connector-python to 8.3.0 (Issue #707) [Neil Cook]
[APERO] apero_remove.py - add apero_remove code to remove obs_dir and/or file prefix/suffix. [Neil Cook]
[APERO] apero.base.drs_db.py - corrections for duplicate and replace_paths functionality. [Neil Cook]
[APERO] add a duplicate and replace_paths function to the database classes (to support copying) [Neil Cook]
[APERO] database_update.py - remove some blank spaces. [Neil Cook]
Apero.science.telluric.gen_tellu.py - add wave mask to only reject snr in orders smaller than 1800um for all instruments. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.289-live’ into v0.7.289-live. [Neil Cook]
[APERO] update version/changelog/documentation. [Neil Cook]
[APERO-ARI] fix when we have no data adding dprtypes to object. [Neil Cook]
[APERO] apero_ri.py - Fix for unique values containing None. [Neil Cook]
[APERO] apero_ri.py - Fix for unique values containing None. [Neil Cook]
[APERO] apero_ri.py - Fix for unique values containing None. [Neil Cook]
[APERO] apero_ri.py - Fix for unique values containing None. [Neil Cook]
[APERO] add spirou_offline_udem profile to ARI. [Neil Cook]
[ARI] Add a reset to apero_ri.py. [Neil Cook]
[APERO] ari_core.py - add ari_user to all files/tables/graphs. [Neil Cook]
[APERO] TElluric airmass limit too low [was 3 now a ratio compared to the airmass] (Issue https://github.com/njcuk9999/apero- utils/issues/203) [Neil Cook]
Merge branch ‘main’ into v0.7.289-live. [Neil Cook]
[APERO] update due to security vulnerability. [Neil Cook]
Merge branch ‘main’ into v0.7.289-live. [Neil Cook]
Merge pull request #730 from njcuk9999/dependabot/pip/pillow-10.0.1. [Neil Cook]

Bump pillow from 9.5.0 to 10.0.1
Bump pillow from 9.5.0 to 10.0.1. [dependabot[bot]]

Bumps [pillow](https://github.com/python-pillow/Pillow) from 9.5.0 to 10.0.1. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](https://github.com/python-pillow/Pillow/compare/9.5.0…10.0.1)

— updated-dependencies: - dependency-name: pillow

dependency-type: direct:production

…
Merge pull request #731 from njcuk9999/dependabot/pip/gitpython-3.1.37. [Neil Cook]

Bump gitpython from 3.1.31 to 3.1.37
Bump gitpython from 3.1.31 to 3.1.37. [dependabot[bot]]

Bumps [gitpython](https://github.com/gitpython-developers/GitPython) from 3.1.31 to 3.1.37. - [Release notes](https://github.com/gitpython-developers/GitPython/releases) - [Changelog](https://github.com/gitpython-developers/GitPython/blob/main/CHANGES) - [Commits](https://github.com/gitpython-developers/GitPython/compare/3.1.31…3.1.37)

— updated-dependencies: - dependency-name: gitpython

dependency-type: direct:production

…
Merge remote-tracking branch ‘origin/v0.7.289-live’ into v0.7.289-live. [Neil Cook]
[APERO] ari-core.py - fix the lbl count on files. [Neil Cook]
[APERO] apero_ri - fix bug with finder charts. [Neil Cook]
[APERO-CHECKS] fix astrom_test (must update database) [Neil Cook]
Apero_prechecks: remove logging when log=False. [Neil Cook]
[APERO] apero_precheck.py - return a table and stop logging. [Neil Cook]
[APERO] install.py - fix problems with prompts when using all from command line arguments (Issue #743) [Neil Cook]
[APERO] ari_pages.py - try to correct pdf url in table. [Neil Cook]
[APERO] aeri_pages.py - try to correct pdf url in table. [Neil Cook]
[APERO] aeri_pages.py - make link to pdf. [Neil Cook]
[APERO] aeri_pages.py - make link to pdf. [Neil Cook]
[APERO] Fix that flat recipe writes E2DSLL when DEBUG_E2DSLL_FILE = False (Issue #740) [Neil Cook]
[APERO] Fix that wave recipes require the debug file to exist (to update their headers) Issue #740. [Neil Cook]
[APERO] Add DRS_DATA_OUT, DRS_DATA_OTHER and LBL_PATH to the startup printout (apero.core.utils.drs_startup.py) Issue #732. [Neil Cook]
[APERO] astrometrics - add properties from simbad (with preferred bibcodes) [Neil Cook]
[APERO] astrometrics - add properties from simbad (with preferred bibcodes) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.289-live’ into v0.7.289-live. [Neil Cook]
[APERO] fix plot_map1 argument (ari finding) [Neil Cook]
[APERO] fix bug in ARI_FINDER params. [Neil Cook]
[APERO] fix plot_map1 argument (ari finding) [Neil Cook]
[APERO] fix bug in ARI_FINDER params. [Neil Cook]
[APERO] fix the filtering of objects. [Neil Cook]
[APERO] fix the filtering of objects. [Neil Cook]
[APERO] fix the WLOG. [Neil Cook]
[APERO] fix the finder_dict not having create. [Neil Cook]
[APERO] fix finder chart SCALE_BAR –> SCALE_SIZE. [Neil Cook]
[APERO] add finder charts to ari. [Neil Cook]
[APERO] work on putting finding charts in ARI. [Neil Cook]
[APERO] work on putting finding charts in ARI. [Neil Cook]
Manual_trigger.py - add an option to override the run.ini file from the command line. [Neil Cook]
Merge branch ‘developer’ into v0.7.289-live. [Neil Cook]
[APERO] update readme versions. [Neil Cook]
[APERO] manage_databases.py - remove dependency on google-sheet columns (future safe) [Neil Cook]
[APERO] fix finding model files. [Neil Cook]
[APERO] report on using DTEMP. [Neil Cook]
[APERO] manage_databases.py - remove dependency on google-sheet columns (future safe) [Neil Cook]
[APERO] continue work to add ARI to apero tools - add live paths. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] continue work to add ARI to apero tools. [Neil Cook]
[APERO] start work to add ARI to apero tools. [Neil Cook]
[APERO] add option for dtemp to apero-lbl. [Neil Cook]
[APERO] update requirements_current.txt to match requirements_developer.txt (Should solve Issue #729) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.288-stable-test’ into v0.7.288-stable-test. [Neil Cook]
[APERO] add lbl log messages to apero log. [Neil Cook]
[APERO] lbl codes - send –program to lbl. [Neil Cook]
[APERO] lbl codes - send –program to lbl. [Neil Cook]
[APERO] apero.science.velocity.gen_lbl.py - only use filename if header_fits_file is None. [Neil Cook]
[APERO] apero.science.velocity.gen_lbl.py - fix typo. [Neil Cook]
[APERO] update lbl “add_output” to better fill the database from header files (for compile use last lblrv input file) [Neil Cook]
[APERO] apero.core.core.drs_database.py - fix problem with INCLUDE_OBS_DIRS and missing the “other” directory. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.288-stable-test’ into v0.7.288-stable-test. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.288-stable-test’ into v0.7.288-stable-test. [Neil Cook]
Add a lock file in the checks to avoid uploading to google sheet at the same time. [Neil Cook]
[APERO] apero.tools.module.listing.drs_get.py - deal better with KW_RUN_ID and KW_PI_NAME being NULL. [Neil Cook]
[APERO] template_tellu.py - fix typo - del variables inside if statement. [Neil Cook]
[APERO] apero_get.py - introduce way to impose file size limit which raises error if failed. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.288-live’ into v0.7.288-live. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.288-live’ into v0.7.288-live. [Neil Cook]
Apero.science.telluric.template_tellu.py - open files manually to avoid memory error (Issue #706) [Neil Cook]
[APERO] apero.core.instruments.spirou.default_constants.py - fix the dprtypes allowed for sim_fp (missing POLAR_FP) - should fix Issue #722. [Neil Cook]
Merge branch ‘v0.7.288-stable-test’ into v0.7.288-live. [Neil Cook]
[APERO] install.py - fix –lbldir argument (should fix Issue #722) [Neil Cook]
Apero.science.telluric.template_tellu.py - do some more clean up. [Neil Cook]
[APERO] apero.science.telluric.template_tellu.py - try to stop memory leak in template creation. [Neil Cook]
[APERO] remove whitespace from HIERARCH ESO OBS PROG ID default_keywords.py. [Neil Cook]
[APERO] update all run.ini files in assets (Issue https://github.com/njcuk9999/apero-drs/issues/720 and https://github.com/njcuk9999/apero-utils/issues/181) [Neil Cook]
[APERO] set complete_run.ini SKIP_XXX to False by default (Issue https://github.com/njcuk9999/apero-drs/issues/720 and https://github.com/njcuk9999/apero-utils/issues/181) [Neil Cook]
[APERO] sort precheck file directories alphabetically (issue https://github.com/njcuk9999/apero-utils/issues/130) [Neil Cook]
[APERO] apero_lbl_compile - skip done should be False - we should always recompute lbl_compile. [Neil Cook]
Merge branch ‘v0.7.287-live’ into v0.7.288-live. [Neil Cook]
[APERO] fix apero_get that when DRSOUTID is given fiber is changed if no fiber present in a DRSOUTID. [Neil Cook]
Listing.drs_get.py - remove fits from any identifer for the filename. [Neil Cook]
[APERO] update date/version/changelog. [Neil Cook]

0.7.288 (2023-08-30)¶

[NIRPS] remove AB from file_Definitions of nirps he and ha. [Neil Cook]
[NIRPS] fix which definitions are used for apero_postprocess for nirps-he and nirps-ha. [Neil Cook]
[APERO] apero_get - fix pid. [Neil Cook]
Error_html.py - fix pid_to_time to allow no pid. [Neil Cook]
[APERO] error_html.py - fix links in date table. [Neil Cook]
[APERO] error_html.py - fix filtering. [Neil Cook]
[APERO] error_html.py - fix filtering. [Neil Cook]
[APERO] add roweven and rowodd. [Neil Cook]
[APERO] error_html.py - fix html styling for recipe page. [Neil Cook]
[APERO] error_html.py - fix problem with from_outlist. [Neil Cook]
[APERO] error_html.py - fix problem with from_outlist. [Neil Cook]
Start error html work. [Neil Cook]
Start error html work. [Neil Cook]
Start error html work. [Neil Cook]
[APERO] add some error handling functions. [Neil Cook]
[APERO] - add a add_html function to markdown functions. [Neil Cook]
Start error html work. [Neil Cook]
[APERO] - add a add_html function to markdown functions. [Neil Cook]
[APERO] add some error handling functions. [Neil Cook]
[APERO] correct making a tar with no files. [Neil Cook]
[APERO] apero_get.py - make tars actually a tar.gz. [Neil Cook]
[APERO] correct dprtype for LBL NIRPS + make default run.ini files set lbl steps skip=False. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.287-live’ into v0.7.287-live. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.287-live’ into v0.7.287-live. [Neil Cook]
[APERO] apero_get - fix arguments. [Neil Cook]
Listing.drs_get.py - change DRS_DATE_OBS to KW_MJDATE (for matching on observed time) [Neil Cook]
[APERO] apero_get - add a timekey to switch between processed and observed. [Neil Cook]
[APERO] apero_get - add indict and outdict (for return analysis) [Neil Cook]
[APERO] apero_get - fix tar file addition. [Neil Cook]
[APERO] apero_get - fix tar file addition. [Neil Cook]
[APERO] apero_get - fix tar file addition. [Neil Cook]
[APERO] reset - ask before reseting all databases. [Neil Cook]
[APERO] reset - ask before reseting all databases. [Neil Cook]
[APERO] update arg on apero_database. [Neil Cook]
[APERO] Update apero_get.py (allow tar creation, filter by runid and get files up to a certain date) [Neil Cook]
[APERO] apero_lbl_ref_nirps_ha.py - create directories before parallelisation. [Neil Cook]
[APERO] apero_lbl - for FP do QC. [Neil Cook]
[APERO] do lbl_compute qc before error reporting. [Neil Cook]
[APERO] Add LBL to apero_reset.py. [Neil Cook]
[APERO] add qc to lbl (for now they always pass) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.287-live’ into v0.7.287-live. [Neil Cook]
Merge branch ‘v0.7.286-stable-test’ into v0.7.287-live. [Neil Cook]
[APERO] can no longer use append for dataframes use pd.concat instead (already implemented in v0.7.287) fixes issue #710. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.287-live’ into v0.7.287-live. [Neil Cook]
[APERO] fix to language database - if row is Nan skip. [Neil Cook]
[APERO] remove EFFRON < 10* RON as a QC parameter. [Neil Cook]
[APERO] update QC limit to 10 * RON. [Neil Cook]
[APERO] add noise combination method. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.287-live’ into v0.7.287-live. [Neil Cook]
Merge branch ‘v0.7.287-live’ of github.com:njcuk9999/apero-drs into v0.7.287-live. [Neil Cook]
Fix broken links not being replaced. [Neil Cook]
Deal with more copy paths existing (overwrite or remove before copy) [Neil Cook]
[APERO] update requirements (downgrade mysql-connector-python) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.287-live’ into v0.7.287-live. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.287-live’ into v0.7.287-live. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.287-live’ into v0.7.287-live. [Neil Cook]
[APERO] fix problem with eff_ron. [Neil Cook]
[APERO] correct gain –> EFF_GAIN. [Neil Cook]
Apero.core.instruments.nirps_* - update comments on MJD_FLUX, RMS_POS, MED_POS. [Neil Cook]
Apero.core.utils.drs_recipe.py - revert forcing value to a string in self.str_arg_list. [Neil Cook]
Apero.core.utils.drs_recipe.py - revert forcing value to a string in self.str_arg_list. [Neil Cook]
[NIRPS] update KW_IDENTIFIER. [Neil Cook]
Add keyword EFF_RON to headers. [Neil Cook]
Add keyword EFF_RON to headers. [Neil Cook]
Setup/install.py - update now we have lbl in the requirements. [Neil Cook]
Add lbl + postprocess recipes to nirps_he and nirps_ha. [Neil Cook]
Update run.ini files. [Neil Cook]
Update run.ini files with LBL and and post_procesing file for nirps. [Neil Cook]
[APERO/LBL] Deal with errors and skipping better. [Neil Cook]
Make Gain a constant (do not use from header) [Neil Cook]
Continue work on running lbl from APERO (test running) [Neil Cook]
Continue work on running lbl from APERO (test running) [Neil Cook]
Continue work on running lbl from APERO (add lbl files to file index database) [Neil Cook]
Continue work on running lbl from APERO. [Neil Cook]
Merge branch ‘v0.7.287-stable-test’ into v0.7.287-live. [Neil Cook]
Add keyword EFF_RON to headers. [Neil Cook]
Continue work on running lbl from APERO. [Neil Cook]
Merge branch ‘v0.7.287-stable-test’ into v0.7.287-live. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.287-stable-test’ into v0.7.287-stable-test. [Neil Cook]
Measure effective readout noise in order to better calculate SNR. Add QC if effective readout noise > 2 * sigdet. [Neil Cook]
Continue work on running lbl from APERO. [Neil Cook]
Allow LBL to be run from APERO [UNFINISHED & UNTESTED] [Neil Cook]
Update date/version/changelog/readme. [Neil Cook]

0.7.287 (2023-08-08)¶

[APERO] Correct that ribbon cannot load in raw file path. [Neil Cook]
[APERO] Correct that ribbon cannot save in raw file path. [Neil Cook]
[APERO] fix apero_get and null/nan passed_all_qc column. [Neil Cook]
[APERO] apero_get if PASSED_ALL_QC is Null we should accept it as passed QC (as we don’t know otherwise) [Neil Cook]
[APERO] drs_markdown.py - if csv_file is None our table does not have rows. [Neil Cook]
[SPRIOU] Correct the RUNID key (was QRUNID now RUNID) [Neil Cook]
[APERO] apero_processing.py - fix issues with which objects go into templates (now only those that are in the obsdirs that are given), if none are given use all obs_dir (we cannot use the astrom list of targets as this contains many objects that don’t exist for an instrument) [Neil Cook]
Deal with processing obsdirs better [UNFINISHED, UNTESTED] [Neil Cook]
[APERO] do not require params[‘INPUTS’][‘PARALLEL’] instead set it to False if not present. [Neil Cook]
[APERO] apero_ccf_spirou.py - fix bug where OBJ_DARK and POLAR_DARK files crash CCF code. [Neil Cook]
[APERO] apero.core.core.drs_base_classes.py - remove FutureWarning calling in on a single element (now get count and then force to int) [Neil Cook]
Merge branch ‘main’ into v0.7.287-live. [Neil Cook]
[APERO] update readme. [Neil Cook]
Merge branch ‘v0.7.285-live’ into v0.7.286-live. [Neil Cook]
Apero.science.calib.background.py - add in local_background_correction image even if not calculating. [Neil Cook]
[NIRPS] Modify the BKGR_BOXSIZE and BKGR_KER_AMP (does not affect SPIROU) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.285-live’ into v0.7.285-live. [Neil Cook]
Drs_precheck, drs_processing.py - allow logging to be turned off (for apero_checks) [Neil Cook]
[APERO] find_objnames can return an empty list, deal with each use case and report error if we do not want this to be empty. [Neil Cook]
[APERO] find_objnames can return an empty list, deal with each use case and report error if we do not want this to be empty. [Neil Cook]
[APERO] find_objnames can return an empty list, deal with each use case and report error if we do not want this to be empty. [Neil Cook]
[APERO] install.py - in dev mode ask user to add all groups. [Neil Cook]
[APERO] install.py - in dev mode ask user to add all groups. [Neil Cook]
[APERO] drs_astrometrics.py - fix using dataframe.append (should be pd.concat) [Neil Cook]

0.7.286 (2023-07-12)¶

Merge remote-tracking branch ‘origin/v0.7.286-live’ into v0.7.286-live. [Neil Cook]
Merge branch ‘v0.7.285-live’ into v0.7.286-live. [Neil Cook]
Drs_astrometrics.py - make sure the user can’t enter a blank name to replace the current name (and that name must be 3 characters long at least). [Neil Cook]
[APERO] update date/version/changelog/notes. [Neil Cook]
Merge branch ‘v0.7.285-live’ into v0.7.286-live. [Neil Cook]
Drs_processing.py - add change to return of _linear_generate_id. [Neil Cook]
Merge branch ‘v0.7.285-live’ into v0.7.286-live. [Neil Cook]
[APERO] recode parallelisation of validation step. [Neil Cook]
[APERO] push back recipemod. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.285-live’ into v0.7.285-live. [Neil Cook]
Apero.tools.module.testing.drs_dev.py - update self.mod–>self.recipemod. [Neil Cook]
Move around drs_precheck.py functions + fix typo in apero_astrometrics (apero_astrometric–>apero_astrometrics) [Neil Cook]
Move around drs_precheck.py functions + fix typo in apero_astrometrics (apero_astrometric–>apero_astrometrics) [Neil Cook]
[APERO] upgrade validation multiprocessing [UNFINISHED, UNTESTED] [Neil Cook]
[APERO] fix getting binned time. [Neil Cook]
[APERO] update getting calibrations - now bin time to local midnight (all observations from the same day will use a calibration closest to the same point - local midnight) [UNFINISHED] [Neil Cook]
[APERO] update getting calibrations - now bin time to local midnight (all observations from the same day will use a calibration closest to the same point - local midnight) [UNFINISHED] [Neil Cook]

0.7.285 (2023-07-05)¶

[APERO] update pool (to fix error) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.285-live’ into v0.7.285-live. [Neil Cook]

# Conflicts: # apero/core/instruments/default/default_constants.py # apero/tools/module/processing/drs_processing.py
[APERO] add REPROCESS_MP_TYPE_VAL (multiprocess valid recipes) and allow linear/process/pool (now difference from multiprocess run recipes with REPROCESS_MP_TYPE) [Neil Cook]
[APERO] attempt to fix pickling issues (mac only problem) [Neil Cook]
[APERO] drs_processing.py - try a fix for pickling on Mac (define recipemod inside parallel function = generate_id) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.285-live’ into v0.7.285-live. [Neil Cook]
[APERO] fix pp QCC key order. [Neil Cook]
[APERO] drs_processing.py - try a fix for pickling on Mac (define recipemod inside parallel function = generate_id) [Neil Cook]
[APERO] attempt to fix pickling issues (mac only problem) [Neil Cook]
[APERO] drs_processing.py - try a fix for pickling on Mac (define recipemod inside parallel function = generate_id) [Neil Cook]
[APERO] fix pp QCC key order. [Neil Cook]
[APERO] drs_processing.py - try a fix for pickling on Mac (define recipemod inside parallel function = generate_id) Issue #702. [Neil Cook]
[APERO] update date/version/changelog. [Neil Cook]

0.7.284 (2023-06-14)¶

[APERO] update binary flags. [Neil Cook]
[APERO] add fiber defintiions to recipe definitions. [Neil Cook]
[APERO] add fiber defintiions to recipe definitions. [Neil Cook]
[APERO] add fiber defintiions to recipe definitions. [Neil Cook]
[NIRPS] apero.science.preprocessing.detector.py - fix read_table ext–>hdu. [Neil Cook]
[APERO] apero.tools.module.processing.drs_processing.py - parallelize the validation. [Neil Cook]
[APERO] remove use of np.int (depricated) [Neil Cook]
Update date/version/changelog. [njcuk9999]

0.7.283 (2023-05-23)¶

Update python modules. [njcuk9999]
[NIRPS] add posemeter values for nirps (mjd, rms, med) to header in preprocessing. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.282-live’ into v0.7.282-live. [Neil Cook]
[APERO] Lower limits for QC in fit_tellu (catch bad snr in template creation) [Neil Cook]
[APERO] H20 to H2O. [Neil Cook]
[NIRPS] Addd new CCF masks for NIRPS-HA and NIRPS-HE (based on lbl_ccf_masks) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.282-stable-test’ into v0.7.282-stable-test. [Neil Cook]
Merge branch ‘v0.7.279-live’ into v0.7.282-stable-test. [Neil Cook]
Drs_markdown.py - allow sectionname to be None. [Neil Cook]
[APERO] only process the ccf for files that pass qc. [Neil Cook]
[APERO] change the QCC for SNR preclean label. [Neil Cook]
[APERO] update version. [Neil Cook]

0.7.282 (2023-04-27)¶

[APERO] apero.core.utils.drs_utils.py - fix ended=0 in rlog. [Neil Cook]
[APERO] correct typo (median missing from methods) [Neil Cook]
[APERO] fix logic when using mean (exptime should be a mean) [Neil Cook]
[APERO] change all means for sums (for saturation flagging) [Neil Cook]
[APERO] increase number of allowed flat files to 100 + add dprtypes before forcing dprtype. [Neil Cook]
[APERO] Need first file to be a ref dprtype file (from file model) [Neil Cook]
[APERO] cannot test type of file for flats (now we are combining) [Neil Cook]
[APERO] FF HIGH PASS must be an integer. [Neil Cook]
[APERO] do not reload the header or data if already loaded (otherwise we can’t override header keys) [Neil Cook]
[APERO] raise the limit on max number of files for apero_loc and apero_flat. [Neil Cook]
[NIRPS] need to deal with multiple file definitions for flat_dark and dark_flat. [Neil Cook]
[NIRPS] need to deal with multiple file definitions for flat_dark and dark_flat. [Neil Cook]
[NIRPS] need to deal with multiple file definitions for flat_dark and dark_flat. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.279-live’ into v0.7.279-live. [Neil Cook]
[APERO] add source of FF_HIGH_PASS_SIZE. [Neil Cook]
[APERO] flat field high pass - adjust the value to 501 pixels (for all instruments) [Neil Cook]
[APERO] low pass the flat to remove low frequency components. [njcuk9999]
[APERO] use the dark_flats and flat_darks in the flat recipe (combine with a sum) –> increased SNR. [Neil Cook]

0.7.281 (2023-04-21)¶

[APERO] replace KW_DPRTYPES spirou list with the nirps list (prevented ccfs for OBJ_SKY and TELLU_SKY) [Neil Cook]
[APERO] drs_markdown.py - add custom cssclass to add_csv_table. [Neil Cook]
Drs_markdown.py - deal with floating image vs one in a container. [Neil Cook]
Drs_markdown.py - deal with floating image vs one in a container. [Neil Cook]
Drs_markdown.py - deal with floating image vs one in a container. [Neil Cook]
Drs_markdown.py - deal with floating image vs one in a container. [Neil Cook]
Drs_markdown.py - deal with floating image vs one in a container. [Neil Cook]
[APERO] apero_get.py - deal with removing hard and symlinks better. [Neil Cook]
[APERO] documentation.conf.py - do not limit body to a max width of 800. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.279-live’ into v0.7.279-live. [Neil Cook]
[APERO] drs_markdown.py - add_divider in markdown function. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.279-live’ into v0.7.279-live. [Neil Cook]
[APERO] precheck: add runid/pi/obs-dir to objects with astrometric entry. [Neil Cook]
[APERO] drs_markdown - properly format section and sub section and add sub sub section. [Neil Cook]
[APERO] ref_seq apero_loc should have ref=True. [Neil Cook]

0.7.280 (2023-04-13)¶

[APERO] add extra apero_preprocess printouts to nirps_he and spirou. [Neil Cook]
[APERO] add debug print out for trying to open via while loop. [Neil Cook]
[APERO] apero.recipes.*.apero_preprocess_* - add more logging messages. [Neil Cook]
[APERO] apero.recipes.*.apero_preprocess_* - add more logging messages. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.279-live’ into v0.7.279-live. [Neil Cook]
[NIRPS] add DRSOUTID for res file e2ds. [Neil Cook]
[APERO] pp_ref add correct keys to pp_ref files for calib db (cannot update using database otherwise) [Neil Cook]
[APERO] make apero_database.py –reset and –update more verbose + fix ended=0 in recipe log update. [Neil Cook]
[APERO] change back to process. [Neil Cook]
[APERO] apero.tools.module.database.database_update.py - add dbkind argument. [Neil Cook]
[APERO] change how the –update and –rest work with apero_database.py. [Neil Cook]
[APERO] change how the –update and –rest work with apero_database.py. [Neil Cook]
[APERO] use pool instead of process. [Neil Cook]
[APERO] update version and add run id to index database. [Neil Cook]

0.7.279 (2023-04-06)¶

[APERO] update run.ini scripts. [Neil Cook]
[APERO] apero.science.telluric.mk_tellu.py - adjust for the slope. [Neil Cook]
[APERO] apero.science.telluric.mk_tellu.py - change frac_valid_min. [Neil Cook]
[APERO] apero.science.mk_tellu - only have the warning once per order. [Neil Cook]
[APERO] apero.science.mk_tellu - correct typo ‘warnings’–>’warning’ [Neil Cook]
[APERO] apero.science.mk_tellu - need to deal with bad orders (set to NaN) in SED. [Neil Cook]
[APERO] apero.science.mk_tellu - need to deal with bad orders (set to NaN) in SED. [Neil Cook]
[APERO] apero.science.mk_tellu - must have some valid points in order to correct image order. [Neil Cook]
[APERO] apero.science.mk_tellu - tapas_trans needs to be per order (typo) [Neil Cook]
[APERO] apero.core.instruments.*.recipe_definitions.py - fix order of the telluric correction. [Neil Cook]
[APERO] apero.science.telluric.mk_tellu - add an additional step to use the tapas transmission to fit the sed residuals to the transmission (iteratively) [njcuk9999]
[NIRPS] add ccf for nirps_ha and nirps_he with slope fit to ccf [SPIROU] add slope fit to ccf. [Neil Cook]
[APERO] apero.science.telluric.mk_tellu - update lowpassfilter + trans file SED creation (filter 3 sigma outliers in hot star SED) [njcuk9999]
[APERO] apero.science.telluric.gen_tellu.py - add tapas_water and tapas_other splines to preclean props. [Neil Cook]
[APERO] apero.tools.recipe.bin.apero_get.py - copy if not doing symlink. [Neil Cook]
[APERO] apero.tools.recipe.bin.apero_get.py - copy if not doing symlink. [Neil Cook]

0.7.278 (2023-03-29)¶

[APERO] apero.tools.recipe.bin.apero_get.py - add nosubdir argument and fix error when symlinks exist. [Neil Cook]
[APERO] apero.io.drs_image.py - do not use removedirs use rmdir - do not remove block dirs. [Neil Cook]
[APERO] apero.io.drs_image.py - do not use removedirs use rmdir. [Neil Cook]
[APERO] apero.io.drs_image.py - do not use removedirs. [Neil Cook]
[APERO] apero.io.drs_image.py: change mkdir –> makedirs. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.276-live’ into v0.7.276-live. [Neil Cook]
[APERO] tools.recipes.bin.apero_get.py - add –obsdir and –pi_name to arguments. [Neil Cook]
[APERO] tools.recipes.bin.apero_get.py - add –obsdir and –pi_name to arguments. [Neil Cook]
[APERO] apero.io.drs_image.py: change mkdir –> makedirs. [Neil Cook]
[NIRPS] apero.science.calib.dark.py - fix typo DRS_RAW_DIR to DRS_DATA_RAW. [Neil Cook]
[NIRPS] add new UNe catalogue for NIRPS-HA and NIRPS_HE. [Neil Cook]
[NIRPS] add new UNe catalogue for NIRPS-HA and NIRPS_HE. [Neil Cook]
[APERO] update apero astrometrics with a –check mode to check current database for duplicates (name, alias, ra+dec crossmatch) [njcuk9999]
[APERO] update apero astrometrics to give aliases with and without spaces/underscores. [njcuk9999]
[APERO] update apero astrometrics to give aliases with and without spaces/underscores. [njcuk9999]
[APERO] update apero astrometrics to give aliases with and without spaces/underscores. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.276-live’ into v0.7.276-live. [njcuk9999]
[APERO] BUGFIX: bug when aliases end with “|” (matches “None” and “Null” thus when there is a null it matches the object with “|” at end. [njcuk9999]

0.7.277 (2023-03-14)¶

[APERO] apero.core.core - properly delete files from database. [Neil Cook]
[APERO] apero.core.utils - deal with switch arguments in function call kwargs (return on True missing) [Neil Cook]
[APERO] aupdate whitelists for nirps. [njcuk9999]
[APERO] apero.base.drs_db.py - remove None’s from list and get via a set (quicker than np.unique) [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.276-live’ into v0.7.276-live. [njcuk9999]
[APERO] apero.science.telluric.gen_tellu.py - Provide better error for tellu preclean CCF curve fit crash + add error to lang database. [Neil Cook]
[APERO] apero.science.calib.wave.py - fix wave sol DV[AB-A] problem. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.276-live’ into v0.7.276-live. [njcuk9999]
[APERO] apero.recipes.*.apero_preprocess_*.py - fix bug when qc_params fails. [Neil Cook]
[APERO] cannot and should not write large median npy files into raw directory. [Neil Cook]
[APERO] update run.ini files. [Neil Cook]
[NIRPS] psuedo_const.py - need OBJECTNAME2 otherwise telluric,sky files fail. [Neil Cook]
[APERO] apero_preprocess_spirou.py - error when qc fils in preprocessing. [njcuk9999]
[NIRPS] pseudo_const.py - must have KW_OBJECTNAME2 in the database. [njcuk9999]
[NIRPS] apero.science.velocity.gen_vel.py - reduce number of decimials in DVRMS to get full comment. [njcuk9999]
[NIRPS] update telluric hot star list. [njcuk9999]
[APERO] do not update database if we are in parallel mode where we assume all files are in database and database has been updated externally. [Neil Cook]
[APERO] fix MKFIT2 (should be AB not A –> use sci_fiber) [Neil Cook]

0.7.276 (2023-02-09)¶

Merge remote-tracking branch ‘origin/v0.7.276-live’ into v0.7.276-live. [njcuk9999]
Allow creation of templates even if qc fails. [Neil Cook]
[APERO] apero.core.core.drs_database.py - fix a problem with headers being of wrong type for s1d. [njcuk9999]
[APERO] allow processing of LED tests (requires a switch to turn off input qc check) [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - allow PP_EVERY and EXT_EVERY for spirou. [Neil Cook]

0.8.001 (2023-01-30)¶

[APERO] update README.md (move developer and main to v0.7.275) [Neil Cook]
[APERO] fix typo apero.science.telluric.gen_tellu.py - image.shape[0] –> range(image.shape[0]) [njcuk9999]
[APERO] update date / version / documentation. [Neil Cook]

0.7.275 (2023-01-27)¶

[APERO] allow masking of bad wavelength regions in telluric correct + mask out bad tranmission. [Neil Cook]
[APERO] apero.science.telluric.template_tellu.py - calculate the s1d template error and n_valid. [Neil Cook]
[APERO] apero.science.telluric.template_tellu.py - calculate the s1d template error and n_valid. [Neil Cook]
Merge branch ‘v0.7.273-live’ into v0.7.267-live. [Neil Cook]
[APERO] recalculate template RMS + linearize template bcols between e2ds and s1d [NIRPS] change MKTEMPLATE_SNR_ORDER 33–>59. [Neil Cook]

0.7.274 (2023-01-25)¶

[APERO] fix not having a –since option. [njcuk9999]
[APERO] apero_go.py - add –setup option. [njcuk9999]
[APERO] check that –since argument is a valid date+ [njcuk9999]
[APERO] add a –since argument to drs_get.py. [njcuk9999]
[APERO] low-pass hot star template + deconv=median for hot stars (update MKTEMPLATE_HOTSTAR_KER_VEL dtype) [njcuk9999]
[APERO] low-pass hot star template + deconv=median for hot stars (update imports) [njcuk9999]
[APERO] low-pass hot star template + deconv=median for hot stars. [njcuk9999]
[NIRPS] apero.science.telluric.gen_tellu.py - finite_res_correction now requires params (For threshold) [njcuk9999]
[NIRPS] fix sky corr being applied twice for nirps and fix convergence. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.273-live’ into v0.7.273-live. [njcuk9999]
[APERO] update install.py module_translation. [Neil Cook]
[NIRPS] gen_tellu.py - filter over bad finite res corrections. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.273-live’ into v0.7.273-live. [Neil Cook]
[NIRPS] update skymodels (error in calculation) [njcuk9999]
[APERO] apero.science.calib.wave.py - update key in table to key in table.colnames. [Neil Cook]
[APERO] update requirements. [Neil Cook]
[APERO] update readme. [Neil Cook]
Merge branch ‘v0.7.273-live’ into developer. [Neil Cook]

# Conflicts: # .gitignore # README.md # apero/core/core/drs_database.py # apero/core/core/drs_startup.py # apero/core/instruments/default/default_config.py # apero/core/instruments/default/default_constants.py # apero/core/instruments/spirou/default_constants.py # apero/core/instruments/spirou/file_definitions.py # apero/core/instruments/spirou/recipe_definitions.py # apero/core/math/general.py # apero/data/spirou/reset/runs/calib_run.ini # apero/data/spirou/reset/runs/complete_run.ini # apero/data/spirou/reset/runs/mini_run.ini # apero/data/spirou/reset/runs/other_run.ini # apero/data/spirou/reset/runs/science_run.ini # apero/data/spirou/reset/runs/trigger_night_calib_run.ini # apero/lang/backup/language.xls # apero/lang/databases/language.xls # apero/recipes/spirou/apero_ccf_spirou.py # apero/recipes/spirou/cal_thermal_spirou.py # apero/science/calib/localisation.py # apero/science/calib/shape.py # apero/science/calib/wave.py # apero/science/extract/berv.py # apero/science/polar/general.py # apero/science/telluric/gen_tellu.py # apero/science/velocity/gen_vel.py # apero/tools/module/setup/drs_processing.py # apero/tools/recipes/bin/apero_processing.py # apero/tools/recipes/spirou/apero_drift_spirou.py # apero/tools/recipes/spirou/apero_expmeter_spirou.py # changelog.md # documentation/working/conf.py # documentation/working/index.rst # documentation/working/main/misc/changelog.rst # version.txt
[APERO] update date/version/docs. [Neil Cook]
Update peak_number rounding issue. [Neil Cook]
Merge remote-tracking branch ‘origin/developer’ into developer. [Neil Cook]
Merge branch ‘master’ into developer. [Neil Cook]
Science.extract.berv.py - get_berv should warn when barycorrpy fails. [Neil Cook]
Merge remote-tracking branch ‘origin/developer’ into developer. [Neil Cook]
Merge remote-tracking branch ‘origin/developer’ into developer. [njcuk9999]
Apero.science.calib.shape.py - Problem with shape when maximum correlation between FPs split between pixels (Issue #668) [njcuk9999]
Apero.core.instruments.spirou.file_definitions.py - RAW_LFC_FP did not have outfunc - add outfunc=out.blank. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - leak_master should be after thermal master. [Neil Cook]
Apero.data.spirou.reset.runs.other_run.ini - add LFCFP and FPLFC to other run.ini file. [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py + recipe_definitions.py - add LFCFP and FPLFC to sequences. [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py + recipe_definitions.py - add LFCFP and FPLFC to sequences. [Neil Cook]
Apero.tools.module.setup.drs_processing.py - _split_string_list - if allow_whitespace must return a list not string. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - _split_string_list should not split by white space unless directly told to (allows spaces in filenames) [njcuk9999]
Apero.recipes.spirou.cal_ccf_spirou.py - make sure A and B can be used as science fibers. [Neil Cook]
Apero.core.instruments.spirou.default_constants.py - update DRIFT_DPRTYPES - (add FP_DARK) [Neil Cook]
Apero.recipes.spirou.cal_thermal_spirou.py - thermal_files are not indexed - correct this. [Neil Cook]
Apero.science.calib.localisation.py + wave.py - add KW_PID to writing functions. [Neil Cook]
Merge remote-tracking branch ‘origin/developer’ into developer. [njcuk9999]
Update README.md. [Neil Cook]

correct typo
Apero.science.telluric.gen_tellu.py - deal with Etienne using 0 as flag - bad bad bad. [njcuk9999]
Tools.recipe.spirou.cal_drift_spirou.py - update output filename. [Neil Cook]
Tools.recipe.spirou.cal_drift_spirou.py - allow OBJ_FP and DARK_FP files (and deal with fibers not containing FP) [Neil Cook]
Apero.science.calib.localisation.py - fix qc logic for MAX_RMPTS_POS and MAX_RMPTS_WID. [Neil Cook]
Apero.core.core.drs_startup.py - pep8 change. [Neil Cook]
Cal_expmeter_spirou.py - update output filename based on input fibers. [Neil Cook]
Apero.core.core.drs_startup.py - try to fix integer scalar bug. [Neil Cook]
Apero.tools.recipes.spirou.cal_expmeter_spirou.py - add –fibers option. [Neil Cook]
Update date/version/changelog/readme/documentation. [Neil Cook]

0.7.273 (2023-01-23)¶

[NIRPS] update telluric list. [njcuk9999]
[APERO] apero.science.telluric.gen_tellu.py - correct typo for failing precleaned files. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.267-live’ into v0.7.267-live. [njcuk9999]
[APERO] correct params[‘INPUTS’] for FINITERES. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.267-live’ into v0.7.267-live. [njcuk9999]
[APERO] update date/version/docs. [Neil Cook]
[NIRPS] update sky_model (ha and he) [njcuk9999]
[APERO] apero.science.telluric.gen_tellu.py - fix spline in finite res. [njcuk9999]

0.7.272 (2023-01-19)¶

[APERO] allow switching on and off of finite res corr (via params and user input) + add header key that finite res was/wasn’t done. [Neil Cook]
[APERO] ref_calib_run.ini should not have RUN_OBS_DIR set to DEFAULT_REF_OBSDIR (we need FP_FP from all nights) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.267-live’ into v0.7.267-live. [njcuk9999]
[APERO] apero.science.telluric.gen_tellu.py - deal with edge effects in wave_to_wave. [Neil Cook]
[APERO] apero.science.calib.gen_calib.py - fix typo in check_fp. [njcuk9999]
[APERO] apero.science.preprocessing.detector.py - flag pixels that have inconsistent intercept in LED. [Neil Cook]
[APERO] apero.science.preprocessing.detector.py - flag pixels that have inconsistent intercept in LED. [Neil Cook]
[APERO] do not do science capacitive coupling correction for HC files. [Neil Cook]
[NIRPS] apero.science.preprocessing.detector - do not sigma clip columns when we are creating a mask. [Neil Cook]
[APERO] apero.science.preprocessing.detector.py - account for NaNs in butterfly maps. [Neil Cook]
[APERO] apero.science.telluric.gen_tellu.py - correct (bad) changes for finite res. [Neil Cook]
[APERO] apero.science.telluric.gen_tellu.py - correct (bad) changes for finite res. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.267-live’ into v0.7.267-live. [Neil Cook]
[NIRPS] correct nirps_correction. [Neil Cook]
[NIRPS] science.preprocessing.detector.py - correct typos. [Neil Cook]
[NIRPS] science.preprocessing.detector.py - correct of the first read of the amplifiers. [Neil Cook]
[NIRPS] science.preprocessing.detector.py - correct of the first read of the amplifiers. [Neil Cook]
[APERO] apero.science.telluric.template_tellu.create_deconvolved_template do not copy over flux (call flux0 as input) [Neil Cook]

0.7.271 (2023-01-17)¶

[APERO] apero.core.math.gen_math.py - add typing in square_medbin. [Neil Cook]
[APERO] science.telluric.gen_tellu.py - fix that qc_exit_tellu_preclean fails without image_e2ds_ini (PRE_SKYCORR_IMAGE) [Neil Cook]
[NIRPS] science.preprocessing.detector.py - fix nirps pp mask. [Neil Cook]
[APERO] correct A and B telluric properly (sky + finite resolution) [Neil Cook]
[APERO] correct A and B telluric properly (sky + finite resolution) [Neil Cook]
[NIRPS] apero.core.utils.drs_utils.py - fix that times are a numpy array. [njcuk9999]
[APERO] correct post_t_file (OHLINE, SKYCORR etc) [Neil Cook]
[APERO] finish adjustments to finite resolution model. [Neil Cook]
[APERO] add finite resolution effects code. [Neil Cook]
[APERO] print progress on capacitive coupling. [Neil Cook]
[NIRPS] add in the capacitive coupling from sci flux (for NIRPS) [Neil Cook]
[APERO] add in the capacitive coupling from sci flux. [Neil Cook]

0.7.270 (2023-01-13)¶

[APERO] correct typo (bug) cavity[0] must have the pedestal added before updating by mean_hc_vel - all wave sols are wrong without this fix. [njcuk9999]
[APERO] typo correct_capacitive_coupling_pattern –> correct_capacitive_coupling. [Neil Cook]
[NIRPS] minor bug fixes for variable resolution. [njcuk9999]
[APERO] correct the capacitive coupling pattern using the amplifier bias model. [Neil Cook]
[APERO] correct the capacitive coupling pattern using the amplifier bias model. [Neil Cook]
[APERO] correct the capacitive coupling pattern using the amplifier bias model. [Neil Cook]
[APERO] correct the capacitive coupling pattern using the amplifier bias model. [Neil Cook]
[APERO] correct the capacitive coupling pattern using the amplifier bias model. [Neil Cook]
[APERO] correct the capacitive coupling pattern using the amplifier bias model. [Neil Cook]
[NIRPS] correct + speed variable resolution convolution, add sky_model for NIRPS HA. [njcuk9999]
[APERO] add in variable resolution for the tellu convolution. [njcuk9999]
[APERO] correct s1d res maps (needed blaze) [njcuk9999]
[APERO] add s1d res amp/fwhm/expo files. [njcuk9999]
Merge branch ‘v0.7.261-live’ into v0.7.267-live. [njcuk9999]
[APERO] apero.core.math.gen_math.py - deal with nans for robust chebyshev. [njcuk9999]

0.7.269 (2023-01-10)¶

[APERO] create s1d res map [unfinished] [Neil Cook]
[NIRPS] sky corr changes. [njcuk9999]
[NIRPS] remove ravel from possible Nones. [Neil Cook]
[NIRPS] remove ravel from possible Nones. [Neil Cook]
[NIRPS] correct typo np.nqnwum –> np.nansum. [Neil Cook]
Merge branch ‘v0.7.261-live’ into v0.7.267-live. [Neil Cook]
[NIRPS] deal with not having the KW_CAV_PEDESTAL key. [Neil Cook]
[NIRPS] add sky correction. [Neil Cook]
[NIRPS] add sky correction. [Neil Cook]
Merge branch ‘v0.7.261-live’ into v0.7.259-nirps-test. [Neil Cook]
[NIRPS] add sky correction. [Neil Cook]
[NIRPS] plan for res convolve change. [Neil Cook]
[NIRPS] add apero_skycorr_nirps_he.py [UNFINISHED] [Neil Cook]
[NIRPS] add sky model correction to telluric mk_tellu and fit_tellu codes. [Neil Cook]

0.7.268 (2022-12-23)¶

[APERO] update apero_database.py database names. [njcuk9999]
[APERO] update date/version/docs/changelog. [njcuk9999]

0.7.267 (2022-12-22)¶

[APERO] change continuity for wave to chebyshev. [Neil Cook]
[APERO] add sigma cut criteria on the CCF FWHM for the mean CCF profile. [Neil Cook]
[APERO] add sigma cut criteria on the CCF FWHM for the mean CCF profile. [Neil Cook]
[APERO] do not do nsig CCF cut for FP. [Neil Cook]
[APERO] set a minimum value for allowed CCF fit (peak CCF < 5sigma) [Neil Cook]

0.7.266 (2022-12-21)¶

[APERO] fix key error with CAVITY_PEDESTAL. [Neil Cook]
[APERO] add res e2ds to wave sol. [njcuk9999]
[APERO] add a resolution e2ds map for amp/fwhm/expo. [Neil Cook]
[APERO] improve wave solution with more cavity fit using chebyshev. [njcuk9999]
[APERO] try making wave solution converge across machines. [Neil Cook]
[APERO] apero.core.math.gen_math.py - update robust_polyfit and robust_chebyfit to be fuzzy at edges. [Neil Cook]
[APERO] apero.core.math.gen_math.py - update robust_polyfit and robust_chebyfit to be fuzzy at edges. [Neil Cook]
[APERO] apero.core.math.gen_math.py - update robust_polyfit and robust_chebyfit to be fuzzy at edges. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.261-live’ into v0.7.261-live. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.261-live’ into v0.7.261-live. [Neil Cook]
[APERO] correct typo. [Neil Cook]
[APERO] apero.core.math.gen_math.py - update robust_polyfit and robust_chebyfit to be fuzzy at edges. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.259-nirps-test’ into v0.7.259-nirps-test. [njcuk9999]

# Conflicts: # apero/data/spirou/telluric/sky_PCs.fits
[APERO] update sky_PCs.fits. [Neil Cook]
[SPIROU] update sky_PCs.fits (needed to be flipped in shape) [njcuk9999]

0.7.265 (2022-12-13)¶

[APERO] storage for optimizing code. [Neil Cook]
[APERO] storage for optimizing code. [Neil Cook]
Merge branch ‘v0.7.261-live’ into v0.7.259-nirps-test. [Neil Cook]
[APERO] implement a locking for orderps file so we don’t try to write it and read it at the same time (should prevent an error we are getting in extraction) [Neil Cook]
[APERO] fix ycents for AB,A,B spirou (change added for NIRPS) in order table. [Neil Cook]
[APERO] fix ycents for AB,A,B spirou (change added for NIRPS) in order table. [Neil Cook]
[APERO] fix ycents for AB,A,B spirou (change added for NIRPS) in order table. [Neil Cook]
Merge branch ‘v0.7.259-nirps-test’ into v0.7.261-live. [Neil Cook]
[APERO] update date/version/docs. [Neil Cook]
[NIRPS] switch sequences for EFF,SKY,SKY and DARK,SKY. [njcuk9999]
[NIRPS] add calculate_dxmap_nirps to both modes (rename from calculate_dxmap_nirpshe) [njcuk9999]
[NIRPS] add calculate_dxmap_nirps to both modes (rename from calculate_dxmap_nirpshe) [njcuk9999]
[APERO] apero.science.extract.gen_ext.py - better handle trying shapel file (when multiple files try to write it at once) [Neil Cook]
[NIRPS] apero.recipes.nirps_ha.apero_preprocess_nirps_ha.py - fix loading of led lat. [Neil Cook]
[APERO] add –plot=4 (select plots) and fix –fpref. [njcuk9999]
[NIRPS] fix LED flat creation + update run.ini files. [Neil Cook]
[NIRPS] fix LED flat creation + combine (for hash code) + save to calibDB. [Neil Cook]

0.7.264 (2022-12-08)¶

[NIRPS] update LED flat creation. [Neil Cook]
[NIRPS] update preprocessing codes to use LED_FLAT from calibrations. [Neil Cook]
[APERO] update apero_get + documentation. [Neil Cook]
[APERO] update apero_get.py. [njcuk9999]
[APERO] apero_get.py allow wildcard for –objnames. [Neil Cook]
[NIRPS] Add LED flat creation to PP_REF. [Neil Cook]
[APERO] update sky model. [njcuk9999]
[APERO] require wavelength solution to be within 7 days if a night calibration. [njcuk9999]
[APERO] try to fix problem with shapel_orderps FileNotFoundError. [Neil Cook]
[APERO] add order table (for extracted files) + WAVE_POLY_TYPE + LOC_POLY_TYPE. [Neil Cook]
[APERO] add order table (for extracted files) + WAVE_POLY_TYPE + LOC_POLY_TYPE. [Neil Cook]
[APERO] add order table (for extracted files) + WAVE_POLY_TYPE + LOC_POLY_TYPE. [Neil Cook]
[APERO] add poly type to loco keys loaded from locofile. [njcuk9999]
[NIRPS] remove extraction bad pixel flagging for HA-A, HA-B, HE-B fibers [APERO] add loc and wave poly coeff type (Chebyshev) [njcuk9999]

0.7.263 (2022-11-30)¶

[NIRPS] change s1d max wavelength. [njcuk9999]
[APERO] add led_flat code + allow forcing only telluric preclean. [njcuk9999]
[APERO] add led_flat. [njcuk9999]
[APERO] allow a constant to determine the min exptime for darks in the dark_ref. [njcuk9999]
[APERO] must add to e2dsoutputs for leak correction to work. [njcuk9999]
[NIRPS] update the list of telluric stars. [njcuk9999]
[NIRPS] apero.tools.module.processing.drs_processing.py - fix skip list with INCLUDE_OBS_DIRS and EXCLUDE_OBS_DIRS (param–> param.listp) [njcuk9999]
[NIRPS] apero.science.gen_ext.py - allow override of fibers for fplines calculation (for FP_FP tests) [njcuk9999]
[NIRPS] apero.science.calib.localisation.py - change max to a percentile in the order loc label (avoids picking up pixels outside order for width measurement) [njcuk9999]
[NIRPS] update nirps_he recipe_definitions (add PP_EVERY and EXT_EVERY) [Neil Cook]

0.7.262 (2022-11-15)¶

[APERO] Add PP_EVERY to pp_seq_opt and EXTRACT_EVERY to eng_seq (used in other_run.ini) to preprocess and extract everything (no calibs) [Neil Cook]
[NIRPS] update HE and HA default wave solution. [Neil Cook]
[NIRPS] updates for nirps HE wave solution. [Neil Cook]
[APERO] update reset.calib.csv and deafult_constants for wave constants. [Neil Cook]
[APERO] update nirps ref wave solutions. [Neil Cook]
[APERO] nirps updates for wave sol. [Neil Cook]

0.7.261 (2022-11-10)¶

[APERO]doc string / typing /pcheck / pep8 update. [Neil Cook]
Merge branch ‘v0.7.259-working’ into v0.7.259-nirps-test. [Neil Cook]
Merge branch ‘v0.7.259-nirps-test’ into v0.7.259-working. [Neil Cook]
[APERO] fix exposure meter. [Neil Cook]
[APERO] doc string/ typing / pcheck / pep8 updates. [Neil Cook]
[APERO] localisation.py - remove cross term between coefficients in the loco fit. [Neil Cook]
[NIRPS] update orders and order position. [Neil Cook]

0.7.260 (2022-11-07)¶

[NIRPS] use chebyshev in the continuity fit. [Neil Cook]
[NIRPS] use chebyshev in the continuity fit. [Neil Cook]
[NIRPS] use chebyshev in the continuity fit. [Neil Cook]
[NIRPS] use chebyshev in the continuity fit. [Neil Cook]
[NIRPS] update number of orders (75–> 74) and LOC_YDET_MIN. [Neil Cook]
[NIRPS] update number of orders (74–> 75) [Neil Cook]
[NIRPS] update LOC_YDET_MAX, LOC_YDET_MAX. [Neil Cook]
[NIRPS] back to 74 orders but move LOC_YDET_MAX. [Neil Cook]
[NIRPS] back to 73 orders but move LOC_YDET_MAX. [Neil Cook]
[NIRPS] update number of orders 73 –> 74. [Neil Cook]
[NIRPS] update number of orders 73 –> 74. [Neil Cook]
[APERO] install.py - fix git python version. [Neil Cook]
[APERO] fix problem with leak_ref not being a hash code file (was just using first file) [Neil Cook]
[APERO] apero.plotting.plot_functions.py - fix broken plot (type reference–>ref) [Neil Cook]
[APERO] add paper to main page. [Neil Cook]
[APERO] fix for badpix (bstatsb) [Neil Cook]
[APERO] update version/date/changelog/docs. [Neil Cook]

0.7.259 (2022-11-04)¶

[APERO] add git branch + git hash + python modules + python version to PARAM_TABLE. [Neil Cook]
[APERO] pep8 and warning fixes. [Neil Cook]
Merge branch ‘v0.7.254-working’ into v0.7.254-cheby. [Neil Cook]

# Conflicts: # apero/core/math/gen_math.py # apero/plotting/plot_functions.py # apero/science/calib/shape.py # apero/science/calib/wave.py # apero/tools/module/utils/inverse.py
[APERO] push chevyshev + clean hot pix lin mini fix into working branch. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.254-cheby’ into v0.7.254-cheby. [Neil Cook]
[APERO] apero.tools.recipes.spirou.apero_expmeter_spirou.py. [Neil Cook]
[APERO] remove linear minimization from clean_hotpix function. [Neil Cook]
[APERO] fixes for chebyshev. [Neil Cook]
[APERO] force jit functions to not use fastmath mode. [Neil Cook]
[APERO] fixes to EA chebyshev code. [Neil Cook]

0.7.258 (2022-10-31)¶

Adding cheby stuff all over the place. [eartigau]
[APERO] make sure assets directory is reset (but copy all “new” files to a backup assets dir) [Neil Cook]
[APERO] re-run template after best telluric correction. [Neil Cook]
[APERO] add zsh profiles to setup dir. [Neil Cook]
[APERO] update import order (pycharm Ctrl+Alt+O to sort) [Neil Cook]
Update date/version/changelog/documentation. [Neil Cook]

0.7.257 (2022-10-25)¶

[APERO] correct columns in apero_stats.py. [Neil Cook]
[APERO] add file index mode to apero_stats.py + write apero_stats_static.txt and apero_stats_varying.txt to msg/report directory. [Neil Cook]
[APERO] remove cook@localhost.mysql.backup file from calib reset (it shouldn’t be here) [Neil Cook]
[APERO] start adding “all” mode to apero_stats.py. [Neil Cook]
[APERO] fix FORCE_REFWAVE flag in get_wavelength function calls. [Neil Cook]
[APERO] add conda and git documentation to other documentation. [Neil Cook]
[APERO] add TODO re: hard coded value. [Neil Cook]
[APERO] add a limit to apero_stats memory mode. [Neil Cook]
[APERO] update apero_stats memory plot. [Neil Cook]
[APERO] add to apero_get documentation. [Neil Cook]
[APERO] test of wave [EXT] memory issue. [Neil Cook]
[APERO] test of wave [EXT] memory issue. [Neil Cook]
[APERO] fix problem with using setup/install.py –update mode. [Neil Cook]
[APERO] update apero_stats plot. [Neil Cook]

0.7.256 (2022-10-13)¶

[APERO] pep8 fixes. [Neil Cook]
[APERO] fixes for adding log start/log end + ccf run_file. [Neil Cook]
[APERO] add LOG_START and LOG_END to log database (and fix END_TIME) - will require new log database. [Neil Cook]
[APERO] improve memory stats plot. [Neil Cook]
[APERO] add an exact requirements module to test all packages being the same. [Neil Cook]
[APERO] fix custom arguments [INPUTS] coming from run.ini file and –mask argument not looking in the assets/ccf_masks directory. [Neil Cook]
[APERO] add a printout to wave_ref_spirou + update apero_overall_flow graph. [Neil Cook]
[APERO] update date/version/changelog/docs. [Neil Cook]

0.7.254 (2022-09-22)¶

[APERO] test fix for pickling PseudoConstants. [Neil Cook]
[APERO] Apply fixes for pickling Run Class. [Neil Cook]
[APERO] apero.science.extract.extraction.py - fix bug is cosmic check res = sx - fx/amp –> res = sx - fx*amp. [Neil Cook]
[APERO] apero.core.utils.drs_startup.py - use np.genfromtxt instead of np.loadtxt as there is a bug in numpy 1.23. [Neil Cook]

0.7.255 (2022-09-30)¶

[APERO] doc + pep8 [gen_calib.py] [Neil Cook]
[APERO] doc + pep8 [flat_blaze.py] [Neil Cook]
[APERO] doc + pep8 [background.py, badpix.py, dark.py] [Neil Cook]
[APERO] update docs. [Neil Cook]
[APERO] update date/version/changelog/docs. [Neil Cook]

0.7.253 (2022-09-29)¶

[APERO] add apero_stats memory table to report directory. [Neil Cook]
[APERO] correct documentation schematics not appearing. [Neil Cook]
[APERO] correct documentation schematics not appearing. [Neil Cook]
[APERO] update versionn/date/docs/changelog. [Neil Cook]

0.7.252 (2022-09-27)¶

[APERO] continue update doc string + pep8. [Neil Cook]
[APERO] continue update doc string + pep8. [Neil Cook]
[APERO] continue update doc string + pep8. [Neil Cook]
[APERO] continue update doc string + pep8. [Neil Cook]
[APERO] apero.core.instruments.*.file_definitions.py - fix typo _WAVESOL_REF –> _wavesol_ref. [Neil Cook]
[APERO] update program descriptions and some doc strings + pep8. [Neil Cook]
[APERO] documentation.unused.v07_docstring_update.txt - add more recipes to check. [Neil Cook]
[APERO] documentation.unused.v07_docstring_update.txt - add more recipes to check. [Neil Cook]
[APERO] apero.science.calib.gen_calib.py - if not required do not cause error. [Neil Cook]
[APERO] correct flat codes - combine method should be “flat” [Neil Cook]
[APERO] apero.io.drs_path.py - reset the listdir function. [njcuk9999]

0.7.251 (2022-09-19)¶

[APERO] update doc strings + pep8 (see v07_docstring_update.txt) [Neil Cook]
[APERO] documentation - add to useful mysql commands. [Neil Cook]
[APERO] update doc strings + pep8 (see progress in v07_docstring_update.txt) [Neil Cook]
[APERO] apero.tools.module.testing.drs_stats.py - for sqlite need the LIKE parameter for recipe. [Neil Cook]
[APERO] apero.tools.module.setup.drs_installation.py - fix arg return of get_sqlite_settings. [Neil Cook]
[APERO] update doc-string + deal with pep8. [Neil Cook]
[APERO] update doc-string + deal with pep8. [Neil Cook]

0.7.250 (2022-09-13)¶

[APERO] update language database. [Neil Cook]
[SPIROU] documentation: add schematics back to recipe_definitions.py. [Neil Cook]
[APERO] update some todo messages. [Neil Cook]
[APERO] update language database to replace some text (in TODO) [Neil Cook]
[APERO] apero.science.extract.gen_ext.py - try to stop errors when order profile exists but cannot be read (parallelisation issue) [Neil Cook]
Update UPDATE_NOTES.txt. [Neil Cook]
Update UPDATE_NOTES.txt. [Neil Cook]
[APERO] apero.recipes.*.apero_fit_tellu*.py - recon must be multiplied by blaze before creating s1d (for proper weighting) [Neil Cook]
[APERO] apero.science.polar.gen_pol.py - fix factor 2 in exponent (from Eder) [Neil Cook]

0.7.249 (2022-09-07)¶

[APERO] setup.install.py - make sure config path is still the full path. [Neil Cook]
[APERO] apero.base.base.py - fix references to allparams. [Neil Cook]
[NIRPS] correct typo apero_PP_REF_nirps –> apero_pp_ref_nirps. [Neil Cook]
[NIRPS] correct typo apero_PP_REF_nirps –> apero_pp_ref_nirps. [Neil Cook]
[APERO] apero.tools.module.setup.drs_installation.py - save install params to DRS_UCONFIG (for re-use / debug) in install.sh. [Neil Cook]
[APERO] apero.tools.module.setup.drs_installation.py - all_params[‘MYSQL’] parameters should be uppercase (to match sqlite) [Neil Cook]
[APERO] apero.tools.module.setup.drs_installation.py - all_params[‘MYSQL’] parameters should be uppercase (to match sqlite) [Neil Cook]
[APERO] apero.core.instruments.default.grouping.py - fix problem where 1 entry leads to a crash. [Neil Cook]
[APERO] fix sqlite installation error (Issue #682) [Neil Cook]
[APERO] apero.base.base.py: typo FILEINDEX –> FINDEX. [Neil Cook]
[APERO] test recipe documentation. [Neil Cook]
[APERO] correct drs_db change. [Neil Cook]
[APERO] update version/date/changelog/documentation. [Neil Cook]

0.7.248 (2022-08-31)¶

[APERO] manage locking better (when no PID), manage databases better (from one place pconst.GET_DB_COLS() + base) [Neil Cook]

0.7.247 (2022-08-29)¶

[APERO] Change object database to astrometric database. [Neil Cook]
[APERO] Change object database to astrometric database. [Neil Cook]
Merge branch ‘v0.7.242-working’ into v0.7.243-working. [Neil Cook]

# Conflicts: # apero/core/core/drs_file.py # apero/tools/module/listing/file_explorer.py

Conflicts fixed
[APERO] update references to INDEX (and make all database lower case for SQL) [Neil Cook]
[APERO] documentation - update files. [Neil Cook]
[APERO] documentation - add sequence graphml/jpg/pdf files. [Neil Cook]
Apero.tools.module.database.database_gui.py - save the hash col before removing it and add it back when saving. [Neil Cook]
Put the readme files back in /bin/ and /tools/ [Neil Cook]
[APERO] apero.science.telluric.template_tellu.py - fix s1d template (in similar way to s1d template) [Neil Cook]

0.7.246 (2022-08-17)¶

[APERO] add to sequence schematics + descriptions. [Neil Cook]
[APERO] update file descriptions + update documentation with file descriptions. [Neil Cook]
[APERO] update file descriptions. [Neil Cook]
[APERO] apero.tools.module.setup.drs_reset.py - correct temporary message. [Neil Cook]
[APERO] apero.tools.module.setup.drs_reset.py - correct file list. [Neil Cook]
[APERO] apero.tools.module.setup.drs_reset.py - speed up reset (or at least display a message) [Neil Cook]
[APERO] documentation - update overview schematics (yed) [Neil Cook]
[APERO] apero.tools.recipes.bin/apero_stats.py - need recipe to be passed (for plotting) [Neil Cook]
[APERO] apero.tools.recipes.bin/apero_stats.py - need recipe to be passed (for plotting) [Neil Cook]
[APERO] apero.science.telluric.gen_tellu.py - change pre-cleaning SNR criteria to be median SNR (not max) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.243-working’ into v0.7.243-working. [Neil Cook]
[APERO] apero.science.telluric.template_tellu.py - [BAD BUG] fix for templates - binning was incorrect if N>50 files was using only the first sqrt(N) files, if N<50 was using only using the first. [Neil Cook]
[APERO] paper - update apero_overall_flow diagram. [Neil Cook]

0.7.245 (2022-08-10)¶

Merge branch ‘v0.7.242-working’ into v0.7.243-working. [Neil Cook]
[APERO] apero.tools.recipes.bin.apero_stats.py - add memory stats to apero_stats.py. [Neil Cook]
Update filenames master–>ref. [Neil Cook]
Update filenames master–>ref. [Neil Cook]
Re-add run.ini files after master–>ref. [Neil Cook]
Re-add run.ini files after master–>ref. [Neil Cook]
Replace “master/MASTER” with “ref/reference” (do not use “master” as a word) [UNTESTED] [Neil Cook]

0.7.244 (2022-08-02)¶

[APERO] core.instruments.*.recipe_defintions.py - missing WAVEREF_EXPECTED from plots. [Neil Cook]
Update mysql_database_commands.rst. [Neil Cook]

Add some extra useful MySQL commands
Add files via upload. [Neil Cook]

add overview for paper

0.7.243 (2022-06-30)¶

[APERO] apero.base.drs_db.py - up the wait time for database connection failure (5s–> 30s) [Neil Cook]
Up the wait time for database connection failure. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.242-working’ into v0.7.242-working. [Neil Cook]
[APERO] deal with nan slices in transmission. [njcuk9999]
Update paper schematics. [Neil Cook]

0.7.242 (2022-06-23)¶

[NIRPS] modify tapas to mask unusable regions. [njcuk9999]
[APERO] tools.module.processing.drs_processing.py - make KW_OBSTYPE condition depend on instrument. [njcuk9999]
[NIRPS] adjust some tellu parameters for nirps. [njcuk9999]
[APERO] remove shortcut to apero_flat_spirou.py in bin dir. [Neil Cook]
Update version/date/changelog/docs. [Neil Cook]

0.7.241 (2022-06-21)¶

[APERO] apero.core.core.drs_file.py - deal with nans better. [njcuk9999]
[APERO] apero.core.core.drs_file.py - deal with nans better. [njcuk9999]
[NIRPS] add a test_fp_dark file definition. [njcuk9999]

0.7.240 (2022-06-17)¶

[APERO] small changes for update to reject database. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [njcuk9999]
[APERO] change slightly how REJECTLIST works (to allow difference between spirou and nirps) [Neil Cook]
[NIRPS] default_constants.py - update GL_OBJ_COL_NAME. [njcuk9999]

0.7.239 (2022-06-14)¶

[APERO] drs_astrometrics.py - ask user for Teff source. [Neil Cook]
[NIRPS] add TEST_DARK_DARK_SKY from EFF,SKY,SKY files and add to engineering seqeuence. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [njcuk9999]
[NIRPS] update hot star list. [Neil Cook]
[NIRPS] fix typo LW_DRS_QC –> KW_DRS_QC. [njcuk9999]
[NIRPS] undo shape change for ha (from he) [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [Neil Cook]
[NIRPS] B fiber should be fit_cavity + fit_achromatic = False. [njcuk9999]
[APERO] save preprocessing files that fail qc to disk but check in all recipes that qc has passed (unless user forces no_in_qc check) [njcuk9999]
[APERO] apero.science.calib.background.py - slightly change how background subtraction is done. [njcuk9999]
[NIRPS] add raw test dark. [Neil Cook]

0.7.238 (2022-06-09)¶

Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [Neil Cook]
[NIRPS] add pp_test_eff_sky file definition. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [njcuk9999]
[APERO] tools.module.processing.drs_trigger.py - put the trigger_table.fits in a standard location (not dependent on recipe run location) [Neil Cook]
[NIRPS] fix for getting object name. [njcuk9999]
[NIRPS] science.extract.extraction.py - remove an extra factor of gain (didn’t matter for SPIRou as gain=1) [njcuk9999]
[NIRPS] update file_definitions.py for RAW_FLUXSTD_SKY. [njcuk9999]
[NIRPS] add TELLU_SKY file definition. [Neil Cook]
[APERO] update date/version/doc/changelog. [Neil Cook]

0.7.237 (2022-06-08)¶

Add FLUX,STD,SKY file definition. [njcuk9999]
[APERO] fixes for trigger + [NIRPS] gain header key change. [njcuk9999]
[APERO] fix drsfile.nosave in copy_header/copy_hdict. [Neil Cook]
[APERO] do not check non calib recipes for calib run. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [njcuk9999]
Deal with store_true action better (when called as an argument) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [njcuk9999]
[APERO] add a nosave option for debug/plotting/information purposes (no writing of files) - bug fix. [Neil Cook]
[APERO] add a nosave option for debug/plotting/information purposes (no writing of files) [Neil Cook]
[APERO] add to trigger code (tested) [Neil Cook]
[APERO] add new wave sol for NIRPS_HA. [njcuk9999]

0.7.236 (2022-06-04)¶

Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [njcuk9999]
[APERO] first commit of very basic trigger. [Neil Cook]
[APERO] apero.io.drs_fits.py - fix read_multi extension being None (deepcopy instead of array) [njcuk9999]
[APERO] fix memory leak with bottleneck + over copying of fits reader. [njcuk9999]
[NIRPS] update nirps_he default wave sol. [njcuk9999]
[APERO] apero.core.instruments.default.deafult_constants.py - BADPIX_ERODE_SIZE and BADPIX_DILATE_SIZE must be integers. [njcuk9999]
[APERO] flat - better deal with bad flat pixels. [njcuk9999]
[APERO] badpix - add erosion + dilution factors for large bad pixels. [njcuk9999]
[APERO] apero.science.extract.extraction.py - fix flat (do not correct too small or too large values) [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [Neil Cook]

# Conflicts: # bin/apero_flat_spirou.py
[NIRPS] add nirps to the documentation. [Neil Cook]
[APERO] todo deal with small number division in the flat. [njcuk9999]
[APERO] better patch edges of large bad pixel regions [NIRPS] update wave sols + catalogue. [njcuk9999]

0.7.235 (2022-05-31)¶

[NIRPS] add in telluric recipes. [njcuk9999]
[NIRPS] apero.tools.module.processing.drs_run_ini.py - add to run.ini files the nirps helios sequence. [njcuk9999]
Add changes to allow helios to be reduced. [njcuk9999]
Pep8 changes. [njcuk9999]
Update default nirps he wave solution + fix typo in WAVE_FIBER_OFFSET_MOD and WAVE_FIBER_SCALE_MOD. [njcuk9999]
Update default nirps he wave solution. [njcuk9999]
WAVEREF_EXPECTED to take diffvelo + allow offset/sclae of wave solution by N pixels. [njcuk9999]
Update header keys for nirps_he. [Neil Cook]

0.7.234 (2022-05-20)¶

Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [njcuk9999]
Add mk_tellu and mk_model to nirps_ha and nirps_he to sequences. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.232-working’ into v0.7.232-working. [Neil Cook]
Add mk_tellu and mk_model to nirps_ha and nirps_he. [Neil Cook]
Long and lat flipped for nirps (whoops) [njcuk9999]
Update tellu white list and default master wave sol for nirps_ha. [njcuk9999]

0.7.233 (2022-05-18)¶

Deal with no pmra/pmde in headers. [njcuk9999]
Update nirps_ha wave sol. [Neil Cook]
Update PP_OBJ_DPRTYPES (add OBJ_SKY) [Neil Cook]
For nirps we need to test whether OBJECT not in obstype (for SKY test) [Neil Cook]
Object type different for nirps - add REPROCESS_OBJECT_TYPES. [Neil Cook]
Add fit_tellu and mk_template for nirps_he/nirps_ha. [Neil Cook]
Update gain header key for nirps. [Neil Cook]
Update exptime for nirps. [Neil Cook]
Some speed up tests. [Neil Cook]
Update date/version/docs/changelog. [Neil Cook]

0.7.232 (2022-05-06)¶

Merge remote-tracking branch ‘origin/v0.7.228-working’ into v0.7.228-working. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.228-working’ into v0.7.228-working. [njcuk9999]
Replace PandasLikeDatabase with PandasLikeDatabaseDuckDB - speeds up post processing by factor of 5. [njcuk9999]
Update date/version/docs/changelog. [Neil Cook]

0.7.231 (2022-05-06)¶

Apero.science.polar.gen_pol.py - shift correctly all parameters stored in headers of the wave solution. [Neil Cook]
Create a pol_calib to store shifted blaze and wave + add WAVE_AB ad BLAZE_AB to p.fits from pol_calib. [Neil Cook]
Add a binary flag for when wave master is forced. [Neil Cook]
Apero.tools.recipes.bin.apero_database.py - add a reset database option. [Neil Cook]
Apero.io.drs_path.py - sort directories and valid_files. [Neil Cook]

0.7.230 (2022-05-04)¶

Apero.science.polar.gen_pol.py - deal with polar failing on orders with all NaN. [njcuk9999]
Mk_template now bins to avoid loading many images + correct berv coverage. [Neil Cook]

0.7.229 (2022-04-29)¶

Apero.data.spirou.databases.reset.calib.csv - uhash must be unique - generate hash for default values. [Neil Cook]
Apero.tools.module.database.manage_database.py - update database creation with additional unique columns in calib/tellu database. [Neil Cook]
Update reset calibration database (need UHASH column) [Neil Cook]
Apero.tools.recipes.bin.apero_explorer.py - correct getting hash arg. [Neil Cook]
Apero.core.core.drs_misc.py - do not use nan for doubles in stats. [Neil Cook]
Apero.core.utils.drs_utils.py - do not use nan for doubles. [Neil Cook]
Update date/version/docs/changelog. [Neil Cook]

0.7.228 (2022-04-28)¶

Add in PID, PDATE to calibration/telluric database add in RAM/SWAP/CPU column to log database. [Neil Cook]
Apero.recipes.spirou.apero_thermal_spirou.py - for DARK_DARK_INT force wave solution to master. [Neil Cook]
Apero.recipes.*.apero_extract_*.py - add way to force wave master in extraction + update recipe_definitions.py. [Neil Cook]

0.7.227 (2022-04-26)¶

Documentation.working.resources.default.descriptions.apero_astrometric s.rst - update the notes on apero_astrometrics. [Neil Cook]
Apero_astrometrics.py - allow aliases to be added and deal with Teff objname better. [Neil Cook]
Apero.tools.module.processing.drs_precheck.py - link conditions to run.ini file supplied (for checking obs_dir etc) [Neil Cook]
Apero.tools.module.drs_processing.py - add UPDATE_IDATABASE_NAME run.ini parameter (to allow turning off update certain databases) [Neil Cook]
Update the default run.ini files. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.225-working’ into v0.7.225-working. [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - fix problem with MJDMID having a NaN (float) value. [njcuk9999]
Apero_extract_spirou.py - add EXP_FPLINE flag. [Neil Cook]
Apero.recipes.spirou.apero_pol_spirou.py - do not allow files that failed qc to be used in polar recipe (by default) flag and return failure. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - remove index database crossmatch for qc mode (not required?) [Neil Cook]

0.7.226 (2022-04-21)¶

Apero.tools.resources.run_in.* - update templates for run.ini files to have UPDATE_INDEX_DATABASE flag. [Neil Cook]
Apero.tools.recipes.bin.apero_processing.py - add UPDATE_INDEX_DATABASE flag so user can not update the index database (needs big warning about doing this) [Neil Cook]
Apero.science.calib.leak.py - add in a second log for fiber loop [untested] [Neil Cook]
Apero.recipes.spirou.apero_leak_master_spirou.py - leak master has no qc - update recipe.log. [Neil Cook]
Apero.core.utils.drs_utils.py - no_qc must update children as well. [Neil Cook]
Apero.core.utils.drs_startup.py - add UPDATE_INDEX_DATABASE to allow not updating index database in apero_processing [UNTESTED] [Neil Cook]
Apero.core.instruments.spirou.default_constants.py - update WAVE_FP_DPRLIST (missed POLAR_FP) [Neil Cook]
Update some typos in default_keywords.py. [Neil Cook]
Correct typo and change NO_DB = False. [Neil Cook]
Apero.base.base.py - update LOG_FLAGS to include QCPASSED. [Neil Cook]
Apero.base.base.py - update LOG_FLAGS to include OBJ. [Neil Cook]
Update date/version/changelog/docs. [Neil Cook]

0.7.225 (2022-04-13)¶

Apero.science.extract.other.py - flag when extraction file has been found (require RecipeLog as input to extract_*_files functions) [Neil Cook]
Apero.core.instruments.*.recipe_definitions.py - add INT_EXT and EXT_FOUND flags to recipes that use apero_extract internally. [Neil Cook]
Apero.core.instruments.*.file_definitions.py - WAVEM_CAV should only be the main science fiber. [Neil Cook]
Apero.base.base.py - add log flag descriptions - can only add flags if the are here. [Neil Cook]

0.7.224 (2022-04-11)¶

Apero.tools.processing.drs_processing.py - update skip_clean_arguments to allow additional arguments. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - apero_water_master should be a master recipe always. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - correct typo “apero_loc.set_flags” –> “apero_extract.set_flags” [Neil Cook]

0.7.223 (2022-04-09)¶

Merge branch ‘v0.7.219-stable-test’ into v0.7.221-working. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.219-stable-test’ into v0.7.219-stable-test. [Neil Cook]
Fix tellurics and thermal problems. [njcuk9999]

0.7.222 (2022-04-03)¶

Update documentation. [Neil Cook]
Update documentation. [Neil Cook]
Update date/version/docs. [Neil Cook]

0.7.221 (2022-04-02)¶

Fixes for outclass (telluric centric fixes) [Neil Cook]
Fix problems with outclass + move running/in_parallel/ended to binary flag + add a flag mode in apero_explorer.py. [Neil Cook]

0.7.220 (2022-03-31)¶

Replace outfunc with outclass (a output file class) [Neil Cook]
Update error for database not found (was ambiguous) [Neil Cook]
Update date/version/docs/changelog. [Neil Cook]

0.7.219 (2022-03-27)¶

Bug fixes after nirps merge. [Neil Cook]
Merge branch ‘v0.7.213-nirps-he’ into v0.7.213-working. [Neil Cook]
Apero.tools.moduile.processing.drs_grouping_functions.py - get_non_file_args(): add an additional check on group being none before assigning obs_dir to group. [Neil Cook]
Add back in pp_master for nirps_he. [Neil Cook]
Re-run run.ini for nirps he. [Neil Cook]
Merge branch ‘v0.7.213-working’ into v0.7.213-nirps-he. [Neil Cook]

# Conflicts: # apero/core/core/drs_file.py
Apero_shape_master_nirps_he.py - update shape for nirps he + start preprocess changes. [Neil Cook]
Add flags to log database and test with preprocessing and loc. [Neil Cook]

0.7.218 (2022-03-24)¶

Apero.core.core.drs_base_classes.py - add binary dictionary (to store flags) - eventually use for log. [Neil Cook]
Apero.core.core.drs_file.py - switch axis in combined table - header keys are columns. [Neil Cook]
Apero.science.telluric.template_tellu.py - template header is now a combined header. [Neil Cook]
Update date/version/changelog/documentation. [Neil Cook]

0.7.215 (2022-03-21)¶

Apero.core.*.recipe_definitions.py - master night non master recipes should not have master=True, night cals should not have thermal master=True. [Neil Cook]
Drs_stats.py - correct typo LOG_FILE –> LOGFILE. [Neil Cook]
Drs_stats.py - add logfile and runstring to output timing stats. [Neil Cook]
Drs_stats.py - add pid to log output. [Neil Cook]

0.7.214 (2022-03-15)¶

Update run.ini files and all negative number of cores (to mean N-abs(cores)) [Neil Cook]
Apero_flat_*.py - remove e2ds saving. [Neil Cook]
Apero.core.constants.param_functions.py + apero.core.core.drs_file.py - add iloc (index database entries) to PARAM_TABLE. [Neil Cook]
Apero.recipes.spirou.apero_flat_*.py - write e2ds and e2dsll for flat files (as debug) [Neil Cook]
Apero.science.extract.gen_ext.py - make sure orderps files are added to index database (and have PARAM_TABLE) [ID by DRS-TEST] [Neil Cook]
Apero.science.calib.dark.py - fix bad naming of dark_master extensions [ID by DRS-TESTS] [Neil Cook]

0.7.216 (2022-03-11)¶

Install.py - fix database_ask criteria for reject database. [Neil Cook]
Install.py - do not validate if –help in args. [Neil Cook]
Update installer with reject database installation. [Neil Cook]
Apero_preprocessing.py - correct reject_infile() [Neil Cook]
Update apero_go.py. [Neil Cook]
Update run.ini files and add reject database to apero_database.py. [Neil Cook]
Update date, version, documentation, changelog. [Neil Cook]

0.7.213 (2022-03-09)¶

Merge branch ‘v0.7.209-neil-test’ into v0.7.208-working. [Neil Cook]
Apero.science.calib.shape.py - try again to close file. [Neil Cook]
Apero.science.calib.shape.py - must close file here. [Neil Cook]
Merge branch ‘v0.7.208-stable-test’ into v0.7.208-working. [Neil Cook]
Apero.tools.recipes.bin.apero_astrometrics.py - add an option to seach proper motion catalogues for the name even if it isn’t found in SIMBAD. [Neil Cook]
Apero.science.preprocessing.gen_pp.py - get the file reject list from the reject database. [Neil Cook]
Merge branch ‘v0.7.208-stable-test’ into v0.7.208-working. [Neil Cook]
Apero_astrometrics - correct bug with multiple teff values. [njcuk9999]

0.7.212 (2022-03-05)¶

Update language database. [Neil Cook]
Merge branch ‘v0.7.208-stable-test’ into v0.7.208-working. [Neil Cook]

# Conflicts: # apero/science/extract/extraction.py
Apero.science.extract.extraction.py - correct typo in extraction. [Neil Cook]
Apero.science.extract.extraction.py - correct typo in extraction. [Neil Cook]
Merge branch ‘v0.7.208-stable-test’ into v0.7.208-working. [Neil Cook]
Apero.tools.module.database.drs_astrometrics.py - make teff selection more logical. [Neil Cook]
Apero.tools.module.database.drs_astrometrics.py - make teff selection more logical. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.208-stable-test’ into v0.7.208-stable-test. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.208-stable-test’ into v0.7.208-stable-test. [njcuk9999]
Apero_astrometrics - correct bug with multiple teff values. [njcuk9999]
Update a todo. [Neil Cook]
Continue adding reject database. [Neil Cook]
Merge branch ‘v0.7.208-stable-test’ into v0.7.208-working. [Neil Cook]
Apeor.plotting.plot_functions.py - remove forced plot option. [Neil Cook]
Apero.tools.module.database.drs_astrometrics.py - deal better with masked rv value (no “–”) [Neil Cook]
Add reject database. [Neil Cook]
Add reject database. [Neil Cook]

0.7.211 (2022-03-03)¶

Apero.science.extraction.py - rearrange equations for speed up. [Neil Cook]
Replace np.nanfunc with mp.nanfunc (speed up) [Neil Cook]
Apero_precheck - get time from sci data if no calibrations. [njcuk9999]
Merge branch ‘v0.7.208-working’ into v0.7.208-stable-test. [Neil Cook]
Apero.core.instruments.*.recipe_definitions.py - update recipe definitions to add calib_required for those calibs that must be checked. [Neil Cook]
Apero.core.core.drs_database.py - only use “USED=1” objects from object database. [Neil Cook]
Apero.tools.module.processing.drs_precheck.py - remove the todo line setting all objs to be refound. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - do not get the index database if in timing mode (we don’t need it) [Neil Cook]
Merge branch ‘v0.7.208-working’ into v0.7.208-stable-test. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - do not crossmatch with index for timing mode. [Neil Cook]
Merge branch ‘v0.7.208-working’ into v0.7.208-stable-test. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - add dt vs start time plot. [Neil Cook]
Merge branch ‘v0.7.208-working’ into v0.7.208-stable-test. [Neil Cook]
Apero.tools.module.processing.drs_precheck.py - use original names for use in astrometrics. [Neil Cook]
Update requirements for astro_visu. [Neil Cook]
Update requirements for astro_visu. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update requirements for LAM (downgrade bottleneck) [Neil Cook]

0.7.210 (2022-02-23)¶

Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Update visualisation test code. [Neil Cook]
Test visualisations. [Neil Cook]

0.7.209 (2022-02-17)¶

Apero.plotting.plot_functions.py.plot_stats_timing_plot - deal with nrows=1 ncols=1. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - deal with None in END_TIME better. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - update timing error. [Neil Cook]
Apero.plotting.plot_functions.py - deal with case where nrows = 1. [Neil Cook]
Apero.tools.module.processing.drs_precheck.py - fix typo. [Neil Cook]
Apero.tools.module.processing.drs_precheck.py - only check obj names for science / hot star observations. [Neil Cook]
Update date/version/docs. [Neil Cook]

0.7.208 (2022-02-11)¶

Copyraw and add version to setup codes, point README.md the documentation. [Neil Cook]
Move the raw sym/copy in apero_get into setup (outside apero frame work) as it is probably only going to be used before installation. [Neil Cook]
Apero.recipes.spirou.apero_postprocess_spirou.py - correct typo filepostfile.out_requiredd –> filepostfile.out_required. [Neil Cook]
Merge branch ‘v0.7.205-stable-test’ into v0.7.205-working. [Neil Cook]
Apero.science.calib.wave.py - remove reference to NAXIS2 and NAXIS1. [Neil Cook]
Apero.tools.recipes.bin.apero_visu.py - for later use. [Neil Cook]
Apero.recipes.*.apero_wave_master_*.py. [Neil Cook]

0.7.207 (2022-02-07)¶

Apero.tools.recipes.bin.apero_get.py - create user_outdir path if it doesn’t exist. [Neil Cook]
Apero.tools.recipes.bin.apero_get.py - add in a raw copy/symlink option. [Neil Cook]
Apero.tools.recipes.bin.apero_get.py - move functionality to module + finish changes to filter by qc failures. [njcuk9999]
Apero.tools.recipes.bin.apero_get.py - only copy those with qc passed. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.205-stable-test’ into v0.7.205-stable-test. [Neil Cook]
Update how null columns are handled. [njcuk9999]
Apero.science.calib.thermal.py - fix ratio1 and ratio2 in Null case (should be ratio) [Neil Cook]
Apero.tools.module.database.drs_astrometrics.py - add way to not check pm (for dev only) [Neil Cook]
Apero.tools.module.database.drs_astrometrics.py - add way to attempt to update all missing teffs. [Neil Cook]
Apero.tools.module.database.drs_astrometrics.py - add way to attempt to update all missing teffs. [Neil Cook]
Apero.tools.module.database.dsr_astrometrics.py - work on updating teffs. [njcuk9999]
Apero.tools.module.database.manage_database.py - separate update and get object database functions. [Neil Cook]
Apero_astrometrics.py - add teff from disk if possible. [Neil Cook]
Update run.ini files. [Neil Cook]
Apero.core.core.drs_database.py - return only OBS_NAMES[objname] [njcuk9999]

0.7.206 (2022-02-03)¶

Update some documentation. [Neil Cook]
Update date/version/changelog/documentation. [Neil Cook]

0.7.205 (2022-02-01)¶

Merge remote-tracking branch ‘origin/v0.7.194-working’ into v0.7.194-working. [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - deal with SKY and CALIB object names. [njcuk9999]
Apero.core.core.drs_database.py - deal with special (calib/sky/test) better when trying to find aliases (don’t check) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.194-working’ into v0.7.194-working. [Neil Cook]
Apero.core.core.drs_fil.py - update DrsInputFile children to have instrument input. [njcuk9999]
Update PP_OBJ_DPRTYPES. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.194-working’ into v0.7.194-working. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.194-working’ into v0.7.194-working. [Neil Cook]

# Conflicts: # apero/tools/recipes/bin/apero_get.py
Obj fix. [Neil Cook]
Find_objname requires rawobjname not objname. [njcuk9999]
Apero.core.core.drs_database.py - save a list of obs names so we don’t do this multiple times per object. [Neil Cook]
Apero.tools.module.processing.drs_run_ini.py - correct pp_seq_opt (set all RUN_PP_XXX to False except those we want as True by default) [Neil Cook]
Continue dealing with aliases to object names. [Neil Cook]
Update documentation. [Neil Cook]
Update documentation. [Neil Cook]
Update documentation. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.194-working’ into v0.7.194-working. [Neil Cook]
Update object database / index database / header fix to check object name aliases for raw data and in preprocessing (everything after this point uses preprocessing names) [Neil Cook]

0.7.204 (2022-01-29)¶

Merge remote-tracking branch ‘origin/v0.7.194-working’ into v0.7.194-working. [Neil Cook]
Updates to apero_astrometrics.py to query pm catalogues for new coords/motions. [Neil Cook]
Apero_leak_master_nirps_he.py - fix extract name (ha–>he) [Neil Cook]
Apero.plotting.plot_functions.py - flip figure rows/cols + stokes parameter. [Neil Cook]
Apero.plotting.plot_functions.py - LSD param typos. [Neil Cook]
Apero.plotting.plot_functions.py - pprops and lprops –> props. [Neil Cook]
Apero.science.polar.lsd.py - linevelo[jpos] –> linevelo[pix] [Neil Cook]
Apero.plotting.plot_functions.py - typo tab:b -> tab:blue. [Neil Cook]
Add labels to plot_polar_fit_cont graph. [Neil Cook]

0.7.203 (2022-01-28)¶

Apero.plotting.plot_functions.py - more plot fixes. [Neil Cook]
Apero.plotting.plot_functions.py - more plot fixes. [Neil Cook]
Apero.plotting.plot_functions.py - more plot fixes. [Neil Cook]
Apero.plotting.plot_functions.py - correct more typos. [Neil Cook]
Apero.plotting.plot_functions.py - correct typo NEXPOSURES –> N_EXPOSURES. [Neil Cook]
Apero.plotting.plot_functions.py - deal with contx being None. [Neil Cook]
Apero.plotting.plot_functions.py - CONT_XBIN, CONT_YBIN -> CONT_POL_XBIN, CONT_POL_YBIN. [Neil Cook]
Apero.plotting.plot_functions.py - FLAT_X –> FLAT_WLDATA. [Neil Cook]
Apero.plotting.plot_functions.py - plot_polar_fit_cont correct plot. [Neil Cook]
Apero.plotting.plot_functions.py - plot_polar_fit_cont correct typo s–>ms. [Neil Cook]
Apero.science.polar.gen_pol.py - typo PLOT_POLAR_FIT_CONT –> POLAR_FIT_CONT. [Neil Cook]
Apero.science.polar.gen_pol.py - typo POLAR_FIT_CONT –> PLOT_POLAR_FIT_CONT. [Neil Cook]
Apero.insturments.spirou.recipe_definitions.py - polar code –exposures should not be required. [Neil Cook]
Apero.core.instruments.*.default_keywords.py - remove KW_THERM_RATIO_2. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.194-working’ into v0.7.194-working. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.194-working’ into v0.7.194-working. [njcuk9999]
Apero.core.core.drs_file.py - deal better with exclude keys in post processing. [njcuk9999]
Apero.core.instruemnts.*.default_constants.py - add LSD MAX LINEDEPTH. [Neil Cook]
Add excess emissivity csv file (default file for the drs) [Neil Cook]
Add excess emissivity changes. [Neil Cook]
Add new lsd masks. [Neil Cook]
Add polar changes (Eder update for 0.7) [Neil Cook]

0.7.202 (2022-01-26)¶

Move leak and thermal to own calib py files and start excess emissivity work. [Neil Cook]
[NIRPS_HE] apero.science.preprocessing.detector.py - account for too much flux between pixels. [Neil Cook]
Correct mini runs for nirps_he and nirps_ha. [Neil Cook]
Update documentation (put examples for apero_get in correct place) [Neil Cook]

0.7.201 (2022-01-25)¶

Updates to get nirps-he working (currently on preprocessing) [Neil Cook]
Update language database. [Neil Cook]
Apero.science.extract.gen_ext.py - correct typo THERMALFF_RATIO to THERMALFF_RATIO_USED. [Neil Cook]
Update lang messages that are warnings/errors to display error code. [Neil Cook]
Apero.core.core.drs_file.py - must copy exclude keys. [Neil Cook]
Apero.core.core.drs_file.py - need to deal with DrsOutFile.exclude_keys = None. [Neil Cook]
Apero.tools.recipes.spirou.apero_postprocess_spirou.py - allow polar code to skip certain files (i.e. if DRSMODE=SPECTROSCOPY or UNKNOWN there will not be any p files to product) [Neil Cook]
Apero.tools.recipes.bin.apero_astrometrics.py - need to add old name to aliases. [Neil Cook]
Apero.tools.recipes.bin.apero_astrometrics.py - need to update astro_obj.objname. [Neil Cook]
Update apero_astrometrics.py and apero_precheck.py with new options. [Neil Cook]
Update docs for dev tools + some optimization. [Neil Cook]

0.7.200 (2022-01-25)¶

Update docs for dev tools + some optimization. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.194-working’ into v0.7.194-working. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.194-working’ into v0.7.194-working. [Neil Cook]
Remove _ = display_func and use of Constants = constants.load() where possible. [Neil Cook]
Add a mode to thermal correction (tapas vs percentile) + add the thermal ratios to header. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.194-working’ into v0.7.194-working. [njcuk9999]
Recipe_definitions for astrometric code wrong. [Neil Cook]
Recipe_definitions for astrometric code wrong. [Neil Cook]
Update requirements pillow + ipython. [Neil Cook]
Apero.science.extract + telluric - fix magic grid (no divide by 1000) [njcuk9999]

0.7.199 (2022-01-21)¶

Update some recipe definitions for dev tools. [Neil Cook]
Apero.science.polar.gen_pol.py - deal with full order having no good (all NaNs) pixels. [njcuk9999]

0.7.198 (2022-01-20)¶

Update documentation descriptions for user tools. [Neil Cook]
Update documentation descriptions for user tools. [Neil Cook]
Update documentation descriptions for user tools. [Neil Cook]
Update documentation descriptions for user tools. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - deal with no unhandled errors found. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - check for PPLOG = None. [Neil Cook]
Apero.tools.recipes.bin.apero_stats.py - error mode requires plog. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - append after errors caught (otherwise x,y and m could be different lengths) [Neil Cook]
Apero.tools.module.drs_documentation.py - fix capitalization (just first word) [Neil Cook]
Only clean auto files if we are redoing all automatically created files. [Neil Cook]
Rearrange doc structure + fix warnings + add tools and dev tools + clean auto files before restarting. [Neil Cook]
Rearrange doc structure. [Neil Cook]
Update documentation code + recipe definitions + file definitions + update docs. [Neil Cook]

0.7.197 (2022-01-13)¶

Merge remote-tracking branch ‘origin/v0.7.194-working’ into v0.7.194-working. [njcuk9999]
Apero.science.calib.flat_blaze.py - add warning message that we are trying sinc fit again + update language database. [Neil Cook]
Apero.science.calib.flat_blaze.py - sometimes does not fit (but not reproducible) try again 5 times and then report error. [Neil Cook]
Apero.recipes.spirou.apero_postprocess_spirou.py - correct error reporting. [njcuk9999]
Apero.core.instruments.spirou.file_definitions.py - cannot take tellu from telluric database (shouldn’t be the closest - should match odometer (KW_IDENTIFIER) [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - TELLU A and B files not in telluric database (should they be?) [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - tellurics from telluric database? [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - t.fits hlink for telluric files should be from database (shouldn’t save if qc wasn’t passed) [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - fix typo OBJ_HC2 –> OBJ_HCTWO. [Neil Cook]

0.7.196 (2022-01-12)¶

Update the language database. [Neil Cook]
Apero.science.calib.gen_calib.py - update pass message for calib delta time + language database. [Neil Cook]
Apero.science.calib.gen_calib.py - update pass message for calib delta time + language database. [Neil Cook]
Apero.science.calib.gen_calib.py - improve error for calib delta time. [Neil Cook]
Problem with error code 09-002 and 09-003. [Neil Cook]
Correction of magic grid function (from lbl changes) [Neil Cook]

0.7.195 (2021-12-27)¶

Apero.tools.module.setup.drs_isntallation.py - user_instrument must be a string. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - self.index is dataframe. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - PID–>KW_PID. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - obtain the index database once and pass dataframe to classes. [Neil Cook]
Update date/version/changelog/docs. [Neil Cook]

0.7.194 (2021-12-22)¶

Merge remote-tracking branch ‘origin/v0.7.193-working’ into v0.7.193-working. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - deal with masked columns and force str/float for all ftable row values (into tabledict) [njcuk9999]
Deal with postprocess wave/blaze from calibration (may not be present in index database) [Neil Cook]
Update language database for template skipped recipes. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py + file_definitions.py - for mini data pol + ccf should only include science_targets. [Neil Cook]
Apero.recipes.spirou.apero_postprocess_spirou.py - move around errors. [njcuk9999]
Apero.core.core.drs_database.py - correct column order in update_header_fix() [Neil Cook]
Apero.core.core.drs_database.py - correct typos OBS_KIND–>OBS_DIR. [Neil Cook]
Astropy (np>1.18) and numba (<1.12) conflict on numpy –> np=1.20.3. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.7.193 (2021-12-20)¶

Apero.recipes.spirou.apero_postprocess_spirou.py - move text to language database. [Neil Cook]
Apero.recipes.spirou.apero_postprocess_spirou.py - combien textentry better. [Neil Cook]
Apero.recipes.spirou.apero_postprocess_spirou.py - better handle error reporting. [Neil Cook]
Apero.recipes.spirou.apero_postprocess_spirou.py - report error numbers. [Neil Cook]
Apero.recipes.spirou.apero_postprocess_spirou.py - report error numbers. [Neil Cook]
Update language database. [Neil Cook]
Apero.recipes.spirou.apero_postprocess_spirou.py + apero.core.core.drs_file.py - add changes to report errors better in post processing. [Neil Cook]
Apero.science.calib.flat_blaze.py - correct strlist for sinc fit (error reporting caused exception which hides actual error) [Neil Cook]

0.7.192 (2021-12-17)¶

Update language database. [Neil Cook]
Apero.science.extract.berv.py - check whether both barycorrpy and pyasl are nan + deal better in pyasl with no distance (and give error when ra/dec are nan because of bad apply_space_motion) [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.182-working’ into v0.7.182-working. [njcuk9999]
Update DrsDatabaseErrors. [Neil Cook]
Update the install module to work with command line args (see install_script.sh) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.182-working’ into v0.7.182-working. [njcuk9999]
Apero.core.instruemnts.spirou.pseudo_const.py - get output type for header/hdict (otherwise drsfile is updated) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.182-working’ into v0.7.182-working. [njcuk9999]
Update FILEDEF_HEADER_KEYS (for spirou to include polar keys) [Neil Cook]
Fixes for errors with full run 211018. [njcuk9999]

0.7.191 (2021-12-15)¶

Apero.tools.module.testing.drs_stats.py - update error mode. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - update error mode. [Neil Cook]
Apero.tools.module.testing.drs_stats.py - update error mode. [Neil Cook]
Add an error mode to the apero_stats.py module. [Neil Cook]
Apero.tools.moduile.recipes.bin.apero_astrometerics.py - finalise design (move functionality to drs_astrometrics.py. [Neil Cook]
Apeor.science.velocity.gen_vel.py - Fix CamelCase column names. [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - make S1D files have tag UniformWavelength/UniformVelocity. [Neil Cook]
Remove auth keys for google sheet. [Neil Cook]
Tools.recipes.bin.apero_astrometrics.py - add code to get/write to googlesheet. [Neil Cook]
Apero.tools.recipes.bin.apero_astrometrics.py - add astrometrics code [unfinished] [Neil Cook]

0.7.190 (2021-12-08)¶

Apero.tools.module.testing.drs_stats.py - fix qc stat plot. [Neil Cook]
Debug printout tables= [Neil Cook]
Debug printout tables= [Neil Cook]
Debug printout tables= [Neil Cook]
Apero.base.drs_db.py - infer table name when getting columns. [Neil Cook]
Apero_stats.py - add qc mode (unfinished) [Neil Cook]
Apero_stats.py - add qc print outs [still need qc plots] [Neil Cook]
Apero_stats.py - add qc mode (unfinished) [Neil Cook]
Setup.install.py - add fix for Issue #676 - weird module version must be set in module_translation. [Neil Cook]

0.7.189 (2021-12-06)¶

Add timing to apero_stats (formly apero_log_stats) - still need QC and error checks. [Neil Cook]
Remove ABSPATH (not indexed) in favour of BLOCK_KIND + OBS_DIR + FILENAME. [Neil Cook]
Allow thermal correction for telescope dark to use internal dark if telescope dark is mising. [Neil Cook]
Re-make run.ini files with changes to thermal code. [Neil Cook]
Re-make run.ini files with changes to thermal code. [Neil Cook]
Apero.tools.module.processing.drs_precheck.py - update precheck to handle exclusive/inclusive drs file lists. [Neil Cook]
Add quality control in preprocessing to catch DARK_DARKs that contain science data - these will not be preprocessed. [Neil Cook]
Update run.ini files + typo in msg. [Neil Cook]
Finish apero_run_ini.py code. [Neil Cook]

0.7.188 (2021-12-01)¶

Continue work on run.ini auto make. [Neil Cook]
Continue work on apero_run_ini.py. [Neil Cook]
Continue work on apero_run_ini.py. [Neil Cook]

0.7.187 (2021-11-24)¶

Apero.tools.module.processing.drs_precheck.py - must mask out other bad nights before comparing the 7 day rule. [Neil Cook]
Apero.tools.module.processing.drs_precheck.py - add a way to filter which nights are actually bad and which nights aren’t. [Neil Cook]
Apero.base.drs_db.py - must set number of tries after super call. [Neil Cook]
Deal with language database trying to connect multiple times. [Neil Cook]
Apero.core.core.drs_argument.py - don’t load database until required. [Neil Cook]
Apero_get.py - problem with AND when no object condition. [Neil Cook]
Apero.base.drs_db.py - fix create index on multiple columns. [Neil Cook]
Apero.tools.module.drs_reset.py - pep8 fixes. [Neil Cook]
Apero.tools.module.drs_reset.py - add faster remove approach (when we have none or a few skip files) [Neil Cook]
Apero.tools.module.database.manage_database.py + apero.core.core.drs_database.py - fix idb_cols.get_index_groups. [Neil Cook]
Remove circular imports to PandasLikeDatabase (move to drs_base_classes.py) [Neil Cook]
Remove requirement for database.tname when tname set in database. [Neil Cook]

0.7.186 (2021-11-23)¶

Apero.core.core.drs_file.py - pep8 move comment. [Neil Cook]
Apero.core.core.drs_argument.py - remove pandas database store. [Neil Cook]
Apero.core.core.drs_database.py + drs_file.py - load the whole database entry for that night. [Neil Cook]
Apero.tools.recipes.bin.apero_get.py - allow no objname. [Neil Cook]

0.7.185 (2021-11-19)¶

Deal with loading. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.182-working’ into v0.7.182-working. [Neil Cook]
Option to turn off using database in arguments calls. [Neil Cook]
Apero.core.instruments.*.file_definitions.py - _wavesol_master_ –> _wavesol_master (removes double __) [Neil Cook]

0.7.184 (2021-11-17)¶

Apero.tools.recipes.dev.apero_run_ini.py - first commit and code for auto generating run.ini files [unfinished] [Neil Cook]
Update UPDATE_NOTES.txt. [Neil Cook]
Apero.core.core.drs_log.py - change recipe type when extract used inside another recipe. [Neil Cook]
Apero.core.utils.drs_startup.py - change recipe type when extract used inside another recipe. [Neil Cook]
Update log dir for recipes calling extract recipe. [Neil Cook]
Update log dir for recipes calling extract recipe. [Neil Cook]
Update UPDATE_NOTES.txt. [Neil Cook]
Apero.core.utils.drs_startup.py + apero.core.core.drs_file + drs_log.py - get the obs_dir (without path) for logging - log messages to subdir. [Neil Cook]

0.7.183 (2021-11-12)¶

Apero.recipe.spirou.apero_extract_spirou.py - add combine method argument. [Neil Cook]
Update date/version/changelog/update notes/documentation. [Neil Cook]

0.7.182 (2021-11-10)¶

Apero.core.core.drs_database.py - do not log error in read_header - pass exception back to handler. [njcuk9999]
Apero.core.core.drs_database.py - when updating index if we can’t get header skip it - bad files should not crash the process here - but we should warn the user. [Neil Cook]
Apero.core.instruments.default.pseudo_const.py - update cleaning of object name now “+” goes to P and “-” goes to M by default. [Neil Cook]

0.7.181 (2021-11-09)¶

Update run.ini files for default skip parameters. [Neil Cook]
Apero.recipes.spirou.apero_ccf_spirou.py - corrections for teff mask change. [Neil Cook]
Apero.core.instruments.default.recipe_definitions.py - update precheck descriptions. [Neil Cook]
Apero.tools.module.processing.drs_precheck.py - update name of precheck module. [Neil Cook]
Apero.tools.recipes.bin.apero_precheck.py + apero.tools.module.processing.drs_precheck.py - add precheck code (check before running apero_processing) for checking raw calibration files, raw telluric files, raw science files and object names (from database vs header) [Neil Cook]
Apero.io.drs_fits.py - correct typo fits.getdata –> fits.getheader. [Neil Cook]

0.7.180 (2021-11-06)¶

Make fure all FTELLU1 and FTELLU2 are FTFIT1 and FTFIT2. [Neil Cook]
Apero.io.drs_fits.py - correct typo fits.getheader –> fits.getdata. [Neil Cook]
Update date/version/changelog/docs/update notes. [Neil Cook]

0.7.179 (2021-11-04)¶

Merge branch ‘v0.7.173-stable-test’ into v0.7.173-obj-res-test. [Neil Cook]
Apero.science.calib.shape.py - deal with shape master having more nights than the max number of shape files (means each group will only have one entry and all were skipped) change to single file groups being kept (just not combined) [njcuk9999]
Apero.io.drs_fits.py - need to deal with getdata for bad files (maybe corrupted but don’t always need all extensions) [Neil Cook]
Science.preprocessing.gen_pp.py need to deal with converting astrometrics from header to required units (assume database is good) [Neil Cook]
Update language database. [Neil Cook]
Add readme to each ccf_mask directory. [Neil Cook]
Default ccf mask now uses Teff (via teff_mask.csv) to assign masks - can still use old method with filename if desired. [Neil Cook]
Apero.science.extract.berv.py - typo set_sources–>set_source. [Neil Cook]

0.7.178 (2021-11-03)¶

Force bad values of plx/rv. [Neil Cook]
Preprocessing + berv correction - simplify to use gsheet(s) and do not match. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - only print about engineering nights once + remove “Removing filters” printout. [Neil Cook]

0.7.177 (2021-11-02)¶

Make sure FTFIT1 and FTFIT2 are in the run.ini files. [Neil Cook]
Apero.core.core.drs_database.py - clear TLOG + typo in comment. [Neil Cook]
Try to improve getting file list from disk (avoid glob due to max open file holders) [Neil Cook]
Remove env files. [Neil Cook]

0.7.176 (2021-10-29)¶

Apero.science.calib.wave.py - deal with no cavity degree polynomial (i.e. from the default master wave sol) [Neil Cook]
Apero.science.calib.wave.py - correct getting cavity polynomial from header. [Neil Cook]

0.7.175 (2021-10-22)¶

Apero.core.math.fast.py - fix weird typo np.array(guess) –> float(guess) [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.173-working’ into v0.7.173-working. [Neil Cook]
Apero.core.math.fast.py - update odd_ratio_mean function. [Neil Cook]

0.7.174 (2021-10-19)¶

Update schematics for paper. [Neil Cook]
Update schematics for paper. [Neil Cook]
Update date/version/changelog/documentation. [Neil Cook]

0.7.173 (2021-10-18)¶

Update language database. [Neil Cook]
Apero.core.core.drs_log.py - update log. [Neil Cook]
Update warning messages to have sublevel. [Neil Cook]

0.7.172 (2021-10-13)¶

Science.telluric.gen_tellu.py - fix the width of the preclean ccf (now a low pass filter) [Neil Cook]
Apero.core.utils.drs_utils.py+ apero.science.calib.dark.py + shape.py - fix the down selection of master files (selected by time) [Neil Cook]
Update the run.ini files + add the fit_tellu res_plot in the plotter functions. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.7.171 (2021-10-08)¶

Apero.science.calib.dark.py + apero.science.calib.shape.py - add limits for the dark master and shape master max number of files. [Neil Cook]
Apero.science.extract.gen_ext.py - fix output for thermal files. [Neil Cook]
Telluric update (EA-210923) - add apero_mk_model_spirou.py + add changes to fit_tellu + pre-cleaning. [Neil Cook]
Apero.recipes.*.apero_wave_*.py - deal with and comment fit_cavity and fit_achromatic better. [Neil Cook]
Update language database. [Neil Cook]
Apero.io.drs_fits.py - read with multifits return better. [Neil Cook]
Update run.ini files that use telluric recipes. [Neil Cook]
Apero.core.instruments.*.recipe_definitions.py - update telluric recipe_definitions.py. [Neil Cook]
Apero.core.instruments.*.file_definitions.py - add TELLU_MODEL to file_definitions.py. [Neil Cook]
Apero.core.instruments.*.default_constants.py - update tellup_ccf_scan_range + thermal_extract_type (e2dsff–>e2ds) [Neil Cook]
Continue work on transmission model update [EA 210923] [Neil Cook]
Continue work on transmission model update [EA 210923] [Neil Cook]

0.7.170 (2021-10-04)¶

Start work on telluric update (EA-210923) [Neil Cook]
Unbreak logging system (conflict with OBS_DIR) [Neil Cook]
Conflict between obs_dir from params and run_file. [Neil Cook]
Wave extraction needs to use master wave sol. [Neil Cook]
Wave extraction needs to use master wave sol. [Neil Cook]
Wave extraction needs to use master wave sol. [Neil Cook]
Apero.core.utils.drs_startup.py - deal with locking params better. [Neil Cook]
Update date/version/docs/changelog. [Neil Cook]

0.7.169 (2021-10-01)¶

Apero.science.extract.gen_ext.py - leak correction must use reference fiber (not science fiber) to scale dark_fp correction. [Neil Cook]
Apero.science.wave.py - add cavity/cavity_deg/mean_hc_vel/err_hc_vel to wprops (for storing in header) [Neil Cook]
Apero.recipes.*.apero_extract_*.py - reference fiber must be extracted first - other fibers use reference fiber for leak correction. [Neil Cook]
Update language database. [Neil Cook]
Apero.core.instruments.*.default_keywords.py - add CDBLEAKR/CDTLEAKR/WCAV/WCAV_DEG/WAVEMHC/WAVEEMHC keywords. [Neil Cook]
Add leakm (file and time) to the extracted header, do not filter master calibrations by dtime for calib vs obs (now use a CalibFile class to store info) [Neil Cook]
Allow run file as an argument to recipes - (–crunfile) this allows passing a constant in the run.ini file when running apero_processing.py. [Neil Cook]

0.7.168 (2021-09-29)¶

Apero.core.core.drs_database.py - deal with unix time better (may be np.nan oir none time –> in these cases set to None) [njcuk9999]
Apero.recipes.*.apero_extract_nirps*.py - correct position in foout 3–>2 2–>1 1–>0. [njcuk9999]
Apero.science.extract.gen_ext.py - LEAK_CORRECTED is in eprops not params. [njcuk9999]

0.7.167 (2021-09-28)¶

Merge branch ‘v0.7.156-working’ into v0.7.166-working. [njcuk9999]
Apero.core.instruments.default.grouping.py - deal with no table (rawtab = None) [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.156-working’ into v0.7.156-working. [njcuk9999]
Merge remote-tracking branch ‘origin/v0.7.156-working’ into v0.7.156-working. [njcuk9999]
Merge branch ‘v0.7.156-working’ of github.com:njcuk9999/apero-drs into v0.7.156-working. [njcuk9999]
Merge branch ‘v0.7.156-working’ of github.com:njcuk9999/apero-drs into v0.7.156-working. [njcuk9999]
Apero.core.core.drs_database.py - deal with removed files from the database. [njcuk9999]
Update language database. [Neil Cook]
Fix error in post products not adding wave files. [Neil Cook]
Update language database. [Neil Cook]
Update update notes. [Neil Cook]
Apero.core.instruments.*.default_constants.py - add DO_CALIB_DTIME_CHECK and MAX_CALIB_DTIME. [Neil Cook]
Apero.science.calib.gen_calib.py - add in a way to check delta time on observation vs calibration. [Neil Cook]
Remove log.txt. [Neil Cook]
Update date/version/changelog/documentation. [Neil Cook]

0.7.166 (2021-09-27)¶

Update language database. [Neil Cook]
Apero.science.calib.wave.py - replace mean rv fit diff with mean of difference of rvs in orders. [Neil Cook]
Apero.core.instruemnts.default.default_keywords.py - the default key=’’ should be key=’NULL’ (otherwise get comments list) [Neil Cook]
Apero.science.telluric.template_tellu.py - correct b_cols. [Neil Cook]

0.7.165 (2021-09-25)¶

Apero.science.calib.wave.py - fix typo WLOG(params, msg) –> WLOG(params, ‘’, msg) [Neil Cook]
Apero.science.calib.gen_calib.py - deal with returning None (cannot case filename to string) [Neil Cook]
Apero.recipes.spirou.apero_extract_spirou.py - correct indices on fbprops. [Neil Cook]
Apero.science.calib.gen_calib.py + apero.science.extract.gen_ext.py - fix calib file being None in wave sol + orderp does n ot have CDTORDP (use MJDMID) [Neil Cook]
Apero.science.calib.shape.py + apero.science.extract.gen_ext.py - use sprops. [Neil Cook]
Apero.recipes.*.apero_extract/flat*.py - push sprops into order_profiles. [Neil Cook]
Apero.recipes.*.apero_shape_*.py - poush sprops into write. [Neil Cook]
Apero.core.instruments.*.file_definitions.py - change orderp_straight to DrsFitsFile. [Neil Cook]
Apero.core.core.drs_file.py - allow coping of hdict / header without drsfile instance. [Neil Cook]
Apero.core.core.drs_database.py - do not fix headers for non fits files. [Neil Cook]
Apero.science.calib.gen_calib.py - fix load_calib_file (add return_time=True) [Neil Cook]
Apero.core.core.drs_database.py - fix ctable output. [Neil Cook]
Add calibration MJDMID to all files that use CDBXXXX (as CBTXXXX) [Neil Cook]

0.7.164 (2021-09-23)¶

Apero.science.calib - wave.py - print out CCFRV as well as DV tests. [Neil Cook]
Apero.core.core.drs_database.py - change message 40-001-00031 from general to debug print out (“Skipping search”) [Neil Cook]
Apero.core.instruments.*.default_constants.py - change cosmic intcut from 10-50 to 50-100. [Neil Cook]
Apero.data.spirou.calib.catalogue_UNe.csv - add red most lines [EA] from large catalogue. [Neil Cook]
Apero.core.instruments.spirou.default_constants.py - add back in order 48 to wave solution. [Neil Cook]

0.7.163 (2021-09-22)¶

Update requirements (untested) [Neil Cook]
Apero.core.instruments.* - make all instruments consistent (groups + other) [Neil Cook]
Apero.tools.module.processing.drs_processing.py - deal with non raw filter keys on raw files (ignore) [Neil Cook]
Update catalogues from Etienne. [Neil Cook]
Flat + wave - combine with sum not median. [Neil Cook]

0.7.162 (2021-09-22)¶

Need to deal with raw keys only. [Neil Cook]
Apero.recipes.spirou.apero_flat_spirou.py - [REVERT] flats should be summed not medianed [EA] [Neil Cook]
Apero.recipes.spirou.apero_flat_spirou.py - flats should be summed not medianed [EA] [Neil Cook]
Update version/date/changelog/documentation. [Neil Cook]

0.7.161 (2021-09-15)¶

Apero.base.base.py + apero.core.core.drs_loy.py - make sure use of DPARAMS and IPARAMS give correct exception. [Neil Cook]
Apero.core.core.data.*.databases.reset* - WAVEM_D –> WAVESOL_DEFAULT. [Neil Cook]
Update UPDATE_NOTES.txt. [Neil Cook]
Apero.core.core.drs_database.py - need to deal with forbidden keys better (comment, history and ‘’ included) [Neil Cook]
Apero.data.*.reset.runs/master_calib_run.ini - typo calib_seq –> master_seq. [Neil Cook]
Requirements_developer.txt - ttkthemes required. [Neil Cook]
Apero.tools.module.database.database_update.py - fix rlog values (now attributes are upper case) [Neil Cook]
Apero.science.extract.gen_ext.py - add debug saving of e2ds uncorrected. [Neil Cook]
Apero.recipes.*.apero_extract_*.py - add recipe to manage_leak_correction arguments. [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - add ‘’ and ‘HISTORY’ to forbidden keys. [Neil Cook]
Remove apero_leak as recipe. [Neil Cook]
Apero.core.core.drs_file.py - skip forbidden header keys. [Neil Cook]

0.7.160 (2021-09-14)¶

Apero.recipe.spirou.apero_extract_spirou.py - get leakcorr from data_dict (i.e. via science.extract.other.py extract_files()) [Neil Cook]
Apero.science.calib.flat_blaze and apero.science.extract.extraction + gen_ext + other - fix blaze keys. [Neil Cook]
Language database update. [Neil Cook]
Apero.core.utils.drs_startup.py - fix logging of DrsCodedException. [Neil Cook]
Apero.core.instruments.*.recipe_definitions.py - add argument –leakcorr to apero_extract. [Neil Cook]
Apero.core.instruments.*.default_constants.py - remove ALLOWED_LEAK_TYPES add CORRECT_LEAKAGE and LEAKAGE_REF_TYPES. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - must not update database in test run for Pool and Process. [Neil Cook]
Update language database. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - deal with runs not in ini files (now skips by default) [Neil Cook]
Apero.core.instruments.*.recipe_definitions.py - for nirps KW_OBJNAME not Calibration use RAW_DPRCATG as CALIB. [Neil Cook]
Apero.data.*.reset.runs.calib_run.ini - add PP_FF to RUN_ and SKIP_ menus. [Neil Cook]
Apero.core.utils.drs_recipe.py - add files to set. [Neil Cook]
Apero.core.utils.drs_recipe.py - need to filter by files (why was this removed?) [Neil Cook]
Apero.tools.module.processing.drs_processing.py - do not update database in test run mode. [Neil Cook]
Apero.core.instruments.*.recipe_definitions.py - pp_seq_opt typo add(apero_extract –> add(apero_preprocess. [Neil Cook]
Apero.core.instruments.*.file_definitions.py - make sure types have outfunc set. [Neil Cook]
Apero.core.instruments.*.recipe_definitions.py - leak_master should use E2DS not E2DSFF (change in where we do leak correction in extraction process) [Neil Cook]
Apero.core.instruments.nirps_ha.file_definitions.py - remove out_wave_hc and out_wave_fp references. [Neil Cook]

0.7.159 (2021-09-10)¶

Add leak to extraction recipe (break up flat blaze corr) [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - add DRS_DATE_NOW (DRSPDATE) to index database. [Neil Cook]
Revert UNe catalogue list. [Neil Cook]
Wave - fix default and master wave solution names. [Neil Cook]

0.7.158 (2021-09-03)¶

Update indexing (index KW_MID_OBS_TIME, KW_OBJNAME, KW_DPRTYPE, KW_OUTPUT, KW_PID, KW_IDENTIFIER) [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py + apero_postprocess_spirou.py - change overwrite to skip - default is now to overwrite. [Neil Cook]
Apero.data.*.reset.runs.complete_run.ini - full_seq should use EXTALL and LEAKALL. [Neil Cook]
Apero.data.spirou.reset.runs.*.ini - update master nights. [Neil Cook]

0.7.157 (2021-08-30)¶

Apero.recipes.spirou.apero_postprocess_spirou.py - set_infile must take params (dealing with multiple possible DrsFitsFiles for single extension) [Neil Cook]
Apero.science.calib.wave.py - remove references to WAVE_FP and WAVE_HC (use WAVE_NIGHT) and WAVEM_FP and WAVEM_HC (use master wave sol) [Neil Cook]
Apero.core.instruments.*.file_definitions.py + recipe_definitions.py - remove old definitions and make sure recipes use the new ones. [Neil Cook]
Apero.core.core.drs_file.py - need to allow multiple drsfiles for some outfile extensions. [Neil Cook]
Update version/date/changelog/documentation. [Neil Cook]

0.7.156 (2021-08-26)¶

Apero.base.drs_db.py - fix backup db directory. [Neil Cook]
Apero.science.telluric.fit_tellu.py - correct scaling on tcorr A and B (needed blazeAB for reconAB not blazeA or blazeB) [Neil Cook]
Apero.science.calib.wave.py - fix master wave. [Neil Cook]
Update date/version/changelog/documents. [Neil Cook]

0.7.155 (2021-08-25)¶

Apero.core.core.drs_database.py - update reset + add key error for PandasDBStorage.get. [Neil Cook]
Apero.tools.recipes.bin.apero_processing.py - move update index db stuff to function (for use elsewhere as well) + add indexdbm to args of process_run_list. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - add an update_index_db function to deal with updates to block kinds (add it to multiprocesses so that after recipe finished all block kinds are updated) [Neil Cook]
Apero.database.database_update.py - correct inputs for index_update. [Neil Cook]
A[erp/cpre/cpre/drs_database.py - add subkey option to reset. [Neil Cook]
Apero.core.core.drs_database.py - add classes PandasDBStorage (for storage) and PandasLikeDatabase (proxy pandas dataframe as database) to allow re-use of same databases / arrays instead of re-querying sql databases. [Neil Cook]
Apero.base.drs_db.py - add to doc string. [Neil Cook]
Apero.core.core.drs_argument.py - only read database once if in parallel mode and store in global way for other iterations. [Neil Cook]
Update requirements - now require pandasql for efficiency. [Neil Cook]
Apero.science.calib.wave.py - wave solution should use WAVE_FP and WAVE_HC not WAVEM_FP and WAVEM_HC. [Neil Cook]
Apero.science.calib.localisation.py - all_labels –> all_labels2. [Neil Cook]

0.7.154 (2021-08-23)¶

Apero.core.instruments.default.grouping.py - better handle masked table: table.mask[colname] not table[colname].mask. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.151-working’ into v0.7.151-working. [Neil Cook]
Repo visualizer: updated diagram. [repo-visualizer]
Workflows.diagram.yml - avoid making new commit on push. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.151-working’ into v0.7.151-working. [Neil Cook]
Repo visualizer: updated diagram. [repo-visualizer]
Apero.base.drs_db.py - update path for sql to be in ~/.apero/ (for backups only) [Neil Cook]
Apero.plotting.plot_functions.py - plots using fiber should have fiber in the suffix. [Neil Cook]
README.md - update code diagram description. [Neil Cook]

0.7.153 (2021-08-20)¶

Repo visualizer: updated diagram. [repo-visualizer]
Update readme and diagram.yml. [Neil Cook]
Repo visualizer: updated diagram. [repo-visualizer]
Update readme and diagram.yml. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.151-working’ into v0.7.151-working. [Neil Cook]
Repo visualizer: updated diagram. [repo-visualizer]
Update readme and diagram.yml. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.151-working’ into v0.7.151-working. [Neil Cook]
Repo visualizer: updated diagram. [repo-visualizer]
Update readme and diagram.yml. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.151-working’ into v0.7.151-working. [Neil Cook]
Repo visualizer: updated diagram. [repo-visualizer]
Update diagram yaml. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.151-working’ into v0.7.151-working. [Neil Cook]
Repo visualizer: updated diagram. [repo-visualizer]
Update diagram yaml. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.151-working’ into v0.7.151-working. [Neil Cook]
Repo visualizer: updated diagram. [repo-visualizer]
Update diagram yaml. [Neil Cook]
Add diagram. [Neil Cook]

add diagram
Update diagram yaml. [Neil Cook]
Try adding codebase diagram. [Neil Cook]
Apero.tools.recipes.bin.apero_get.py - fix problems with blank fields. [Neil Cook]
Apero.tools.recipes.bin.apero_get.py - deal with filter_items equal to None. [Neil Cook]
Param func listp and listd need ‘required’ keyword argument. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.151-working’ into v0.7.151-working. [Neil Cook]
Apero.core.instruments.defualt.recipe_definitions.py - name of apero_get typo anme –> name. [Neil Cook]

0.7.152 (2021-08-05)¶

Update loc regions text. [Neil Cook]
Apero.core.instruments.default.grouping.py - pol group must remove masked rows. [Neil Cook]
Apero.core.core.drs_file.py - deal with math = “None” (for polar combine –> return first header value) [Neil Cook]
Update date/version/changelog/docs. [Neil Cook]
Update date/version/changelog/docs. [Neil Cook]
Apero.science.calib.wave.py - wfp_target_rv None –> 0.0 (so not Null in header) [Neil Cook]

0.7.151 (2021-07-29)¶

Apero.science.calib.wave.py - wfp_target_rv None –> 0.0 (so not Null in header) [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - remove_std_hkeys True by default + add Recon/ReconErr to s.fits file + add tag for UniformWavelength and UniformVelocity. [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - update FORBIDDEN_KEYS definitions. [Neil Cook]
Apero.core.instruments.default.grouping.py - polar sequences must be for same object + correct _is_numeric function. [Neil Cook]
Apero.core.core.drs_file.py - combine filename column names should not end in .fits + remove std hkeys by default. [Neil Cook]

0.7.150 (2021-07-24)¶

Apero.science.preprocessing.detector.py - fix issue with cosmic correction being slow - need to correct intercept + errslope. [Neil Cook]
Remove databases and update gitignore. [Neil Cook]
Apero.science.calib.wave.py - update wave qc (limit to 2 m/s between fibers) and add back in the ccf rv qc (again qc at 2 m/s) [Neil Cook]
Apero.core.math.gen_math.py - add todo to fix this function (can take a long time) [Neil Cook]
Add start_time and end_time to log database. [Neil Cook]
Apero.base.drs_db.py - fix commit problem with sqlite3. [Neil Cook]
Apero.recipes.*.apero_preprocess_*.py - move cosmic ray correction before shift. [Neil Cook]
Apero-drs-full.setup.install.py + setup_lang.py - add way to get lang code without using apero (so we can check modules) otherwise if modules don’t exist we can’t import apero.base. [Neil Cook]

0.7.149 (2021-07-21)¶

Apero.base.drs_db.py - add changes to make sqlite work again. [Neil Cook]
Sqlite3 no longer works - test it. [Neil Cook]
Apero.core.instruments.default.grouping.py - need to deal with NUMEXP and CMPLTEXP being blank - remove them (adds 3 ms to polar grouping) [Neil Cook]
Update date/version/changelog/update notes. [Neil Cook]

0.7.148 (2021-07-16)¶

Update .gitignore. [Neil Cook]
Update language database. [Neil Cook]
Update language database + add install text to language database (using langdb proxy) [Neil Cook]
Add text to language database. [Neil Cook]
Apero.science.localisation.py - add loc im regions plot. [Neil Cook]
Setup.install.py - scikit-image –> skimage in module_translation. [Neil Cook]
Update language database. [Neil Cook]
Add pp_ff and ext_ff to runs. [Neil Cook]
Apero.core.core.drs_database + apero.core.utils.drs_utils.py + apero.tools.module.processing.drs_processing.py - fix problem with include/exclude list of obs_dirs. [Neil Cook]
Update documentation, date, version, changelog. [Neil Cook]

0.7.147 (2021-07-14)¶

Update language database. [Neil Cook]
Apero.science.calib.wave.py - update echelle orders calculation + up limits on WAVE_CCF_RV_THRES_QC. [Neil Cook]
Force recipes that are master to give error on qc failure. [Neil Cook]

0.7.146 (2021-07-13)¶

Apero.core.instruments.nirps_ha.default_constants.py - up the nirps qc limit to 20 m/s. [Neil Cook]
Apero.science.calib.wave.py - match_fplines to get dv from wave meas. [Neil Cook]

0.7.145 (2021-07-13)¶

Apero.science.calib.wave.py - need to sort both to the same length (assumes 1. they are sorted by peakn 2. there are no duplicates) [Neil Cook]
Apero.science.calib.flat_blaze.py - deal with blaze failing even simple fix (remove cubic term) [Neil Cook]
Update wave sol to fix problem with dv measurement between A,B and C rel to AB. [Neil Cook]

0.7.144 (2021-07-09)¶

Try to fix wave master solution. [Neil Cook]
Try to fix wave master solution. [Neil Cook]
Try to fix wave master solution. [Neil Cook]
Update documentation + add recipe sequence auto doc. [Neil Cook]
Update documentation + add recipe sequence auto doc. [Neil Cook]
Update documentation. [Neil Cook]
Apero.science.calib.flat_blaze.py - load_calib_file must use fiber argument!! [Neil Cook]
Apero.core.instruments.spirou.default_constants.py - WAVE_CAVITY_FIT_DEGREE too high, change from 11 –> 7. [Neil Cook]

0.7.143 (2021-07-06)¶

Apero.science.extract.berv.py - make sure berv warning is on by default. [Neil Cook]
Update date / version / documentation. [Neil Cook]

0.7.142 (2021-07-05)¶

Update documentation. [Neil Cook]
Change grouping to only allow a maximum number of files in a group. [Neil Cook]
Update documentation. [Neil Cook]
Add nirps_he mode. [Neil Cook]
Update wave solution. [Neil Cook]

0.7.141 (2021-07-02)¶

Add auto-doc recipe definitions. [Neil Cook]
Apero.core.instruments.nirps_ha.pseudo_const.py - correct typo remove filename from get_drs_mode. [Neil Cook]

0.7.140 (2021-06-30)¶

Apero.tools.module.documentation - add css + table formatting. [Neil Cook]
Apero.tools.module.documentation - add to file definitions documentation nirps + spirou. [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - expand psuedo_consts loading certain variables only once. [Neil Cook]
Apero.science.calib.shape.py - correctiong for infiles for outfile3+ (nirps hcfiles None) [Neil Cook]

0.7.139 (2021-06-29)¶

Update documentation based on file_definitions page. [Neil Cook]
Add way to compile list of file definitions. [Neil Cook]
Apero.core.instruments.nirps_ha.default_constants.py - change the localisation ydet max value limit from 4060–>4050. [Neil Cook]
Apero.core.utils.drs_startup.py - add DrsCodedException as known error type (expected) [Neil Cook]
Apero.core.instruments.nirps_ha.file_definitions.py - add OBJ_SKY, OBJ_TUN, TEST_HCONE_HCONE, TEST_FP_HCONE, TEST_HCONE_FP, TEST_DARK_FP. [Neil Cook]
Apero.core.core.drs_file.py - get id file error keys from psuedo const. [Neil Cook]
Apero.core.instruments.nirps_ha.file_definitions.py - add FLAT,LED to known raw file types. [Neil Cook]
Update reset.object.csv file based on current googlesheet (so we don’t have to recheck we supply this as default) [Neil Cook]

0.7.138 (2021-06-29)¶

Database fixes - FLOAT–>DOUBLE, order file names for skipping, fix grouping for polar files (pol not running) [Neil Cook]
Remove PPM from nirps run.ini files. [Neil Cook]
Update requirements (no longer a test) [Neil Cook]
Update master night for nirps. [Neil Cook]
Update pseudo const for nirps. [Neil Cook]
Update date/version/changelog/docs. [Neil Cook]

0.7.137 (2021-06-25)¶

Finish delete table app for apero_database.py (–delete) [Neil Cook]
Apero.tools.module.database.manage_db_gui.py - work on app to delete / manage tables. [Neil Cook]
Few fixes for database indexing. [Neil Cook]

0.7.136 (2021-06-23)¶

Apero.core.utils.drs_utils.py - forgot param_kind in log key loop. [Neil Cook]
Continue database indexing overhaul. [Neil Cook]
Apero.base.drs_db.py - add index column. [Neil Cook]
Optimize database using index columns and define all sql data types properly (to aid speed up + indexing) [Neil Cook]
Apero.io.drs_path.py - add listdirs, nofiles and listfiles functions (for quick directory/file listings) [Neil Cook]
Apero.core.math.gen_math.py - rename ‘slice’ to ‘imslace’ (avoid using standard name) [Neil Cook]
Apero_wave_night_nirps_ha.py - do not update smart_fp_mask here (only in master) [Neil Cook]
Apero_wave_night_spirou.py - do not update smart_fp_mask here (only in master) [Neil Cook]
Turn off cosmic correction for NIRPS - broken (Etienne will fix later) [Neil Cook]

0.7.135 (2021-06-21)¶

Apero.core.core.drs_database - add todo on how we deal with unique columns. [Neil Cook]
Try to speed up processing pre-indexing. [Neil Cook]
Try to speed up processing pre-indexing. [Neil Cook]
Try to speed up processing pre-indexing. [Neil Cook]
Apero.core.core.drs_file.py - self.abspath should be a string here. [Neil Cook]

0.7.134 (2021-06-18)¶

Apero.core.core.drs_database.py - last modified date a problem with many files. [Neil Cook]
Update nirps preprocessing. [Neil Cook]
Apero_preprocess_nirps_ha.py - need to add etiennes code for fixing first pixel in amp. [Neil Cook]
Update version/date/changelog/update notes. [Neil Cook]
Fix apero_postprocess_spirou.py - fix db infiles. [Neil Cook]

0.7.133 (2021-06-17)¶

Keep adding drs output files with infiles (for the database) - brute force approach –> find blanks in database (we missed some) [Neil Cook]
Keep adding drs output files with infiles (for the database) - brute force approach –> find blanks in database (we missed some) [Neil Cook]
Add KW_INSTRUMENT + add infiles column to the index database. [Neil Cook]

0.7.132 (2021-06-15)¶

Update requirements_test.txt. [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - fix drs_mode. [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - add instrument to the keywords. [Neil Cook]
Apero.core.instruments.spirou.pseudo_const.py - update DRSMODE - spectroscopy only for P16,P16 everything else with P2 or P4 or P14 or P16 is POLAR (if valid in both channels) [Neil Cook]

0.7.131 (2021-06-14)¶

Apero.core.instruments.*.file_definitions + default_keywords.py - make sure raw files check instrument header key. [Neil Cook]
Apero.core.instruments.spirou.pseudo_const.py - add polar rhomb positions that are valid for spectroscopy (P2,P4,P14,P16) unless specific polar combination. [Neil Cook]
Add out directory to the reset code. [Neil Cook]

0.7.130 (2021-06-12)¶

Work on apero_get.py. [Neil Cook]
Updates to echelle order numbers to wave solution - add to header. [Neil Cook]
Add echelle order numbers to wave solution. [Neil Cook]

0.7.129 (2021-06-11)¶

Updates to localisation - now tested on mini data 1+2 spirou, + nirps 20210218. [Neil Cook]
Code space for echelle orders + change wave_night __NAME__ to wave_night (was wave_master) [Neil Cook]
Apero_get.py - new tool to get any file from the drs - currently code not copied see apero-utils/general/apero_get/apero_get.py for the draft code. [Neil Cook]

0.7.128 (2021-06-09)¶

Updates to localisation. [Neil Cook]
Apero.tools.recipes.bin.apero_database.py - add a mode to update reset.object.csv using either a dfits text file or a read of all current raw files. [Neil Cook]
Continue changes to update localisation for SPIRou and NIRPS. [Neil Cook]
Upgrade the localisation using new recipe from EA (use blob finding) [Neil Cook]
Fix installation bug (Issue #669) [Neil Cook]

0.7.127 (2021-06-02)¶

Apero.core.utils.drs_startup.py - must update recipe.inpudir and recipe.in_block_str when in_block_str is a block kind (and forced) [Neil Cook]
Apero.core.utils.drs_startup.py - deal with in_block_str being a path as well as the current working directory containing block kind as a directory (would break here before) [Neil Cook]
Apero.science.calib.wave.py - need a return to res_fit_super_gauss function. [Neil Cook]
Merge branch ‘master’ into v0.7.126-working. [Neil Cook]

# Conflicts: # README.md
Update README.md. [Neil Cook]

correct typo
Update version/date/changelog/update notes/documentation. [Neil Cook]

0.7.126 (2021-06-01)¶

Apero.science.calib.wave.py - fix res map to work for NIRPS (gaussian fit vs super-gaussian fit for spirou) [Neil Cook]

0.7.125 (2021-05-31)¶

Apero.science.preprocessing.gen_pp.py - handle request.get() exception or going to the wrong link (table inconsistent) [Neil Cook]
Update wave codes for NIRPS and SPIRou - now can remove orders from any part of the detector. [Neil Cook]
Update some doc strings + unused arguments in wave codes. [Neil Cook]
Update nirps default wave grid (for cut 71) [Neil Cook]

0.7.124 (2021-05-27)¶

Update nirps default wave grid (for cut 71) [Neil Cook]
Wave sol changes for NIRPS_HA full detector. [Neil Cook]

0.7.123 (2021-05-26)¶

Apero.recipes.nirps_ha.apero_wave_master_nirps_ha.py - add back in the FP file check. [Neil Cook]
Apero.recipes.science.calib.wave.py - modify wave code for nirps. [Neil Cook]
Setup.newprofile.py - (re)create yamls after updating them. [Neil Cook]
Apero.science.extract.extraction.py - clean up calculate_blaze_flat_sinc args. [Neil Cook]
Apero.science.calib.flat_blaze.py - make med filter size a constant (for each instrument) [Neil Cook]
Apero.recipes.*.apero_extract_*.py - quicklook remove wavesol. [Neil Cook]
Apero.plotting.plot_funcitons.py - type frame1.set_ylim –> frame2.set_ylim. [Neil Cook]
Apero.core.utils.drs_recipe.py + others - deal with DRS_OBJ_NAME + DRS_OBJ_NAMES. [Neil Cook]
Apero.instruments.nirps_ha.recipe_definitions.py - apero_pp_master needed group_func + group_column. [Neil Cook]
Apero.core.instruments.default.grouping.py - need to deal with rawtab=None. [Neil Cook]
Apero.instruments.*.pseudo_const.py - sort out objname + null text. [Neil Cook]
Apero.core.instruments.*.default_constants.py - add FF_BLAZE_SINC_MED_SIZE. [Neil Cook]
Apero.base.base.py - write_yaml Path–>str + pep8. [Neil Cook]
Apero.core.instruments.spirou.default_keywords.py - use OBJECT not OBJNAME (reversal of last weeks change) [Neil Cook]
Update date / version / changelog / documentation. [Neil Cook]

0.7.122 (2021-05-25)¶

Apero.recipes.nirps_ha.apero_wave_master_nirps_ha.py - pep8 updates. [Neil Cook]
Apero.core.instruments.spirou.pseudo_const.py - if OBJNAME is None use OBJECT header key. [njcuk9999]
Apero.core.core.drs_Database.py + apero.core.instruments.spirou.pseudo_const.py - address Null vs None values in database. [njcuk9999]
Apero.core.instruments.spirou.pseudo_const.py - need to add objectname and objectname2 for index database. [njcuk9999]

0.7.121 (2021-05-21)¶

Apero.plotting.html.py latex.py plot_functions.py - add typing doc strings and pep8. [Neil Cook]
Apero.plotting.html.py latex.py plot_functions.py - add typing doc strings and pep8. [Neil Cook]
Apero.recipes.nirps_ha.apero_wave_master_nirps_ha.py + spirou/apero_wave_master_spirou.py - remove debug hc + fp lines. [Neil Cook]
Apero.recipes.nirps_ha.apero_wave_master_nirps_ha.py + spirou/apero_wave_master_spirou.py + apero.science.calib.wave.py - move offset code and apply to spirou and nirps. [Neil Cook]
Update berv keys + remove HIERARCH keys + remove pp keys from post products (to be in-line with CADC) [Neil Cook]
Apero.core.core.drs_file.py - make sure we copy all post file properties (explains why header_add were disappearing) [Neil Cook]
Apero.core.instruments.nirps_ha.default_constants.py - WAVEREF_HC_BOXSIZE from 5–>13. [Neil Cook]
Apero.base.base.py - remove future warning –> error. [Neil Cook]
Apero.plotting.core.py - update typing/doc strings. [Neil Cook]
Apero.plotting.core.py - update typing/doc strings. [Neil Cook]

0.7.120 (2021-05-19)¶

Apero.science.preprocessing.gen_pp.py - update resolve_target (python typing) [Neil Cook]
Apero.science.calib.gen_calib.py - fix from logging issues in check_fp + add doc strings + typing. [Neil Cook]
Apero.core.core.drs_database.py - load_db does not log by default. [Neil Cook]
Apero.core.utils.drs_startup.py - add database settings to the display print out. [Neil Cook]

0.7.119 (2021-05-19)¶

Test requirements + fix some warnings + add way to filter warnings (db mysql connection need func to ignore internal warnings as they are weird) [Neil Cook]
Database - backup databases before deleting (in case I’m being stupid and delete them without realising) [Neil Cook]
Apero.setup.newprofile.py - update error message for invalid path / apero profile name + change cprint sys.exit message to red. [Neil Cook]
Apero.setup.*.py - update installation doc strings + pep8 + bring newprofile.py inline with changes to install.py. [Neil Cook]

0.7.118 (2021-05-17)¶

Apero.setup.install.py + apero.tools.module.setup.drs_installation.py - fix problem with database tables going to “MAIN” and problem with upper case vs lower case apero profile names (force lower) [Neil Cook]
Apero.data.spirou.reset.calibdb - remove master_calib_SPIROU.txt (not longer used) [Neil Cook]
Apero.data.nirps_ha.databases.reset.calib.csv - test 41 orders first for wave solution. [Neil Cook]
Apero.science.extract.berv.py - add todo to check epoch for spirou. [Neil Cook]
Apero.science.calib.shape.py - Problem with shape when maximum correlation between FPs split between pixels (Issue #668) [Neil Cook]
Must deal with having no epoch - assume it is the observation time in this case. [Neil Cook]
Update version to 0.7.117, update docs, date, changelog. [Neil Cook]

0.7.117 (2021-05-15)¶

Apero.science.calib.gen_calib.py - objname can be Null or None - deal with this. [Neil Cook]
Make sure SKY is checked in OBJECT and OBJNAME even when TRG_TYPE is set. [Neil Cook]

0.7.116 (2021-05-13)¶

Apero.science.calib.wave.py - make sure qc failure prints to screen. [Neil Cook]
Apero.core.utils.drs_utils.py - some rlog columns were still wrong –> correct humantime, groupname, levelcrit, qc_values, errormsgs. [Neil Cook]
Apero.recipes.spirou.apero_wave_master_spirou.py - for master solution need an offset test after first HC lines calculation (this is because default wave solution can be off from master night if master night is far from when the default wave solution was made) [Neil Cook]
Update mini_run files to have SCIENCE_TARGETS = All by default. [Neil Cook]
Continue work on recreating databases from files on disk. [Neil Cook]

0.7.115 (2021-05-10)¶

Update language database. [Neil Cook]
Add functionality to update databases from files on disk (index, log, calib, tellu) [Neil Cook]
Apero.data.spirou.reset.runs.*.ini - correct run.ini with THI and THT. [Neil Cook]
Apero.core.core.drs_file.py + apero.io.drs_fits.py - make sure headers are copied to extensions - was isinstance(header[it], Header) now isinstance(header[it], (Header, fits.Header)) [Neil Cook]

0.7.114 (2021-05-06)¶

CADC output fixes. [Neil Cook]
More fixes for nirps into 0.7 (works up to apero_flat) [Neil Cook]
Fixes for quicklook sequence. [Neil Cook]

0.7.113 (2021-05-04)¶

Update runs for NIRPS (LOC(M)AB –> LOC(M)A, LOC(M)C –> LOC(M)B) [Neil Cook]
Update to code to bring NIRPS to 0.7. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - leak_master must be after thermal masters. [Neil Cook]
Apero.science.calib.wave.py - add printouts for calc_wave_lines. [Neil Cook]
Apero.science.calib.flat_blaze.py - correct problem with blaze in new mini data set (local minima) [Neil Cook]
Update language database. [Neil Cook]
Equalise nirps with spirou. [Neil Cook]
Add program + parallel to log database + add switches for DEBUG files. [Neil Cook]
Update UPDATE_NOTES.txt. [Neil Cook]

0.7.112 (2021-04-30)¶

Make sure keys are added before argparse. [Neil Cook]
Only update drs_processing.py Run runstring once. [Neil Cook]
Correct typo ‘–parallel’ –> ‘ –parallel’ [Neil Cook]
Deal with using –parallel argument (stops index database updating in a recipe run) [Neil Cook]
Update language database. [Neil Cook]
Apero.core.core.drs_argument.py - add parallel argument. [Neil Cook]
Update language database. [Neil Cook]

0.7.111 (2021-04-28)¶

Apero.science.preprocessing.gen_pp.py - add bad list checker. [Neil Cook]
Update language database. [Neil Cook]
Update language database. [Neil Cook]
Apero.tools.recipe.bin.apero_processing.py - index certain block kinds to avoid indexing during recipe runs. [Neil Cook]
Apero.science.polar.gen_pol.py - correct typo STOKESI_CONTINUUM_DETECTION_ALGORITHM –> STOKESI_CONTINUUM_DET_ALG. [Neil Cook]
Update language database. [Neil Cook]
Apero.tools.recipe.bin.apero_processing.py - try to stop re-indexing of the database occuring. [Neil Cook]
Get_wavesol requires either ‘infile’ OR (‘header’ and ‘nbpix’) not both - correct. [Neil Cook]

0.7.110 (2021-04-27)¶

Apero.core.utils.drs_utils.py - add running to param table (rlog.running) [Neil Cook]
Apero.science.wave.py - correct typo *margs –> args=margs. [Neil Cook]
Move text to language database + update language database. [Neil Cook]
Move text to language database and constants to instrument/default definitions. [Neil Cook]
Fix mk tellu add_wave_keys. [Neil Cook]

0.7.109 (2021-04-23)¶

Move wave.py –> wave_old.py and move wave2.py –> wave.py (and move last required functions from wave_old.py –> wave.py) + move wave_master_old + wave_night_old to apero/tools/recipes/spirou/ [Neil Cook]
Change recipe names cal_ obj_ –> apero_ [Neil Cook]
Update changelog + update notes. [Neil Cook]
Update version/date/changelog/update notes. [Neil Cook]

0.7.108 (2021-04-22)¶

Fix grouping + fix emailing + fix run.ini files. [Neil Cook]
Update run.ini files with LOCAB LOCC (previously LOC) and LOCMAB LOCMC (previously LOCM) [Neil Cook]
Apero.core.core.drs_database.py - fix drsfile being NpyFile. [Neil Cook]
Apero.science.calib.wave2.py - must read hc and fp e2ds files in process_fibers. [Neil Cook]
Fix plot_waveref_expected with large outliers. [Neil Cook]
Update wave sol with ea fixes. [Neil Cook]

0.7.107 (2021-04-20)¶

Apero.tools.module.processing.py + apero.tools.recipes.bin.apero_processing.py - remove reset from processing. [Neil Cook]
Add NIRPS 0.6 changes. [Neil Cook]
Apero.core.core.drs_file.py - make sure obs_dir is cleaned of block_path (via block_kind) [Neil Cook]
Remove reset options from processing (do via apero_reset.py if required) [Neil Cook]
Update nirps definitions with changes to 0.7 (note nirps still on 0.6 and needs adding - this just changes 0.7 changes to code left over before 0.6 divergence) [Neil Cook]
Apero.science.calib.wave.py - correct type (this is for wave2) - eventually move wave -> wave_old. [Neil Cook]
Allow for recipe kind from input args + update recipe defintions with new recipe kinds for all sequences. [Neil Cook]
Apero.recipes.spirou - move old wave sols to _old and new from _ea to main (no extra suffix) [Neil Cook]

0.7.106 (2021-04-20)¶

Fix grouping + shortnames + set running on construction (__init__) [Neil Cook]
Catch warnings on astroquery import. [Neil Cook]
Apero.recipes.spirou.cal_wave_*_ea_spirou.py - fix cavity file. [Neil Cook]
Apero.core.core.drs_database.py - change rtype –> recipe_type + add recipe_kind. [Neil Cook]
Apero.core.core.drs_argument.py - add recipe kind global argument. [Neil Cook]
Fix grouping for polar code + change sequences arguments for polar code. [Neil Cook]
Apero.core.instruments.grouping.py - work on the grouping for polar files. [Neil Cook]
Fixes to cal_wave_master_ea and cal_wave_night_ea. [Neil Cook]

0.7.105 (2021-04-15)¶

Move ea wave functions from wave to wave2. [Neil Cook]
Apero.science.calib.wave2.py - continue work on ea wave sol. [Neil Cook]
Apero.recipes.spirou.cal_wave_*_ea_spirou.py - continue update to wave master + night ea. [Neil Cook]
Apero.plotting.plot_functions.py - add legend_no_alpha + plot_wave_hc_resmap + plot_wave_hc_resmap_old. [Neil Cook]
Apero.core.math.py - add centered_super_gauss function (for wave res map) [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - add plot to cal_wave_master_ea_spirou.py. [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - add WAVERES file (copy of WAVERESHC) [Neil Cook]
Apero.core.instruments.*.default_keywords.py - add wave res keywords. [Neil Cook]
Apero.recipe.spirou.cal_wave_master_ea_spirou.py - add WAVESOURCE to wprops. [Neil Cook]

0.7.104 (2021-04-13)¶

Apero.core.instruments.spirou.recipe_definitions.py - add SUIM_CCF_RV_FIT to summary plots. [Neil Cook]
Apero.recipe.spirou.cal_wave_master_ea_spirou.py - continue work with EA on new wave sol. [Neil Cook]
Apero.science.gen_pol.py - add more info to question. [Neil Cook]
Make sure user can turn off saving to the database. [Neil Cook]
Continue with polar update. [Neil Cook]
Update sequence overview flow charts. [Neil Cook]
Apero.core.core.drs_file.py + apero.science.polar.gen_pol.py - corrects to polar code. [Neil Cook]

0.7.103 (2021-04-10)¶

Fix ccf typo + drs_file.DrsPath distinguish between abspath and obs_dir and block_kind. [Neil Cook]
Apero.core.core.drs_file.py - make block paths real paths (try to fix Issue #660) [Neil Cook]
Remove references to DRS_DS9_PATH and DRS_LATEX_PATH - either get from shutil.which or don’t use. [Neil Cook]
Remove references to DRS_DS9_PATH and DRS_LATEX_PATH - either get from shutil.which or don’t use. [Neil Cook]
Apero.core.instruments.*.default_keywords.py - add lsd keywords + lsd file. [Neil Cook]
Apero.science.calib.gen_calib.py - correct typo block_ind –> block_kind. [Neil Cook]
Apero.core.core.drs_file.py - sort out length of data, header, names, datatype, dtype. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - add polar to sequences and run.ini files [still requires grouping] [Neil Cook]
Polar update - add writing polar files [unfinished - needs lsd files] [Neil Cook]
Polar update - add writing polar files [unfinished - needs lsd files] [Neil Cook]
Change return of drs_file.combine. [Neil Cook]

0.7.102 (2021-04-08)¶

Continue work on polar lsd code integration. [Neil Cook]
Continue work on polar lsd code integration. [Neil Cook]
Continue work on polar lsd code integration. [Neil Cook]
Continue work on polar lsd code integration. [Neil Cook]
Continue work on polar lsd code integration. [Neil Cook]

0.7.101 (2021-04-06)¶

Continue work on polar code integration. [Neil Cook]
Continue work on polar code integration. [Neil Cook]
Continue work on polar lsd integration. [Neil Cook]
Continue work on polar code integration. [Neil Cook]
Continue work on polar code integration. [Neil Cook]
Merge pull request #666 from njcuk9999/v0.7-zsh. [Neil Cook]

Add zsh support
Add zsh to setup files. [Thomas Vandal]
Add first version of zsh files. [Thomas Vandal]

0.7.100 (2021-04-02)¶

Apero.recipes.spirou.obj_pol_spirou.py + science.polar.gen_pol.py - continue work on polar code. [Neil Cook]
Apero.core.core.drs_file.py - add to Block class (fileset) + move get_file_definition here + add get_infile_infilename function. [Neil Cook]
Move get_file_definition to drs_file.py. [Neil Cook]
Start work on polar code. [Neil Cook]
Apero.base.drs_db.py - hide connection debug printout - use later to profile. [Neil Cook]

0.7.099 (2021-03-31)¶

Apero.base.drs_db.py - up the wait time to reconnect to 5+-1s * 20 (max 120s) - brute force hack to try to make connections wait longer. [Neil Cook]
Apero.base.drs_db.py - up the wait time to reconnect to 10+-2s (from 0.1+-0.1) - brute force hack to try to make connections wait longer. [Neil Cook]
Apero.base.drs_db.py - up the wait time to reconnect to 2+-1s (from 0.1+-0.1) - brute force hack to try to make connections wait longer. [Neil Cook]
Apero.base.drs_db.py - save error from exception. [Neil Cook]
Apero.base.drs_db.py - and connection timing. [Neil Cook]
Apero.base.drs_db.py - try again after connection failure. [Neil Cook]
Apero.core.core.drs_file.py + science.telluric.fit_tellu.py - clear a possible back log of npy writing + do not populate output dictionary for npy files (not required - they shouldn’t be in the index database) [Neil Cook]

0.7.098 (2021-03-29)¶

Apero.base.drs_db.py - add extra info to connection() error message. [Neil Cook]
Apero.recipes.spirou.obj_pol_spirou.py - start integrating polar code. [Neil Cook]
Apero.base.drs_db.py - allow dbname to be unset (dbname=’NULL’) [Neil Cook]
Apero.tools.module.setup.drs_reset.py - try to remove files but give warning and continue if failed. [Neil Cook]
Apero.base.drs_db.py - add table name to error. [Neil Cook]
Apero.base.drs_db.py - make errors more explicit (database name) + close cursor and connections. [Neil Cook]

0.7.097 (2021-03-27)¶

Apero.base.drs_db.py - correct database exception error. [Neil Cook]
Apero.science.extract.berv.py - **bprops should be props=bprops. [Neil Cook]
Apero.base.drs_db.py - problem with shallow copy on values + need to deal with masked column in gtable (re: input_gaiaid) [Neil Cook]
Apero.base.drs_db.py - continue integration of changes to the database connection + add “out” files to index database + fix apero_explorer pandas.to_sql erasing UNIQUE column. [Neil Cook]

0.7.096 (2021-03-25)¶

Apero.base.drs_db.py - continue work on _conn_ replacement. [Neil Cook]
Apero.base.drs_db.py - we cannot connect until we are going to do something –> move all _conn_ inside places where we actually use the database - only connect (then importantly disconnect) each time we do something - do not keep connection open. [Neil Cook]
Apero.io.drs_fits.py - deal with not being able to remove a file because it doesn’t exist (try to test existence again) [Neil Cook]
Apero.recipes.*.cal_badpix_*.py - combine DARK_DARK same_type=False (want to combine DARK_DARK_TEL and DARK_DARK_INT) [Neil Cook]
Update date/version/changelog/update notes. [Neil Cook]

0.7.095 (2021-03-24)¶

Merge branch ‘v0.7.090-test-stable’ into v0.7.090-work. [Neil Cook]
Merge pull request #662 from njcuk9999/v0.7.090-sql-reconnect. [Neil Cook]

Update drs_db to reconnect upon cursor creation failure
Add KW_OUTPUT for pp files + KW_PID for combined files + recipe in index database. [Neil Cook]
Merge branch ‘v0.7.090-test-stable’ into v0.7.090-work. [Neil Cook]
Apero.base.drs_db.py - add doc string for connect class and move all connections here. [Neil Cook]

0.7.094 (2021-03-19)¶

Undo unnecessary changes. [cusher]
Update drs_db to reconnect upon cursor creation failure. [cusher]
Apero.base.drs_db.py - add doc string for connect class and move all connections here. [Neil Cook]
Apero.base.drs_db.py - add connection timeout for mwsql connection. [Neil Cook]
Apero.base.drs_db.py - add connection timeout for mwsql connection. [Neil Cook]

0.7.093 (2021-03-17)¶

Apero.core.core.drs_file.py - get_hkey_2d dim1/dim2 should be integers. [Neil Cook]
Apero.data.spirou.reset.runs.other_run.ini - add LFCFP and FPLFC to other run.ini file. [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py + recipe_definitions.py - add LFCFP and FPLFC to sequences. [Neil Cook]

0.7.092 (2021-03-13)¶

Apero.tools.module.processing.drs_processing.py - fix duplicate entries (pp + raw) and make badpix dark_dark inclusive (int + tel) [Neil Cook]
Apero.tools.module.processing.drs_processing.py - change using defaults from warning to normal message. [Neil Cook]
Apero.core.instruments.spirou.recipe_defintiions.py + blank_run.ini - add a blank sequence (for apero testing and maybe loading raw files to index database) [Neil Cook]
Apero.tools.module.setup.drs_processing.py - _split_string_list should not split by white space unless directly told to (allows spaces in filenames) [Neil Cook]

0.7.091 (2021-03-11)¶

Update spirou_map_sections.graphml. [Neil Cook]
Fix display_func + processing obs_dir. [Neil Cook]
Add spirou map sections (for documenation and paper) [Neil Cook]
Params.snapshot_table –> add recipe to args. [Neil Cook]
Recipes - remove params from log functions. [Neil Cook]
Apero.io.drs_fits.py - add find_named_extensions + update_extension. [Neil Cook]
Apero.core.utils.drs_utils.py - rtype <–> block_kind. [Neil Cook]
Apero.core.utils.drs_startup.py - change rtype and block_kind for recipe.log. [Neil Cook]
Apero.core.core.drs_misc.py - raise value error for non-string name in display_func. [Neil Cook]
Remove RecipeLog from drs_log.py. [Neil Cook]
Apero.core.core.drs_file.py - add update_param_table function. [Neil Cook]
Apero.core.core.drs_database.py - add update param table to calib/tellu file update. [Neil Cook]
Apero.core.constants.param_functions.py - update snapshot_table to have recipe.log parameters. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.7.090 (2021-03-09)¶

Apero.core.core.drs_file.py - catch numpy_load failure. [Neil Cook]

0.7.089 (2021-03-06)¶

Need gaiadr for AstroObject. [Neil Cook]
Apero.science.calib.wave.py - correct typo. [Neil Cook]
Apero.core.instruments.*.deafult_keywords.py - add KW_GAIA_DR (for future determining against dr2/dr3. [Neil Cook]
Recipes: .inputtype–>.in_block_str .outputtype–>.out_block_str. [Neil Cook]
Apero.recipes.*.obj/out_postprocess_*.py - DIRNAME–>OBS_DIR, kind–>block_kind. [Neil Cook]
Apero.core.instruments.spirou.default_constants.py - add POLAR_DARK and POLAR_FP to DPRTYPES. [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - DIRNAME–>OBS_DIR, KIND–>BLOCK_KIND. [Neil Cook]
Apero.core.core.drs_file.py - kind–>block_kind. [Neil Cook]

0.7.088 (2021-03-04)¶

Apero.core.core.drs_database.py - deal with null values in index database hkeys. [Neil Cook]
General.py –> gen_xxx.py, processing fixes. [Neil Cook]

0.7.087 (2021-03-03)¶

Rework directory/nightname (str –> DrsPath, night–>obs_dir), remove whitelist (–>include list) and blacklist (–>exclude list) [Neil Cook]
Rework directory (str –> DrsPath) - [unfinished] [Neil Cook]

0.7.086 (2021-02-27)¶

Apero.science.calb.wave.py - need to worry about updating e2ds files with multiple extensions. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - need to add POLAR_FP and POLAR_DARK to obj types. [Neil Cook]
Apero.io.drs_fits.py - warnings for Table.read (with multiple tables) [Neil Cook]
Apero.core.instruments.*.default_constants.py - add REPROCESS_OBJ_DPRTYPES. [Neil Cook]
Apero.core.core.drs_file.py - correct __log__ [Neil Cook]
Apero.tools.module.database.manage_databases.py + apero.recipes.bin.apero_database.py - add kill switch for database stuck with processes (apero_database.py –kill) [Neil Cook]

0.7.085 (2021-02-26)¶

Need to be able to kill database connections. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - do not add nightname if already a master sequence. [Neil Cook]
Apero.science.calib.shape.py - lin_transform_vect should be list. [Neil Cook]
Correct typos with snapshot_table input. [Neil Cook]
Apero.core.utils.drs_recipe.py - deal with directory separately from file/files (due to needing path between filename and raw/tmp/red path. [Neil Cook]
Apero.core.core.drs_file.py - fix headers + dout/hout. [Neil Cook]
Apero.core.core.drs_database.py - condition now comes from uhash for index and object dbs. [Neil Cook]
Apero.base.drs_db.py - get condition from uhash if unique_cols is populated + deal with unique exception text better (force lower case) [Neil Cook]
Apero.recipes.spirou.cal_ccf_spirou.py - make sure A and B can be used as science fibers. [Neil Cook]

0.7.084 (2021-02-24)¶

Apero.core.core.drs_database.py - deal with unique keys in database. [Neil Cook]
Update language database. [Neil Cook]
Apero.core.core.drs_database.py - allow for unique columns (by using a hash column) in INDEX and HASH databases. [Neil Cook]
Apero.core.core.drs_database.py - allow for unique columns (by using a hash column) in INDEX and HASH databases. [Neil Cook]
Remove breakpoint/breakfunc (use debugger) + add hdict to snapshot table + replace most write_file with write_multi + snapshot tables. [Neil Cook]
Change display_func (remove breakpoints/breakfuncs) + start adding parameter table to outputs (write_multi first) [Neil Cook]

0.7.083 (2021-02-20)¶

Apero.core.constants.param_functions.py - add used functionality to keep track of uses of parameters in a recipe (for output table) [Neil Cook]
Continue work on new wave solution by EA [UNFINISHED - solution diverges on mean2error while loop) [Neil Cook]
Continue work on new wave solution by EA [UNFINISHED - solution diverges on mean2error while loop) [Neil Cook]
Continue work on new wave solution by EA [UNFINISHED - requires new calc_wave_lines func for HC and FP lines) [Neil Cook]

0.7.082 (2021-02-18)¶

Update UPDATE_NOTES.txt. [Neil Cook]
Apero.science.wave2 - add EA code for new wave solution. [Neil Cook]
Apero.core.core.drs_file.py - drsfile can be ‘table’ therefore have to check if drsfile is DrsInputFile or else deepcopy. [Neil Cook]
Apero.core.constants.param_functions.py - must check for INSTRUMENT (as this is used in installation when yaml may not exist) [Neil Cook]

0.7.081 (2021-02-12)¶

Apero.science.calib.wave.py - typing for generate_res_files. [Neil Cook]
Apero.science.calib.wave.py - correct generate_res_file (should return names for extensions) [Neil Cook]
Apero.base.base.py - add profile to all database tables - so you can change each table in settings. [Neil Cook]
Apero.tools.module.setup.drs_installation.py - change install message (to be more clear) [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py + apero.core.core.drs_file.py - add a tag to out_post files + add NEXT to primary. [Neil Cook]

0.7.080 (2021-02-11)¶

Update UPDATE_NODATE.txt. [Neil Cook]
Update language database. [Neil Cook]
Apero.core.insturments.spirou.pseudo_const.py - get_drs_mode() - only set DRS_MODE for OBSTYPE=”OBJECT” [Neil Cook]
Add extension names to all extensions. [Neil Cook]
Apero.core.insturments.spirou.recipe_definitions.py - add quick_seq (for trigger use) [Neil Cook]
Apero.core.utils.drs_startup.py - setup() must load psuedo constants with an instrument (as FILEMOD/RECIPEMOD for recipes / files with no instrument come from here) [Neil Cook]
Apero.core.core.drs_log.py - need to allow logger to have params as an input. [Neil Cook]
Apero.core.constants.param_functions.py - load_config need a default option (instrument=None) [Neil Cook]
Update constants.load, constants.pload (do not define instrument) + attempt a better way to read (get first ext automatrically) / write fits (do not write in primary) [Neil Cook]
Get instrument from base.IPARAMS not from definition. [Neil Cook]

0.7.079 (2021-02-10)¶

Update extraction cosmic ray rejection [UNTESTED] [Neil Cook]
Apero.recipes.spirou.cal_thermal_spirou.py - thermal_files are not indexed - correct this. [Neil Cook]
Update UPDATE_NOTES.txt. [Neil Cook]
Apero.tools.module.error.find_error.py + apero.tools.recipes.dev.apero_langdb.py - add –find option to langdb.py that launches find_error gui. [Neil Cook]
Apero.core.instruments.spirou.pseudo_const.py - pep8 clean up. [Neil Cook]
Apero.base.drs_db.py - surround all connections to cursor with the “with” statement to make sure connections are closed in all circumstances (i.e. Ctrl+C) [Neil Cook]

0.7.078 (2021-02-09)¶

Apero.core.instruments.spirou - add POLAR_FP and POLAR_DARK (similar to OBJ_FP and OBJ_DARK) for polar files with SBRHB1_P and SBR2_P keys used to distinguish between spectroscopy and polarimetry. [Neil Cook]
Apero.setup.newprofile.py - fix code to copy profile files in 0.7 format. [Neil Cook]
Add switch between pool and process (REPROCESS_MP_TYPE) [Neil Cook]

0.7.077 (2021-02-08)¶

Setup.install.py - add mysql-connector to module_translation. [Neil Cook]
Update requirements. [Neil Cook]
Apero-drs-spirou.recipe_definitions.py - change grouping for obj_pp_recipe. [Neil Cook]
Apero.recipe.spirou.obj_postprocess_spirou.py - remove unused imports. [Neil Cook]
Apero.core.core.drs_file.py - add clear file to postprocess. [Neil Cook]

0.7.076 (2021-02-04)¶

Apero.core.core.drs_file.py - allow set_infile to take a filename. [Neil Cook]
Apero.core.instruments.spirou.recipe_defintions.py - add obj_pp_recipe. [Neil Cook]
Apero.recipes.spirou.obj_postprocess_spirou.py - convert out_postprocess to a per file (for apero_processing.py and multiple cores) [Neil Cook]
Apero.tools.recipes.spirou - move tellu_db files here. [Neil Cook]
Apero.science.telluric.gen_tellu.py - change FWHM_PIXEL_PSF –> FWHM_PIXEL_LSF. [Neil Cook]
Apero.ploting.plot_functions.py - add tellup_clean_oh to definitions. [Neil Cook]
Apero.data.spirou.reset.runs.complete_run.ini - remove commit() to database outside for loops (commit each entry) [Neil Cook]
Apero.core.instruments.spirou.recipe_defintions.py - remove obj_mk_tellu_db and obj_fit_tellu_db from full sequence. [Neil Cook]
Remvoe commit() to database outside for loops (commit each entry) [Neil Cook]
Apero.core.core.drs_database.py - only check last modified for raw files. [Neil Cook]

0.7.075 (2021-02-03)¶

Add thermal flow diagram. [Neil Cook]
Make sure PyQt5 is installed. [Neil Cook]
Apero.science.preprocessing.detector.py - fix mask1+mask2 –> xpand_mask now data is fixed. [Neil Cook]
Apero.plotting.core.py - remove Qt4Agg (not supported in matplotlib 3.3+) [Neil Cook]
Apero.core.core.drs_file.py - allow read_data to return data (and not set self.data) [Neil Cook]

0.7.074 (2021-02-02)¶

Apero.tools.module.setup.drs_installation.py - clean profile names. [Neil Cook]
Apero.science.preprocessing.detector.py - do not do expand_mask. [Neil Cook]
Apero.core.instruments.default.default_constants.py - PP_COSMIC_BOXSIZE should be an integer. [Neil Cook]
Apero.core.core.drs_database.py - make sure checking last_mod done correctly (exclude_files + last_mod should be arrays not pandas table columns) [Neil Cook]
Update language database. [Neil Cook]
Update requirements + apero-pip env. [Neil Cook]
Apero.tools.module.setup.drs_reset.py - deal with not having index/log database in reduced/tmp resets. [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - replace all non alphanumeric characters (except “_”) with _ (then remove double __) [Neil Cook]
Apero.base.drs_db.py - add tname_in_db function to check tables in database for database.tname. [Neil Cook]
Apero.core.core.drs_database.py - add a last_modified check for raw files (to update them if they’ve changed) [Neil Cook]
Update date/version/changelog/update notes/documentation. [Neil Cook]

0.7.073 (2021-01-29)¶

Update UPDATE_NOTES.txt. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - deal with “switch” arguments (should be user defined only) [Neil Cook]
Apero.core.core.drs_file.py - deal with not selecting DEBUG-uncorr files (assume they don’t have runargs) [Neil Cook]
Apero.science.preprocessing.detector.py - finish correct_cosmics function + add typing. [Neil Cook]
Apero.recipes.*.cal_preprocess_*.py - add changes to add correct_cosmics functionality. [Neil Cook]
Apero.core.math.general.py - add xpand_mask function (for pp cosmic) [Neil Cook]
Apero.core.instruments.*.default_keywords.py - add PP_COSMIC keywords. [Neil Cook]
Apero.core.instruments.*.default_constants.py - add PP_COSMIC constants. [Neil Cook]

0.7.072 (2021-01-27)¶

Apero.recipe.spirou.cal_preprocess_spirou.py - start adding cosmic ray reject code. [Neil Cook]
Apero.core.core.drs_file.py - add loading all extensions to drs_file.get_data. [Neil Cook]
Apero.science.calib.localisation.py + wave.py - add KW_PID to writing functions. [Neil Cook]
Apero.core.instruments.default.default_constants.py - add PLOT_TELLUP_CLEAN_OH to __all__ [Neil Cook]
Update language database. [Neil Cook]

0.7.071 (2021-01-26)¶

Apero.science.telluric.gen_tellu.py - add EA’s changes to sky model. [Neil Cook]
Apero.science.calib.wave.py - add KW_PID to wave writing functions. [Neil Cook]
Apero.plotting.plot_functions.py - add plot_tellup_clean_oh function. [Neil Cook]
Apero.data.spirou.telluric - update sky_PCs.fits. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - add TELLUP_CLEAN_OH to plots. [Neil Cook]
Apero.core.instruments.*.default_constants.py - add TELLUP_OHLINE_NBRIGHT. [Neil Cook]

0.7.070 (2021-01-22)¶

Documentation - todo.rst - add to known issues. [Neil Cook]
Apero.tools.module.setup.drs_installation.py - fix hasattr. [Neil Cook]
Update setup/envs/apero-pip. [Neil Cook]
Apero.science.telluric.gen_tellu.py - deal with Etienne using 0 as flag - bad bad bad. [Neil Cook]
Apero.core.core.drs_file.py - do not check metric for DARK_DARK and HC_HC. [Neil Cook]

0.7.069 (2021-01-20)¶

Update language database. [Neil Cook]
Apero.core.core.drs_file.py - need to deal with metric removing all files. [Neil Cook]
Update typo in documentation WAVE_{FIBER} –> LEAKM_{FIBER} [Neil Cook]
README.md - update typo - WAVE_{FIBER} –> LEAKM_{FIBER} [Neil Cook]
Apero.core.core.drs_file.py - must update kind when forced_dir. [Neil Cook]
Apero.core.core.drs_database.py - must update kind when forced_dir. [Neil Cook]
Apero.core.core.drs_argument.py - must update kind when forced_dir. [Neil Cook]

0.7.068 (2021-01-19)¶

Apero.tools.module.processing.drs_processing.py - need to make sure directory is set to None if not the master recipe. [Neil Cook]
Update TODO. [Neil Cook]
Apero.recipes.spirou.* - make sure recipes with two levels end log1 as well as log2. [Neil Cook]
Apero.core.utils.drs_utils.py - edit how we write_logfile when set present (only log set) else log self. [Neil Cook]
Apero.recipes.spirou.cal_thermal_spirou.py - must update some header keys to match cal_thermal (not cal_extract that was used internally) [Neil Cook]
Update todo. [Neil Cook]
Apero.plotting.core.py - matplotlib.use does not have warn argument in 3.3.3. [Neil Cook]

0.7.067 (2021-01-15)¶

Apero.core.instruemnts.spirou.file_definitions.py - add remove_drs_hkeys and remove_std_hkeys. [Neil Cook]
Apero.recipes.*.out_postprocess_{instrument}.py - add processing header updates. [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - add NON_CHECK_DUPLICATE_KEYS, FORBIDDEN_OUT_KEYS methods. [Neil Cook]
Apero.core.instruments.*.default_keywords.py - add post_exclude argument where required. [Neil Cook]
Apero.core.instruments.*.default_constants.py - add POST_HDREXT_COMMENT_KEY. [Neil Cook]
Apero.core.core.drs_file.py - add header modifications to DrsOutFile (and DrsOutFileExtension) [Neil Cook]
Apero.core.constants.constant_functions.py - add post_exclude to Keyword class. [Neil Cook]

0.7.066 (2021-01-14)¶

Apero.core.instruemtns.spirou.file_definitions.py - add TODOs re: meeting with Chris. [Neil Cook]
Update documentation. [Neil Cook]
Apero.tools.recipe.dve.apero_constants.py - add way to generate glossary from constants/keywords. [Neil Cook]
Apero.base.base.py - add bool to the STRTYPES. [Neil Cook]
Apero.instruments.default.default_keywords.py - add descriptions for Keywords. [Neil Cook]
Update todo/update notes. [Neil Cook]
Apero.tools.recipes.dev.apero_constants.py - add check that dev wants to clean constants (and return success/fail) [Neil Cook]
Update descriptions of Const. [Neil Cook]
Apero.tools.module.utils.constants_tools.py - simplify description tool - manually edit after. [Neil Cook]

0.7.065 (2021-01-13)¶

Apero.tools.module.utils.constants_tools.py - add todo to change adding descriptions to constants. [Neil Cook]
Update todo and update notes. [Neil Cook]
Apero.tools.recipes.dev.apero_constants.py - add a tool for dealing with constants. [Neil Cook]
Apero.tools.module.testing.drs_dev.py - fix mod from ImportModule. [Neil Cook]
Apero.tools.module.setup.drs_installation.py - add settings for apero_constants.py. [Neil Cook]
Apero.core.utils.drs_startup.py - fix mod from dev recipes. [Neil Cook]
Correct typos in default_consts. [Neil Cook]
Apero.core.core.drs_file.py - remove dprtype filter on combine metric 1 (accept all files) [Neil Cook]

0.7.064 (2021-01-11)¶

Update TODO list. [Neil Cook]
Update language database. [Neil Cook]
Apero.core.core.drs_file.py - metric 1 only valid for specific types - deal with this. [Neil Cook]
Apero.core.instruments.*.default_constants.py - add COMBINE_METRIC_THRESHOLD1 and COMBINE_METRIC1_TYPES. [Neil Cook]
Apero.core.core.drs_file.py - add metric for rejecting combine files. [Neil Cook]
Apero.core.instruments.*.default_constants.py - add COMBINE_THRESHOLD. [Neil Cook]

0.7.063 (2021-01-08)¶

Update language database. [Neil Cook]
Update update_notes + readme + todo.rst. [Neil Cook]
Apero.recipes.nirps_ha.out_postprocess_nirps_ha.py - copy over work from SPIRou to NIRPS (placeholder until we have a post process file for NIRPS) [Neil Cook]
Apero.core.instruments.* - update recipe_definitions.py and file_definitions.py (and copy to NIRPS) [Neil Cook]
Apero.tools.module.processing.drs_processing.py - add add_non_file_args function (to deal with setting –night, –wnightlist, –bnightlist from processing) [Neil Cook]
Apero.recipe.*.out_{instrument} –> apero.recipe.*.out_postprocess_{instrument} [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - make all out file types not required. [Neil Cook]
Update run.ini files with out_postprocess. [Neil Cook]
Apero.core.instruments.*.default_constants.py - add POST_CLEAR_REDUCED and POST_OVERWRITE to constants. [Neil Cook]
Apero.core.core.drs_file.py - update process_links and return success/failure. [Neil Cook]

0.7.062 (2021-01-07)¶

Apero.recipes.spirou.out_spirou.py - continue work on out_spirou.py. [Neil Cook]
Apero.core.instruments.spirou.output_filenames.py - continue work on post_file (outfunc) [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - update out files (continued work) [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - reformat index_keys. [Neil Cook]
Apero.core.core.drs_file.py - move output_dictionary to DrsInputFile, and continue work on DrsOutFile. [Neil Cook]
Core.core.drs_database.py - fix hkeys loop in IndexDatabase.get_entries() and add _hkey_condition. [Neil Cook]
Tools.recipe.bin.apero_listing.py + apero.core.core.drs_database.py - update apero_listing.py to handle wrong number of columns. [Neil Cook]

0.7.061 (2021-01-06)¶

Apero.recipes.out_spirou.py - continue adding code to process post_process files. [Neil Cook]
Apero.core.instruments.spirou.* - add post_file options. [Neil Cook]
Apero.core.instruments.*.default_config.py - add DRS_DATA_OUT directory (for post processed files) [Neil Cook]
Setup.install.py + apero.tools.module.setup.drs_installation.py - add database options from command line. [Neil Cook]

0.7.060 (2021-01-05)¶

Update language database and todo list. [Neil Cook]
Tools.module.database.database_gui.py - fix saving of database (table should be database.tname not self.kind) [Neil Cook]
Apero.* - add first work for post processing (out_{instrument}.py) [Neil Cook]
Apero.core.instruments.*.default_keywords.py - add KW_IDENTIFIER. [Neil Cook]
Core.core.drs_file.py - add DrsOutFileExtension and DrsOutFile for post processing of files. [Neil Cook]
Update default_constants.py default_keywords.py pseudo_const.py. [Neil Cook]
Update language database + update notes. [Neil Cook]
Apero.science.telluric.gen_tellu.py - get template from user definition (if present) [Neil Cook]
Documentation - add cal_shape_spirou_schematic. [Neil Cook]
Update documentation. [Neil Cook]
Update file_definitions.py and recipe_definitions.py. [Neil Cook]
Apero.core.core.drs_file.py - make checksum upper case. [Neil Cook]

0.7.059 (2020-12-24)¶

Update object database. [Neil Cook]
Apero.tools.module.database.manage_databases.py - update make_object_reset (OBJNAME–>OBJECT) [Neil Cook]
Update notes and todo. [Neil Cook]
Apero.tools.module.setup.drs_reset.py - for reseting tmp/red dirs also reset databases. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - add shortname to processing for all recipes. [Neil Cook]
Apero.science.calib.wave.py - add wave coeffs table. [Neil Cook]
Update language database. [Neil Cook]
Apero.core.utils.drs_utils.py - add sname (shortname) and rtype (raw/tmp/red) [Neil Cook]
Apero.core.utils.drs_startup.py - add rtype tp recipe log (raw/tmp/red) [Neil Cook]
Apero.core.utils.drs_recipe.py - add short name. [Neil Cook]
Apero.core.instruments.default.pseudo_const.py - change columns. [Neil Cook]
Apero.core.core.drs_file.py - checksum for filename (untested) [Neil Cook]
Apero.core.core.drs_database.py - add delete row functions (for reset) [Neil Cook]
Core.core.drs_argument.py - add special shortname argument (to carry short name forward to recipe) [Neil Cook]

0.7.058 (2020-12-22)¶

Update todo + UPDATE_NOTES.txt. [Neil Cook]
Apero.science.preprocessing.gen_pp.py - deal with being offline (warning + skip step) [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - deal with multiple __ in a row (replace with _) [Neil Cook]
Tools.recipes.spirou.cal_drift_spirou.py - added support for OBJ_FP and DARK_FP for cal_drift. [Neil Cook]
Apero.science.calib.shape.py - max_dxmap_info must have three terms. [Neil Cook]

0.7.057 (2020-12-22)¶

Update todo (more tasks) [Neil Cook]
Apero.tools.module.database.manage_databases.py - add the new astro_obj.update_objects. [Neil Cook]
Apero.science.preprocessing.gen_pp.py - add an update target method to astro_obj. [Neil Cook]
Update todo. [Neil Cook]
Apero.science.calib.shape.py - pep8 too long line. [Neil Cook]
Apero.core.utils.drs_utils.py - set log_file and plot_dir to “Not Set” [Neil Cook]
Apero.core.utils.drs_startup.py - add back log file and correct typo kwargs –> skwargs. [Neil Cook]
Apero.core.instruments.*.default_constants.py - correct PP_BAD_EXPTIME_FRACTION. [Neil Cook]
Apero.science.calib.localisation.py - fix qc logic for MAX_RMPTS_POS and MAX_RMPTS_WID. [Neil Cook]
Apero.tools.recipe.spirou.cal_expmeter_spirou.py - add –fibers input to choose fibers to add to mask. [Neil Cook]
Apero.core.core.drs_misc.py - try to fix integer scalar bug. [Neil Cook]

0.7.056 (2020-12-20)¶

Re-save shape master schematic. [Neil Cook]
Add shape master schematic + add tools pages (empty for now) [Neil Cook]
Add to localisation documentation. [Neil Cook]
Add update object database to apero_processing.py. [Neil Cook]

0.7.055 (2020-12-17)¶

Add 10% exptime limit in preprocessing. [Neil Cook]
Update documentation. [Neil Cook]

0.7.054 (2020-12-16)¶

Update todo/update notes and documentation. [Neil Cook]
Update todo list. [Neil Cook]
Update todo list. [Neil Cook]
Add apero_database.py - to import csv file to database and export database to csv file. [Neil Cook]
Update language database. [Neil Cook]
Update documentation. [Neil Cook]
Apero.base.drs_base + apero.lang.core.drs_lang.py - drs_base.BETEXT from langdb.csv and language proxy from same function. [Neil Cook]
Update version/date/changelog/documentation. [Neil Cook]

0.7.053 (2020-12-15)¶

Apero-drs.setup.install.py - update requirements path and weird import modules (not equal to module name) [Neil Cook]
Correct requirements. [Neil Cook]
Update todo list. [Neil Cook]
Apero.tools.recipe.bin.apero_reset.py - must work out files to exclude before warn statement. [Neil Cook]
Apero.tools.module.setup.drs_instllation.py - add database installation steps. [Neil Cook]
Apero.lang.core.drs_lang.py - need to check whether language database has a table yet (and don’t try getting it if it doesn’t exist yet) [Neil Cook]
Apero.base.base.py - try getting all parameters from allparams (if we are updating an installation these all will be filled, if installing for first time some will be filled) [Neil Cook]

0.7.052 (2020-12-14)¶

Update documentation. [Neil Cook]
Only resolve objects for OBJ_FP and OBJ_DARK + do not add multiple rows for KW_OBJNAME. [Neil Cook]

0.7.051 (2020-12-12)¶

Continue updating documentation. [Neil Cook]
Core.instrument.spirou.default_constants.py - change central column to 2044 (was 2500 - why?) [Neil Cook]
Update documentation. [Neil Cook]

0.7.050 (2020-12-10)¶

Update todo list. [Neil Cook]
Apero_reset.py + apero_processing.py - do not warn if reset log file is present (and skip it) [Neil Cook]
Update language database. [Neil Cook]
Apero.documentation.working.user.general.todo.rst - update todo list. [Neil Cook]
Apero.plotting.core.py - deal with plt = None. [Neil Cook]
Apero.tools.moduile.processing.drs_processing.py - deal with no plt import. [Neil Cook]

0.7.048 (2020-12-10)¶

Apero.core.instruments.default.grouping.py + apero.tools.module.processing.drs_processing.py - add master value to set directory name. [Neil Cook]
Apero.lang - force the encoding (remove bad characters) [Neil Cook]
Apero.lang - update reset files. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - revert to Process (Pool is not working) [Neil Cook]
Apero.lang.core.drs_lang.py - make sure reset csv files are utf-8 encoded. [Neil Cook]

0.7.047 (2020-12-07)¶

Apero-drs.apero.base.drs_db.py - user and host must come from arguments. [Neil Cook]
Apero-drs.apero.base.drs_db.py - must reset path after call to super. [Neil Cook]
Apero-drs.apero.base.drs_db.py - path must be set before we check mysql. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - try fixing freezing Pool. [Neil Cook]

0.7.046 (2020-12-04)¶

Apero.data.nirps_ha.calibdb.MASTER_WAVE_NIRPS_HA.fits - update default wave solution. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - import matplotlib to close plots. [Neil Cook]
Apero.plotting.core.py - move import for matplotlib to separate function (import_matplotlib) [Neil Cook]
Apero.data.nirps_ha.reset.calibdb - Add Etiennes new MASTER_WAVE file for NIRPS. [Neil Cook]
Apero.io.drs_fits.py - deal with HIERARCH keys and keys longer than 8 characters better. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - deal with not using recipe. [Neil Cook]

0.7.045 (2020-12-02)¶

Update language database. [Neil Cook]
Apero.core.utils.drs_recipe.py - move class_name outside __init__ [Neil Cook]
Apero.core.instruments.default_keywords.py - add combine_method for keywords that require it. [Neil Cook]
Apero.core.instrument.*.pseudo_const.py - add class_name. [Neil Cook]
Apero.core.core.drs_file.py - update combine to include updating the headers. [Neil Cook]
Apero.core.core.drs_base_classes.py - move class_names outside __init__ [Neil Cook]
Apero.core.constants.constant_functions.py - add combine_method to Keyword Class. [Neil Cook]
Update todo list. [Neil Cook]
Apero.core.instruments.default.grouping.py - continue work on grouping. [Neil Cook]
For key, item in self.__dict__ –> for key, item in self.__dict__.items() [Neil Cook]

0.7.044 (2020-12-01)¶

Apero.tools.module.processing.drs_processing.py - for skip add nightname to whitelist. [Neil Cook]
Apero.science.telluric.template_tellu.py - typo get_key –> get_hkey. [Neil Cook]
Apero.core.utils.drs_recipe.py - add a group_func storage in recipe instance. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - add group funcs for all functions to be used in apero_processing. [Neil Cook]
Apero.tools.module.processing.drs_grouping_functions.py + apero.core.instruments.default.grouping.py - add grouping functions - so apero_processing can use custom functions to group files/args for processing. [Neil Cook]

0.7.043 (2020-11-30)¶

Update todo/update/docs. [Neil Cook]
Apero.science.telluric - add berv coverage to template construction. [Neil Cook]
Add plot_mktemp_berv_cov to plot_functions.py. [Neil Cook]
Update language database. [Neil Cook]
Apero.core.instruments.*.default_constants.py default_keywords.py - add berv correction keywords/constants. [Neil Cook]

0.7.042 (2020-11-27)¶

Apero.base.drs_db.py - correct typo values–> values=values. [Neil Cook]
Core.instruments.*.pseudo_const.py - add FIBER_LOC. [Neil Cook]
Apero.science.calib.localisation.py - update cent/wid coefficient tables. [Neil Cook]
Apero.base.drs_db.py - force table to be set. [Neil Cook]

0.7.041 (2020-11-26)¶

Apero.base.drs_base.py - do not call exception - raise exception. [Neil Cook]
Apero.base.drs_db.py - correct self.database.get to include table. [Neil Cook]
Update todo list + documentation. [Neil Cook]
Update language database. [Neil Cook]
Apero.tools.module.database.manage_database.py - must do a super call in Database Exception + set self.tname after super (MySqlDatabasE) [Neil Cook]
Apero.base.drs_db.py - remove reference to ‘MAIN’ (replace with database.tname) - so mysql can write to different tables - make sql tname be {kind}_{profile} from database.yaml. [Neil Cook]
Apero.apero.instruments.spirou.recipe_defintions.py - add masknormmode option. [Neil Cook]
Apero.science.velocity.general.py - add in ccf mask norm options. [Neil Cook]
Update documentation. [Neil Cook]
Update update notes + todo. [Neil Cook]
Apero.core.core.drs_database.py - if all rows have rawfix=1 don’t do loop. [Neil Cook]
Apero.core.core.drs_database.py - do not fix header if rawfix == 1. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - add some print statements about progress + update language database. [Neil Cook]
Apero.tools.recipes.dev.apero_langdb.py - add reload option (to reload the database from reset files but not regenerate reset files) [Neil Cook]
Update language database. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - format global condition better. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - only show overwriting value if original value was not null (None) + move all conditional filters that are not recipe specific outside the recipe loop. [Neil Cook]
Apero.core.utils.drs_recipe.py - filter objects in SCIENCE_TARGETS and TELLURIC_TARGETS by tstars+ostars (i.e. all on disk) [Neil Cook]

0.7.040 (2020-11-25)¶

Update documentation. [Neil Cook]
Apero.core.utils.drs_recipe.py - correct typo value –> objname. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.000-pre’ into v0.7.000-pre. [Neil Cook]
Apero.tools.processing.drs_processing.py - correct SQL logic for conditions. [Neil Cook]
Apero.core.utils.drs_recipe.py + tools.module.processing.drs_processing.py - add template stars to process_adds/add_extra/update_args. [Neil Cook]
Apero.base.drs_db.py - correct arg for error (DatabaseError) [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - add teplate_required to tellu_seq and science_seq. [Neil Cook]
Apero.science.preprocessing.gen_pp.py - have to search colnames of table. [Neil Cook]
Apero.tools.module.processing.py - deal with RECAL_TEMPLATE = False and rejecting objnames with templates. [Neil Cook]
Apero.science.telluric.template_tellu.py - add list_current_templates function. [Neil Cook]
Apero.core.utils.drs_recipe.py - add template_required flag (to be added in sequences) [Neil Cook]
Apero.core.instruments.spirou.py - add template_required to MKTELLU3,4 FTELLU2,3. [Neil Cook]
Apero.data.*.reset.runs - correct typo: RECAL_TEMPALTES –> RECAL_TEMPLATES. [Neil Cook]

0.7.039 (2020-11-24)¶

Update language database. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - add code to set science_targets and telluric_targets from command line args + add rejecting via odometer codes. [Neil Cook]
Apero.core.instruments.*.default_constants.py - add ODOCODE_REJECT_GSHEET_ID and ODOCODE_REJECT_GSHEET_NUM to constants. [Neil Cook]
Apero.science.preprocessing.gen_pp.py - add getting the rejection list from googlesheet. [Neil Cook]
Apero.data.*.reset.runs.*run.ini - add USE_ODO_REJECTLIST and RECAL_TEMPLATES to run.ini files. [Neil Cook]
Apero.core.instruments.default.recipe_definitions.py - add –science_targets and –telluric_targest to argumnets of apero_processing. [Neil Cook]
Apero.core.core.drs_text.py - add cull_leading_trailing function. [Neil Cook]

0.7.038 (2020-11-23)¶

Apero.recipes.spirou.obj_mk_template_spirou.py + science.telluric.tempalte_tellu.py - deal with copying hdict/header better. [Neil Cook]
Apero.core.core.drs_file.py - try to populate output_dict (for index database) differently. [Neil Cook]
Apero - telluric - add TEMPLATE TIME to mk_tellu / fit_tellu products. [Neil Cook]
Apero.science.telluric.template_tellu.py - add a generate_template_hash function. [Neil Cook]
Apero.* - telluric - add number of files and template hash for better id of template. [Neil Cook]
Apero.recipes.spirou.cal_preprocess_spirou.py - add object database outside for loop. [Neil Cook]
Add first test of a setup.py. [Neil Cook]
Update requirements/environments. [Neil Cook]
Update environments to use mostly pip - astropy 4.1. [Neil Cook]
Apero.science.calib.localisation.py - add coefficients as tables in the fits files. [Neil Cook]

0.7.037 (2020-11-20)¶

Apero.lang.core.drs_lang.py - only report when tkey is not tvalue (otherwise we get duplication) [Neil Cook]
Update language database. [Neil Cook]
Apero.core.utils.drs_startup.py - add python modules being used to log. [Neil Cook]
Apero.base.base.py - add RECOMM_USER and RECOMM_DEV. [Neil Cook]
Update requirements_developer.txt and rint must be a single number (not array) [Neil Cook]

0.7.036 (2020-11-18)¶

Update installation. [Neil Cook]
Update installation. [Neil Cook]
Update installation. [Neil Cook]
Update installation. [Neil Cook]
Update installation. [Neil Cook]
Apero.lang.core.drs_lang.py - deal with no language database and return proxy to language database. [Neil Cook]
Apero.base.drs_db.py - add a proxy language database (for when we don’t have access to the database) [Neil Cook]
Update changelog/version/date/documentation/language database. [Neil Cook]

0.7.035 (2020-11-18)¶

Apero.tools.module.processing.drs_processing.py - do not worry about nulls - all raw filters should be present in index database. [Neil Cook]
Apero.core.utils.drs_recipe.py - remove files from add_filters (should only be raw filters because we use raw files) [Neil Cook]
Apero.core.core.drs_file.py - if column is masked don’t filter by it. [Neil Cook]

0.7.034 (2020-11-17)¶

Apero.* - correct problems with textentry. [Neil Cook]
Apero.base.* apero.core.core.* - add/update import rules. [Neil Cook]
Apero.base.* - move none base modules to core.core. [Neil Cook]
Apero.base.drs_exceptions.py - reorganise exceptions. [Neil Cook]
Apero.* - replace TextEntry with textentry. [Neil Cook]

0.7.033 (2020-11-14)¶

Update language database. [Neil Cook]
Apero.base.drs_base.py drs_db.py drs_text.py + lang.core.drs_lang.py - use BETEXT base_error and base_printer. [Neil Cook]
Apero.core.instruments.default.pseudo_const.py - move LANG_DB_COLUMNS to base.py (same with INSTRUMENTS definition) [Neil Cook]
Apero.tools.recipe.dev.apero_langdb.py - update for new language database. [Neil Cook]
Apero.tools.module.database.manaage_database.py - deal with change to language db functionality. [Neil Cook]
Update language database files. [Neil Cook]
Apero.core.core.drs_database.py - move language database stuff to drs_db.py. [Neil Cook]
Apero.base.* - start moving around base functionality (for base lang/print/error integration) [UNFINISHED] [Neil Cook]
Apero.base.drs_base.py - add place to add base base functions. [Neil Cook]
Apero.base.drs_db.py - add BaseDatabaseManager and LanguageDatabase classes. [Neil Cook]
Apero.base.base.py - add language variables to base and re-organise order of base constants. [Neil Cook]

0.7.032 (2020-11-12)¶

Apero.core.core.drs_argument.py - change sql column names to not be reserved names and change X==Y -> X=Y. [Neil Cook]
Apero.base.drs_db.py - pandas functions have to be abstracted. [Neil Cook]
Apero.recipes.*.cal_wave_* + apero.science.calib.wave.py - add calls to database and missing database keys. [Neil Cook]
Apero.core.utils.drs_utils.py - allow log database from parent. [Neil Cook]
Apero.base.drs_db.py - add doc strings to new functions. [Neil Cook]
Apero.base.drs_db.py + apero.core.core.drs_database.py + apero.tools.module.database.database_gui.py + manage_databases.py - modify MySQL feature (after testing) [Neil Cook]

0.7.031 (2020-11-10)¶

Apero.science.preprocessing.gen_pp.py - do not hard code googlesheet columns - now defined at top and separate from database col names. [Neil Cook]
Apero.tools.module.database.database_gui.py + manage_databases.py - add path back to database_wrapper. [Neil Cook]
Apero.core.utils.drs_startup.py - deal with reloading filemod and recipemod when instrument changes. [Neil Cook]
Apero.core.core.drs_database.py - deal with sqlite3 vs mysql (with paths) [Neil Cook]
Apero.base.drs_db.py - make sure all table names end with _TABLE (to avoid SQL commands) [Neil Cook]

0.7.030 (2020-11-09)¶

Apero.tools.module.database.manage_database.py - replace calls to drs_db.Database with drs_db.database_wrapper and calls to ‘MAIN’ table with self.kind. [Neil Cook]
Apero.tools.module.database.database_gui.py - replace calls to drs_db.Database with drs_db.database_wrapper and calls to ‘MAIN’ table with self.kind. [Neil Cook]
Apero.science.preprocessing.gen_pp.py - replace calls to drs_db.Database with drs_db.database_wrapper and calls to ‘MAIN’ table with self.kind. [Neil Cook]
Apero.core.core.drs_database.py - replace calls to drs_db.Database with drs_db.database_wrapper and calls to ‘MAIN’ table with self.kind. [Neil Cook]
Apero.base.drs_db.py - start implementing MySQL as an alternative to sqlite [UNFINISHED/UNTESTED] [Neil Cook]
Apero.tools.recipes.bin.apero_log_stats.py - update to use from database. [Neil Cook]

0.7.029 (2020-11-04)¶

Apero.tools.resources.images.spirou_logo.png - tmp icon for apero explorer app. [Neil Cook]
Apero.tooks.recipe.bin.* - remove instrument from arguments (now from DRS_UCONFIG install yaml) [Neil Cook]
Apero.tools.module.setup.drs_installation.py - deal with reset and validate codes no longer needing instrument. [Neil Cook]
Apero.tools.module.database.database_gui.py - add is_openable and load_file functions to database handler + add option if file is open to open it (in right click popup menu) [Neil Cook]
Apero.core.utils.drs_startup.py - check that instrument is None or matches install.yaml (in DRS_UCONFIG) [Neil Cook]
Apero.core.instruments.default.recipe_definitions.py - remove all instrument arguments (now get from DRS_UCONFIG install yaml) [Neil Cook]
Apero.base.drs_db.py - fix backup replace path. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - remove RESET_LOGFITS. [Neil Cook]
Apero.data.*.reset.runs.* - remove references to reset_logfits - now a database. [Neil Cook]
Apero.science.calib.wave.py - wavefile must have params. [Neil Cook]
Apero.science.extract.berv.py - correct typo DPRTPYE–>DPRTYPE. [Neil Cook]

0.7.028 (2020-10-30)¶

Recipes - update get_berv parameters. [Neil Cook]
Apero.science.extract.berv* - finish update to berv code (using. [Neil Cook]
Apero.recipes.*cal_extract_* - update args for get_berv. [Neil Cook]
Apero.io.drs_fits.py - make sure get function pushes NaN back to np.nan. [Neil Cook]

0.7.027 (2020-10-29)¶

Update update notes + add update header file. [Neil Cook]
Apero.science.prepreocessing.py - make AstroObject pickeable. [Neil Cook]
Apero.sciience.extract.berv2.py - redo berv code now object resolving done in preprocessing [UNFINISHED] [Neil Cook]
Apero.recipes.spirou.cal_preprocess_spirou.py - add the resolve_target function to update header. [Neil Cook]
Apero.io.drs_fits.py - add a set_key function (for using a keywordstore) [Neil Cook]
Apero.data.database.reset.object.csv - update colnames. [Neil Cook]
Apero.core.instruments.*.deafult_keywords.py - add DRS_{RESOLVE} keywords. [Neil Cook]
Apero-drs.apero.core.core.drs_database.py - cahnge “GAIAID” –> GAIA_COL_NAME. [Neil Cook]

0.7.026 (2020-10-28)¶

Apero.data.spirou.database.reset.object.csv - update object reset file (with new values) [Neil Cook]
Apero.tools.module.database.manage_database.py - must load objdbm. [Neil Cook]
Apero.tools.moduile.database.manage_database.py - update object database and add new way to reset object csv file. [Neil Cook]
Apero.science.preprocessing.py - move general.py –> gen_pp.py. [Neil Cook]
Apero.recipes.spirou.cal_preprocess - todo - resolve target. [Neil Cook]
Apero.core.instruments.spirou.default_keywords.py - update objra/objdec to ra_deg and dec_deg. [Neil Cook]
Apero.core.instruments.default.pseudo_const.py - update columns for object database (sources) [Neil Cook]
Apero.core.instruments.*.default_constants.py - update OBJ_LIST constants. [Neil Cook]
Apero.core.core.drs_database.py - make sure obj database adds sources + use set (update row) when gaia id exists (do not add a new row) [Neil Cook]

0.7.025 (2020-10-26)¶

Apero.tools.module.processing.drs_processing.py - run_process function - generate_run_table requires module not recipe (should be the recipe to run not the recipe it is called from) [Neil Cook]
Apero.science.telluric.gen_tellu.py - update get_non_tellu_objs for use with index database. [Neil Cook]
Apero.recipes.spirou.obj_fit_tellu_db_spirou.py + obj_mk_tellu_db_spirou.py + obj_spec_spirou.py - updaet with database interface. [Neil Cook]
Apero.core.utils.drs_utils.py - make sure filters are stripped of leading/trailing white spaces. [Neil Cook]

0.7.024 (2020-10-23)¶

Apero.tools.module.processing.drs_processing.py - modify run_process to work with index database. [Neil Cook]
Apero.recipes.spirou.obj_mk_tellu_db_spirou.py - start work to fix this [UNFINISHED] [Neil Cook]
Apero.core.utils.drs_utils.py - allow update_index_db to take in a database (so we don’t read many times), modify find_files to accept lists of filters. [Neil Cook]
Apero.core.core.drs_database.py - add a get_entries method to LogDatabase (for skip table) [Neil Cook]
Apero.core.instruments.default.pseudo_const.py - add aliases column from object database. [Neil Cook]
Apero.core.core.drs_database.py - add to object database functions. [Neil Cook]

0.7.023 (2020-10-21)¶

Apero.tools.module.database.manage_databases.py - log database should use LOG_DB_COLUMNS from pconst. [Neil Cook]
Apero.core.utils.drs_utils.py - load database on creation. [Neil Cook]
Apero.core.utils.drs_startup.py - change drs_log.RecipeLog to drs_utils.RecipeLog. [Neil Cook]
Apero.core.instruments.default.pseudo_const.py - group is sql keyword - use groupname. [Neil Cook]
Apero.tools.module.database.database_gui.py - list_database now returns classes - fix return and get paths. [Neil Cook]
Apero.core.core.drs_file.py - remove_insuffix in args should be None not False (leave to default value unless set) [Neil Cook]

0.7.022 (2020-10-20)¶

Apero.core.core.drs_file.py - catch bad files in last_modified. [Neil Cook]
Apero.base.drs_db.py - exectue –> execute. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - remove obj_mk_tellu_db and obj_fit_tellu_db from limited_seq. [Neil Cook]
Apero.recipes.spirou.obj_fit_tellu_db_spirou.py - remove apero.io.drs_text (apero.base.drs_text) [Neil Cook]
Apero.core.core.drs_file.py - only add last_modified time if file exists - and set used = 0 if file doesn’t exist (for some reason) [Neil Cook]
Apero-base.drs_db.py - in colnames use self._execute (to catch the database lock) [Neil Cook]

0.7.021 (2020-10-15)¶

Apero.core.core.drs_database.py - add_entries func add doc string. [Neil Cook]
Apero.base.drs_db.py - try to deal with sqlite database is locked error (try again up to a max wait time) [Neil Cook]
Apero.science.telluric.gen_tellu.py - preclean filepath should be from telluric database directory (Issue #651) [Neil Cook]
Apero.science.polar.general.py - update polar recipe with bug from Issue #648. [Neil Cook]

0.6.132 (2020-10-15)¶

Apero.science.telluric.gen_tellu.py - preclean filepath should be from telluric database directory (Issue #651) [Neil Cook]
Apero.data.spirou.reset.runs - reformat run.ini files (more logical order) [Neil Cook]
Update polar code - Issue #648. [Neil Cook]
Update language database. [Neil Cook]
Add .run to .gitignore. [Neil Cook]
Apero_processing.py - add ptime. [Neil Cook]
Apero.core.math.general.py - correct math for iuv_spline nanmask –> ~nanmask. [Neil Cook]
Apero.core.math.general.py - deal with too many NaNs in spline - correct eargs. [Neil Cook]
Apero.core.math.general.py - deal with too many NaNs in spline. [Neil Cook]
Apero.science.telluric.gen_tellu.py - correct what goes into the headers for TQCCL and TQCCP (was qc_values –> qc_logic,qc_pass) [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - EXTOBJ –> EXTTELL. [Neil Cook]
Merge branch ‘developer’ into working. [Neil Cook]
Merge branch ‘master’ into developer. [Neil Cook]
Merge branch ‘master’ into working. [Neil Cook]
Update README.md. [Neil Cook]

update processing tables in README.md
Update README.md. [Neil Cook]

update readme.md pp_seq_opt
Update processing tables in README.md. [Neil Cook]
Merge remote-tracking branch ‘origin/developer’ into developer. [Neil Cook]
Update drs_database.py. [Neil Cook]

removed chmod to 644
Apero.tools.module.processing.drs_processing.py - send_email should be False not ‘False’ [Neil Cook]

0.7.020 (2020-10-14)¶

Apero - continue adding log features. [Neil Cook]
Apero.core.utils - start adding log database. [Neil Cook]
Apero.tools.module.setup.drs_installation.py - fix create_symlinks. [Neil Cook]
Apero-drs.setup.install.py - os.environ[CARD] requires a str not a Path. [Neil Cook]
Apero-drs.setup.install.py - must activate DRS_UCONFIG in environ. [Neil Cook]
Apero.base.base.py - need to reload iparams and dparams after creating yaml files. [Neil Cook]
Apero.base.base.py - for installation we cannot have DPARAMS and IPARAMS. [Neil Cook]
Setup.install.py - have __file__ path absolute. [Neil Cook]
Setup.install.py - add print statement (For test) [Neil Cook]
Apero.tools.module.setup.drs_installation.py - DRS_DATA_RECUC: ‘red’–>’reduced’ [Neil Cook]
Udpate language database. [Neil Cook]

0.7.019 (2020-10-14)¶

Apero.tools.module.setup.* - create yamls and update database creation. [Neil Cook]
Apero-drs/config - remove redundant ini files. [Neil Cook]
Apero.tools.module.gui.general.py - get DRS_UCONFIG from base. [Neil Cook]
Apero.tools.module.database - update paths to use database yaml file. [Neil Cook]
Apero.io.drs_lock.py - need max wait time (used to be database setting) [Neil Cook]
Apero.core.instruments.*.default_config.py - remove database settings (now in yaml) [Neil Cook]
Apero.core.core.drs_database.py - change how set path works. [Neil Cook]
Apero.core.constants.param_functions.py - only cache when from_file is True (otherwise don’t ever read files) [Neil Cook]
Apero.base.py - add yaml reading functions here. [Neil Cook]
Apero-drs/* - work on yaml inputs for install + database. [Neil Cook]
Apero.science.extract.other.py - deal with exceptions/errors from extrecipe better. [Neil Cook]
Apero.recipes.spirou.cal_dark_master_spirou.py - set nightname to ‘other’ [Neil Cook]
Apero.core.utils.drs_startup.py - test is mod is None (as well as mod instance None) [Neil Cook]
Apero.core.instruments.*.recipe_definitions.py - typo intputtype –> inputtype. [Neil Cook]
Apero.core.core.drs_file.py - typo DRS_CALIB_DB –> DRS_DATA_ASSETS. [Neil Cook]
Apero.core.core.drs_argument.py - deal with directory better. [Neil Cook]
Apero.data.spirou.reset.runs.*.ini - reorganise run.ini files. [Neil Cook]

0.7.018 (2020-10-11)¶

Apero-drs.apero.science.calib.badpix.py - chaange recipe.outputdir to recipe.outputtype. [Neil Cook]
Sort out disambiguity between inputdir outputdir inputtype outputtype (former should be None or Path, later should be ‘raw’, ‘red’, ‘tmp’, ‘calib’, ‘asset’ etc) [Neil Cook]

0.7.017 (2020-10-10)¶

Apero.core.utils.drs_startup.py - parg –> pargs[parg] for settings params. [Neil Cook]
Apero.core.core.drs_file.py - outfile must update params. [Neil Cook]
Apero.core.utils.drs_startup.py - need to update input files with params (after we have added to them) [Neil Cook]
Apero.core.core.drs_database.py - need to not check dirname if check=False (in DatabaseManager.set_path) [Neil Cook]
Apero.core.core.drs_argument.py - need to deal with empty types in _check_file_logic. [Neil Cook]

0.7.016 (2020-10-10)¶

Add default calibdb/objectdb csv files for NIRPS. [Neil Cook]
Apero.core.utils.drs_utils.py - find_files correct typing pd.dataframe –> pd.DataFrame. [Neil Cook]
Apero.core.utils.drs_startup.py - do not check path of index database here - sometimes we may not have it (only on reset?) [Neil Cook]
Update language database. [Neil Cook]
Apero.core.utils.drs_recipe.py - frecipe must get params (it changed previously) [Neil Cook]
Apero.core.instruments.nirps_ha.deafult_config.py - update some settings for database (c.f. spirou) [Neil Cook]
Apero.core.instruments.default.pseudo_const.py - correct columns for index_database columns. [Neil Cook]
Apero.core.core.drs_file.py - correct remove_insuffix default value should be None. [Neil Cook]
Apero.core.utils.drs_utils.py - write a new find_files function that uses the index database. [Neil Cook]
Move find_files to drs_utils.py. [Neil Cook]
Apero.core.utils.drs_recipe.py - change location of get_output_dir and get_input_dir. [Neil Cook]
Apero.core.core.drs_file.py - move get_dir get_input_dir and get_output_dir here. [Neil Cook]
Apero.core.core.drs_database.py - add _update_params so we only update database when new request comes in (unless forced) [Neil Cook]
Core.core.drs_argument.py - update check directory and check file to use indexdb instead of opening headers. [Neil Cook]
Apero.base.drs_db.py - count should return an int. [Neil Cook]

0.7.015 (2020-10-08)¶

Apero.tools.recipe.bin.apero_listing.py - update listing to update index database. [Neil Cook]
‘reduced’ –> ‘red’, from apero.core.core import drs_database. [Neil Cook]
Update language database. [Neil Cook]
Apero.io.* - sort out imports. [Neil Cook]
Apero.core.util.drs_utils.py - sort out imports. [Neil Cook]
Apero.core.utils.drs_startup.py - get IndexDatabase (for recipe_setup) [Neil Cook]
Apero.core.instruments.*.recipe_definitions.py - change ‘reduced’ to ‘red’ [Neil Cook]
Apero.core.core.drs_log.py - move setup_inputs to drs_recipe.py. [Neil Cook]
Apero.core.core.drs_file.py - update write functions (add runstring and kind for index database) [Neil Cook]
Apero.core.core.drs_database.py - deal with no instrument + move drs_database.py from core.utils.drs_database.py. [Neil Cook]
Apero.core.core.drs_argument.py - add IndexDatabase to Argument Checks (unfinished) [Neil Cook]
Core.constants.param_functions.py - deal with no value in listp and dictp. [Neil Cook]
Apero.base.drs_db.py - typo :param columns: –> :param column: [Neil Cook]

0.7.014 (2020-10-07)¶

Update language database. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - continue integrating index database. [Neil Cook]
Apero.core.utils.drs_database.py - continue work integrating index database. [Neil Cook]
Apero.core.instruemnts.*.default_constants.py - change REPROCESS columns (for index database) [Neil Cook]
Apero.core.core.drs_file.py - change kwargs for hkeys in NpyFile. [Neil Cook]
Apero.tools.recipe.bin.apero_processing.py - continue work integrating index database. [Neil Cook]
Apero.core.utils.drs_recipe.py + apero.tools.module.processing.drs_processing.py - move processing/reprocessing functionality to drs_processing. [Neil Cook]
Apero.core.utils.drs_database.py - continue work on index database. [Neil Cook]
Apero.base.drs_db.py - add count and unique functions. [Neil Cook]

0.7.013 (2020-10-07)¶

Apero.tools.module.processing.drs_processing.py + apero.recipes.bin.apero_processing.py - start update with IndexDatabase (unfinished) [Neil Cook]
Apero.science.polar.general.py - change KW_ACQTIME to KW_MJDEND. [Neil Cook]
Update language database. [Neil Cook]
Apero.core.utils.drs_utils.py - modify update_index_db. [Neil Cook]
Apero.core.utils.drs_recipe.py - deal with filemod better. [Neil Cook]
Apero.core.utils.drs_database.py - continue working on IndexDatabaseManager. [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - update drs_finput with hkeys (still need to do this for nirps) [Neil Cook]
Apero.core.instruments.deafult_keywords.py - KW_ACQTIME –> MJDEND. [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - adjust pseudo const for index files. [Neil Cook]
Apero.core.core.drs_file.py - change kwargs to hkeys. [Neil Cook]
Apero.base.drs_db.py - add command to database error (on execute) [Neil Cook]
Apero.core.math.general.py - add nan spline to account for iuv_spline going wrong (with NaNs len < k + 1) [Neil Cook]

0.7.012 (2020-10-05)¶

Apero.tools.recipes.bin.apero_processing.py - start adding IndexDatabase functionality. [Neil Cook]
Apero.tools.module.setup.drs_reset.py - change create_databases–>manage_database. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - start adding IndexDatabase functionality. [Neil Cook]
Apero.tools.module.database.manage_database.py - renamed from create_databases.py. [Neil Cook]
Update language database. [Neil Cook]
Apero.io.drs_path.py - allow copytree to log. [Neil Cook]
Apero.core.utils.py - add utils module for functions that must import from all other utils. [Neil Cook]
Core.utils.drs_database.py - add features to IndexDatabaseManager. [Neil Cook]
Apero.core.instruments.*.pseudo_const.py - add INDEX_HEADER_KEYS and modify INDEX_DB_COLUMNS. [Neil Cook]
Core.core.drs_file.py - tag some functions to be changed to database functions. [Neil Cook]
Apero.base.drs_misc.py - allow get_uncommon_paths to accept Path as well as string. [Neil Cook]
Apero.base.drs_db.py - add column names to set function. [Neil Cook]
Change drs_database2.py –> drs_database.py. [Neil Cook]

0.7.011 (2020-10-02)¶

Apero.tools.module.setup.drs_reset.py - create databases after reseting files (otherwise databases are removed) [Neil Cook]
Apero.io.drs_image.py - unix_char_code moved from drs_startup to drs_misc. [Neil Cook]
Apero.science.calib.dark.py - add out_fmt for get_mid_obs_time. [Neil Cook]
Apero.science.calib.shape.py - add out_fmt for get_mid_obs_time. [Neil Cook]

0.7.010 (2020-10-01)¶

Apero.science.telluric.gen_tellu.py - get_non_tellu_objs add doc string. [Neil Cook]
Apero.recipes.spirou.obj_mk_template_spirou.py - key is just filetype now (fiber separate) filetype_fiber –> filetype. [Neil Cook]
Apero.core.utils.drs_database2.py - allow iarmass/tau_Water/tau_others to be string (to handle ‘None’) [Neil Cook]
Apero.science.telluric.fit_tellu.py - number of trans files should be one less than length (but mask <= instaed of <) [Neil Cook]
Apero.science.wave.py - fix file for out_wave_fp/out_wave_hc. [Neil Cook]
Apero.recipes.spirou.obj_fit_tellu_spirou.py + obj_mk_template_spirou.py - add database=telludbm for tellu database functions. [Neil Cook]
Apero.recipe.spirou.cal_dark_master_spirou.py - drs_fits –> drs_file import. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - EXTOBJ –> EXTTELL + continue update to new database system for tellurics. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - EXTOBJ –> EXTTELL. [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - TELLU_CONV should be of wavem_fp or wavem_hc drs file type. [Neil Cook]
Apero.core.core.drs_file.py - add filename as arg to construct_filename (used for certain outfuncs) [Neil Cook]
Apero.base.drs_db.py - only open cursor when require and close it after to avoid locking. [Neil Cook]

0.7.009 (2020-09-30)¶

Apero.science.telluric.gen_tellu.py - move database interface over from old text database to new sql database. [Neil Cook]
Apero.recipes.spirou.obj_fit_tellu_spirou.py - add database inpout to telluric.tellu_preclean. [Neil Cook]
Apero.io.drs_fits.py, io.drs_image.py, io.drs_lock.py, io.drs_path.py, io.drs_table.py - add import rules (to avoid circular imports) [Neil Cook]
Apero.core.utils.drs_database2.py - update telluric database manager. [Neil Cook]
Apero.core.utils.drs_data.py - add npy file type. [Neil Cook]
Apero.core.core.drs_file.py - reformat get_hkey. [Neil Cook]
Apero.base.drs_db.py - add colnames function and _decode_value function. [Neil Cook]
Move DrsFits functions from apero.io.drs_fits to apero.core.core.drs_file (they should be with the class not IO functions) - functions moved: get_index_files, find_files, find_raw_files, combine, fix_header, id_drs_file, get_mid_obs_time, _get_files, _get_path_and_check, [Neil Cook]
Update processing tables in README.md. [Neil Cook]
Update UPDATE_NOTES.txt (probably prematurely) [Neil Cook]
Update requirements (split into conda/pip for those installating using these lists) [Neil Cook]
Move apero-drs/misc to apero-utils repo. [Neil Cook]

0.7.008 (2020-09-29)¶

Apero.io.drs_fits.py - need to deal with key == ‘’ [Neil Cook]
Apero-drs.misc.tools.profiler.apero_profiler.py - add recipe profiler. [Neil Cook]

0.7.007 (2020-09-25)¶

Apero.io.drs_table.py - pickling/python typing/docstrings. [Neil Cook]
Apero.io.drs_path.py - continue pickling/python typing/docstrings. [Neil Cook]
Apero.base.drs_text.py - move test_format here from drs_table.py. [Neil Cook]

0.7.006 (2020-09-24)¶

Apero.io.drs_lock.py - make sure classes are pickle-able, add python typing and docstrings. [Neil Cook]
Apero.io.drs_image.py drs_lock.py - continue pickling/typing/docstring. [Neil Cook]
Apero.core.instruments - fix pep8. [Neil Cook]

0.7.005 (2020-09-22)¶

Drs_fits.find_files – add filters arg (dict) [Neil Cook]
Apero.io.drs_fits.py - continue pickling/typing/docstring adding. [Neil Cook]
Apero.io.drs_fits.py - start pickling/python typing/doc string. [Neil Cook]
Misc.tools.copy_master_db.py - code to only copy master database. [Neil Cook]

0.7.004 (2020-09-19)¶

Setup.install.py - correct typo barycorrp=y –> barycorrpy. [Neil Cook]
Build documentation. [Neil Cook]
Apero.tools.module.documentation.drs_changelog.py - change how we produce changelog.rst. [Neil Cook]
Apero.science.extract.berv.py - remove func as input parameter. [Neil Cook]
Apeor.core.utils.drs_startup.py - instrument = ‘None’ not just None. [Neil Cook]
Apero.core.core.drs_file.py - copy output_dict + datatype + dtype from instance2. [Neil Cook]
Build documentation. [Neil Cook]
Build documentation. [Neil Cook]
Build documentation. [Neil Cook]
Add empty recipe documentation. [Neil Cook]
Apero.io.drs_fits.py - close the hdu and for now keep the image in primary hdu (remove later) [Neil Cook]
Apero.core.utils.drs_database.py - remove chmod 644 for copying to databases. [Neil Cook]
Apero.core.core.drs_file.py - deep copy header/hdict when copying file. [Neil Cook]

0.7.003 (2020-09-16)¶

Add .run to .gitignore. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - add TODO to see if we can see whats wrong (later) [Neil Cook]
Apero.science.* - fix after debug run. [Neil Cook]
Apero.plotting.core.py - deal with no pdfpath set (skip commit) [Neil Cook]
Apero.core.recipes.*.* - update after debug run. [Neil Cook]
Update language database. [Neil Cook]
Apero.io.drs_fits.py - fix after debug run. [Neil Cook]
Apero.core.math.fast.py - remove display_func from jit function. [Neil Cook]
Apero.core.instruments.*.file_definitions.oy - update out_orderp_straight. [Neil Cook]
Apero.core.core.*.py - fix issues after debug run. [Neil Cook]
Apero.core.constants.param_funtions.py - chagne ConfigError–>DrsCodedException. [Neil Cook]

0.7.002 (2020-09-15)¶

Apero.core.utils.drs_recipe.py - correction for typing/structural changes. [Neil Cook]
Apero.io.drs_fits.py - drs_file must have params. [Neil Cook]
Apero.io.drs_path.py - update get_uncommon_path. [Neil Cook]
Apero - apero.core.drs_log –> apero.core.core.drs_log + instrument = None –> instrument = ‘None’ [Neil Cook]
Apero.core.instruments.*.output_filenames.py - generalize inputs. [Neil Cook]
Apero.core.core.drs_file.py - make changes to DrsInputFile.check_params. [Neil Cook]
Apero.core.core.drs_argument.py - change recipe.drs_params –> recipe.params. [Neil Cook]
Apero.core.constants.param_functions.py - instrument variable should be tested for null test None and ‘None’ [Neil Cook]
Apero.base.drs_misc.py - fix drs_misc.get_uncommon_path (first path should be the longest) [Neil Cook]
Apero.base.drs_exceptions.py - Exit has not __init__ [Neil Cook]
Apero.core.utils.drs_startup.py - add doc strings/python typing. [Neil Cook]

0.7.001 (2020-09-14)¶

Apero.core.utils.drs_recipe.py - continue typing/pickling/docstrings. [Neil Cook]
Apero.tools.module.processing.drs_processing.py - send_email should be False not ‘False’ [Neil Cook]

0.7.000 (2020-09-10)¶

Apero-drs.misc.tools.create_science_targets.py - add telluric targets (may want to upload these too) [Neil Cook]
Merge branch ‘master’ into v0.7.000-pre. [Neil Cook]

# Conflicts: # UPDATE_NOTES.txt # apero/core/instruments/default/default_config.py # apero/core/utils/drs_startup.py # apero/io/drs_fits.py # apero/recipes/spirou/pol_spirou.py # apero/science/telluric/gen_tellu.py # apero/tools/module/processing/drs_processing.py
Merge pull request #645 from njcuk9999/developer. [Neil Cook]

Developer –> master v0.6.131
Update date/version/changelog/docs/update notes/read me. [Neil Cook]
Apero.recipes.spirou.pol_spirou.py - hack from Issue #639 re: linear algebra error. [Neil Cook]
Identical? [Neil Cook]
Apero.core.core.drs_startup.py - format of splash update. [Neil Cook]
Update date/version/docs/changelog. [Neil Cook]
Update object query list. [Neil Cook]
Issue #644 - deal with table = None in generate_run_list + add –test=True to codes which use processing (obj_mk_tellu_db an dobj_fit_tellu_db) [Neil Cook]
Apero.tools.module.setup.drs_processing.py - deal with table being None (just to test if things work with this option) [Neil Cook]
Apero.recipes.spirou.obj_fit_tellu_db_spirou.py - add break point and TEST_RUN = True for test. [Neil Cook]
Apero.io.drs_fits.py - remove breakpoint. [Neil Cook]
Apero.io.drs_fits.py - try to fix copying comments. [Neil Cook]
Apero.recipes.nirps_ha.cal_pp_master_nirps_ha.py - move break point to test error. [Neil Cook]
Apero.io.drs_fits.py - deal with header key not being str. [Neil Cook]
Apero.io.drs_fits.py - deal with header key not being str. [Neil Cook]
Apero.recipes.nirps_ha.cal_wave_master_nirps_ha.py – move breakpoint. [Neil Cook]
Apeor.data.nirps_ha.calib - add catalogue_UNe.csv file. [Neil Cook]
Apero.science.extract.general.py - remove breakpoint apero.core.instruments.default.default_constants.py - make LEAKM_WSMOOTH an int. [Neil Cook]
Apero.science.extract.general.py - move breakpoint. [Neil Cook]
Apero.io.drs_image.py - deal with only one image in large_image_median (return image without medianing) [Neil Cook]
Apero.recipes.nirps_ha.cal_shape_nirps_ha.py – move break point. [Neil Cook]
Apero.recipes.nirps_ha.cal_shape_nirps_ha.py – move break point. [Neil Cook]
Apero.recipes.nirps_ha.cal_shape_nirps_ha.py – add break point. [Neil Cook]
Apero.recipes.spirou.obj_fit_tellu_spirou.py + science/telluric/fit_tellu.py + gen_tellu.py + mk_tellu.py - fix problem with qc for tellu pre clean. [njcuk9999]
Update requirements_current.txt. [Neil Cook]

security dependency requires update
Merge pull request #642 from njcuk9999/developer. [Neil Cook]

Developer - Master
Apero - moved drs_file from apero.core.utils –> apero.core.core (used in drs_argument.py) - continue pickling/docstring/python-typing of apero.core.utils.drs_recipe. [Neil Cook]
Apero - start changes to DrsRecipe (linearizing, pickling, doc strings, python typing) [Neil Cook]
Apero - fix usage of Dict[value-type] –> Dict[key-type, value-type] [Neil Cook]
Apero - change get_key & read_header_key–>get_hkey, read_header_key_2d_list–>get_hkey_2d, read_header_key_1d_list–>get_hkey_1d. [Neil Cook]
Apero.core.utils.drs_file.py - finish upgrade of drs_file (pickling/docstrings/python typing) [Neil Cook]
Apero - manage getting data and header via DrsFitsFile.get_data() and DrsFitsFile.get_header() – used to be .data and .header. [Neil Cook]
Apero-drs.misc.problems.visu_calibs.py - add plotting option. [Neil Cook]
Apero-drs.misc.problems.visu_calibs.py - visualizer for which calibration was chosen for which star. [Neil Cook]
Issue #644 - deal with table = None in generate_run_list + add –test=True to codes which use processing (obj_mk_tellu_db an dobj_fit_tellu_db) [Neil Cook]
Apero.core.utils.drs_file.py - continue work on docstring/python typing/pickling. [Neil Cook]
Apero.core.utils.drs_file.py - continue work on docstring/python typing/pickling. [Neil Cook]
Apero.core.utils - continue with doc string / python typing / pickling. [Neil Cook]
Apero.io.drs_fits.py - try to fix copying comments. [Neil Cook]
Apero.io.drs_fits.py - deal with header key not being str. [Neil Cook]
Apero.core.constants.param_functions.py - pep8 cleanup. [Neil Cook]
Apero.io.drs_image.py - continued correction to large_median_image (for when there is 1 file) [Neil Cook]
Apeor.data.nirps_ha.calib - add catalogue_UNe.csv file. [Neil Cook]
Apero.core.instruments.default.default_constants.py - make LEAKM_WSMOOTH an int. [Neil Cook]
Apero.io.drs_image.py - deal with only one image in large_image_median (return image without medianing) [Neil Cook]
Apero.utils.drs_data.py - continue adding doc strings. [Neil Cook]
Apero.core.math - update pickling/docstrings/python typing + move DrsMathException to drs_exceptions.py. [Neil Cook]
Apero.io.drs_fits.py - change call to pconst.HEADER_FIXES. [Neil Cook]
Apero.core.utils.drs_startup.py - chagne wlog to logger in RecipeLog construction. [Neil Cook]
Apero.core.instruments.default.pseudo_const.py - change typing of REPORT_KEYS() [Neil Cook]
Core.core.drs_log.py - finish pickling/typing/docstrings. [Neil Cook]
Apero.core.constants.param_functions.py - move base classes out of here and move capitalise_keys to drs_text.py + pep8 changes. [Neil Cook]
Apero.core.constants.param_functions.py - move base classes out of here and move capitalise_keys to drs_text.py. [Neil Cook]
Apero.core.constants.constant_functions.py - move CKCaseINSDict here (requires Const and Keyword classes) [Neil Cook]
Apero.core.instruments - update docstrings/typing/pickling. [Neil Cook]
Apero.base.drs_text.py - move capitalise_key to here (from param_functions.py) [Neil Cook]
Apero.base.drs_base_classes.py - add base classes here. [Neil Cook]
Apero - remove usage of apero.core in favour of apero.core.core.drs_log and apero.core.utils.drs_startup. [Neil Cook]
Apero - move pcheck/find_params to param_functions and make class (to add WLOG) - change all calls to pcheck/find_params. [Neil Cook]
Apero.core.core.drs_log.py - add typing/pickling/docstrings [UNFINISHED] [Neil Cook]
Apero.core.param_functions.py - correct pep8. [Neil Cook]
Apero.recipes.spirou.obj_fit_tellu_spirou.py + science/telluric/fit_tellu.py + gen_tellu.py + mk_tellu.py - fix problem with qc for tellu pre clean. [Neil Cook]
Misc.tool.screate_science_targets.py - update arg list. [Neil Cook]
Update language database. [Neil Cook]
Apero.core.utils.drs_recipe.py - keywordargument kind = ‘kwarg’ not ‘kwargs’ [Neil Cook]
Apero.core.core.instruments.*.recipe_definitions.py - remove all references to nargs (not used- set by dtype) [Neil Cook]
Apero.core.core.drs_argument.py - must define kind otherwise crash in self.exception. [Neil Cook]
Core.core.constants.param_functions.py - CKKCaseINSDict should not force to lists (copy/paste error) [Neil Cook]
Apero.core.utils.drs_recipe.py - update set_arg and set_kwarg remove **kwargs and explicitly type arguments. [Neil Cook]
Apero.core.instruments.*.recipe_definitons.py - change path= –> parent= [Neil Cook]
Apero.core.core.drs_argument.py - pos can be int str or None. [Neil Cook]
Misc.tools.create_science_targets.py - update target list. [Neil Cook]
Apero.base.drs_misc.py - move get_uncommon_path to drs_misc.py. [Neil Cook]
Core.core.drs_argument.py - add pickling and python type checking to all classes and functions. [Neil Cook]
Merge branch ‘developer’ into v0.7.000-pre. [Neil Cook]

# Conflicts: # README.md # apero/core/instruments/default/default_config.py
Apero.core.utils.drs_recipe.py + drs_startup.py + tools.module.processing.drs_processing.py + tools.module.testing.drs_dev.py - change call to constants.getmodnames: path –> return_paths. [Neil Cook]
Apero.core.core.drs_argument.py + drs_log.py - move textwrap to apero.base.drs_text.py. [Neil Cook]
Apero.base.* + apero.core.constants.* - add python type checking, pickle-able classes and doc strings. [Neil Cook]
Apero.base.* - make all classes pickle-able. [Neil Cook]
Apero.core.core.drs_log.py + apero.core.utils.drs_startup.py - change how Colors class works. [Neil Cook]
Apero.base.* - update pep8 and python type checking for base module. [Neil Cook]
Apero.science.calib.general.py + localisation.py + shape.py - make sure calib file return is string. [Neil Cook]
Apero.io.drs_fits.py - import pathlib. [Neil Cook]
Apero.science.calib.wave.py - remove break ppoint. [Neil Cook]
Apero.io.drs_fits.py - add some python type checking. [Neil Cook]
Apero.core.utils.drs_database2.py - add some python type checking. [Neil Cook]
Apero.data.spirou.database.reset.calib.csv - update default keys WAVE_D –> WAVEM_D. [Neil Cook]
Update language database. [Neil Cook]
Apero.* - move fiber in get_dbkey() to argument in load_calib_file. [Neil Cook]
Apero.recipes.*.* - remove params from add_calib_file and add_tellu_file. [Neil Cook]
Apero.* - continue adding drs_database2 functionality. [Neil Cook]
Core.utils.drs_database2.py - add_calib_file + add_tellu_file add a copy_files option. [Neil Cook]
Save language.xls. [Neil Cook]
Apero-drs.misc.tools.create_science_targets.py - update target list. [Neil Cook]
Apero.io.drs_path.py - move drs_break. [Neil Cook]
Apero.core.utils.drs_database* - continue work on database update. [Neil Cook]
Apero.core.utils.drs_recipe.py + drs_startup.py - move calls to drs_break. [Neil Cook]
Apero.lang.core - move calls to drs_break. [Neil Cook]
Apero.recipes + apero.science + apero.tools - move around calib db stuff. [Neil Cook]
Apero.core.instruments.*.* - add/modify calib db constants. [Neil Cook]
Apero.core.core.drs_log.py - move dispaly_func call. [Neil Cook]
Apero.core.constants.param_functions.py - move break_point + display_func + get_relative_folder + _copy_pdb_rc + _remove_pdb_rc + _get_prev_count. [Neil Cook]
Apero.base.drs_misc.py - move display_func here and _get_prev_count. [Neil Cook]
Apero.base.drs_exceptions.py - add base_printer. [Neil Cook]
Apero.base.drs_break.py - move break function here. [Neil Cook]
Apero.base.base.py - add PDB_RC_FILENAME. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.7.000-pre’ into v0.7.000-pre. [Neil Cook]
Update README.md. [Neil Cook]

update pp_seq_opt
Move base functionality to apero.base and update all codes with changes - correct bugs. [Neil Cook]
Move base functionality to apero.base and update all codes with changes. [Neil Cook]
Apero.tool.smodule.database.database_gui.py - fix crash in pandastable + add way to save/update sql database. [Neil Cook]
Apero.data.spirou.reset.runs.calib_run.ini - add calib_run.ini example. [Neil Cook]
Apero.core.core.drs_database2.py - add typing and doc strings to database function. [Neil Cook]
Apero.core.math.fast.py + general.py - add typing to most functions. [Neil Cook]
Merge branch ‘v0.6.130-pre’ into v0.7.000-pre. [Neil Cook]

# Conflicts: # UPDATE_NOTES.txt
Core.instruments.*.pseudo_const.py - make all obj names upper. [Neil Cook]
Core.core.drs_database2.py - add empty database for when we don’t have a dataframe. [Neil Cook]
Merge branch ‘v0.6.130-pre’ into v0.7.000-pre. [Neil Cook]
Apero.science.telluric.fit_tellu.py - must mask expo_water/expo_others for trans files. [Neil Cook]
Merge branch ‘v0.6.130-pre’ into v0.7.000-pre. [Neil Cook]
Apero.science.telluric.gen_tellu.py - nanmin –> nanmax. [Neil Cook]
Apero.recipes.spirou.obj_mk_tellu_spirou.py - pep8 white space before operator. [Neil Cook]
Core.core.drs_database2.py + tools.module.database.* - continue to add and test database functionality. [Neil Cook]
Core.core.drs_database2.py + tools.module.database.* - continue to add and test database functionality. [Neil Cook]
Core.core.drs_database2.py + tools.module.database.* - continue to add and test database functionality. [Neil Cook]
Merge branch ‘v0.6.130-pre’ into v0.7.000-pre. [Neil Cook]
Apero.core.instruments.*.default_config.py - add database filenames. [Neil Cook]
Apero.core.drs_database2.py - first commit - start work on buliding database class. [Neil Cook]
Merge branch ‘v0.6.130-pre’ into v0.7.000-pre. [Neil Cook]

# Conflicts: # apero/data/spirou/telluric/tapas_all_sp.fits.gz # apero/tools/module/processing/__init__.py # apero/tools/recipes/bin/apero_database.py
Apero.tools.module.gui.database_gui.py + apero.tools.recipes.bin.apero_database.py - add first commit of database gui. [Neil Cook]
Move drs_processing.py and drs_trigger.py to processing tools.module.processing (from setup) [Neil Cook]
Move drs_processing.py and drs_trigger.py to processing tools.module.processing (from setup) [Neil Cook]
Apero.science.calib.wave.py - add_hkey values–>value. [Neil Cook]
Apero.science.calib.wave.py - correct TREGIONS. [Neil Cook]
Apero.io.drs_data.py - fix fit_1m fit_ll filename input to load_text_file. [Neil Cook]
Update UPDATE_NOTES.txt. [Neil Cook]
Apero.io.drs_path.py - pep8 changes. [Neil Cook]
Apero.tools.reicpes.*.cal_pphotpix_spirou.py - DRS_DATA_ASSET –> DRS_DATA_ASSETS. [Neil Cook]
Apero.tools.module.setup.drs_reset.py - copy tree when reseting + construct path for assets path. [Neil Cook]
Apero.tools.module.setup.drs_processing.poy - deal with no skip table. [Neil Cook]
Apero.science.telluric.gen_tellu.py - DRS_DATA_ASSET –> DRS_DATA_ASSETS + change output to get_whitelist/get_blacklist. [Neil Cook]
Science.calib.wave.py - DRS_DATA_ASSET –> DRS_DATA_ASSETS. [Neil Cook]
Apero.recipes.spirou.obj_*_tellu_* - change return to get_blacklist/get_whitelist. [Neil Cook]
Apero.io.drs_data.py - DRS_DATA_ASSET —> DRS_DATA_ASSETS. [Neil Cook]
Apero-drs.setup.install.py - add –assetdir definition. [Neil Cook]
Apero.tools.reicipes.bin.apero_reset.py - add a reset for assets directory. [Neil Cook]
Apero.tools.recipes.bin.apero_mkdb.py - make calib + telluric database from assets dir. [Neil Cook]
Apero.tools.module.setup.drs_reset.py - deal with reseting assets dir + relative dirs from there. [Neil Cook]
Apero.tools.module.setup.drs_installation.py - add assets dir to installed directory list. [Neil Cook]
Apero.tools.recipes.*.cal_pphotpix_*.py - make hotpix file + debug file spawn from assets dir. [Neil Cook]
Apero.science.telluric.gen_tellu.py - make get_whiltelist/get_blacklist files spawn from assets dir. [Neil Cook]
Apero.science.calib.wave.py - make update_smart_fp_mask file spawn from assets dir. [Neil Cook]
Apero.io.drs_data.py - make all relfolders relative to assets directory. [Neil Cook]
Apero.core.instruments.*.default_constants.py - make ./data paths relative to assets dir. [Neil Cook]
Apero.data - move around assets (eventually move out and online) [Neil Cook]
Apero.core.instruments.*.default_config.py - update paths to assets. [Neil Cook]
Apero.core.constants.constant_functions.py - force dtype in Constant.__init__ to Union[None, str, type] [Neil Cook]
Move old INTROOT code to apero-utils. [Neil Cook]
Apero-drs.misc.database_test - update test database files. [Neil Cook]
Apero-drs.misc.tools.create_science_targets.py - update target lists and version. [Neil Cook]

0.6.131 (2020-08-27)¶

Update version in readme for master/developer/working. [Neil Cook]
Update date/version/changelog/update notes. [Neil Cook]
Update date/version/changelog/update notes. [Neil Cook]
Update date/version/changelog/update notes. [Neil Cook]

0.6.130 (2020-08-21)¶

Update README.md. [Neil Cook]

update pp_seq_opt
Update UPDATE_NOTES.txt. [Neil Cook]
Core.instruments.*.pseudo_const.py - make all obj names upper. [Neil Cook]
Apero.science.telluric.fit_tellu.py - must mask expo_water/expo_others for trans files. [Neil Cook]
Apero.core.instruments.spirou.default_constants.py - set FTELLU_NUM_TRANS to 20. [Neil Cook]
Apero.recipes.spirou.obj_fit_tell_spirou.py - add tpreprops to inputs of gen_abso_pca_calc. [Neil Cook]
Science.telluric.fit_tellu.py - add a trans file mask based on expo_h2o and expo_others (and use closest N trans files to science object) [Neil Cook]
Apero.core.instruments.*.file_definitions.py + recipe_definitions.py - add ABSO1_NPY (for trans expo_h2o+exp_others vector) [Neil Cook]
Apero.core.instruments.*.default_constants.py + default_keywords.py - add KW_FTELLU_NTRANS and FTELLU_NUM_TRANS. [Neil Cook]
Apero.science.telluric.gen_tellu.py - nanmin –> nanmax. [Neil Cook]
Apero.science.telluric.gen_tellu.py - when saving pre-clean only mask to exp(-2) not exp(-1) [Neil Cook]
Apero.science.telluric.gen_tellu.py - make sure we don’t spline outside magic grid. [Neil Cook]
Update UPDATE_NOTES.txt. [Neil Cook]
Merge remote-tracking branch ‘origin/v0.6.130-pre’ into v0.6.130-pre. [Neil Cook]
Update wave.py. [Neil Cook]

apero.science.calib.wave.py - add_hkey values–>value
Apero.recipes.spirou.obj_fit_tellu_spirou.py - add break point for EA. [Neil Cook]
Apero-drs.misc.INTROOT - move old INTROOT code to apero-utils. [Neil Cook]
Apero.science.calib.wave.py - correct TREGIONS. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - make sure q2dsff file links to correct file. [Neil Cook]
Update language database. [Neil Cook]
Apero.science.extract.general.py - add write_extraction_files_ql function (to write quick look files) [Neil Cook]
Apero.recipes.spirou.cal_extract_spirou.py - add quick look switches. [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - add Q2DS and Q2DSFF files for quicklook. [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - add quick look e2ds/e2dsff files. [Neil Cook]
Apero.core.instruments.*.default_constants.py - add EXT_QUICK_LOOK constant value. [Neil Cook]
Apero.tools.recipes.spirou.cal_drift_spirou.py - clean up. [Neil Cook]
Apero.core.core.drs_startup.py - remove type function (doesn’t work as :type:) [Neil Cook]
Update the update notes (work in progress) [Neil Cook]
Apero.tools.recipe.spirou.cal_drift_spirou.py - add first version of cal_drift_spirou. [Neil Cook]
Apero.recipes.*.cal_shape_master_*.py - correct ALLOWED_FP_TYPES (didn’t break but would on change of input) [Neil Cook]
Merge remote-tracking branch ‘origin/developer’ into v0.6.130-pre. [Neil Cook]

# Conflicts: # UPDATE_NOTES.txt
Merge remote-tracking branch ‘origin/developer’ into developer. [njcuk9999]
Apero.science.calib.shape.py - filenames must be filtered as well (append to valid_files) [njcuk9999]
Apero.science.extract.general.py - correct typo from release. [njcuk9999]
Update object query list. [njcuk9999]
Update mtl sync codes. [njcuk9999]
Apero.tools.recipes.spirou.cal_drift_spirou.py - first commit plan for cal_drift_spirou.py. [Neil Cook]
Apero-drs.apero.science.calib.wave.py - add header keys NBO/NREGIONS and update gaussian params with names in hdr. [Neil Cook]
Apero-drs.tools.recipes.*.* - update instrumental tool recipe names to follow conventions. [Neil Cook]
Apero.science.telluric.template_tellu.py - copy data and delete infile when done (hopefully stops having so many fits file open at once) [Neil Cook]
Apero.io.drs_fits.py - readfits - add options to copy data implicity (slower) [Neil Cook]
Apero.core.core.drs_file.py - read_file/read_data/read_header - add option to copy data implicitly. [Neil Cook]
Apero-drs.update_notes.txt - update update notes. [njcuk9999]
Apero.data.spirou.reset.runs.* - update runs and add complete + other run.ini. [njcuk9999]
Apero-drs.README.md - update read me with latest version. [njcuk9999]
Apero.core.instruments.*.recipe_definitions.py - update args for thermal. [njcuk9999]
Apero.data.spirou.reset.runs.*run.ini - update THIM and THTM –> THI_M and THT_M. [njcuk9999]
Update changelog/date/version/update notes/documentation. [njcuk9999]

0.6.129 (2020-07-29)¶

Apero.science.calib.general.py - add check_fp and check_fp_files functionality. [njcuk9999]
Apero.recipes.spirou.cal_shape_master_spirou.py + cal_shape_spirou.py + cal_wave_master_spirou.py + cal_wave_night_spirou.py - check 2d fp files are good to use before using them! [njcuk9999]
Apero.io.drs_image.py - correct typo in comment. [njcuk9999]
Apero.core.instruments.*.default_constants.py - add in check fp constants. [njcuk9999]
Apero.core.instruments.*.file_definitions.py - add LFC_FP to file types (Issue #641) [njcuk9999]
Apero.plotting.plot_functions.py + apero.science.extract.general.py - remove reference to wave (change to wavemap) [njcuk9999]
Apero.plotting.plot_functions.py - remove reference to wave (change to wavemap) [njcuk9999]
Apero.science.calib.flat_blaze.py - try curve_fitting two ways (when first method fails) [njcuk9999]
Misc.problems.spikes.* - add test codes for EA. [njcuk9999]

0.6.128 (2020-07-28)¶

Apero.science.extract.general.py - address spikes in s1d data (EA changes) [njcuk9999]
Apero.io.drs_fits.py + apero.lang.core.drs_exceptions.py - get the filename from abspath and don’t print in DrsHeaderError. [njcuk9999]
Apero.core.core.drs_file.py + apero.core.instruments.*.pseudo_const.py + apero.io.drs_fits.py + apero.lang.core.drs_exceptions.py - add checks for header key and deal with exception of not finding them properly + update language database. [njcuk9999]
Apero.core.core.drs_file.py - rvalue and value do not exist. [njcuk9999]
Apero.core.core.drs_file.py - add breakpoint to test error. [njcuk9999]
Apero.core.core.drs_file.py - must check that id header keys exist and report error it not + update language db. [njcuk9999]
Update version/date/changelog/documentation/update notes. [njcuk9999]

0.6.127 (2020-07-24)¶

Apero.tools.modeul.setup.drs_processing.py - filter objects by dprtype and obstype. [njcuk9999]
Apero.core.core.drs_recipe.py - have to make sure string is not in null text before making a string list. [njcuk9999]
Apero.core.core.drs_recipe.py - add break point to test mk_template with All. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - only keep log entries that finished (we will only skip finished recipes) [njcuk9999]
Update language database. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - remove breakpoint + only keep unique entries in skip_storage. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - need to remove all arguments until we find one to keep (as –args might have spaces after them) [njcuk9999]
Apero.tools.module.setup.drs_processing.py - change skip runstring comparison from adding all arguments to just keeping required arguments. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - add –master to skip remove args (added after this step) [njcuk9999]
Apero.tools.module.setup.drs_processing.py - move breakpoint. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - move breakpoint. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - update breakpoint to test thermal/wave/extract. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - add add_set_kwargs to add optional args to runstring (for skip check comparison) [njcuk9999]
Apero.tools.module.setup.drs_processing.py - move break point. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - move break point. [njcuk9999]
Apero.lang.core.drs_execptions.py + core.core.drs_log.py - remove @profile. [njcuk9999]
Apero.lang.core.drs_execptions.py - add @profile. [njcuk9999]
Apero.core.core.drs_log.py - add more @profile. [njcuk9999]
Apero.core.core.drs_log.py - add @profile to test speed. [njcuk9999]

0.6.126 (2020-07-23)¶

Apero.tools.module.setup.drs_processing.py - add break point and test timings. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - add break point and test timings. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - only strip recipe.name not column. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - strip .py from name. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - add break point to test skipping. [njcuk9999]
Apero.io.drs_fits.py - make sure wnightnames and bnightnames are defined. [njcuk9999]
Apero.io.drs_fits.py - deal with filtering files by whitelist/blacklist nightnames (accept ‘All’) [njcuk9999]
Apero.core.core.drs_log.py - correct missing lang.drs_text. [njcuk9999]
Apero.tools.modules.setup.drs_processing.py + apero_processing.py - re-work skipping file feature and change SCIENCE_TARGETS/TELLUIRC_TARGETS to “All” [njcuk9999]
Update language database. [njcuk9999]
Apero.io.drs_text.py - add null_text and true_text functions for determining with text is unset/true. [njcuk9999]
Apero.data.*.reset.runs.* - update all ini files. [njcuk9999]
Core.core.drs_recipe.py - when SCIENCE_TARGETS is None use “other stars” list (non-tellurics) + allow TELLUIC_TARGETS and SCIENCE_TARGETS = ALL or None. [njcuk9999]
Change from apero.lange import drs_text –> from apero import lang. [njcuk9999]

0.6.125 (2020-07-22)¶

Apero.science.telluric.gen_tellu.py - some pep8 correction. [njcuk9999]
Apero.science.telluric.gen_tellu.py - correct argument of 40-019-00043. [njcuk9999]
Apero.core.core.drs_log.py - add_level does not have WLOG –> self.wlog. [njcuk9999]
Apero.core.core.drs_log.py + drs_startup.py - RecipeLog cannot use WLOG (get it from construction) [njcuk9999]
Update README.md. [njcuk9999]
Merge branch ‘neil’ into working. [njcuk9999]
Merge branch ‘neil_tellu’ into neil. [njcuk9999]

# Conflicts: # apero/recipes/spirou/obj_fit_tellu_spirou.py # apero/recipes/spirou/obj_mk_tellu_spirou.py
Update language database. [njcuk9999]
Move text to language database. [njcuk9999]
Update language database. [njcuk9999]
Update date/version/changelog/documentation. [njcuk9999]
Merge branch ‘neil’ of https://github.com/njcuk9999/apero-drs into neil. [njcuk9999]
Os.walk should alwawys follow symbolic links. [njcuk9999]
Update object database (now 65 entries) [njcuk9999]
Update the windows setup files (to include forcing utf8) - Issue #640. [njcuk9999]
Merge pull request #632 from njcuk9999/neil. [Neil Cook]

Neil –> Working (based on mini run test error)
Merge pull request #631 from njcuk9999/neil. [Neil Cook]

Neil –> Working (for mini data test)

0.6.124 (2020-07-21)¶

Update language database. [njcuk9999]
Apero.science.telluric - remove language database todos. [njcuk9999]
Apero.telluric.fit_tellu.py - undo import removal. [njcuk9999]
Apero.telluric.fit_tellu.py - fit_tellu_write_corrected must have nprops as input. [njcuk9999]
Apero.telluric.fit_tellu.py - correct blaze correction. [njcuk9999]
Apero.recipe.spirou.obj_fit_tellu_spirou.py + apero.science.telluric.fit_tellu.py - do not normalize by the blaze, just apply the recon. [njcuk9999]
Apero.recipe.spirou.obj_fit_tellu_spirou.py + apero.science.telluric.fit_tellu.py - must get blaze/wave inside function and normalize inside. [njcuk9999]
Apero.recipe.spirou.obj_fit_tellu_spirou.py + apero.science.telluric.fit_tellu.py - fix arguments for correct_other_science. [njcuk9999]
Apero.recipes.spirou.obj_fit_tellu_spirou.py - try out the correction of A and B files + add break point to test. [njcuk9999]
Apero.data.core.pdbrc_full - rename .pdbrc. [njcuk9999]
Apero.core.instruments.*.output_filenames.py - remove calibration date prefix. [njcuk9999]
Core.constants.param_functions.py - change name of default .pdbrc file (to avoid deletion if in that directory) [njcuk9999]
Apero.recipes.spirou.obj_fit_tellu_spirou.py + science.telluric.fit_tellu.py - the spectrum must be divided by the recon_abso_res not the recon_abso. [njcuk9999]
Apero.science.telluric.fit_tellu.py - recon is flatten so abso_e2ds needs to be too (49,4088)–>200312. [njcuk9999]
Apero.science.telluric.gen_tellu.py - need at least k+1 points to spline. [njcuk9999]

0.6.123 (2020-07-18)¶

Apero.core.instruments.*.default_keywords.py - add parents for KW_MKTELL_THRES_TFIT and KW_MKTELL_TRANS_FIT_UPPER_BAD. [Neil Cook]
Apero.science.telluric.fit_tellu.py - add back in KW_MKTELL_THRES_TFIT and KW_MKTELL_TRANS_FIT_UPPER_BAD. [Neil Cook]
Apero.core.*.default_constants.py + default_keywords.py - add back in MKTELLU_THRES_TRANSFIT and MKTELLU_TRANS_FIT_UPPER_BAD. [Neil Cook]
Aper.science.telluric.gen_tellu.py - put back in break points. [Neil Cook]
Apero.science.telluric.mk_tellu.py - remove tau from plot. [Neil Cook]
Apero.science.telluric.gen_tellu.py - add tpclfile to index file. [Neil Cook]
Apero.recipe.spirou.obj_*_tellu_spirou.py - end logging properly when file skipped. [Neil Cook]
Apero.recipe.spirou.obj_*_tellu_spirou.py - add printout validating files. [Neil Cook]
Apero.science.telluric.gen_tellu.py - add that we read pclean from file. [Neil Cook]
Apero.science.telluric.gen_tellu.py - correct typo. [Neil Cook]
Core.instruments.*.default_keywords.py - move CCF water/others to header (from images) [Neil Cook]
Apero.io.drs_fits.py - _read_fitsmulti - add log option. [Neil Cook]
Apero.science.telluric.gen_tellu.py - compare file basenamse for tpclfile. [Neil Cook]
Apero.recipe.spirou.obj_mk_tellu_spirou.py - add break point to see loading of preclean file. [Neil Cook]
Apero.science.telluric.mk_tellu.py - mixed up recov_airmass and recov_water (blame EA) [Neil Cook]
Apero.science.telluric.* - remove FINER_CWIDTH and KW_MKTELL_FIN_CONV_WID. [Neil Cook]
Apero.science.telluric.* - remove FINER_CWIDTH and KW_MKTELL_FIN_CONV_WID. [Neil Cook]
Apero.science.telluric.__init__.py - remove unused alias. [Neil Cook]
Apero.science.telluric.mk_tellu.py - remove lowpassfilter (to math module) + sort out unused header keys/unused constants. [Neil Cook]
Apero.science.telluric.gen_tellu.py - remove load_tapas_convolved function + edit iteration msg. [Neil Cook]
Aper.recipes.spirou.obj_mk_tellu_spirou.py - remove tapas conv not needed in mk_tellu any more (done in tellu pre-clean) + rename calculate_telluric_absorption to calculate_tellu_res_absorption. [Neil Cook]
Recipes.spirou.obj_fit_tellu_spirou.py - fit_tellu must load_conv_tapas for first time (not done in mk_tellu any more) [Neil Cook]
Core.math.genearl.py - add lowpassfilter function from EA. [Neil Cook]
Core.instruments.*.default_keywords.py - remove unused keywords. [Neil Cook]
Core.instruments.*.default_constants.py - remove unused constants. [Neil Cook]
Apero.science.telluric.mk_tellu.py - update lowpassfilter. [Neil Cook]
Apero.core.instruments.spirou.default_constants.py - change conv width and orders. [Neil Cook]
Apero.science.telluric.gen_tellu.py - trans_mask must be floats when saved to fits. [Neil Cook]
Apero.core.core.drs_file.py - correct typo mapf slist–>list. [Neil Cook]
Apero.science.telluric.gen_tellu.py - corrections with EA. [Neil Cook]
Apero.plotting.plot_functions.py - correct set_title. [Neil Cook]
Apero.plotting.plot_functions.py - add plot definitions + correct gauss function guess/return. [Neil Cook]
Apero.science.telluric.gen_tellu.py - add print outs and edit mas files (no title) [Neil Cook]
Apero.science.telluric.gen_tellu.py - make sure we can deal with conv_paths unset (none found) [Neil Cook]
Aper.core.instruments.*.file_definitions.py - add dbname/dbkey for TELLU_TAPAS. [Neil Cook]
Apero.science.telluric.gen_tellu.py - update ohline filename + ravel ohpcshift + add warning to sky_model < 0. [Neil Cook]
Apero.core.instruments.*.file_definitons.py - fix out_tellu_spl_npy. [Neil Cook]
Apero.core.instruments.*.default_constants.py - correct typo TELLUP_ABSO_EXP_KEXP –> TELLUP_ABSO_EXPO_KEXP. [Neil Cook]
Apero.science.telluric.gen_tellu.py - deal with no pclean files found. [Neil Cook]
Apero.science.telluric.gen_tellu.py - do not require clean files (may not exist) [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - add out_tellu_pclean to file sets out_file and tellu_file. [Neil Cook]
Apero.science.telluric.gen_tellu.py mk_tellu.py - fix imports. [Neil Cook]
Apero.recipes.spirou.obj_*_tellu_spirou.py - add break points to test EA changes. [Neil Cook]

0.6.122 (2020-07-17)¶

Apero.science.telluric.template_tellu.py - add possible todo later. [Neil Cook]
Misc.hybrid_tellu.hybrid_tellu.py - add EA changes after questions. [Neil Cook]
Apero.recipes.spirou.*tellu*.py + science.telluric.*.py - continue to add EA pre-cleaning changes. [Neil Cook]
Apero.plotting.plot_functions.py - add plot_tellup_wave_trans and plot_tellup_abso_spec functions for tellu pre-cleaning. [Neil Cook]
Apero.core.instruments.*.recipe_definition.py - add plots and outputs to obj_mk_tellu and obj_fit_tellu recipe definitions. [Neil Cook]
Apero.core.instruments.spirou.file_definitions.py - add out_tellu_pclean file. [Neil Cook]
Apero.core.instruments.*.default_keywords.py - add KW_TELLUP keywords. [Neil Cook]
Apero.core.instruments.*.default_constants.py - add TELLUP constants + PLOT constants. [Neil Cook]
Core.core.drs_file.py - add listtype argument and deal with booleans and list dtype better + add mapf to add_hkey method to add string lists. [Neil Cook]

0.6.121 (2020-07-16)¶

Misc.hybrid_tellu.hybrid_tellu.py - add questions for EA about code. [Neil Cook]
Apero.science.telluric.gen_tellu.py - add EA telluric pre-cleaning. [Neil Cook]
Apero.science.telluric.* - general.py –> gen_tellu.py in imports. [Neil Cook]
Apero.recipes.spirou.obj_fit_tellu_spirou.py - temp add params here (for constants file) [Neil Cook]
Aper.core.math.gauss.py - add gauss_function_nodc. [Neil Cook]
Apero.core.instruemnts.spirou.file_definitions.py - add out_tellu_abso_npy. [Neil Cook]
Apero-drs.misc.hybrid_tellu.* - add temp space for EA pre-cleaning code. [Neil Cook]
Obj_fit_tellu_spirou.py - prep for EA precleaning changes. [Neil Cook]
Apero.science.telluric.* - rearrange telluric functions. [Neil Cook]
Data.spirou.telluric.* - add telluric pre-cleaning data. [Neil Cook]
Apero.plotting.plot_functions.py - add label change to cron plot. [Neil Cook]
Core.core.drs_database.py - do not load image/header if not required. [Neil Cook]
Apero.recipes.spirou.obj_fit_tellu_spirou.py - add break point for EA changes. [Neil Cook]
Apero.science.telluric.general.py - correct typo. [Neil Cook]
Apero.recipes.spirou.obj_fit_tellu_spirou.py + science.telluric.general.py - add adjustments to test fit tellu. [Neil Cook]

0.6.120 (2020-07-14)¶

Apero.* - remove break points. [Neil Cook]
Apero.tools.module.setup.drs_processing.py - remove break point. [Neil Cook]
Apero.recipes.spirou.obj_fit_tellu_spirou.py - add correct_other_science to correct fibers A and B for tellurics. [Neil Cook]
Apero.science.velocity.general.py - add todo about filename. [Neil Cook]
Core.core.drs_log.py - deal with directory (nightname) not defined - go into “other” directory. [Neil Cook]
Apero.science.telluric - change where Templates/BigCubes are saved to (no info about nightname) - fix. [Neil Cook]
Apero.science.telluric - change where Templates/BigCubes are saved to (no info about nightname) [Neil Cook]
Apero.science.telluric - change where Templates/BigCubes are saved to (no info about nightname) [Neil Cook]
Apero.science.telluric.general.py - continue etiennes changes. [Neil Cook]

0.6.119 (2020-07-13)¶

Apero.science.telluric.general.py - must set key for header (remove later) [Neil Cook]
Apero.recipes.spirou.obj_mk_tellu_spirou.py + science.telluric.general.py - start adding changes for EA telluric cleaning. [Neil Cook]
Update README.md. [Neil Cook]
Misc.tools.apero_diff.py - update paths. [Neil Cook]
Apero.recipe.spirou.poly_spirou_new.py - continue updating polar code. [Neil Cook]
Apero.recipes.spirou.cal_extract_spirou.py - undo commentation. [Neil Cook]
Apero.io.drs_data.py - update colnames from load_sp_mask_lsd. [Neil Cook]
Apero.data.spirou.lsd - add masks. [Neil Cook]
Remove apero.data.core.runs.* [Neil Cook]
Apero.core.instruments.spirou.recipe_definitions.py - add obj_fit_tellu to full_seq. [Neil Cook]
Apero.core.instruments.*.recipe_defintiions.py - make obj_mk_tellu_db and obj_fit_tellu_db non master recipes (do not require master night to run these) [Neil Cook]
README.md - remove some formatting. [Neil Cook]

0.6.118 (2020-07-09)¶

Apero.science.extract.crossmatch.py + science.extract.crossmatch.py - move breakpoint. [njcuk9999]
Apero.science.extract.crossmatch.py - add break point to investigate obj table. [njcuk9999]
Apero.core.constants.param_functions.py - add normpath (see Issue #635) [njcuk9999]
Apero.recipes.spirou.pol_spirou.py - add back in constants removed for upgrade (Issue #639) [njcuk9999]
Apero.science.velocity.general.py - replace hard coded C with reffiber form pseudo constants (FIBER_KINDS) [njcuk9999]

0.6.117 (2020-07-07)¶

Misc.tools.create_science_targets.py - add all priority targets to string. [njcuk9999]
Apero.io.drs_fits.py - deal with INFs and -INFs in floats (for headers) –> pipe to string INF/-INF. [njcuk9999]
Aper.core.math.general.py - create a better exception when len(x) < k+1 in iuv_spline. [njcuk9999]
Apero.core.core.drs_log.py - divide up errors better. [njcuk9999]
Apero.science.telluric.general.py - if column is filename make it absolute paths. [njcuk9999]

0.6.116 (2020-07-06)¶

Update the readme (working version update) [njcuk9999]
Update date/version/changelog/documentation. [njcuk9999]

0.6.115 (2020-07-04)¶

Update language database. [njcuk9999]
Apero.io.drs_fits.py - move printouts to language database. [njcuk9999]
Apero.io.drs_fits.py - only print out whitelisted/blacklisted if night dir not seen before. [njcuk9999]
Apero.io.drs_fits.py - modify blacklist/whitelist logic. [njcuk9999]
Apero.io.drs_fits.py - do not scan all directories when whitelist/blacklist used. [njcuk9999]
Update language database. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - add PI_NAMES filter. [njcuk9999]
Apero.core.instruments.*.default_constants.py - add REPROCESS_PINAMECOL constant. [njcuk9999]
Apero.data.spirou.reset.runs.*run.ini - add PI_NAME variable. [njcuk9999]
Apero.core.core.drs_recipe.py - must check filter values for None/’None’ and ‘’ and skip filter for values that are unset. [njcuk9999]

0.6.114 (2020-07-04)¶

Apero.core.coire.drs_file.py + apero.tools.module.setup.drs_processing.py - deal with None/’None’,’’ values in filedict (assume true as not set by file) [njcuk9999]
Apero.core.core.drs_recipe.py - move break_point. [njcuk9999]
Apero.core.core.drs_recipe.py - correct typo with filters from file_filters. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - modify break point. [njcuk9999]
Apero.core.core.drs_recipe.py - deal with multiple file filters. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - add break point to test filters. [njcuk9999]
Drs_file.py - change debug output in check_table_keys and update language database. [njcuk9999]
Apero.core.core.drs_startup.py + apero.core.core.drs_startup.py - add state string return and fix test run returns. [njcuk9999]
Aper.tools.recipe.bin.apero_processing.py + apero.core.core.drs_startup.py - add keys parameter to allow custom copying of variables from __main__ namespace. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - pass pid, success, passed properly back to processing from each job. [njcuk9999]
Apero.io.drs_fits.py + apero.recipes.*.*.py - combine need recipe (for indexing) [njcuk9999]
Apero.core.core.drs_log.py - make sure set_plot_dir has correct arguments. [njcuk9999]
Apero.core.core.drs_log.py - set_plot_dir update children (and write to file) [njcuk9999]
Apero.plotting.core.py - recipe.log.set_plot_dir takes params. [njcuk9999]
Apero.* - replace RAW_OUTPUT_KEYS, REDUC_OUTPUT_KEYS and RAW_OUTPUT_KEYS with OUTPUT_FILE_HEADER_KEYS. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - add pid to returns from linear process (for pickup by trigger) [njcuk9999]
Apero.plotting.html.py - html figure should be just the basename (not the absolute path) [njcuk9999]
Apero.plotting.core.py - update plot location in log when updated in plot. [njcuk9999]
Apero.core.instruments.default.pseudo_const.py - add pid and fiber to reduced dir index.fits. [njcuk9999]
Core.core.drs_startup.py - add nightname to index.fits and sort by lat modified. [njcuk9999]
Core.core.drs_log.py - add set_plot_dir and plot_dir attribute to add plot directory to log.fits. [njcuk9999]

0.6.113 (2020-07-02)¶

Update language database. [njcuk9999]
Apero.science.telluric.general.py - add print out for number of files/tpyestr for get_tellu_objs. [njcuk9999]
Apero.science.telluric.general.py - add function get_tellu_objs to get telluric objects from telluric database. [njcuk9999]
Apero.recipes.spirou.obj_mk_tempalte_spirou.py - distinguish between getting files from disk or telluric database (telluric database files are cleaned for QC) [njcuk9999]
Misc.tools.apero_diff.py - fix bug. [njcuk9999]
Apero.science.telluric.general.py - load_tellu_file func add return_entires and allow user to set mode + fit_tellu_quality_control - use snr qc for ftellu only. [njcuk9999]
Core.instruments.*.default_constants.py + default_keywords.py - add back in some missing FTELLU constants + modify QC keywords. [njcuk9999]
Core.core.drs_database.py - add a mode=”ALL” to get_key_from_db. [njcuk9999]
Apero.core.core.drs_recipe.py - inherit filters from given files (only if not already in filter list) [njcuk9999]
Apero.core.instruments.spirou.file_definitions.py - add outfunc to raw_lfc_lfc. [njcuk9999]
Apero.core.instruments.spirou.recipe_definitions.py - add to engineering sequences. [njcuk9999]

0.6.112 (2020-06-29)¶

Apero.core.core.drs_recipe.py - only do pconst.DRS_OBJ_NAME if value is a string. [njcuk9999]
Apero.io.drs_fits.py - must sort the kwargs by the sortmask for files. [njcuk9999]
Apero.data.spirou.reset.runs/science_run.ini - correct typo. [njcuk9999]
Apero.core.instruments.spirou.recipe_defintions.py - make sure tellu_seq and science_seq only extraction OBJ_FP and OBJ_DARK files. [njcuk9999]
Update language database. [njcuk9999]
Tools.recipes.spirou.update_berv.py - add prefix removal. [njcuk9999]

0.6.111 (2020-06-27)¶

Tools.recipes.spirou.update_berv.py - update berv code to account for more extracted files and fibers. [njcuk9999]
Apero.core.core.drs_file.py - output dict needs to look in (1) hdixt (1) header. [njcuk9999]
Apero.science.extract.general.py - add break point to explore problem with indexing. [njcuk9999]
Make sure os.walk returns sorted files. [njcuk9999]
Make sure all glob.glob and os.listdir and Path.glob are sorted alphabetically. [njcuk9999]
Apero.science.extract.berv.py + apero.science.extract.crossmatch.py - add hdr objname for objects without valid simbad object name. [njcuk9999]
Apero.science.extract.crossmatch.py - correct typo intable –> table. [njcuk9999]
Apero.science.extract.berv.py - add debug print out of final input berv parameters. [njcuk9999]
Apero.science.extract.crossmatch.py - carefully force data type for columns in object look up table (inlookuptable function) [njcuk9999]
Apero.science.extract.berv.py - refractor some variables names (to distinguish from other variables) [njcuk9999]
Apero.io.drs_table.py - add force_dtype_col function to deal with making sure columns are required data types. [njcuk9999]
Apero.core.core.drs_log.py - deep copy anything in pcheck (should not be a shallow copy) [njcuk9999]
Apero.recipes.spirou.cal_extract_spirou.py - add breakpoint. [njcuk9999]

0.6.110 (2020-06-25)¶

Apero.tools.module.setup.drs_processing.py - remove break point (error fixed) [njcuk9999]
Apero.science.calib.general.py - make sure objname_inputs is upper case (for comparison with file case) [njcuk9999]
Recipes.*.cal_extract_*.py - log1.writelog –> log1.write_logfile. [njcuk9999]
Misc.tools.create_science_targets.py - add additional files to archive. [njcuk9999]
Apero.core.core.drs_recipe.py - find science_targets and clean them (as well as telluric targets) - to match drs preprocessing objnames. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - add breakpoints to see crash. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - move science target definitions. [njcuk9999]
Changelog.md - update some old syntax. [njcuk9999]
Apero.tools.module.setup.drs_processing.py - move where science_targets is updated. [njcuk9999]
Update science_targets (after clean up) [njcuk9999]
Apero.tools.module.setup.drs_processing.py - add break point to test problem. [njcuk9999]
Misc.tools.create_science_targets.py - add a list of science targets to the tar.gz file list. [njcuk9999]

0.6.109 (2020-06-24)¶

Apero.plotting.plot_functions.py - catch NaNs and deal with them in the plot. [njcuk9999]
Apero.science.velocity.general.py - wsum2 cannot be negative (attempt 2) [njcuk9999]
Apero.science.velocity.general.py - wsum2 cannot be negative either. [njcuk9999]
Misc.tools.update_header_keys.py - deal with missing headers better + add subdir / no subdir options. [njcuk9999]
Update language database. [njcuk9999]
Science.velocity.general.py - wsum cannot be less than zero otherwise wnoise is complex - set wnoise to inf if wsum is zero (we divide by wnoise later –> set ccf noise and ccf snr to NaN) [njcuk9999]
Find all places where OBJNAME is used (not from the header) and pass value through pp header fix code for objname (in a consistent way) [njcuk9999]

0.6.108 (2020-06-22)¶

Apero.science.velocity.general.py - change spline_weight(omask_centers)to sweights. [njcuk9999]
Apero.science.velocity.general.py - add a weight to ignore bad (not mask=good) sections of ccf. [njcuk9999]
Apero.science.velocity.general.py - add break point to investigate crash. [njcuk9999]
Apero.misc.tools.update_header_keys.py - make parallel. [njcuk9999]
Apero.io.drs_text.py - remove debug print outs and deal with empty string (set to None) [njcuk9999]

0.6.107 (2020-06-20)¶

Apero.science.extract.other.py - get nightname from filename dir and dirname from the dir of the night name - file can change this. [njcuk9999]
Apero.core.core.drs_startup.py - add debug printouts. [njcuk9999]
Apero.core.core.drs_startup.py + drs_recipe.py - need to make force_dirs from recipe. [njcuk9999]
Apero.core.core.drs_startup.py - need to deal with indir/outdir being none before checking abspath. [njcuk9999]
Apero.core.core.drs_startup.py - need to check if force input/output dir argument has been used - if it has need to update recipe.inputdir and/or recipe.outputdir and update INPATH, OUTPATH. [njcuk9999]
Apero.core.core.drs_recipe.py - add option if force is true to read input/output dir from recipe definition (now updated if force is on from raw/tmp/reduced to abspath) [njcuk9999]
Apero.science.extract.other.py - force indir for extraction (combined files are stored in the reduced dir) [njcuk9999]
Core.core.drs_startup.py - add getting of forec_indir/outdir and push into get_input/output_dir functions (overwrites default raw/tmp/reduced etc dirs) [njcuk9999]
Core.core.drs_recipe.py - modify get_input_dir and get_output_dir and make force input/outdur special arguments. [njcuk9999]
Core.core.drs_argument.py - add force input and output dirs. [njcuk9999]
Update date/version/changelog/documentation. [njcuk9999]

0.6.106 (2020-06-18)¶

Apero.core.core.drs_file.py - add is_combined and combined list to keys, in combine function change the basename (i.e. 123, 124, 125 –> 12F3T5) and save combined to reduced. [njcuk9999]
Apero.core.core.drs_startup.py - make sure inpath, nightname and output are strings. [njcuk9999]
Apero.io.drs_fits.py - write combined file to the reduced folder (with the new file name) [njcuk9999]
Apero.io.drs_text.py - add common_text and combine_uncommon_text functions to handle list of files –> single filename. [njcuk9999]
Update language database. [njcuk9999]
Apero.science.calib.badpix.py - change writing badpix file to use flat file (only important for processing with output names) [njcuk9999]
Core.instruments.spirou.recipe_defintions.py - change order of arguments (cal_shape_master) - just important for processing with output names. [njcuk9999]
Core.instruemnts.spirou.file_definitions.py - change badpix out files to use flat_flat. [njcuk9999]
Core.instruments.*.file_definitions.py - change badpix dark_dark –> flat_flat. [njcuk9999]

0.6.105 (2020-06-17)¶

Misc.tools.valid_raw_directories.py - add a WORKSPACE for rawsym as well as raw. [njcuk9999]
Misc.tools.apero_diff.py - only work out the fraction of finite pixels. [njcuk9999]
Misc.ea_alder32_code.py - possible solution to file naming issue. [njcuk9999]
Apero.tools.module.setup.drs_installation.py - correct _create_link (Issue #630) [njcuk9999]
Science.calib.general.py - remove breakpoint. [njcuk9999]
Apero.science.calib.background.py - add break point in cal_loc. [njcuk9999]
Apero.science.calib.background.py - add break point in cal_loc. [njcuk9999]

0.6.104 (2020-06-16)¶

Misc.database_test.database.* - first test and commit of database overhaul. [njcuk9999]
Apero.science.preprocessing.detector.py - correct return to nirps_correction. [njcuk9999]
Apero.science.preprocessing.detector.py - make sure we read the mask in get pp master and record to header (nirps_ha) [njcuk9999]
Apero.data.nirps_ha.engineering.hotpix_pp.csv - add file to default files. [njcuk9999]
Apero.core.instruments.nrips_ha.recipe_definitons.py + data.nrips_ha.reset.runs - update run.inis and sequences for nirps. [njcuk9999]

0.6.103 (2020-06-15)¶

Apero.core.instruments.nirps_ha - update nirps recipes after spirou changes. [njcuk9999]
Apero.recipes.nirps_ha - update nirps recipes after spirou changes. [njcuk9999]
Misc.tools.update_header_keys.py - add hack tool to update certain header keys on mass (no warning - careful of use!) [njcuk9999]
Apero.data.spirou.reset.calibdb - update master wave solution + master_calib_SPIROU.txt (use more recent wave solutions + different for each fiber) [njcuk9999]
Apero.science.velocity.general.py - add additional check for no valid pixels after blaze cut (keep) –> should avoid NaNs when no lines in order (Issue #622) [njcuk9999]
Update the language database. [njcuk9999]
Merge remote-tracking branch ‘origin/neil’ into neil. [njcuk9999]
Apero.science.velocity.general.py - add break point to investigate Issue #622. [njcuk9999]

0.6.102 (2020-06-12)¶

Merge pull request #629 from njcuk9999/working. [Neil Cook]

Working –> Developer (tested with mini-run successfully)
Update README.md. [Neil Cook]
Merge pull request #627 from njcuk9999/neil. [Neil Cook]

Neil –> working
Apero.core.instruments.spirou.recipe_defintions.py - allow –plot to go to -1 (dev mode plot NOTHING) - not recommended for general use. [njcuk9999]
Misc.tools.valid_raw_directories.py - add code to test the validity of an APERO raw directory. [njcuk9999]
Misc.tools.apero_mtl_sync_master.py - update version and local path. [njcuk9999]
Merge pull request #626 from njcuk9999/working. [Neil Cook]

Working
Merge pull request #625 from njcuk9999/neil. [Neil Cook]

Neil
Update install.py and requirements_current.txt. [njcuk9999]
Update date/version/changelog/documentation. [njcuk9999]
Apero.science.telluric.general.py - remove break point. [njcuk9999]
Apero.core.instruments.*.file_defintiions.py + apero.core.instruments.default.output_filenames.py - use basename instead of filename (avoids confusion in file defintions with set_file) [njcuk9999]
Apero.core.instruments.default.output_filenames.py - be more careful with filename when setting a file (should not be a path) [njcuk9999]
Apero.science.telluric.general.py - add break point to test tellu bug. [njcuk9999]
Update date/version/changelog/documentation. [njcuk9999]
Misc.tools.apero_diff.py - add time/version/id key to file - and order columns better for output. [njcuk9999]
Apero.core.core.drs_database.py - need to lock db files while they are being read (to avoid two or more cores opening at once) [njcuk9999]
Apero-drs.misc.tools.apero_diff.py - add code to compare two DRS reductions. [njcuk9999]
Apero.core.core.drs_file.py - correct typo - os.abspath –> os.path.abspath. [njcuk9999]
Update date/version/changelog. [njcuk9999]
Merge pull request #621 from njcuk9999/working. [Neil Cook]

Working –> Developer
Merge pull request #620 from njcuk9999/neil. [Neil Cook]

tools.module.setup.drs_installation.py - Path(in_tool_path) –> str(i…
Merge pull request #619 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #618 from njcuk9999/neil. [Neil Cook]

Neil –> working

0.6.101 (2020-06-09)¶

Apero.science.velocity.general.py - remove breakpoint (problem solved) - Issue #623. [njcuk9999]
Apero.core.core.drs_file.py - make filename absolute path in all cases (Issue #623) [njcuk9999]
Add break point to test Issue 623. [njcuk9999]
Apero.tools.module.setup.drs_installation.py - value.exists() –> not value.exits() (Issue #624) [njcuk9999]

0.6.100 (2020-06-08)¶

Misc/tools/apero_diff.py - code to find differences between two reductions. [njcuk9999]
Apero.science.calib.dark.py - add back in the dark removal of the low frequency dark. [njcuk9999]
Apero.recipe.spirou.cal_extract_spirou.py - remove breakpoints. [njcuk9999]
Apero.core.instruments.spirou.default_constants.py - add HCONE and HCTWO to THERMAL_CORRECTION_TYPE2. [njcuk9999]
Move the break point. [njcuk9999]
Move the break point. [njcuk9999]
Apero.science.velocity.general.py - move breakpoint. [njcuk9999]
Apero.science.velocity.general.py - add break point fto fit_fp_peaks. [njcuk9999]
Update the apero_mtl_sync codes. [njcuk9999]
Requirements_current.txt - add pyyaml requirement. [njcuk9999]
Update env with yaml/pyyaml. [njcuk9999]
Tools.module.setup.drs_installation.py - Path(in_tool_path) –> str(in_tool_path) [njcuk9999]
Apero-drs.setup.install.py - correct typo Path(drs_path) –> str(drs_path) [njcuk9999]
Update date/version/changelog/update notes/documentation. [njcuk9999]

0.6.099 (2020-06-04)¶

Misc.tools.ccf_drift_plot.py - add another ccf header key plot. [njcuk9999]
Update update-notes for version 0.6.098. [njcuk9999]
Apero.tools.module.setup.drs_installation.py - correct typo join( –> joinpath( [njcuk9999]
Apero-drs.setup.envs.README.md - add a read me to detail how to use/mask conda env files. [njcuk9999]
Setup.env.apero-env-2020-06-03.txt - add env pip install copy. [njcuk9999]
Setup.env.apero-env-2020-06-03.txt - add yml conda env copy. [njcuk9999]
Setup.env.apero-env-2020-06-03.txt - add explicit environment copy. [njcuk9999]
Update date/version/changelog/documentation. [njcuk9999]

0.6.098 (2020-06-01)¶

Apero.plotting.plot_functions.py - adjust ccf plot. [njcuk9999]
Apero.plotting.plot_functions.py - update scale and add legend to plot_ccf_photon_uncert. [njcuk9999]
Apero.science.velocity.general.py - correct rv_noise for compute_ccf_fp. [njcuk9999]
Apero.science.velocity.general.py - correct rv_noise. [njcuk9999]
Apero.science.velocity.general.py - add breakpoint to test bug. [njcuk9999]
Apero.science.velocity.general.py - add EA calculation of DVRMS CC (from CCF) [njcuk9999]
Apero.science.velocity.general.py - remove redundant 1/1/x –> x. [njcuk9999]
Apero.plotting.plot_functions.py - Update plot_ccf_photon_uncert for ccf + sp noise. [njcuk9999]
Core.instruments.*.default_keywords.py - remove KW_CCF_MEAN_RV_NOISE (now use KW_CCF_DVRMS_SP and KW_CCF_DVRMS_CC) [njcuk9999]
Apero.tools.module.setup.drs_installation.py - add str. [njcuk9999]
Apero.tools.module.setup.drs_installation.py - add int/float/bool. [njcuk9999]
Update date/version/changelog/documentation. [njcuk9999]

0.6.097 (2020-05-30)¶

Setup.install.py and setup.newprofile.py - change os.path to pathlib.Path. [njcuk9999]
Apero.tools.module.setup.drs_installation.py - replace os.path with pathlib.Path. [njcuk9999]
Apero.io.drs_path.py - change copy tree to use pathlib.Path. [njcuk9999]
Apero.core.constants.param_functions.py - allow get_relative_folder to accept pathlib.Path. [njcuk9999]
Apero.core.instruments.*.default_keywords.py - add KW_CCF_DVRMS_SP and KW_CCF_DVRMS_CC keyword arguments. [njcuk9999]
Apero.science.velocity.general.py - add a photon noise per order calculation and save to ccf table/header. [njcuk9999]
Documnetation.working.user.general.todo.rst - update todo list. [njcuk9999]
Apero.recipes.spirou.pol_spirou_new.py and science.polar.general_new.py - continue work on new polar code from @eder. [njcuk9999]
Apero.data.spirou.reset.runs.mini_run.ini - add extra science targets (rv standards) [njcuk9999]
Apero.core.instruments.*.default_constants.py - remove polar consts (for now) [njcuk9999]

0.6.096 (2020-05-27)¶

Setup.newprofile.py - add TODO as setup file is at the wrong path and needs fixing. [njcuk9999]
Apero.core.math.general.py - add back in continuum function for now (until new polar code ready) [njcuk9999]
Td_data/apero-drs/setup/newprofile.py - add debug and clean options. [njcuk9999]
Misc.tools.ccf_plot.py - separate out science and reference fiber results into frames for plot. [njcuk9999]
Apero.recipes.spirou.pol_spirou_new.py and science.polar.general_new.py - continue polar update from @eder. [njcuk9999]

0.6.095 (2020-05-25)¶

Test for git version adding for EA. [njcuk9999]
Apero.science.calib.dark.py - make large_image_median –> large_image_combine and specify the median math mode (same as before but changed input) [njcuk9999]
Apero.recipes.spirou.cal_shape_master_spirou.py + apero.science.calib.shape.py + apero.io.drsimage.py - make large_image_median –> large_image_combine and use a mean to combine fpcube and return fpmaster instead. [njcuk9999]
Apero.science.calib.shape.py - add back break point to investiage fpdata shape error. [njcuk9999]

0.6.094 (2020-05-24)¶

Apero.science.calib.shape.py - need to increase row every iteration row+=1. [njcuk9999]
Apero.io.drs_image.py + apero.science.calib.shape.py - move break point. [njcuk9999]
Apero.io.drs_image.py - add breakpoint to figure out problem. [njcuk9999]
Apero.io.drs_image.py - correct typo b_it –> f_it. [njcuk9999]
Apero.io.drs_image.py - add more printouts. [njcuk9999]
Apero.io.drs_image.py - make sure bins are scaled by number of pixels in image0. [njcuk9999]
Apero.io.drs_image.py - make sure npy files have leading zeros. [njcuk9999]
Apero.io.drs_image.py - remove dirs until filepath does not exist. [njcuk9999]
Apero.io.drs_image.py + science.calib.dark.py and science.calib.shape.py - allow reading of fits and npy files in large_image_median. [njcuk9999]
Apero.io.drs_image.py - fix npyfilelist. [njcuk9999]
Apero.io.drs_image.py - clean up and fix typo. [njcuk9999]
Apero.io.drs_image.py - correct typo wargs -> *wargs. [njcuk9999]
Apero.science.calib.dark.py - correct outdir (no directory defined) [njcuk9999]
Update date/version/changelog/documentation. [njcuk9999]
Apero.recipes.spirou.cal_wave_master_spirou.py and apero.science.calib.wave.py - add rv difference bettwen fibers QC. [njcuk9999]
Apero.core.instruments.*.default_connstants.py - add WAVE_CCF_RV_THRES_QC. [njcuk9999]
Apero.recipes.spirou.cal_wave_night_spirou.py + cal_wave_master_spirou.py + apero.science.calib.wave.py - remove break points and printouts –> fixed? [njcuk9999]
Apero.recipes.spirou.cal_wave_night_spirou.py + cal_wave_master_spirou.py + apero.science.calib.wave.py - remove break points and test fix. [njcuk9999]
Apero.recipes.spirou.cal_wave_night_spirou.py + cal_wave_master_spirou.py + apero.science.calib.wave.py - add printouts to test differences (with breakpoints) [njcuk9999]
Apero.recipes.spirou.cal_wave_night_spirou.py + apero.science.calib.wave.py - add more breakpoints. [njcuk9999]
Updaet date/version/changelog/documentation. [njcuk9999]

0.6.093 (2020-05-22)¶

Apero.science.calib.wave.py - add force fiber to get wavesolution - do not use wprops in night_wavesolution (use only wavemap and wavefile) [njcuk9999]
Apero.recipes.*.cal_wave_night_*.py - night_wavesolution now does not take wprops as input - only take wavemap and wavefile, and force fiber to be fiber=fiber (not use fiber) [njcuk9999]
Apero.science.calib.wave.py - force two iterations of each wave solution, first time with AB, second time with own solution. [njcuk9999]
Apero.science.calib.wave.py - force two iterations of each wave solution, first time with AB, second time with own solution. [njcuk9999]
Apero.recipe.spirou.cal_wave_master_spirou.py - correct rkeys/wkeys. [njcuk9999]
Apero.science.calib.wave.py - create process_fibers function - loop around fibers and run night_wavesolution (update dcavity and hclines/fplines when master is run) [njcuk9999]
Apero.recipes.spirou.cal_wave_master_spirou.py - change way we calculate A, B and C (after AB, both AB, A, B and C are calculated in same way as night solution) [njcuk9999]
Apero.recipe.spirou.cal_wave_night_spirou.py - change fpfiles –> rawfplines. [njcuk9999]
Apero.science.calib.wave.py - add waveinit and nbpix to nprops. [njcuk9999]
Apero.recipes.spirou.cal_wave_master_spirou.py and cal_wave_night_spirou.py - add WFP_FILE. [njcuk9999]
Apeor.core.constants.param_functions.py - make sure source is not None. [njcuk9999]
Apeor.core.constants.param_functions.py - correct typo np.ndarr –> np.ndarray. [njcuk9999]
Apero.recipes.spirou.cal_wave_master_spirou.py and cal_wave_night_spirou.py - move the break point. [njcuk9999]
Apero.recipes.spirou.cal_ccf_spirou.py - add other key sources. [njcuk9999]
Core.lang.core.drs_lang_db.py - add new terms. [njcuk9999]
Core.constants.param_functions.py - add typing to param dict. [njcuk9999]
Apero.core.core.drs_file.py - add nameattr (get_instanceof is now more generic) [njcuk9999]
Core.constants.constant_functions.py - change _DisplayText –> DisplayText. [njcuk9999]

0.6.092 (2020-05-20)¶

Apero.recipes.spirou.pol_spirou_new.py + apero.science.polar.general_new.py - continue adding eders new polar recipe. [njcuk9999]
Apero.recipes.spirou.cal_wave_night_spirou.py - add break point to wave night. [njcuk9999]
Apero.core.instruments.*.default_constants.py - add back THERMAL_CORRECT (why did it get removed?) [njcuk9999]

0.6.091 (2020-05-20)¶

Apero.science.polar.general_new.py - add PolarObjOut getting of tellu and ccf files. [njcuk9999]
Apero.recipes.spirou.pol_spirou_new.py + apero.science.polar.general_new.py - continue work on loading polar files (finding ccf + tellu files) [njcuk9999]
Apero.core.instruments.default.output_filenames.py - change wlog import. [njcuk9999]
Apero.core.core.drs_file.py - add reconstruct_filename to get another filename close to input one (i.e. change of fiber) [njcuk9999]
Misc.tools.wave_drift_comp.py - remove second plt.close() [njcuk9999]
Apero.science.calib.wave.py - move break point to test rvs. [njcuk9999]
Apero.science.calib.wave.py - add print out about saving fp mask. [njcuk9999]
Misc.tools.ccf_plot.py - update how we get values. [njcuk9999]
Update language database. [njcuk9999]
Apero.science.calib.wave.py - change how we construct outfile for update_smart mask. [njcuk9999]
Misc.tools.wave_drift_compy.py - separate the frames into individual figures. [njcuk9999]
Apero.science.calib.wave.py - correct typo in update_smart_mask u.nm –> uu.nm. [njcuk9999]
Apero.core.instruments.spirou.recipe_definitions.py - add WAVENIGHT plots to wave master. [njcuk9999]
Update flow diagram for cal_wave_master. [njcuk9999]
Apero.science.calib.wave.py - remove inverse of fit_ll_d polynomial (not required any more) [njcuk9999]

0.6.090 (2020-05-15)¶

Apero.science.calib.shape.py - update construct_master_fp to use large image median (better memory handlings to avoid memory errors) [njcuk9999]
Apero.science.calib.dark.py - update construct_master_dark to use large image median (better memory handlings to avoid memory errors) [njcuk9999]
Apero.science.calib.wave.py - add WFP_FILE for HC solution (set to None) [njcuk9999]
Apero.science.calib.wave.py - correct typo read_header_keys –> read_header_key. [njcuk9999]
Apero.science.calib.wave.py - add update_smart_fp_mask function to re- generate smart-fp-mask. [njcuk9999]
Apero.recipes.spirou.cal_wave_master_spirou.py - after wave solution calculated add a night wave solution for master fiber + add option to update smart FP mask after cavity poly updated. [njcuk9999]
Apero.core.instruments.*.default_constants.py - add WAVE_CCF_SMART_MASK constants (for re-generating smart mask) [njcuk9999]
Misc.problems.test_crossmatch.py - add pascals most recent query/gaia link. [njcuk9999]

0.6.089 (2020-05-14)¶

Misc.tools.wave_drift_comp.py - update wave drift code plot to add diff plot. [njcuk9999]
Documentation.working._static.yed - update cal_wave_master flow diagrams. [njcuk9999]
Apero.science.extract.general.py - in write_extraction_files exclude_groups=loc for e2dsfile (get them just from loc file later) [njcuk9999]
Apero.science.calib.wave.py - read WFP_FILE from header, add WAVEINIT (WAVE INIT key at this point is same as WAVEFILE) - could differ after this, change value of WFP_FILE to wprops[‘WFPFILE’], when writing wave solutions update WAVEFILE, WAVETIME, WAVESOURCE and WFP_FILE to the new file itself, for copy_original_keys new to avoid copying wave keys from hcfile. [njcuk9999]
Cal_wave_night_spirou.py - get back nprops from night write wavesol - pass these to update e2ds HC and FP files, return updated hc and fp e2ds files, use these to populate ccf output. [njcuk9999]
Apero.recipes.spirou.cal_wave_master_spirou.py - move write_ccf function and use updated e2ds files to populate it. [njcuk9999]

0.6.088 (2020-05-13)¶

Apero.tools.recipes.utils.get_grid_models.py - get the goettingen and convert to single table. [njcuk9999]
Apero.science.velocity.general.py - modify get_ccf_mask and ccf_calculation with EA changes. [njcuk9999]
Apero.science.calib.dark.py and shape.py - add large image median funtionality (as untested + unused versions) [njcuk9999]
Apero.io.drs_image.py - add npy_filelist, npy_fileclean and large_image_median (untested) [njcuk9999]
Apero.core.instruments.spirou.recipe_definitions.py - add modifications to pol_spirou_new. [njcuk9999]
Core.core.drs_startup.py - add unix_char_code function (to spawn from PID) [njcuk9999]
Misc.updates_to_drs.new_ccf_ea_2020-05-13.py - another iteration by EA. [njcuk9999]
Apero.science.polar.general_new.py - use as staging ground for eders changes (compared to 0.6+ version in general.py) [njcuk9999]
Apero.science.berv.py - if infile is not defined should use header only to get berv keys. [njcuk9999]
Apeor.recipes.spirou.pol_spirou_new.py - start filling out code (compared to Eders version and 0.6+ version and 0.5 version) [njcuk9999]
Apero.core.instruments.spirou.recipe_definitions.py - add pol_spirou_new (for eders updates) [njcuk9999]

0.6.087 (2020-05-12)¶

Apero.recipes.nirps_ha.cal_preprocess_nrips_ha.py - add header as arg to pp.nirps_correction. [njcuk9999]
Apero.core.instruments.*.* - update nirps_ha with changes to spirou. [njcuk9999]
Misc.updates_to_drs.mf_ccf_mask_may2020.py - add EA code for injestion into the drs. [njcuk9999]
Apero.science.calib.wave.py - do not use FIBER_WAVE_TYPEs for non master wave solution (i.e. use AB, A, B and C not just AB, C) [njcuk9999]
Apero.core.instruments.*.default_constants.py - be more descriptive about littrow HC and FP constants. [njcuk9999]
Apero.recipe.nirps_ha.py - update changes in nirps_ha recipes (from spirou) [njcuk9999]

0.6.086 (2020-05-11)¶

Update language database. [njcuk9999]
Setup.install.py - allow the user (on crash) to enter a path themselves and try again (for Claires issue that I cannot reproduce) [njcuk9999]
Apero.core.core.drs_recipe.py - check against input_dir (from recipe definitions) [njcuk9999]
Apero.core.core.drs_argument.py - remove break point - error fixed. [njcuk9999]
Apero.core.core.drs_argument.py - add break point to fix error. [njcuk9999]
Apero.recipes.spirou.cal_wave_master_spirou.py and cal_wave_night_spirou.py - add velocity.write_ccf to these codes (to save CCF for FPs) [njcuk9999]
Apero.core.instruments.spirou.recipe_defintions.py - add CCF_RV to cal_wave_master and cal_wave_night. [njcuk9999]
Documentation.working._static.yed.* - update spirou_map_all graphs/pdfs. [njcuk9999]

0.6.085 (2020-05-09)¶

Misc.problems.shell_vs_call.py - first commit of shell vs call test code for Andres/LAM. [njcuk9999]
Documentation.working._static.yed.apero_cal_wave_master.* - update cal_wave_master flow diagram. [njcuk9999]
Documentation.working._static.yed.apero_cal_wave_master.* - add cal_wave_master flow diagram. [njcuk9999]
Apero_rv - add code, wrapper and utility functions for new ccf code (thanks to EA and his requirements) [njcuk9999]
Apero.tools.recipe.spirou.get_ext_fplines.py - add file/dprtype/object printout. [njcuk9999]

0.6.084 (2020-05-06)¶

Apero-drs.setup.install.py - add detailed debug of root/cwd/pythonpath and sys.path. [njcuk9999]
Apero-drs.setup.install.py - add another debug printout. [njcuk9999]
Apero.tools.module.setup and setup.install.py - add debug mode. [njcuk9999]
Apero.tools.module.setup.drs_installation.py + setup.install.py - add –clean_no_warning for those who like deleting data without prompts (Issue #579) [njcuk9999]
Update date/version/changelog/documentation. [njcuk9999]

0.6.083 (2020-05-05)¶

Recipes.spirou.cal_extract_spirou.py + toools.recipes.spirou.get_ext_fplines.py - change EXT_FPLIST –> EXT_FPLINES. [njcuk9999]
Apero.tools.recipes.spirou.get_ext_fplines.py - have to set plot location. [njcuk9999]
Science.extract.general.py - add debug print outputs when fiber and dprtype are incorrect. [njcuk9999]
Apero.io.drs_fits.py - HEADER_FIXES requireds hdict input and output. [njcuk9999]
Core.instruments.*.pseudo_const.py - require hdict to be populated. [njcuk9999]
Misc.tools.apero_mtl_sync_master.py - add tmp files to uploads. [njcuk9999]
Apero.tools.recipes.spirou.get_ext_fplines.py - first commit of extract fplines (separate from extract code) [njcuk9999]
Apero.tools.module.testing.drs_dev.py - add mod to temp RecipeDefinition. [njcuk9999]
Apero.science.extract.general.py - add ref_fplines function. [njcuk9999]
Apero.science.calib.wave.py - add a required condition to get_wavelines. [njcuk9999]
Apero.recipes.spirou.cal_wave_night_spirou.py - add fiber to get_wavelines. [njcuk9999]
Apero.recipes.*.cal_extract_spirou.py - add fplines creation. [njcuk9999]
Core.instruments.*.recipe_defintions.py - add EXT_FPLINES. [njcuk9999]
Core.instruments.*.file_definitions.py - add ext_fplines. [njcuk9999]
Core.instruments.default_constant.py - add WAVE_FP_DPRLIST to constants. [njcuk9999]
Core.core.drs_log.py - add doc string for find_param. [njcuk9999]
Core.instruments.spirou.default_config.py - change calibDB mode to closest. [njcuk9999]
Merge branch ‘developer’ of https://github.com/njcuk9999/apero-drs into developer. [njcuk9999]
Update README.md. [Neil Cook]

update versions
Merge pull request #617 from njcuk9999/developer. [Neil Cook]

Developer
Merge pull request #608 from njcuk9999/developer. [Neil Cook]

Developer
Merge pull request #605 from njcuk9999/developer. [Neil Cook]

Developer –> master
Merge pull request #585 from njcuk9999/working. [Neil Cook]

Working –> Master
Setup.install.py - kill infinite loop to find apero. [njcuk9999]
Merge pull request #616 from njcuk9999/working. [Neil Cook]

Working
Merge pull request #615 from njcuk9999/neil. [Neil Cook]

update update notes/todo/known issues
Update update notes/todo/known issues. [njcuk9999]
Merge pull request #614 from njcuk9999/neil. [Neil Cook]

neil –> working
Update date/version/changelog/documentation. [njcuk9999]
Merge pull request #607 from njcuk9999/working. [Neil Cook]

Working
Merge pull request #606 from njcuk9999/neil. [Neil Cook]

update readme
Merge pull request #604 from njcuk9999/working. [Neil Cook]

Working –> Developer
Merge pull request #603 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #591 from njcuk9999/working. [Neil Cook]

Working –> Developer
Merge pull request #590 from njcuk9999/neil. [Neil Cook]

neil –> working
Merge pull request #589 from njcuk9999/working. [Neil Cook]

Working –> Developer
Merge pull request #587 from njcuk9999/neil. [Neil Cook]

Neil override: neil –> working
Merge pull request #582 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #581 from njcuk9999/neil. [Neil Cook]

Merge allowed

0.6.082 (2020-05-04)¶

Apero.tools.resources.setup.apero.*.* - update the MKL environment exports. [njcuk9999]
Update language database. [njcuk9999]
Apero.io.drs_fits.py - add the getting of a time variable from the index files and sort by it before returning - all files should be in date order at point of return. [njcuk9999]
Apero.tools.recipes.spirou.update_berv.py - remove from __future__ import. [njcuk9999]
Apero.recipe.spirou.cal_shape_master_spirou.py + apero.science.calib.shape.py - get dxrms and pass to qc (Issue #602) [njcuk9999]
Core.instruments.*.default_constants.py - add SHAPE_MASTER_DX_RMS_QC value (Issue #602) [njcuk9999]
Core.core.drs_database.py - remove break point. [njcuk9999]
Apero..science.calib.shape.py - get rms value for dx-min(ddx) (Issue #602) [njcuk9999]
Apero.science.extract.crossmatch.py - add back warnings for issues with crossmatching - were only debug messages (Issue #612) [njcuk9999]
Apero.core.instruments.*.default_constants.py - update gaia url for tap query (Issue #612) [njcuk9999]
Apero.core.core.drs_file.py - need to return False if copy_cards has a group argument but header key not found in defined keywords. [njcuk9999]
Update date/version/changelog/documentation. [njcuk9999]

0.6.081 (2020-05-01)¶

Science.calib.wave.py - only update dd_cavity when indcavity is None (not the opposite) [njcuk9999]
Apero-drs.requirements_current.txt - change PIL–> Pillow. [njcuk9999]
Update the date/version/changelog/documentation. [njcuk9999]
Misc.tools.ccf_plot.py - update plot. [njcuk9999]
Aspero.science.calib.wave.py - remove break_point. [njcuk9999]
Aspero.science.calib.wave.py - do not update the d_cavity when a input dcavity (indcavity) is provided. [njcuk9999]
Apero.plotting.plot_functions.py - add a ylabel for wave night hist graph. [njcuk9999]

0.6.080 (2020-04-30)¶

Apero.core.core.drs_file.py - correct header card copy bug (Issue #611) [njcuk9999]
Apero.core.instruemnts.*.default_keywords.py - correct KW_INFILE2 and KW_INFILE3. [njcuk9999]
Apero.plotting.plot_functions.py - remove frame 3. [njcuk9999]
Plotting.plot_functions.py and science.calib.shape.py - remove frame 3, function get_offset_sp and xpeak2 etc. [njcuk9999]
Plotting.plot_functions.py and science.calib.shape.py - remove frame 3, function get_offset_sp and xpeak2 etc. [njcuk9999]
Apero.science.calib.general.py - deal with n_entries == 1 for filename not equal to None. [njcuk9999]
Apero.science.calib.general.py - n_entries must = 1 (only need one fpmaster) [njcuk9999]
Apero.science.calib.general.py - fix value if it is a filename/DrsFitsFile instance. [njcuk9999]
Cal_shape_master_spirou.py - params[‘INPUTS’][‘FPMASTER’][0][0] [njcuk9999]
Cal_shape_master_spirou.py - filename for FPMASTER should be [0] [njcuk9999]
Update language database. [njcuk9999]
Apero.science.calib.shape.py - typo arg –> args. [njcuk9999]
Apero.science.calib.shape.py - if we have no HC lines do not try to find Nth line fppeak using HC (assume that it is correct from fp) [njcuk9999]
Update language database. [njcuk9999]
Apero.science.calib.shape.py - add break_point to test error. [njcuk9999]
Apero.core.instruments.spirou.default_constants.py - go back to new line list. [njcuk9999]
Misc.tools.mk_master_hc_cat.py - change path of wave_hclines. [njcuk9999]
Update wave calib files. [njcuk9999]
Apero.core.instruments.spirou.default_constants.py - change wave catalogue back to original. [njcuk9999]
Apero.science.calib.wave.py - remove sigclip mask. [njcuk9999]
Apero.science.calib.shape.py - pep8 update. [njcuk9999]
Apero.science.calib.wave.py - add break point from EA. [njcuk9999]
Apero.core.instruments.default.default_constants.py - WAVE_LINELIST_START should be an integer. [njcuk9999]
Apero.io.drs_data.py - correct typo data_start –> datastart. [njcuk9999]
Apero.core.instruments.spirou.default_constants.py - change linelist start to line 1. [njcuk9999]
Apero.core.core.drs_file.py and science.extract.general.py - add copy_header function (in addition to copy_hdict) and for s1d files copy the header from the e2ds file not the hdict (which only has new keys in) - Issue #610) [njcuk9999]
Apero.science.extract.general.py - add break point to investigate no header in s1d. [njcuk9999]
Update date/version/changelog/documentation. [njcuk9999]

0.6.079 (2020-04-28)¶

Update language database. [njcuk9999]
Misc/tools/mk_master_hc_cat.py + data.spirou.calib.catalogue_UNe.csv - code to update the hc linelist. [njcuk9999]
Apero.core.instruemnts.spirou.defalut_constants.py - update catalogue file and fmt. [njcuk9999]
Apero.core.instruments.spirou.default_constants.py - pep8 adjustment. [njcuk9999]
Apero.plotting.plot_functions.py - add summary descriptions for two wave night summary plots. [njcuk9999]
Apero.science.calib.wave.py - add wave_expected (after) plot for hc and fp. [njcuk9999]
Apero.scioence.calib.wave.py - and catch warning statement around madmask. [njcuk9999]
Update language database. [njcuk9999]
Science.calib.wave.py - remove breakpoint + and range for second iteration. [njcuk9999]
Apero.plotting.plot_functions.py - correct wave night figures. [njcuk9999]
Apero.science.calib.wave.py - add break point to test EA new code. [njcuk9999]
Plotting.plot_functions.py - correct typo kwargs[‘waveref’] –> kwargs[‘waverefs’] [njcuk9999]
Core.instruments.*.default_keywords.py - correct typo groupu–>group. [njcuk9999]
Apero.core.instruments.default.default_constants.py - remove PLOT_WAVENIGHT_DIFFPLOT from __ALL__ [njcuk9999]
Apero.science.calib.wave.py - add EA updates to night_wavesolution. [njcuk9999]
Recipes.spirou.cal_wave_night_spirou.py - add fiber to inputs of night_wavesolution (for plot saving) [njcuk9999]
Plotting.plot_functions.py - modify wave night plotting (wavenight_iterplot + wavenight_histplot) and remove wavenight_diffplot after ea changes. [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - modify debug/summary plots after EA changes. [njcuk9999]
Update language database. [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - remove WAVENIGHT_DIFFPLOT from debug plot list. [njcuk9999]
Core.instruments.default_constants.py and default_keywords.py - add/remove/modify wave night constants/keywords with new update from EA. [njcuk9999]
Misc.tools.ccf_plot.py - update graph. [Neil Cook]

0.6.078 (2020-04-27)¶

Recipes.nirps_ha.cal_preprocessing_niprs_ha.py - update pp for nirps (from spirou updates) [njcuk9999]
Recipes.spirou.cal_preprocessing_spirou.py and science.preprocessing.general.py - fix qc to print only when log=True + redo QC after iteration loop. [njcuk9999]
Misc.tools.wave_drift_comp.py - test drift in fibers. [njcuk9999]
Apero.recipe.spirou.cal_preprocess_spirou.py - deal with a QC after a shift in pixels. [njcuk9999]
Update date, version, changelog, documentation. [njcuk9999]

0.6.077 (2020-04-24)¶

/locale/ –> /lang/ [njcuk9999]
Apero.locale –> apero.lang. [njcuk9999]
Io.drs_fits.py + science.preprocessing.identification.py - fix for preprocessing to use input file (was changed due to copyother change) [njcuk9999]
Apero.science.preprocessing.detector.py - add a border mask to remove hotpix that lie near the edge (we need to scan around them so these are not useful) [njcuk9999]
Apero.io.drs_data.py + apero.science.preprocessing.detector.py - format hotpix table correctly. [njcuk9999]
Apero.core.instruments.*.default_constants.py - add back in PP_CORRUPT_MED_SIZE. [njcuk9999]
Apero.science.calib.wave.py - add rhcl and rfpl to output (for saving to file) [njcuk9999]
Core.instruments.spirou.file_definitions.py + recipe_definitions.py - add WAVE_HCLIST and WAVE_FPLIST. [njcuk9999]
Recipes.spirou.cal_wave_master_spirou.py + science.velocity.general.py - remove the wave test code. [njcuk9999]
Recipe.spirou.cal_wave_master_spirou.py + science.velocity.general.py - push correct e2ds fiber into ccf code. [njcuk9999]
Science.calib.wave.py - data llprops[‘LL_FINAL’] –> wprops[‘WAVEMAP’] [njcuk9999]
Recipes.spirou.cal_wave_master_spirou.py + science.velocity.general.py - add wavetest to test wavemap values. [njcuk9999]
Science.calib.wave.py - add master wave sol to solutions (after plotting) [njcuk9999]
Recipes.spirou.cal_wave_master_spirou.py science.calib.wave.py science.velocity.general.py - move break points. [njcuk9999]

0.6.076 (2020-04-22)¶

Apero.science.calib.wave.py - correct wave fp header keys. [njcuk9999]
Apero.core.instruemnts.spirou.default_constants.py - add smart FP mask as default from EA. [njcuk9999]
Add updated cavit length equation files. [njcuk9999]
Add EA smark fp mask from cavity file. [njcuk9999]
Science.velocity.general.py - deal with bounds and change remove wide peaks criteria. [njcuk9999]
Science.velocity.general.py - deal with bounds and change remove wide peaks criteria. [njcuk9999]
Science.velocity.general.py - remove exception breakpoints. [njcuk9999]
Science.velocity.general.py - adjust dc and shape p0 values. [njcuk9999]
Apero.science.velocity.general.py - add breakpoints to fit fp exceptions (For test) [njcuk9999]
Science.velocity.general.py - deal with bounds being out-of-bounds. [njcuk9999]
Apero.science.velocity.general.py - add back in pcov. [njcuk9999]
Apero.science.velocity.general.py - correct bounds. [njcuk9999]
Apero.science.velocity.general.py - add bounds to fp fit. [njcuk9999]
Science.velocity.general.py - add break point to test. [njcuk9999]
Apero.science.velocity.general.py - set peak_spacing = 5 (old drs value) [njcuk9999]
Apero.science.calib.wave.py and apero.science.velocity.general.py - remove params from fit_fp_peaks. [njcuk9999]

0.6.075 (2020-04-21)¶

Apero.science.velocity.general.py - reduce the peak criteria to half the order peak size. [njcuk9999]
Apero.science.velocity.general.py - change outputs for fit_fp_peaks. [njcuk9999]
Apero.science.velocity.general.py - dcpenormpercentak –> dcpeak. [njcuk9999]
Apero.science.velocity.general.py - fix typo normpercentile –> normpercent. [njcuk9999]
Science.calib.wave.py - move print outs to language database. [njcuk9999]
Update language database. [njcuk9999]
Apero.science.velocity.general.py - deal with curve_fit warnings. [njcuk9999]
Apero.science.calib.wave.py - add warnings back to code. [njcuk9999]
Update language database. [njcuk9999]
Apero.core.instruments.default_keywords.py - add KW_WFP_WIDUSED for storing width per order. [njcuk9999]
Apero.science.calib.wave.py - move constants to wave file and update header. [njcuk9999]
Apero.science.velocity.general.py - move constants to constants files. [njcuk9999]
Core.instruments.*.default_constants.py + default_keywords.py - adjust wave fp constants after fp finding update. [njcuk9999]
Science.calib.wave.py - need new cond2 for FP. [njcuk9999]
Science.calib.wave.py - add breakpoint to test get_master_lines. [njcuk9999]
Science.velocity.general.py - change limit 0.3 –> 0.1. [njcuk9999]
Science.calib.wave.py - remove breakpoint. [njcuk9999]
Science.calib.wave.py - update output from line fit. [njcuk9999]
Core.instruments.*.default_contants.py - update cavity file. [njcuk9999]
Science.velocity.general.py - change EWPEAK to PEAK2PEAK and modify remove_wide_peaks (width is peak to peak not normalized width) [njcuk9999]
Core.instruemnts.spirou.default_constants.py - change WAVE_FP_NORM_WIDTH_CUT from 0.25 to 15. [njcuk9999]
Science.velocity.general.py - add fit_fp_peaks function. [njcuk9999]
Science.calib.wave.py - FP should use ea_airy function. [njcuk9999]
Science.velocity.general.py - determine fp peak size from the data (median of all peak widths) [njcuk9999]
Science.velocity.general.py - modify the FP peak finding (now use the ea_airy function) [njcuk9999]
Core.math.general.py - add ea_airy_function (for FP peak finding) [njcuk9999]
Core.insturments.spirou.default_constants.py - change the border and box size for FP peak finding (now using ea_airy) [njcuk9999]
Science.velocity.general.py - add breakpoint to test gaussian. [njcuk9999]

0.6.074 (2020-04-20)¶

Apero.core.math.__init__.py - add gauss_beta_function. [njcuk9999]
Misc.problems.new_ccf_code.py - add EA changes to give option to play with convolution kernel. [njcuk9999]
Misc.nirps_tools.correct_sims.py - write code to correct the headres of simulations. [njcuk9999]
Apero.science.velocity.general.py - swap gaussian fit fot gaussian_beta fit in function=measure_fp_peaks. [njcuk9999]
Apero.science.calib.wave.py - change inverse coefficient fit for updating pixel_ref (rpixels –> rwaveref) [njcuk9999]
Apero.core.math.gauss.py - add gauss_beta_function for ((x-x0)/sigma)^beta. [njcuk9999]

0.6.073 (2020-04-18)¶

Apero.science.calib.wave.py - add iteration for WAVEREF plot. [njcuk9999]
Apero.plotting.plot_functions.py - update the title depending on where used. [njcuk9999]
Documentation.working.user.general.known_issues.rst - update known issues. [njcuk9999]
Science.calib.wave.py - update plot (give before and after) [UNFINISHED] [njcuk9999]

0.6.072 (2020-04-17)¶

Apero.plotting.plot_functions.py and science.velocity.general.py - update wave fiber plot size + add fiber name to ccf fp plot. [njcuk9999]
Apero.plotting.plot_functions.py - make markers smaller. [njcuk9999]
Wave codes - pep8 corrections. [njcuk9999]
Science.calib.wave.py - correct typo WAVE_OTHERFIBER –> WAVE_FIBER_COMPARISON. [njcuk9999]
Update todo list. [njcuk9999]
Science.velocity.general.py - do not limit fp ccf to fiber c (AB,A,B valid too) [njcuk9999]
Apero.recipes.spirou.cal_wave_master_spirou.py - only do main code for master_fiber and then add functionality to process other fibers (fit from FPLINES) + CCF and write loops. [njcuk9999]
Apero.plotting.plot_functions.py - add plot_wave_fiber_comparison. [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - add wave_fiber_comp plots. [njcuk9999]
Update language database. [njcuk9999]
Core.instruments.default.default_constants.py - add wave fiber constants. [njcuk9999]
Documentation.working.user.general.known_issues.rst - update known issues. [njcuk9999]
Misc.problems.new_ccf_code.py - update CCF_RV_NULL and add IN_RV (copy from apero-utils) [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - add EXTRACT_S1D_WEIGHT to debug plots. [njcuk9999]
Core.core.drs_log.py - change typo fmt–>format. [njcuk9999]
Science.calib.wave.py - add wave time to hc and fp solutions. [njcuk9999]
Science.velocity.general.py - make null_targetrv. [njcuk9999]
Core.instrument.*.default_constant.py - NULLVAL for RV is now a abs limit. [njcuk9999]

0.6.071 (2020-04-16)¶

Apero.recipes.nirps_ha.cal_preprocess_nirps_ha.py - change instrument SPIROU –> NIRPS_HA. [njcuk9999]
Apero.io.drs_data.py - load_hotpix fmt is ‘csv’ not ‘None’ [njcuk9999]
Apero.io.drs_data.py - read_table default table is fits. [njcuk9999]
Core.core.drs_log.py - Table.read log –> fmt=’fits’ [njcuk9999]
Tools.recipe.bin.apero_processing.py - remove old break point. [njcuk9999]
Tools.module.setup.drs_processing.py - if we have to find the recipe set the file mod after finding it. [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - replace _run with _seq and add engineering sequence (hc1_hc1 extract, fp_fp extract, dark_fp extract) [njcuk9999]
Data.spirou.reset.runs.* - update sequences _run –> _seq. [njcuk9999]
Recipes.spirou.cal_wave_night_spirou.py - remove one of the breakpoints. [njcuk9999]
Core.instruments.spirou.file_definitions.py - add back in thermal e2ds with correct kw_output. [njcuk9999]
Recipes.spirou.cal_wave_night_spirou.py - add breakpoint for testing. [njcuk9999]

0.6.070 (2020-04-15)¶

Core.instruments.spirou.recipe_defintions.py - add EXTRACT_S1D_WEIGHT. [njcuk9999]
README.md - update raw file table. [njcuk9999]
Apero.tools.recipes.bin.apero_mkdb.py - skip master files. [njcuk9999]
Update language database. [njcuk9999]
Tools.recipes.bin.apero_mkdb.py - skip master default files. [njcuk9999]
Core.core.drs_file.py + io.drs_fits.py - do not report error from read header in id. [njcuk9999]
Core.instruments.spirou.file_definitions.py - out_wave_night - WAVE_FP –> WAVE_NIGHT. [njcuk9999]
Science.extract.other.py - correct KW_OUTPUT for thermal files. [njcuk9999]
Core.core.drs_file.py + io.drs_fits.py - deal with copyother and trying to open files with wrong extensions. [njcuk9999]
Data.spirou.reset.runs.mini_run.ini - set reset_run to False by default. [njcuk9999]
Core.core.drs_file.py in check_read get load_data option from call args. [njcuk9999]
Core.core.drs_file.py in check_read get load_data option from call args. [njcuk9999]
Tools.recipes.bin.apero_mkdb.py - do not get data when identifying file. [njcuk9999]
Core.core.drs_file.py - read file after copying parameters (so datatype is correct) [njcuk9999]
Core.core.drs_file.py - do not copy over drsfile.datatype from infile (in copyother) [njcuk9999]
Instruments.spirou.file_definitions.py - update KW_OUTPUT (should be WAVEM) [njcuk9999]
Core.core.drs_database.py - fix error in writing to database. [njcuk9999]
Science.calib.wave.py - add WAVETIME to nprops (for header) [njcuk9999]
Recipe.spirou.cal_wave_night_spirou.py + science.calib.wave.py - add input dcavity for fibers A,B,C (use cavity width from AB) [njcuk9999]
Core.instrument.*.default_keywords.py - add dcavity source. [njcuk9999]

0.6.069 (2020-04-09)¶

Recipe.spirou.cal_ccf_spirou.py - correct typo rv_props1 –> rv_props2 for WAVESOURCE. [njcuk9999]
Core.instruments.spirou.recipe_defintions.py - add tmp (commented) polar recipe. [njcuk9999]
New_ccf_code.py - add help. [njcuk9999]
Core.core.drs_log.py and io.drs_lock.py - correct write statement (log–> mode=a) [njcuk9999]

0.6.068 (2020-04-08)¶

Science.velocity.general.py - add rv wave source to ccf header. [njcuk9999]
Misc.old - move cal_wave_spirou.py [old code] to misc. [njcuk9999]
Science.calib.wave.py - add wave time to wprops + add it to header when present (i.e. in add_wave_keys) [njcuk9999]
Recipes.spirou.cal_ccf_spirou.py - add wave source for rv fiber to header. [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - remove old cal_wave. [njcuk9999]
Cpre.instruments.*.default_keywords.py - modify ccf rv wave keys. [njcuk9999]
Cal_ccf_spirou.py - save rv wavefile, rv wave time and rv time diff (file->wave) to header. [njcuk9999]
Core.instruments.*.defaults_keywords.py - add KW_CCF_RV_WAVEFILE, KW_CCF_RV_WAVETIME and KW_CCF_RV_TIMEDIFF (for ccf) [njcuk9999]
Misc.problems.new_ccf_code.py - update code, make it completely independent of the drs + add writing file + add switch for OBJ and FP + add plots (and plot switch) [njcuk9999]

0.6.067 (2020-04-07)¶

Split create_pp_hotpix.py into two bits - one for each instrument + update for drs integration (via drs_dev tmp functions) [njcuk9999]
Science.preprocessing.detector.py - update get hot pixel function to load ypix and xpix from file. [njcuk9999]
Apero.io.drs_data.py - change load_full_flat_pp to load_hotpix. [njcuk9999]
Data.spiroiu.engineering.hotpix_pp.csv - update hotpix file for spirou. [njcuk9999]
Core.instruments.*.default_constants.py - modify pp constants for new hotpix function/file. [njcuk9999]

0.6.066 (2020-04-07)¶

Add a hotpix mask for spirou. [njcuk9999]
Tools.recipes.utils.README.md - add a directory for utilities. [njcuk9999]
Tools.recipe.utils.create_pp_hotpix.py - add EA hotpix generator. [njcuk9999]
Tools.recipes.spirou.update_berv.py - rename from cal_update_berv.py. [njcuk9999]
Core.math.general.py - add in the normal_fraction math function. [njcuk9999]

0.6.065 (2020-04-03)¶

Replace open+read/write+close –> with open+read/write. [njcuk9999]
Tools.recipes.spirou.expmeter_spirou.py - change copy_hdict –> copy_original_keys. [Neil Cook]
Tools.recipes.spirou.expmeter_spirou.py - corerct code after testing. [Neil Cook]
Core.core.drs_file.py - make add_hkey accept list or tuple for keywordstore. [Neil Cook]
Tools.recipes.spirou.expmeter_spirou - add saving to file (using drs_dev FileDefinitions and Tmp files) [Neil Cook]
Tools.module.testing.drs_dev.py - add TmpInputFile, TmpFitsFile and TmpNpyFile and FileDefinition to allow external file defintions (for tools and testing) [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Tools.recipes.spirou.expmeter_spirou.py - move exposuremeter constants to constants file (use params) [njcuk9999]
Core.instruments.*.default_constants.py - add exposure meter constants. [njcuk9999]
Misc/tools/apero_mtl_sync_master.py - add master sync code. [Neil Cook]

0.6.064 (2020-04-02)¶

Update language database. [njcuk9999]
Io.drs_lock.py - deal with locking and removing files bug (Impossible error should now be impossible) [njcuk9999]
Core.core.drs_database.py - check calibration is copied after copying (so we don’t update database if there was an uncaught error) [njcuk9999]
Documentation.working.user.general.todo.rst - update todo list. [njcuk9999]
Tools.recipes.spirou.expmeter_spirou.py - continue work on functionality. [njcuk9999]
Io.drs_fits.py - add function add_header_key (for when we don’t have a drs fits file) [njcuk9999]
Core.math.general.py - add inverse functionality to rot8. [njcuk9999]
Update readme. [njcuk9999]
Update date/version/changelog/update notes. [njcuk9999]

0.6.063 (2020-04-01)¶

Apero.data.spirou.reset.runs.mini_run.ini - turn off MKTELLDB and FTELLDB runs (use individuals) [njcuk9999]
Apero.recipes.spirou.cal_leak_spirou.py - qcparams is a dict –> user ref fiber. [njcuk9999]
Apero.recipes.spirou.cal_leak_spirou.py - add qc to log.fits. [njcuk9999]
Core.instruments.default.recipe_definitions.py - master is reserved keyword –master –> –mlog. [njcuk9999]
Recipe.spirou.expmeter_spirou.py - continue work on exposuremeter. [Neil Cook]
Science.telluric.general.py - fix core.get_file_definition. [Neil Cook]
Tools.recipe.spirou.expmeter_spirou.py - add params to arguments of simage_to_drs. [Neil Cook]
Tools.module.utils.inverse.py - add required keys. [Neil Cook]
Science.telluric.general.py - provide fiber fot TELLU_CONV. [Neil Cook]
Tools.recipes.spirou.expmeter_spirou.py - add telluric map (from mask making) - UNFINISHED. [Neil Cook]
Tools.module.utils.inverse.py - move imports to top. [Neil Cook]
Science.telluric.general.py - add second way to get TELLU_CONV if not defined in outputs. [Neil Cook]
Io.drs_fits.py - add two conditions to find files with fibers _fiber_ or _fiber. [Neil Cook]
Tools.recipes.spirou.expmeter_spirou.py - add changes to use inverse.py code. [njcuk9999]
Tools.module.utils.inverse.py - add drs_image_shape function and reference full image size from params and make calc_central_localisation take filename or header. [njcuk9999]
Core.instruments.*.default_constants.py - add in IMAGE_X_FULL and IMAGE_Y_FULL (for reference) [njcuk9999]
Core.instruments.default.pseudo_const.py - add INDIVIDUAL_FIBERS function. [njcuk9999]
Tools.module.utils.inverse.py - add changes with order profile. [Neil Cook]
Update version/date/documentation/changelog. [Neil Cook]

0.6.062 (2020-03-31)¶

Tools.module.utils.inverse.py - test out making straight image and shifting by x and y. [Neil Cook]
Core.core.drs_log.py - correct typo (‘DRS_RECIPE_KIND’ is not None) –> (params[‘DRS_RECIPE_KIND’] is not None) [Neil Cook]
Core.core.drs_log.py - deal with DRS_DATA_MSG_FULL set to None. [Neil Cook]
Core.isntruments.default.default_config.py - add to __ALL__ [Neil Cook]
Core.isntruments.default.default_config.py - add some constant that are set in drs_setup (for when we are not using setup) [Neil Cook]
Science.calib.general.py - check that inputs is in params (may not be) [Neil Cook]
Core.core.drs_recipe.py - add a quick way to make a recipe (using params) [Neil Cook]
Tools.recipes.spirou.exposuremeter_spirou.py and module.utils.inverse.py - start work on inversing drs (exspoure meter etc) [njcuk9999]
Core.core.drs_recipe.py - directory must be an absolute path (if we are in the reduced folder it wont be without these changes –> causes an error later) [njcuk9999]
Core.core.drs_argument.py - paths for commonpath must be absolute –> enforce this explicitly. [njcuk9999]
Core.core.drs_argument.py - add breakpoint to test error. [njcuk9999]
Core.core.drs_recipe.py - break_point to test error. [njcuk9999]
Core.core.drs_recipe.py - deal with sys.argv having a full path as first argument (don’t know why this is happening) [njcuk9999]
Core.core.drs_recipe.py - remove path from recipe name (for argparse) [njcuk9999]
Science.velocity.general.py - add EA changes from new_ccf_code test. [njcuk9999]
Misc.problems.new_ccf_code.py - add EA fixes. [njcuk9999]

0.6.061 (2020-03-29)¶

Science.telluric.general.py - correc typo KW_FTELLU_TEMP –> KW_FTELLU_TEMPLATE. [Neil Cook]

0.6.060 (2020-03-28)¶

Misc.problems.new_ccf_code.py - add comments. [Neil Cook]
Misc.problems.new_ccf_code.py - add better plot for EA. [Neil Cook]
Misc/problems/new_ccf_code.py - correction to stand alone ccf code. [njcuk9999]
Misc/problems/new_ccf_code.py - stand alone test of ccf code. [njcuk9999]
Science.velocity.general.py - add in the condition that targetrv is equal to the null value (-9999.99 for spirou) [njcuk9999]
Update language database. [njcuk9999]
Core.instruments.*.default_constants.py - add CCF_OBJRV_NULL_VAL. [njcuk9999]
Core.instruments.spirou.default_keywords.py - correct typo KW_FTELLU_TEMPLATEKW_FTELLU_TEMPLATE –> KW_FTELLU_TEMPLATE. [njcuk9999]
Recipes.spirou.obj_fit_tellu_spirou.py and science.telluric.general.py - add a keyword for which template was used (or if not set to None) [njcuk9999]
Core.instruments.*.default_keywords.py - add KW_FTELLU_TEMPLATE. [njcuk9999]
Core.core.drs_file.py - change drs_path() –> drs_path.numpy_load() [njcuk9999]
Core.core.drs_database.py + drs_file.py io.drs_path.py science.telluric.general.py - replace np.load with drs_path function (mitigate certain errors?) [njcuk9999]

0.6.059 (2020-03-26)¶

Update date/version/changelog/documentation. [njcuk9999]
Core.core.drs_database.py - fix typo master in entries –> master in entries.colnames. [Neil Cook]
Core.core.drs_database.py - add break point to test database error. [njcuk9999]
Science.extract.general.py - correct leakage correction (extimage –> extimage[order_num]) [njcuk9999]
Science.velocity.general.py - add breakpoint to test error. [njcuk9999]
Science.velocity.general.py - null value of targetrv is not NaN - if so deal with it. [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - change default_ref of ccf to CCF_NO_RV_VAL. [njcuk9999]
Core.instruments.default.default_constants.py - add CCF_NO_RV_VAL (set to np.nan) [njcuk9999]
Update language database. [njcuk9999]
Io.drs_lock.py - add exceptions and warnings for os.remove and os.removedirs (should not crash in lock) [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - change ccf –rv default from None to ‘None’ [njcuk9999]
Core.instruments.*.default_config.py - add TELLU_DB_MATCH and DB_MATCH. [njcuk9999]
Core.core.drs_file.py locale.core.drs_text.py and science.telluric.general.py - allow np.load to have allow_pickle. [njcuk9999]
Core.core.drs_database.py - add a different db match for telluric and calibration database. [njcuk9999]

0.6.058 (2020-03-24)¶

Tools.module.setup.drs_processing.py - correct test for TEST_RUN. [njcuk9999]
Tools.recipes.bin.apero_processing.py - add breakpoint. [njcuk9999]
Tools.recipes.bin.apero_processing.py - remove breakpoint. [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - update leak files in sequences (should be e2dsff fiber AB) [njcuk9999]
Tools.module.setup.drs_processing.py - change message when just a test. [njcuk9999]
Recipes.bin.apero_processing.py - add breakpoint to test leakage error. [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - change cal_leak inputtype e2ds –> reduced. [njcuk9999]
Core.core.drs_database.py - ‘master’ should only be used for databases with ‘master’ column. [njcuk9999]
Data.spirou.reset.runs - update run.ini files. [njcuk9999]
Tools.module.setup.drs_processing.py - do not check for master if recipe is None. [njcuk9999]
Science.velocity.general.py - add warning to suppress warning about NaNs in greater than mask. [njcuk9999]
Science.velocity.general.py - add threshold for the blaze. [Neil Cook]
Update language database. [njcuk9999]
Science.velocity.general.py - mask mask_centers and mask_weights to just fall in the order in question. [njcuk9999]
Core.instruments.*.default_keywords.py - change WNTDWAVEB –> WNTDWAVB. [njcuk9999]
Cal_wave_night_spirou.py - add breakpoint to investigate bug. [njcuk9999]
Core.instruemnts.spirou.recipe_defintions.py - cal_leak should not be a master recipe. [njcuk9999]

0.6.057 (2020-03-24)¶

Apero.tools.module.setup and setup/*.py - add newprofile script to add a new profile quickly (copy of currently in use) [njcuk9999]
Science.velocity.general.py - need to set ccf to NaN if mask has no values for this order. [njcuk9999]
Update language database. [njcuk9999]
Science.velocity.general.py - add breakpoint to test error. [njcuk9999]
Science.velocity.general.py - add a nansum to ccf_ord. [njcuk9999]
Science.velocity.general.py - add a nansum to ccf_ord. [njcuk9999]
Science.velocity.general.py - add break point. [njcuk9999]
Recipes.spirou.cal_badpix_spirou.py - remove breakpoint in cal_badpix. [njcuk9999]
Tools.module.setup.drs_processing.py - correct –master ==True –> True. [njcuk9999]
Tools.module.setup.drs_processing.py - add –master=True. [njcuk9999]
Core.core.drs_argument.py - –master now has to be True or False. [njcuk9999]
Core.core.drs_argument.py - correct wlog type (should be debug) [njcuk9999]
Update language database. [njcuk9999]
Core.core.drs_argument.py - update _IsMaster function (no arguments) [njcuk9999]
Tools.module.setup.drs_processing.py - change master arg to have no arguments. [njcuk9999]
Tools.module.setup.drs_processing.py - add push to add –master arg for master recipes. [njcuk9999]
Recipes.spirou.cal_badpix_spirou.py - add break point (to test) [njcuk9999]
Update language database. [njcuk9999]
Core.core.drs_startup.py - add comment for debug_key. [njcuk9999]
Core.core.drs_recipe.py - get master from input_parameters and update ‘IS_MASTER’ if True. [njcuk9999]
Core.core.drs_database.py - remove is_master from database get_entry, now modify mask2 (always keep master calibrations) [njcuk9999]
Core.core.drs_argument.py - add is_master argument (make any recipe a master) [njcuk9999]
Update language database. [njcuk9999]
Data.*.reset.calibdb.master_calib_*.txt - add master column to default master db files. [njcuk9999]
Core.instruments.*.default_config.py - add column to calib_db_cols (master) [njcuk9999]
Core.core.drs_database.py - add column to calibration database (master) and if recipe is master except from “older” [njcuk9999]

0.6.056 (2020-03-22)¶

Core.instruments.spirou.file_defintions.py - save badpix from dark not flat. [njcuk9999]
Update language database. [njcuk9999]
Core.core.drs_database.py - correct error message 00-002-00006. [njcuk9999]
Core.instruments.*.pseudo_const.py - add MASTER_DB_KEYS function. [njcuk9999]
Core.drs_database.py - get master keys from pseudo consts. [njcuk9999]
Core.core.drs_startup.py - add a IS_MASTER key to params (True when recipe is a master recipe) [njcuk9999]
Core.core.drs_database.py - if database case = ‘older’ and we have a master but no older use closest. [njcuk9999]

0.6.055 (2020-03-22)¶

Io.drs_fits.py - pep8 change. [njcuk9999]
Core.instruemnts.*.pseduo_const.py - BERV outputs should use BERV key (make it clear) [njcuk9999]
Core.instruments.*.default_keywords.py - update KW_MID_OBSTIME_METHOD (more consistent) [njcuk9999]
Core.core.drs_recipe.py - only check required for dtype = file/files. [njcuk9999]
Core.core.drs_argument.py - DrsArgument required is True by default for args and False by default for kwargs. [njcuk9999]
Core.instruments.*.pseudo_const.py - correct typo need first element in list (not the list itself) [njcuk9999]
Core.instruments.*.pseudo_const.py - correct typo KW_OBNAME -> KW_OBJNAME. [njcuk9999]
.gitignore - ignore all python files in tools. [njcuk9999]
Tools.module.setup.drs_processing.py - fix nightname needed for non- trigger run. [njcuk9999]
Data.spirou.rset.runs - update run.ini files with leakage codes. [njcuk9999]
Core.instruments.spirou.recipe_defintions.py - update the sequences with leakage codes. [njcuk9999]
Data.spirou.reset.calibdb.master_calib_SPIROU.txt - add default leak master files to calibDB (only to use when we don’t have any files) [njcuk9999]
Data.spirou.ccf - add new masks from Andres. [njcuk9999]
Data.reset.calibdb - add MASTER_LEAK files. [njcuk9999]
Science.velocity.general.py - deal with unset targetrv (input target rv for ccf) - if unset try to get key from header - else set it to zero. [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - change the default value of –rv (for ccf) to None (i.e. unset) [njcuk9999]
Core.instruments.spirou.default_constants.py - change default mask to masque_sept18_andres_trans50.mas. [njcuk9999]
Core.instruments.*.default_config.py - change CALIB_DB_MATCH to ‘older’ - no matter where on a night we are it should always use calibrations before. [njcuk9999]
Core.instruments.*.pseduo_const.py - add fix for object name having spaces (#Issue 598) – now have key DRSOBJN. [njcuk9999]
Core.instruments.*.default_keywords.py - add OBJECTNAME and change OBJNAME to DRSOBJN (new keyword just for drs) [njcuk9999]
Update date/version/changelog/documentation. [Neil Cook]

0.6.054 (2020-03-10)¶

Sciecne.extract.general.py - continue adding leak functionality. [Neil Cook]
Apero.science.calib.flat_blaze.py - allow flat to be loaded quietly. [Neil Cook]
Recipes.spirou.cal_leak_spirou.py - continue work on EA implementation - add save_uncorrected_ext_fp and write_leak functions. [Neil Cook]
Recipes.spirou.cal_leak_master_spirou.py - add cprops (for header keys) and pipe to write_leak_master. [Neil Cook]
Update language database. [Neil Cook]
Io.drs_strings.py - add module for generic string manipulation [TODO: find other generic functions and move here] [Neil Cook]
Io.drs_path.py - add copyfile function (with logging) [Neil Cook]
Core.instruments.*.default_keywords.py - add LEAK header keywords. [Neil Cook]
Core.instruments.*.file_definitions.py - add out_leak_master to out_file set and calib_file set. [Neil Cook]
Core.instruments.*.defalut_constants.py - add LEAK and EXT_S1D parameters. [Neil Cook]
Core.core.drs_file.py - add an include/exclude part to wild cards so we can search header for specific header keys + add get_qckeys method. [Neil Cook]

0.6.053 (2020-03-09)¶

Recipes.spirou.cal_leak_spirou.py and science.extract.general.py - add function dark_fp_regen_s1d [Neil Cook]
Recipes.*.cal_extract_*.py - get s1d infile from params (EXT_S1D_INTYPE) formally hardcoded to E2DSFF. [Neil Cook]
Core.instruments.*.default_constants.py - add EXT_S1D_INTYPE to constants. [Neil Cook]
Core.instruments.*.default_constants.py - add EXT_S1D_INTYPE to constants. [Neil Cook]
Recipe.spirou.cal_leak_spirou.py and science.extract.general.py - add outputs to extgen.correct_dark_fp function and make changes to function return. [Neil Cook]
Documentation.working._static.yed.spirou_all.graphml - save flow diagram for spirou. [Neil Cook]
Tools.module.setup.drs_processing.py - fix call to _linear_process group should be a keyword argument (Issue #599) [Neil Cook]
Core.instruments.spirou.default_keywords.py - update rv keyword OBSRV –> OBJRV. [Neil Cook]

0.6.052 (2020-03-05)¶

Cal_leak_master_spirou.py - deal num_files = 0. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.*.default_constants.py - add blaze_norm_percentile (CCF_BLAZE_NORM_PERCENTILE) [Neil Cook]
Science.velocity.general.py - EA corrections to RV CCF (normalisation) [Neil Cook]

0.6.051 (2020-03-04)¶

Science.extract.general.py - add leak functions. [Neil Cook]
Apero.recipes.spirou.cal_leak_spirou.py - continue with EA adaptation. [Neil Cook]
Update language database. [Neil Cook]
Core.isntruments.spirou.recipe_definitons.py - update cal_leak. [Neil Cook]
Core.instruments.spirou.default_constants.py - comment these out for now. [Neil Cook]
Core.instruments.nirps_ha.default_keywords.py [APERO] - add KW_LEAK_CORR. [Neil Cook]
Core.instruments.default.default_keywords.py - add KW_LEAK_CORR keyword. [Neil Cook]

0.6.050 (2020-03-03)¶

Science.extract.general.py [APERO] - add correct_master_dark_fp correct_dark_fp master_dark_fp_cube get_extraction_files functions [UNFINISHED] [Neil Cook]
Documentation.working._static.yed.spirou_map.graphml [APERO] - add leak to spirou flow diagram. [Neil Cook]
Recipe.spirou.obj_mk_tellu_spirou.py [SPIROU] - correct typo. [Neil Cook]
Recipes.spirou.cal_leak_spirou.py - first commit add start of cal_leak code (from EA code) [Neil Cook]
Recipes.spirou.cal_leak_master_spirou.py - continue work on implementing EA’s code. [Neil Cook]
Update language database. [Neil Cook]
Io.drs_fits.py [APERO] - deal with not having nightname column for tmp/reduced index files. [Neil Cook]
Core.instruments.*.recipe_definitions.py - update cal_leak_master and add cal_leak. [Neil Cook]
Core.instruments.*.file_definitions.py [APERO] - set intype for out_leak_master. [Neil Cook]
Core.instruments.*.pseudo_const.py - add FIBER_KINDS (science and reference) [Neil Cook]
Core.instruments.*.default_constants.py [APERO] - add LEAKM and LEAK constants. [Neil Cook]
Core.core.drs_file.py [APERO] - read_header_key_1d_list - update input and param dict. [Neil Cook]

0.6.049 (2020-03-02)¶

Tools.module.setup.drs_processing.py [APERO] - move find_raw_files, _get_path_and_check, _get_files to io.drs_fits. [Neil Cook]
Recipes.spirou.cal_leak_master_spirou.py [APERO] - first commit [UNFINISHED] of the master leakage creation recipe. [Neil Cook]
Nrips_ha.cal_pp_master_nirps_ha.py [NIRPS] - add nirps master pp code to get flat_flat mask. [Neil Cook]
Recipes.* and tools.* - correct call to drs_fits.find_files (now requires recipe for raw finding) [Neil Cook]
Io.drs_fits.py [APERO] - update find_files to correctly find raw files, add find_raw_files function, move fix_header to here. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.nirps_ha.file_definitions.py [NIRPS] - replace fiber AB,A,B,C with A,B. [Neil Cook]
Core.instruments.spirou.file_definitions.py [SPIROU] - add out_leak_master. [Neil Cook]
Core.instruments.spirou.default_constants.py - add ALLOWED_LEAKM_TYPES. [Neil Cook]
Core.instruments.*.recipe_definitions.py [APERO] - move DrsRecipe construction closer to each recipe + add to recipe list + add cal_leak_master + add cal_pp_master. [Neil Cook]
Core.instruments.*.pseudo_const.py [APERO] - add VALID_RAW_FILES to instruments seperately. [Neil Cook]
Core.instruments.nirps_ha.file_definitions.py [NIRPS] - add out_pp_master file for the mask master flat pp file + add out_leak_master for leak_master code + remove polar file definitions. [Neil Cook]
Core.instruments.nirps_ha.default_keywords.py - add a PPMSTR_NSIG keyword to keep track when it is used. [Neil Cook]
Core.instruments.nirps_ha.default_constants.py - add ALLOWED_PPM_TYPES PPM_MASK_NSIG PP_MEDAMP_BINSIZE and ALLOWED_LEAKM_TYPES. [Neil Cook]
Default.default_keywords.py [NIRPS] - add PPMSTR_NSIG constants (for nirps pp correction) [Neil Cook]
Core.instruments.default.default_constants.py - add PPM and LEAKM keywords. [Neil Cook]
Core.core.drs_startup.py - deal with case in find_files where we do not have full params set up yet (i.e. WLOG will crash) –> raise ConfigError. [Neil Cook]
Core.core.drs_recipe.py - when we have a master recipe set directory from params[‘MASTER_NIGHT’] [Neil Cook]
Update changelog/date/version/documentation. [Neil Cook]
Update changelog/date/version/documentation. [Neil Cook]

0.6.048 (2020-02-28)¶

Documentation.working.user.general.todo.rst - update todo list. [Neil Cook]
Tools.recipes.spirou.exposuremeter_spirou.py - first commit of exposure meter code [UNFINISHED] [Neil Cook]
Tools.recipes.spirou - move cal_update_berv.py to tools. [Neil Cook]
Io.drs_fits.py - add “night” to find_files (to filter just one night) [Neil Cook]
Update language database. [Neil Cook]
Tools.module.setup.drs_processing.py - correct NIGHT_NAME –> NIGHTNAME and cause exception when TRIGGER=True and NIGHTNAME unset. [Neil Cook]
Update run.ini files (NIGHT_NAME –> NIGHTNAME) [Neil Cook]
Tools.module.setup.drs_processing.py - update how filters are obtained and add error when incorrect. [Neil Cook]
Update language database. [Neil Cook]
Data.spirou.reset.runs.trigger_night_calbi_run.ini - correct run and skip pp parameters. [Neil Cook]
Readme.md - update sequences. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add pp_run_opt (preprocessing with options – must turn all off to only select one) [Neil Cook]
Data.spirou.reset.runs.trigger*.ini - add pp seqeunce elements. [Neil Cook]
Tools.module.setup.drs_processing.py - add trigger from file. [Neil Cook]
Core.instruments.spirou.recipe_defintions.py - add pp_run_sci sequence (preprocess OBJ_DARK, OBJ_FP only) [Neil Cook]
Update run.ini files. [Neil Cook]
Core.core.drs_recipe.py - deal with having no files in a recipe that requires files. [Neil Cook]
Update language database. [Neil Cook]
Tools.module.setup.drs_processing.py - add section to stop processing recipes when we are in trigger mode. [Neil Cook]
Tools.module.setup.drs_processing.py - update_run_table needs to take value from rlist if already populated. [Neil Cook]
Tools.module.setup.drs_processing.py - deal with trigger run when removing engineering nights (i.e. deal with when we have no objects in a directory) [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.default.recipe_defintions.py - update dtype for –trigger argument. [Neil Cook]
Update language database. [Neil Cook]
Documentation.working.user.general.todo.rst - update todo list. [Neil Cook]
Core.instruments.default.recipe_defintions.py - add –trigger option to apero_processing.py. [Neil Cook]
Drs_installation.py – check “clean” argument for update. [Neil Cook]
Setup.install.py - pass args to update. [Neil Cook]
Setup.install.py - print that we are locating install path. [Neil Cook]
Tools.module.setup.drs_reset.py – do not remove head when removing paths in clean install. [Neil Cook]
Io.drs_lock.py - add checks in __remove_empty__ for symbolic links. [Neil Cook]
Core.constants.param_functions.py - add check for stty for posix os. [Neil Cook]
Update requirements (in .txt and install.py) [Neil Cook]
Update version/date/changelog/documentation. [Neil Cook]

0.6.047 (2020-02-27)¶

Documentation.working.dev.developer_guide.rst [APERO] - add another section todo. [Neil Cook]
Science.extract.general.py [APERO] - pep8 change. [Neil Cook]
Documentation.working.user.genearl.todo.rst - update todo list. [Neil Cook]
Tools.recipe.bin.apero_go.py [APERO] - a program to aid finding where data directories are (try cd <quote>python apero_go.py INSTRUMENT –data<quote> to change to data dir. [Neil Cook]
Recipes.spirou.cal_wave_* - change how we update hc and fp files once wave solution is updated (correct e2ds/e2dsff/e2dsll and remake s1dw/s1dv) [Neil Cook]
Io.drs_lock.py - make all lock normal print outs debug print outs (hide unless in debug mode) [Neil Cook]
Data.spirou.reset.runs.hc_run.ini - update run/skip section. [Neil Cook]
Data.spirou.reset.runs.*.ini - update RUN_INI_FILES (more appropriate names + updated values) [Neil Cook]
Core.instruments.*.recipe_defintions.py - add wave plot (extract_s1d) [Neil Cook]
Core.instruments.default.recipe_definitions.py [APERO] - add apero_go.py tools recipe. [Neil Cook]
README.md - add short name to sequence description. [Neil Cook]

0.6.046 (2020-02-27)¶

Tools.recipe.bin.apero_processing.py - add a save stats call to save to stats file. [Neil Cook]
Tools.module.setup.drs_processing.py [APERO] - save a stats fits and stats txt to run folder (under stats) [Neil Cook]
Tools.module.setup.drs_installation.py - fix force resets without warning. [Neil Cook]
Update language database. [Neil Cook]

0.6.045 (2020-02-26)¶

Tools.module.setup.drs_installation.py - deal with tool sub-dirs not existing (first time install) [Neil Cook]
../setup/install.py - search up levels for apero. [Neil Cook]
Tools.module.setup.drs_installation.py - correct in_tool_path (how we add bin sub-dir) [Neil Cook]
Tools.module.setup.drs_installation.py - correct valid_path for validation recipe. [Neil Cook]
Tools.module.setup.drs_installation.py - make tool links generic (based on sub-dirs) + make paths os independent. [Neil Cook]
Apero.tools.resources.setup.* - update paths to add multiple sub- paths. [Neil Cook]
Apero.tools.recipes - move general –> bin and add instrument tool directories. [Neil Cook]

0.6.044 (2020-02-24)¶

Science.preprocessing.detector.py [NIRPS] - add nirps preprocessing functions from EA [UNFINISHED + QUESTIONS] [Neil Cook]
Misc.nrips_tools.nirps_pp.py - copy over EA preprocessing code. [Neil Cook]
Recipes.nirps_ha.cal_preprocess_nirps_ha.py [NIRPS] - copy over SPIROU code and implement EA changes [UNFINISHED] [Neil Cook]
Core.math.general.py [APERO] - add medbin function. [Neil Cook]
Core.core.drs_startup.py - allow llmain to be dict or None (via Union) [Neil Cook]

0.6.043 (2020-02-22)¶

Update documentation. [Neil Cook]
Working.user.genearl.todo.rst - update todo list. [Neil Cook]
Misc.tools.apero_mtl_sync.py - finish off code (formally mtl_sync.py) [Neil Cook]

0.6.042 (2020-02-20)¶

Working.user.general.todo.rst [APERO] - update todo list. [Neil Cook]
Core.math.general.py [APERO] - pep8 change to robust nan std function. [Neil Cook]
Data.nirps_ha.reset.calibdb.MASTER_WAVE_NIRPS_HA.fits - add a first attempt at wave solution for NIRPS_HA from optical model. [Neil Cook]
Science.extract.general.py [NIRPS] - NIRPS does not have thermal make these keys added to header conditional on presence in eprops. [Neil Cook]
Science.calib.flat_blaze.py [NIRPS/SPIROU] - change keep, rms and nan some outliers in flat. [Neil Cook]
Recipes.nirps_ha.cal_shape_nirps_ha.py [NIRPS] - convert cal_shape from spirou code. [Neil Cook]
Recipes.nirps_ha.cal_shape_master_nirps_ha.py [NIRPS] - remove hc and dxmap stuff from spirou code. [Neil Cook]
Recipes.nirps_ha.cal_flat_nirps.py [NIRPS] - add flat/blaze code (converted from spirou) [Neil Cook]
Recipes.nirps_ha.cal_extract_nirps_ha.py [NIRPS] - add extraction code (converted from spirou) [Neil Cook]
Update database. [Neil Cook]
Core.math.general.py - add robust_nanstd function. [Neil Cook]
Core.instruments.spirou.recipe_defintions.py - update shape master help example. [Neil Cook]
Core.instruments.nirps_ha.recipe_defintions.py - remove hc inputs/outputs from shape master. [Neil Cook]
Core.instruments.nirps_ha.pseudo_const.py [NIRPS] - update FIBER_LOC_COEFF_EXT. [Neil Cook]
Core.instruments.nirps_ha.default_constants.py [NIRPS] - change SHAPE_UNIQUE_FIBERS, QC_FF_MAX_RMS, EXT_RANGE1, EXT_RANGE2, EXT_S1D_WAVEEND, EXTRACT_S1D_PLOT_ZOOM1, EXTRACT_S1D_PLOT_ZOOM2. [Neil Cook]
Misc.tools.mtl_sync.py - remove requirement of using apero. [Neil Cook]

0.6.041 (2020-02-20)¶

Misc.tools.mtl_sync.py - first commit (code for users to get data from montreal) [Neil Cook]
Remove unused doc files. [Neil Cook]
Update documentation. [Neil Cook]
Tools.module.documentation.drs_documentation.py - replace copy_tree –> copytree (from drs_path) [Neil Cook]
Io.drs_path.py [APERO] - add copytree function (copies all files from src to dst) [Neil Cook]
Apero.science.calib.shape.py - remove private functions in shape. [Neil Cook]
Recipes.nirps_ha.cal_shape_master_nirps_ha.py - copy over code from spirou. [Neil Cook]
Plotting.plot_functions.py [APERO] - update loc plot and shape plot. [Neil Cook]
Data.*.reset [APERO] - update master wave solutions (distinguish spirou and nirps_ha) [Neil Cook]
Core.instruments.*.file_defintions.py [APERO] - correct out_dark files (suffix needs underscore) [Neil Cook]
Core.instruments.*.default_constants.py [NIRPS] - update loc constants + update comment for LOC_COLUMN_SEP_FITTING. [Neil Cook]

0.6.040 (2020-02-18)¶

Apero.science.calib.badpix.py and localisation.py [APERO] - RAW_TO_PP_ROTATION and pep8 changes. [Neil Cook]
Recipes.spirou.cal_preprocess_spirou.py [SPIROU] - update header key KW_BERV_OBSTIME_METHOD –> KW_MID_OBSTIME_METHOD. [Neil Cook]
Recipes.nirps_ha.*.py [NIRPS] - add cal_badpix, cal_dark_master, cal_loc for nirps_ha. [Neil Cook]
Io.drs_image.py [APERO] - link rotate_image function to math.genearl.rot8. [Neil Cook]
Io.drs_data.py [APERO] - fix arguments to error 00-012-00001. [Neil Cook]
Update documentation. [Neil Cook]
Update documentation. [Neil Cook]
Data.nirps_ha [NIRPS] - rename data folder from nirps –> nirps_ha. [Neil Cook]
Apero.core.math.general.py [APERO] - add rot8 function to deal with rotation modes of images. [Neil Cook]
Core.instruments.spirou.default_constants.py - add RAW_TO_PP_ROTATION value. [Neil Cook]
Core.instruments.nirps_ha.default_constants.py - tweak NIRPS values from SPIROU values. [Neil Cook]
Core.instruments.default.recipe_definitions.py [APERO] - get instruments from Constants. [Neil Cook]
Core.instruments.default.default_constants.py [APERO] - add RAW_TO_PP_ROTATION constant. [Neil Cook]

0.6.039 (2020-02-17)¶

Documentaqtion/working/dev/developer_guide.rst [APERO] - add github interface as section. [Neil Cook]
Core.instruments.nirps_ha.recipe_definitions.py - change spirou references to nirps_ha. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py [SPIROU] - rename internal instance names obj_pol_spirou and obj_spec_spirou –> obj_pol and obj_spec. [Neil Cook]
Documentation.working._static.yed.spirou_map_2020-01-22_all.graph [SPIROU] - update yed graph. [Neil Cook]
Recipes.nirps_ha.cal_dark_nirps_ha.py - copy over spirou recipe. [Neil Cook]
Update the language database [APERO] add nirps files as duplicates of spirou for start. [Neil Cook]
Core.instruments.nirps_ha.pseudo_const.py [NIRPS] - update splash from spirou –> nirps. [Neil Cook]
Core.instruments.deafult.default_config.py [NIRPS] - add NIRPS_HA to list of instruments. [Neil Cook]
Tools.module.setup.drs_installation.py [APERO] - force userconfig to have a os.sep as last character. [Neil Cook]
NIRPS: start config file copy. [Neil Cook]

0.6.038 (2020-02-10)¶

Tools.recipes.general.apero_log_stats.py - remove hard coded path. [Neil Cook]
Printout of the limited_run.ini on mini_data for apero_processing.py 2020-02-10 13:56:00. [Neil Cook]
Update yed graphs. [Neil Cook]
Update yed graphs. [Neil Cook]
Update changelog. [Neil Cook]
Update python versions, yed graphs and update notes. [Neil Cook]
Update readme/known_issues/todo. [Neil Cook]
Update date/version/changelog/documentation. [Neil Cook]

0.6.037 (2020-02-07)¶

Core.core.drs_recipe.py - add a pre-filter of table (so we are not scanning all files every time) [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - filelogic must be exclusive for mk_tellu, fit_tellu and pol_spirou + update sequences (only e2dsff not e2ds) [Neil Cook]
Documentation - add yed graphs. [Neil Cook]
Documentation.working - update python installation, code links. [Neil Cook]
Documentation.output - update docs. [Neil Cook]
Tools.module.drs_documentation.py - update ssh host. [Neil Cook]
Update date/version/changelog/documentation. [Neil Cook]

0.6.036 (2020-02-05)¶

Plotting.latex.py - must clean characters [ and ] - leads to error in pdflatex. [Neil Cook]
Science.calib.wave.py + science.calib.wave1.py - update master wave to look for all master wave types and generate new error if none found. [Neil Cook]
Recipe.spirou.obj_mk_tellu_spirou.py + obj_fit_tellu_spirou.py - update headers to use correct wave solutions for outputs. [Neil Cook]
Plotting.core.py - add numpy import. [Neil Cook]
Update language database. [Neil Cook]
Recipe.spirou.obj_mk_template_spirou.py and science.telluric.general.py - update wave solution of template. [Neil Cook]
Recipes.test.demo_spirou.py - add param dict section. [Neil Cook]
Spirou.recipe_definitions.py - add old_run (with no master/night wave) [Neil Cook]

0.6.035 (2020-02-04)¶

Update the language database. [Neil Cook]
Tools.module.testing.drs_dev.py - add a demo class to store demo functions (keep out of demo as they would just confuse the point) [Neil Cook]
Recipes.test.demo_spirou.py - add a recipe that demonstrates the different features of APERO. [Neil Cook]
Locale.core.drs_text.py - add a language level in cache data so we are name.instrument.language cache. [Neil Cook]
Locale.core.drs_lang_db.py - move dictionary to static call (once per import) – loads quicker. [Neil Cook]
Data.spirou.demo - add demo data. [Neil Cook]
Core.core.drs_log.py - correct the language must be a string not a list. [Neil Cook]
Testing.drs_dev.py - add module to allow recipe definition to come from recipe (used to add rmod to core.setup) [Neil Cook]
Science.extract.berv.py - use_pyasl in quiet mode in barycorrpy (just for calculating bervmax) [Neil Cook]
Science.extract.berv.py - allow berv to be calculated quietly. [Neil Cook]
Core.core.drs_startup.py - allow recipe definition to come from input (i.e. define in recipe - for initial testing) [Neil Cook]
Add new blank codes with recipe definition inline. [Neil Cook]
Remove from __future__ import division imports (no longer supporting python 2) [Neil Cook]
Misc.tools.cal_update_berv.py - add switch for skipping. [Neil Cook]
Apero.science.extract.berv.py - use pyasl to measure berv maximum. [Neil Cook]
Misc.tools.cal_update_berv.py - update .write–>.write_file. [Neil Cook]
Recipes.spirou.cal_wave_master_spirou + cal_wave_night_spirou - add TODOs to update s1d files AFTER new wave solution generated. [Neil Cook]
Apero.plotting.plot_functions.py - deal with all NaNs in flux[mask] - only set ylim if values are finite. [Neil Cook]
Apero.plotting.core.py - add a set_interactive method to try to change backend. [Neil Cook]

0.6.034 (2020-02-03)¶

Documentation.working.dev.developer_guide.rst - add more sections to dev section [UNFILLED] [Neil Cook]
Update language databases. [Neil Cook]
Core.core.drs_file.py - change get_keyword_instance –> get_instanceof (more generic) [Neil Cook]
Core.constants.param_functions.py - write all doc strings [UNFINISHED] up to end of ParamDict. [Neil Cook]
Core.constants.constant_functions.py - fill out all doc-strings. [Neil Cook]
Core.cosntants.__init__.py - add comment to catch_sigint. [Neil Cook]
README.md - add changes to sequences (now doing cal_wave_master) [Neil Cook]
Update date/version/changelog/documentation. [Neil Cook]

0.6.033 (2020-01-31)¶

Add flow diagram for locking wait times. [Neil Cook]
Plotting.latex.py - add switch to turn on/off latex pdf making + add fix to latex command to make it non-interactive (Issue #586) [Neil Cook]
Plotting.latex.py - add -interaction=nonstopmode to not allow latex to pause running on error. [Neil Cook]
Core.core.drs_recipe.py - remove breakpoint. [Neil Cook]
Tools.module.setup.drs_processing.py - deal with unset event (non- parallel process) [Neil Cook]
Core.core.drs_argument.py - make sure reicpe is updated before we run display_func. [Neil Cook]
Core.instruments.default.default_config.py - update the value of debug mode (only print at debug>=10) [Neil Cook]
Core.constants.constants_functions.py - update types in doc string. [Neil Cook]
Core.core.drs_recipe.py - move break_point to exception. [Neil Cook]
Core.core.drs_recipe.py - add breakpoint to address error. [Neil Cook]
Core.core.drs_recipe.py - add breakpoint to address error. [Neil Cook]
Constants.constant_functions.py - add doc strings. [Neil Cook]
Core.core.drs_file.py - add display_funcs and pep8 changes. [Neil Cook]

0.6.032 (2020-01-30)¶

Dark_fp_run.ini - add dark fp run script. [Neil Cook]
Core.instruments.spirou.recipe_defintions.py - add pp_run and dark_fp_run sequences. [Neil Cook]
Io.drs_lock.py - make sure we do not remove lock path (drs_msg_path/lock/) [Neil Cook]

0.6.031 (2020-01-29)¶

Core.core.drs_file.py - update display_func for hkeys_exist. [Neil Cook]
Core.core.drs_argument.py - add comments to special arg make functions + display func to DrsArgument. [Neil Cook]
Core.core.drs_argument.py - add display func + pep8 corrections. [Neil Cook]
Core.core.drs_recipe.py - change DRSArgumentParser –> DrsArgumentParser. [Neil Cook]
Core.core.drs_argument.py - add display_funcs and comments for Parser functions. [Neil Cook]
Misc.updates_to_drs.mk_night_wave.py - add dymanic paths to EA code. [Neil Cook]
Science.extract.telluric.general.py - change read –> readfits. [Neil Cook]
Science.extract.general.py - change read –> read_file. [Neil Cook]
Science.calib.background.py + badpix.py + dark.py - change read –> readfits. [Neil Cook]
Recipe.spirou.cal_wave_night_spirou.py - pep8 changes. [Neil Cook]
Locale.core.drs_exceptions.py - add __main__ section. [Neil Cook]
Io.drs_fits.py - change read –> readfits. [Neil Cook]
Drs_data.py - change read –> readfits. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add force extract options. [Neil Cook]
Locale.core.drs_lang_db.py - move constant/params text to dict (linked to language database) [Neil Cook]
Core.core.drs_file.py - change read –> read file. [Neil Cook]
Core.core.drs_database.py - change read to readfits (and read_database) [Neil Cook]
Core.constant.param_functions.py - add display_func and comments. [Neil Cook]
Core.constants.constant_function.py - add comments and display func. [Neil Cook]
Update language database. [Neil Cook]

0.6.030 (2020-01-28)¶

Plotting.plot_functions.py - pep8 clean up. [Neil Cook]
Science.calib.wave1.py - add hclines and fplines arguments to get_master_lines (to get lists from file) and for reference file use these arguments to start with the master. [Neil Cook]
Plotting.plot_functions.py - copy x and y in wave night plot function and catch nan in greater than less than with the “with warnings” command. [Neil Cook]
Add display_func. [Neil Cook]
Update date/version/changelog/documentation. [Neil Cook]

0.6.029 (2020-01-27)¶

Data.spirou.reset.runs.limited_run.ini - update default limited_run.ini. [Neil Cook]
Update spirou flow map. [Neil Cook]
Recipes.spirou.cal_wave_night_spirou.py - remove breakpoint. [Neil Cook]
Locale.core.drs_exception.py - add wlogbasic (basicalogger wrapper with same args as WLOG) [Neil Cook]
DrsFitsFile.read –> read_file. [Neil Cook]
Core.core.drs_log.py - move display_func main to param_functions - keep here the use of wlog and textentry (too low in param_functions) [Neil Cook]
Core.core.drs_file.py - add display_funcs and change read–>read_file. [Neil Cook]
Core.core.drs_database.py - add display funcs. [Neil Cook]
Core.core.drs_argument.py - update func_name comments - no access to inputs cannot breakfunc here. [Neil Cook]
Core.constants.constant_functions.py - add messages to show func_name breakfunc can’t work here (too low) [Neil Cook]
Recipes.spirou.cal_wave_night_spirou.py - correct typo set –> set_sources. [Neil Cook]
Recipes.spirou.cal_wave_night_spirou.py - add rv properties to nprops. [Neil Cook]
Science.calib.wave1.py - add wavefile, wavesource, nbo, deg to nprops. [Neil Cook]
Core.core.drs_startup.py - breakpoint –> break_point. [Neil Cook]
Core.constants.__init__.py - breakpoint –> break_point. [Neil Cook]
Core.constants.param_functions.py - rename breakpoint –> break_point. [Neil Cook]
Recipes.spirou.cal_wave_night_spirou.py - add breakpoint to check errors. [Neil Cook]
Recipes.spirou.cal_wave_night_spirou.py - replace hcfile and fpfile for hc_e2ds_file and fp_e2ds_file. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - key WAVE_NIGHT_WAVE –> WAVEMAP_NIGHT. [Neil Cook]
Spirou_map – update flow chart. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add shape to master sequence. [Neil Cook]
Spirou_map – update flow chart. [Neil Cook]
Recipe.spirou.cal_shape_master_spirou.py - add way to load fpmaster from file/calibDB – FOR DEBUG ONLY. [Neil Cook]

0.6.028 (2020-01-24)¶

Science.calib.shape.py - EA changes to shape (remove corr_dx_from_fp) [Neil Cook]
Add new spirou flow maps. [Neil Cook]
Recipe.spirou.cal_shape_master_spirou.py - add breakpoint for debugging. [Neil Cook]
Plotting.plot_functions.py - change corr_dx_from_fp_arr to shifts. [Neil Cook]
Language database. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add changes for wave master/night. [Neil Cook]
Misc.tools.compare_e2ds.py - add code to compare used calibrations between two e2ds files. [Neil Cook]
Update spirou flow graph maps. [Neil Cook]

0.6.027 (2020-01-23)¶

Science.calib.wave1.py - corrections after EA changes. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add rv plots to cal_Wave_night definition. [Neil Cook]
Core.instruments.spirou.default_constants.py - adjust WAVE_LITTROW_QC values. [Neil Cook]

0.6.026 (2020-01-22)¶

Science.calib.wave1.py - disable the littrow QC (still breaking) [Neil Cook]
Recipe.spirou.cal_wave_master_spirou.py + science.calib.wave1.py - continue work on EA fixes. [Neil Cook]
Plotting.plot_functions.py - remove line and add markers to wave night plot. [Neil Cook]
Core.math.general.py - deal with median = 0 (over half the points are zero) [Neil Cook]
Core.instruments.*.default_constants.py + core.instruments.spirou.recipe_defintions.py - add PLOT_WAVENIGHT_HISTPLOT. [Neil Cook]
Documentation.working._static.yed - add yed diagrams. [Neil Cook]

0.6.025 (2020-01-21)¶

Misc.tools.nirps_lsf.py - EA tool to get the line spread function for NIRPS. [Neil Cook]
Recipes.spirou.cal_wave_master_spirou.py, cal_wave_night_spirou.py and science.calib.wave1.py - continue work on EA changes to wave solution master/night combo. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - correct cal_wave_night outputs and plots. [Neil Cook]
Core.instruments.spirou.file_defintions.py - correct typo in out_wavem_fp WAVE_FP –> WAVEM_FP. [Neil Cook]
Core.instruments.spirou.default_constants.py - update WAVE_HC_TFIT_ORDER_FIT_CONT. [Neil Cook]
Core.core.drs_file.py - added exclude groups to copy_original_keys. [Neil Cook]

0.6.024 (2020-01-20)¶

Recipes/spirou.cal_wave_*.py + science.calib.wave*.py - continue work on implementing EA changes. [Neil Cook]
Science.telluric.general.py - remove breakpoint. [Neil Cook]
Science.extract.general.py - correct add_wave_keys. [Neil Cook]
Plotting.plot_functions.py - correct where we get nbo + add title. [Neil Cook]
Update language database. [Neil Cook]
Data.core..pdbrc - add alias commands to pdbrc for ease of use. [Neil Cook]
Core.instruments.spirou.default_constants.py - change wave fit degree from 4 –> 5 (EA: 4th order does not catch structure) [Neil Cook]
Core.core.drs_startup.py - add DebugExit class to catch pdb/ipdb exits. [Neil Cook]
Core.core.drs_recipe.py - add make_breakfunc (special argument) [Neil Cook]
Core.core.drs_log.py - allow display_func to have break at function name (if –breakfunc used) [Neil Cook]
Core.core.drs_database.py - fix display func. [Neil Cook]
Core.constants.param_functions.py - fix breakpoint to have levels (set by .pdbrc) [Neil Cook]
Core.core.drs_argument.py - add break function special argument. [Neil Cook]

0.6.023 (2020-01-17)¶

Io.drs_lock.py - add some randomisation to the 240 reset. [Neil Cook]
Io.drs_lock.py - reset the lock file after 240 seconds (can help with stuck lock files) [Neil Cook]
Science.extract.berv.py - must define iteration for using use_barycorrpy (due to locking – both iterations will use same lock files) [Neil Cook]
Recipes/spirou.cal_wave_master_spirou.py + science.calib.wave1.py - make changes for cal_wave_master (UNFINISHED) [Neil Cook]
Science.calib.shape.py - fix poly_cavity (should be un-inverted) [Neil Cook]
Io.drs_lock.py - need to re-check that path exists when creating lock file. [Neil Cook]
Misc nirps directory. [Neil Cook]

0.6.022 (2020-01-16)¶

Setup.install.py and pythoninstallion.rst - update recommended way to install python and modules. [Neil Cook]
Setup/install.py - add comments on how installed (after installing conda) [Neil Cook]
Reipces.spirou.cal_wave_master_spirou.py - add cavity_poly for FP master lines (always use the most up-to-date version) [Neil Cook]
Science.calib.wave.py - move master line const to const file, move location of cavity file, add valid line print out to get_master_lines, add fp_fit paramets to llprops. [Neil Cook]
Science.calib.shape.py - replace getting cavity file from old to new location (made in wave solution) [Neil Cook]
Recipe.spirou.cal_wave_master_spirou.py - make note that we need to decide when/how to update cavity file. [Neil Cook]
Io.drs_data.py - remove cavity file loading. [Neil Cook]
Data.spirou.calib - update cavity files. [Neil Cook]
Core.instruments.*.deafult_constants.py - remove cavity length constants. [Neil Cook]
Cal_wave_master_spirou.py - fix inputs to get_master_lines. [Neil Cook]
Plotting.plot_functions.py - fix waveref plot (for get_master_lines) [Neil Cook]
Core.instruments.spirou.file_definitions.py - fix pep8 + change hclist_master nad fplist_master to drs_finput. [Neil Cook]
Core.instruments.*.default_constants.py - add WAVEREF constants. [Neil Cook]

0.6.021 (2020-01-15)¶

Science.calib.wave.py - correct typos. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - change WAVEM_HCLL –> WAVE_HCLL. [Neil Cook]
Core.instruments.spirou.file_definitions.py - remove WAVEHCLL master (redundant) [Neil Cook]
Scuebce.telluric.general.py - add lower and upper bounds for hband coming from constants. [Neil Cook]
Plotting.plot_functions.py - add better comments and fix pep8. [Neil Cook]
Core.instruments.*.default_constants.py - add MKTELLU_HBAND_LOWER and MKTELLU_HBAND_UPPER and change MKTELLU_QC_AIRMASS_DIFF from 0.1 –> 0.3. [Neil Cook]
Plotting.plot_functions.py - change style on plot point. [Neil Cook]
Science.telluric.general.py - only use good_domain for the absorption fit. [Neil Cook]
Science.telluric.general.py - test of good_domain (1500 to 1750 nm) [Neil Cook]
Core.instruments.spirou.recipe_definitions.py + science.telluric.general.py - add –use_template. [Neil Cook]
Plotting.plot_functions.py - normalise for plotting. [Neil Cook]
Plotting.plot_functions.py - correct measured transmission for plotting. [Neil Cook]
Plotting.plot_function.py + science.telluric.general.py - correct plotting when having a template. [Neil Cook]
Science.telluric.general.py - add breakpoint. [Neil Cook]
Core.core.drs_log.py - fix typo lists should be appended for qc values + add master log analysier (add to apero_log_stats later?) [Neil Cook]
Recipes.spirou.obj_mk_template_spirou.py - fix qc params when skipping object (must be lists) [Neil Cook]

0.6.020 (2020-01-14)¶

Core.core.drs_log.py - make log more readable + add qc columns. [Neil Cook]

0.6.019 (2020-01-13)¶

Update master_tellu_SPIROU.txt. [Neil Cook]
Update documentation. [Neil Cook]
Update version/date/changelog/documentation. [Neil Cook]

0.6.018 (2020-01-10)¶

Recipes.spirou.obj_mk_template_spirou.py - add logging for when file is skipped (and qc passes) [Neil Cook]
Recipe.dev.apero_changelog.py and module.documentation.drs_changelog.py - need to format changelog so it works as .rst file (for documentation) [Neil Cook]
Update documentation. [Neil Cook]
Tools.module.documentation.drs_documentation.py - make sure we copy the contents of output folder not the folder itself. [Neil Cook]
Tools.recipes.dev.apero_documentation.py - add update option to making documentation (for updating doc website) [Neil Cook]
Tools.module.testing.drs_log_stats.py - make sure path is in nights list + sort by htime. [Neil Cook]
Tools.resources.setup.apero.bash.setup* - correct typo – missing speech mark. [Neil Cook]
Science.calib.wave.py - seperate master and old wave writing functions + add in night qc and write functions. [Neil Cook]
Cal_wave_night_spirou.py - add in ccf computation. [Neil Cook]
Cal_wave_master_spirou.py - change writing functions to master functions (to separate from cal_wave – old) - master now writes to key WAVEM. [Neil Cook]
Update the master_*_SPIROU.txt files - default master files now WAVEM_D_{fiber} [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - need a set of files for master (can remove non-master if we go with master/night recipes) [Neil Cook]
Core.instruments.spirou.file_definitions.py - need a set of files for master (can remove non-master if we go with master/night recipes) [Neil Cook]
Core.instruments.spirou.default_keywords.py - group all wave header keys. [Neil Cook]
Core.core.drs_startup.py - add argument ‘required’ to get_file_definition to allow not finding a key and return None if this is the case. [Neil Cook]
Core.core.drs_log.py - add pipes to the end of each qc to ease splitting in log analysis. [Neil Cook]
Update language database. [Neil Cook]
Science.calib.wave.py - move logs to language database. [Neil Cook]
Setup.install.py - remove blank spaces. [Neil Cook]
Update date/version/changelog/documentation. [Neil Cook]

0.6.017 (2020-01-08)¶

Setup.install.py - add dev section to modules (sphinx, ipdb, gitchangelog) [Neil Cook]
Core.instruments.default.recipe_definitions.py - change dtype to ‘bool’ [Neil Cook]
Tools.recipe.general.apero_log_stats.py - allow saving of all the log files to one file. [Neil Cook]
Tools.module.testing.drs_log_stats.py - update recipe print outs. [Neil Cook]
Tools.module.testing.drs_log_stats.py - correct error/warn sample. [Neil Cook]
Tools.module.testing.drs_log_stats.py - correct typo. [Neil Cook]
Tools.module.testing.drs_log_stats.py - keep all error/warning messages and use error/warn samples to keep just one for each code. [Neil Cook]
Update language database. [Neil Cook]
Tools.module.testing.drs_log.stats.py - add separations between warnings/errors. [Neil Cook]
Tools.module.testing.drs_log_stats.py - add print out of unique errors/warnings. [Neil Cook]
Tools.module.testing.drs_log_stats.py - change eval –> int. [Neil Cook]
Drs_startup.py log file should use group (only used to save where log files are correctly) [Neil Cook]
Tools.module.testing.drs_log_stats.py - try to locate log file if not found immediately. [Neil Cook]
Tools.module.testing.drs_log_stats.py - add check if log file exists. [Neil Cook]
Plotting.core.py - try fix to plt.show, plt.close. [Neil Cook]
Core.constants.constant_functions.py - add parent/author to set method. [Neil Cook]
Correct README.md. [Neil Cook]
Sciecne.calib.wave.py - correct typo IC_LITTROW –> WAVE_LITTROW, move wave night params to config. [Neil Cook]
Constants - start adding parents to keywords and add wave_night constants. [Neil Cook]
Tools.module.testing.drs_log_stats.py - change where we get the log fits file from. [Neil Cook]
Data/spirou/reset/runs/batch_run.ini - correct batch run as example of EA mini_data. [Neil Cook]
Tools/resource/setup/* - update all environmental variables. [Neil Cook]
Misc.tools.ccf_plot.py - basic plot to plot all ccfs for a given object (minus the mean) [Neil Cook]
Setup.install.py - astropy must be v3.2 or greater. [Neil Cook]
Tools.recipes.dev.apero_changelog.py - update locations of docs. [Neil Cook]
Tools.recipes.dev.apero_documentation - add codes to build documentation [unfinished] [Neil Cook]
Re-build documentation. [Neil Cook]
Update documentation (add fontawesome icons) [Neil Cook]
Core.instruments.default.recipe_definitions.py - add remake_doc (apero_documentation) to recipe definitions. [Neil Cook]
Reorganise documentation - move build into working dir and have an output dir. [Neil Cook]
Update date/version/changelog. [Neil Cook]
Update docs - known_issues and todo. [Neil Cook]
Tools.module.documentation.drs_changelog.py - add function to update a file based on a prefix and add in a suffix. [Neil Cook]
Tools.recipes.dev.apero_changelog.py - add doc changes to changelog (including copying changelog) [Neil Cook]

0.6.016 (2020-01-06)¶

Misc.updates_to_drs.mk_night_wave.py - question for EA. [Neil Cook]
Science.calib.wave.py - continue work adding wave night functions. [Neil Cook]
Recipe.spirou.cal_wave_night_spirou.py - continue work on EA code. [Neil Cook]
Plotting.plot_functions.py - add wave night plots. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add debug plots to wave night recipe def. [Neil Cook]
Core.instruments.*.default_constants.py - add wave night plots to constants. [Neil Cook]
Science.velocity.general.py - add ccf per order normalisation to table 2 of ccf output. [Neil Cook]
Continue work adding cal_wave_night functionality. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add cal_wave_night recipe. [Neil Cook]
Core.instruments.spirou.file_definitions.py - correct typo in raw file definition. [Neil Cook]
Io.drs_lock.py - mkdir can be accessed by two parallel processes at the same time - try 10 times with a sleep timer to allow one to complete and other to pass on before raising an error (due to e.g. bad file path) [Neil Cook]
Tools.module.setup.drs_processingl.py - if we have a master item do not skip if file is missing (cause error) [Neil Cook]
Tools.resources.setup.* - add alias to installation dir. [Neil Cook]
Setup/inall.py - add –name to install.py to allow different profiles to be set up on the same system. [Neil Cook]
Update changelog/version/date. [Neil Cook]
Add apero-data and gitignore contents. [Neil Cook]
Core.instruments.default.deafult_config.py - change default locations to a relative location. [Neil Cook]
Core.core.drs_startup.py - do not index if there are no outputs (including lock) [Neil Cook]
Tools.recipe.general.apero_validate.py - remove recipe log from non- instrument recipe. [Neil Cook]

0.6.015 (2020-01-04)¶

Io.drs_lock.py - remove unused imports. [Neil Cook]
Io.drs_fits.py - all writing to file must be locked (for parellisation) based on filename. [Neil Cook]
Science.telluric.general.py - change write –> write_file. [Neil Cook]
Science.polar.general.py - change write –> write_file. [Neil Cook]
Science.extract.general.py - change write –> write_file. [Neil Cook]
Science.calib.wave.py - change write –> write_file. [Neil Cook]
Science.calib.shape.py - change write –> write_file. [Neil Cook]
Science.calib.localisation.py - change write –> write_file. [Neil Cook]
Science.calib.flat_blaze.py - change write –> write_file. [Neil Cook]
Science.calib.dark.py - change write –> write_file. [Neil Cook]
Science.calib.badpix.py - change write –> write_file. [Neil Cook]
Recipe.spirou.cal_wave_spirou.py - change write –> write_file. [Neil Cook]
Recipe.spirou.cal_Wave_master_spirou.py - change write –> write_file. [Neil Cook]
Recipe.spirou.cal_thermal_spirou.py - change write –> write_file. [Neil Cook]
Recipes.spirou.cal_preprocess_spirou.py - change write –> write_file. [Neil Cook]
Recipes.spirou.cal_extract_spirou.py - change write –> writelog. [Neil Cook]
Core.core.drs_file.py - change write –> write_file (more unique) [Neil Cook]

0.6.014 (2020-01-03)¶

Io.drs_lock.py - make all lock files under the DRS_DATA_MSG path (not the group modified path) [Neil Cook]
Io.drs_lock.py - add absolute path to the files. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Core.core.drs_log.py - if use_group=False need to reset drs_data_msg (otherwise it will already have group name in even if group=None) [Neil Cook]
Tools.module.setup.drs_reset.py - remove breakpoint. [Neil Cook]

0.6.013 (2020-01-02)¶

Continue work on sphinx documentation (html and linux) [njcuk9999]
Recipes.spirou.cal_extract_spirou.py - remove breakpoint. [Neil Cook]
Core.core.drs_startup.py - make sure log file does not use group (different groups may need to lock same file) [Neil Cook]
Core.core.drs_log.py - give an option to turn off using group. [Neil Cook]
Recipes.spirou.cal_extract_spirou.py - force breakpoint. [Neil Cook]
Recipes.spirou.cal_extract_spirou.py - add breakpoint to help find problem. [Neil Cook]
Core.core.drs_log.py - pep8 correction. [Neil Cook]

0.6.012 (2019-12-31)¶

Start of documentation with Sphinx. [njcuk9999]

0.6.011 (2019-12-23)¶

Core.core.drs_log.py - try to catch log problems. [Neil Cook]
Update date/version/changelog/readme. [Neil Cook]

0.6.010 (2019-12-19)¶

Science.calib.wave.py + recipes.spirou.cal_wave_master_spirou.py - add hc/fp line creation from EA. [Neil Cook]
Core.instruments.*.default_constants.py - add PLOT_WAVEREF_EXPECTED. [Neil Cook]
Plotting.plot_functions.py - add plot_waveref_expected. [Neil Cook]
Io.drs_data.py - add a raw mode for getting the cavity file. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.spirou.py - add plot WAVEREF_EXPECTED for hc/fp lines. [Neil Cook]
Core.instrumnets.*.pseudo_const.py - add FIBER_DPR_POS (correct dpr type for fiber) [Neil Cook]
Core.instruments.spirou.file_defintions.py - add dbname,key and datatype for hc and fp master line files. [Neil Cook]
Re-make directories (if they don’t exist) [Neil Cook]
Io.drs_lock.py - replace __remove__empty__ function. [Neil Cook]
Core.core.drs_log.py - only continue with DRS_DATA_MSG_FULL if it exists. [Neil Cook]
Core.core.drs_startup.py - fix location of where we define drs_data_msg_full the first time. [Neil Cook]
Core.core.drs_startup.py - must pass group to log dir. [Neil Cook]
Tools.module.setup.drs_processing.py - deal with KeyboardInterrupt. [Neil Cook]
Drs_log.py - sort out log structure. [Neil Cook]
Drs_reset.py - should not remove read of path. [Neil Cook]
Update the reset codes to reset log.fits files. [Neil Cook]
Core.core.drs_startup.py - only use recipe.log if recipe_kind = ‘recipe’ [Neil Cook]
Core.core.drs_log.py - set logfitsfiles name from constants. [Neil Cook]
Core.instruments.default.default_config.py - add DRS_LOG_FITS_NAME. [Neil Cook]
Update language database. [Neil Cook]
Io.drs_lock.py - replace print statements for WLOG. [Neil Cook]
Add reset options to run files. [Neil Cook]
Remove recipe.log from non-recipe scripts (i.e. tools) [Neil Cook]
Core.core.drs_startup.py - address not initially having instrument for DRS_RECIPE_KIND. [Neil Cook]
Core.core.drs_startup.py - correctly manage KeyboardInterrupts. [Neil Cook]
Correctly manage KeyboardInterrupts. [Neil Cook]
Core.core.drs_log.py - add way to add an error (if found at the right time) [Neil Cook]
Core.instruments.default.pseudo_const.py and io.drs_lock.py - update drs_data_msg path (to full path) [Neil Cook]
Core.core.drs_startup.py - get recipe kind and add to params and figure out how to log to files only once we have correct information. [Neil Cook]
Core.core.drs_log.py - add recipe_kind to recipe_log. [Neil Cook]
Core.instruments.*.recipe_definitions.py - add a kind to every recipes (“test”,”recipe”,”tool”,”processing”) for logging. [Neil Cook]
Core.core.drs_recipe.py - add a recipe kind (for logging) [Neil Cook]
Core.core.drs_log.py - sort logs into night names and by recipe_kind. [Neil Cook]
Core.core.drs_log.py - add group and runstring to recipe log fits file. [Neil Cook]
Update date/version/changelog/readme. [Neil Cook]
Update doc string. [Neil Cook]

0.6.009 (2019-12-18)¶

Core.core.drs_log.py + drs_log_stats.py - add option to save time of file and then do log analysis on –since –before log files only. [Neil Cook]
Recipes/test/blank_spirou.py - blank recipe. [Neil Cook]
Update doc strings for recipes. [Neil Cook]
Misc/updates_to_drs/mk_night_wave.py - EA code to do nightly wavelength solution. [Neil Cook]
Plotting.plot_functions.py - log scale on some wave plots. [Neil Cook]
Science.calib.wave.py - update wave triplet fit by EA. [Neil Cook]
Science.calib.wave.py - add breakpoint to look at wave res map problem. [Neil Cook]
Science.calib.wave.py - EA changes to triplets fit. [Neil Cook]
Recipe/spirou/cal_wave_spirou.py - force initial wavelength solution as the master. [Neil Cook]
Core.instruments.spirou.default_constants.py - change the number of triplet iterations to 1. [Neil Cook]
Science.calib.wave.py - EA modifications to triplet fitting. [Neil Cook]
Update changelog.md to include core.core.drs_recipe fixes. [Neil Cook]
Core.core.drs_recipe.py - add other list arguments – attempt to correct bug. [Neil Cook]
Core.core.drs_recipe.py - add other list arguments (i.e. –fpfiles=X Y Z) as separate elements of str_arg_list. [Neil Cook]
Core.core.drs_recipe.py - add other list arguments (i.e. –fpfiles=X Y Z) as separate elements of str_arg_list. [Neil Cook]
Update date/version/changelog/readme. [Neil Cook]

0.6.008 (2019-12-17)¶

README.md - correct typo “processing” –> “apero_processing” [Neil Cook]
Setup/install.py - install.update does not require “args” as input. [Neil Cook]
Drs_log_stat - reset the code to remove xytext change (doesn’t work currently) [Neil Cook]
Science.calib.wave.py - add EA changes (no linear_minimisation now use wave_lmfit) [Neil Cook]
Update language database. [Neil Cook]
Core.core.drs_startup.py - only start in quiet mod if fkwargs[‘quiet’] is True. [Neil Cook]
Core.core.drs_recipe.py - fix bug introduced by having –arguments only (need to append all list items to string for self.str_arg_list. [Neil Cook]
Core.instruments.spirou.default_constants.py - tweak hc tfit order fit continuum parameters (EA) [Neil Cook]
Core.instruments.spirou.default_constants.py - change hc tfit order fit continuum constants (EA) [Neil Cook]
Core.instruments.spirou.default_constants.py - lower the values of the wave hc tfit order fit continnum (EA) [Neil Cook]
Science.calib.wave.py - add breakpoint to test problem. [Neil Cook]
Science.calib.wave.py - attempt fix of wave solution triplets rms diverging. [Neil Cook]
Science.calib.wave.py - add breakpoint. [Neil Cook]
Science.calib.flat_blaze.py - EA played with bounds. [Neil Cook]
Tools.recipes.general.apero_log_stats.py - tweak plot. [Neil Cook]
Tools.recipes.general.apero_log_stats.py - tweak plot. [Neil Cook]
Tools.recipes.general.apero_log_stats.py - add recipe mode - correct bug. [Neil Cook]
Tools.recipes.general.apero_log_stats.py - add recipe mode. [Neil Cook]
Plotting.plot_functions.py - correct pep8. [Neil Cook]
Science.calib.wave.py - remove break points. [Neil Cook]
Science.calib.flat_blaze.py - add comments to EA new additions. [Neil Cook]
Science.calib.dark.py - correct bug dark_time must be an array. [Neil Cook]
Changelog/readme/date/version. [Neil Cook]

0.6.007 (2019-12-16)¶

Tools/bin/apero_log_stats.py - start adding options for stats on specific recipes. [Neil Cook]
Science/extract/other.py - add extra printout to show files were extracted and loaded from extraction (before silent in log) [Neil Cook]
Science/extract/extraction.py - add extra arguments for calculate_blaze_flat_sinc. [Neil Cook]
Science.calib.flat_blaze.py - fix issue with fitting blaze function (and given better error if curve_fit fails) [Neil Cook]
Science.calib.dark.py and science.calib.shape.py - make sure files for cubes are deep copied (try to prevent memory issues) [Neil Cook]
Cal_wave_spirou.py - update convergence test on hc solution (EA bug fix) [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.default.recipe_definitions.py - add recipe argument to log stats. [Neil Cook]
Data.core.runs - limited_run.ini - update the default limited run. [Neil Cook]
Install.py / drs_installation.py - Allow user to define all userinputs from the command line (Issue #579) [Neil Cook]
Drs_startup.py - need to re-set the instrument when found in params. [Neil Cook]
Update changelog/data/version/readme. [Neil Cook]

0.6.006 (2019-12-13)¶

Update non-instrument specified recipes (and make sure apero_processing can be run correctly from main call. [Neil Cook]
Drs_startup.py - need to be careful when we don’t have an instrument set. [Neil Cook]
Setup.install.py - correct help string. [Neil Cook]
Tools.module.testing.drs_log_stats.py + tools.recipes.general.py - add log stat code to apero_log_stats.py. [Neil Cook]
Plotting.plot_functions.py - add plot_logstats_bar plot. [Neil Cook]
Core.instruments.default.recipe_definitions.py - add logstats recipe. [Neil Cook]
Update language database and add recipe to apero_tools. [Neil Cook]
Tools.module.documentation.drs_changelog.py - update VERSIONSTR/DATESTR with changes to const files. [Neil Cook]
Update default_config/default_constants with groups and some descriptions. [Neil Cook]
Core.core.drs_startup.py - allow quiet to be passed from fkwargs. [Neil Cook]
Core.core.drs_log.py - move textwrap to constants. [Neil Cook]
Core.constants.param_functions.py - add “from_file” and “cache” optiosn to load_config (for installation purposes) [Neil Cook]
Core.constants.constant_functions.py - move textwrapper here, add description to constants, add write_line method for writing user configs + add ‘=’ to end of update string to make constants unique. [Neil Cook]
Setup.install.py + drs_installation.py - add an update mode to the install.py (and fix reset bug) [Neil Cook]

0.6.005 (2019-12-12)¶

Updates to installation script (UNFINISHED) [Neil Cook]
Io.drs_lock.py - change warning message (name.lock) [Neil Cook]
Cal_preprocessing_spirou.py - typo fix qc inputs. [Neil Cook]
Core.core.drs_recipe.py - change “-” to “–” [Neil Cook]
Update tools with recipe log. [Neil Cook]
Science.telluric.genearl.py - return qc_params and passed in qc functions. [Neil Cook]
Core.core.drs_log.py - add no_qc and RECIPE to log file and only write newlog on add_level. [Neil Cook]
Cal_thermal_spirou.py - add no_qc. [Neil Cook]
Science.preprocessing.general.py - add quality control to function. [Neil Cook]
Science.calib.badpix.py - remove redundant code. [Neil Cook]
Modify recipes and add recipe logging. [Neil Cook]

0.6.004 (2019-12-12)¶

Recipe.spirou.* - test locking [not working yet] [Neil Cook]
Io.drs_lock.py - provide function to lock function. [Neil Cook]
Core.ocre.drs_startup.py - setup the recipe log. [Neil Cook]
Core.core.drs_recipe.py - add a self.log to store to RecipeLog. [Neil Cook]
Core.core.drs_log.py - add RecipeLog. [Neil Cook]
Make sure all arguments that are words start with – [Neil Cook]
Update date/changelog/version. [Neil Cook]

0.6.003 (2019-12-10)¶

Update README.md. [Neil Cook]
Tools.module.listing.file_explorer.py - deal with no ds9 path set (Issue #576) [Neil Cook]
Fix typos for apero_validate and apero_reset (Issue #577) [Neil Cook]
Core.instruments.default.pseudo_const.py - modify logfile to have .log and latex to replace .log (make unique) [Neil Cook]
Core.instruments.default.default_config.py - DRS_DS0_PATH and DRS_PDFLATEX_PATH should be str not ‘path’ (Issue #576) [Neil Cook]
Localisation - remove breakpoints. [Neil Cook]
Update readme (cal_preprocessing –> cal_preprocess) [Neil Cook]
Localisation.py - fix bug with loc order 0. [Neil Cook]
Science.calib.localisation.py - move break point. [Neil Cook]
Science.calib.localisation.py - changes to fix loc. [Neil Cook]
Cal_loc_spirou.py - move break point. [Neil Cook]
Cal_loc_spirou.py - add breakpoint to test qc failure. [Neil Cook]
Tools.module.setup.py - drs_installation.py - add to clean install message. [Neil Cook]
README.md - update read me with extra comments. [Neil Cook]
Prepare cal_wave_master_spirou.py. [Neil Cook]
Tools.module.setup.drs_installation.py - update ‘apero-validate.py’ –> ‘apero_validate.py’ [Neil Cook]
Recipes.spirou.cal_wave_spirou.py - correct typo in comment. [Neil Cook]
Science.calib.wave.py - add a TODO. [Neil Cook]
Tools.modules.setup.drs_processing.py - correct returns for prerun_test() [Neil Cook]
Change the file_explorer name. [Neil Cook]
Core.core.drs_recipe.py - fix telluric test. [Neil Cook]
Update config/changelog/readme/version. [Neil Cook]

0.6.002 (2019-12-09)¶

Core.core.drs_recipe.py - change souce of tellurics (shouldn’t be here) [Neil Cook]
Get whitelist for tellurics in drs_processing.py. [Neil Cook]
Tools.module.setup.drs_processing.py - add a pre-run test to test if files exist before running. [Neil Cook]
Tools.module.listing.file_explorer.py - update plotting function and check before loading ds9. [Neil Cook]
Science.velocity.general.py - remove old function (create_drift_file) [Neil Cook]
Science.extract.crossmatch.py - add simbad query (when we have no ra and dec and only have object name) [Neil Cook]
Science.calib.wave.py - remove todo. [Neil Cook]
Science.calib.localisation.py - add rorder to params (for plotting) [Neil Cook]
Science.calib.flat_blaze.py - make it clear calculate_blaze_flat should not be used. [Neil Cook]
Recipes.spirou.cal_shape_master_spirou.py - remove master cube npy debug. [Neil Cook]
Plotting - add general use image/plot functions + add cursor + add main() and allow use without recipe defined + add new graph type “show” [Neil Cook]
Update language database. [Neil Cook]
Io.drs_table.py - remove redundant lock checks (new system works better) [Neil Cook]
Io.drs_lock.py - push messages into language database. [Neil Cook]
Io.drs_data.py - remove todo. [Neil Cook]
Core.math.gauss.py - remove todo here. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add plots that were missing. [Neil Cook]
Core.instruments.default.file_defintions.py - remove unused file objects. [Neil Cook]
Core.instruments.default.recipe_definitions.py - add Help strings. [Neil Cook]
Core.instruments.*.default_*.py - add config/constants/keyword args. [Neil Cook]
Core.core.drs_recipe.py - deal with TELLURIC_TARGETS being set to None (get all) [Neil Cook]
Core.core.drs_log.py - remove old WLOG string warning. [Neil Cook]
Core.core.drs_database.py - set Database constants from constants files. [Neil Cook]
Core.core.drs_argument.py - add help string for set_quiet. [Neil Cook]
Convert readme.md to pdf. [Neil Cook]
Add subsections to contents in README.md. [Neil Cook]
Add descriptions for each recipe in the README.md. [Neil Cook]
Correct typo in readme. [Neil Cook]
Update changelog/version/date. [Neil Cook]
Correct typos in file_definitions. [Neil Cook]
Update the read me with recipe + output descriptions. [Neil Cook]

0.6.001 (2019-12-06)¶

Remove old breakpoints. [Neil Cook]
Science.calib.wave.py - add breakpoint for debugging. [Neil Cook]
Flat_blaze.py - fix bug with sinc fitting (bounds for quad and cube parameters to constraining) [Neil Cook]
Add error dumps directory. [Neil Cook]
Io.drs_lock.py - make all lock files go to the log/lock dir and add a way to remove all empty ones of these (after processing is complete) using drs_lock.reset_lock_dir. [Neil Cook]
Update the Lock (not longer need lockdir –> will all go to log directory (under the a lock dir) [Neil Cook]
Update README.md. [Neil Cook]
Update README.md. [Neil Cook]
Io.drs_lock.py - remove the lock directory if directory is empty. [Neil Cook]
Science.calib.wave.py - badvalues must be a string list. [Neil Cook]
Core.core.drs_startup.py - random seed needs to be set to randomise the cores. [Neil Cook]

0.5.124 (2019-12-05)¶

Tools.module.setup.drs_processing.py - set multi_process back to group by core (Process) [Neil Cook]
Tools.module.setup.drs_processing.py - correct typo manager.event –> manger.Event. [Neil Cook]
Update language database. [Neil Cook]
Parallel test2 - test out Pool (from @cusher) [Neil Cook]
Tools.modules.setup.drs_processing.py - test out Pool (from @cusher) [Neil Cook]
Add second parallel check based on @cusher example. [Neil Cook]
Update log and group names (slightly shorter - no host) [Neil Cook]
Update analyse_logs.py. [Neil Cook]
Core.core.drs_startup.py - add a random set of charaters to the end of pid to make unique. [Neil Cook]
Add contents to main README.md. [Neil Cook]
Update default run scripts. [Neil Cook]
Tools.module.setup.drs_reset.py - change empty dir param (typo) [Neil Cook]
Update paths given changes to tool name/location. [Neil Cook]
Update paths given changes to tool name/location. [Neil Cook]
Remove dashes from program names to allow importing. [Neil Cook]

0.5.123 (2019-12-05)¶

Core.drs_startup.py - make sure pids are really unlikely to be the same (add random component) [Neil Cook]
Io.drs_lock.py - deal with folder/queue files disappear during lock process. [Neil Cook]
Misc/problems/* - add copy to analyse log files for preprocessing + modify the parallel test. [Neil Cook]
Tools.module.setup.drs_processing.py - change grouping –> only number of cores files per group (instead of total/cores per group per recipe) [Neil Cook]
Recipe/spirou/cal_preprocess_spirou.py - change error message. [Neil Cook]

0.5.122 (2019-12-04)¶

Misc.problems.parellel_test_20191203.py - minimum working version of parallisation problem. [Neil Cook]
Misc.problems.parellel_test_20191203.py - minimum working version of parallisation problem. [Neil Cook]
Core.core.drs_startup.py - add SystemExit to the possible exceptions to catch. [Neil Cook]
Add an export command to file_explorer. [Neil Cook]
Tools.module.setup.drs_installation.py - make optional programs not create “None” path. [Neil Cook]
Tools.module.setup.drs_installation.py - fix typo. [Neil Cook]
Setup/install.py - check for python 3. [Neil Cook]
Add ds9/pdflatex to the codes. [Neil Cook]
Add DRS_DS9_PATH and DRS_PDFLATEX_PATH to constants. [Neil Cook]
Tools.module.setup.drs_installation.py - macs still suck. [Neil Cook]
Tools.module.setup.drs_installation.py - macs suck. [Neil Cook]

0.5.121 (2019-12-02)¶

Add README.md to bin and dev tool folders. [Neil Cook]
Change __INSTRUMENT__ = None to __INSTRUMENT__ = ‘None’ and move tools/bin and tools/dev to the new loc + add chmod + symlinks. [Neil Cook]
- make file_explorer.py work again. [Neil Cook]
Add runs to default user config files. [Neil Cook]
Add README.md to reset run files. [Neil Cook]
Tools.bin.reset.py + drs_reset.py - add run files to reset. [Neil Cook]
Core.instruments.*.default_config.py - add DRS_RESET_RUN_PATH. [Neil Cook]
Add reset run files. [Neil Cook]
Science.preprocessing.identification.py - fileset must be string to go into .join. [Neil Cook]
Core.instruments.spirou.file_definitions.py - add the pp_lfc_lfc to pp_file set. [Neil Cook]
Science.calib.general.py - catch warnings for unphysical pixel nan setting. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.120 (2019-11-29)¶

Replace old locking mechanism with new one. [Neil Cook]
Science.calib.general.py - fix upper and lower limit after conversion to electrons. [Neil Cook]
Science.extract.extraction.py - change breakpoint location. [Neil Cook]
Change breakpoint location. [Neil Cook]
Update language database. [Neil Cook]
Science.calib.flat_blaze.py - add breakpoint. [Neil Cook]
Tools.module.setup.drs_installation.py - correct install messages. [Neil Cook]
Apero/tools/module/setup/drs_installation.py + setup.install.py - update the installation after Etienne’s first attempt. [Neil Cook]
Update README.md. [Neil Cook]
Processing add to README.md. [Neil Cook]
Drs_startup + drs_lock - continue to test the locking mechanism. [Neil Cook]
Drs_startup + drs_lock - continue to test the locking mechanism. [Neil Cook]
Drs_startup + drs_lock - continue to test the locking mechanism. [Neil Cook]
Drs_startup + drs_lock - continue to test the locking mechanism. [Neil Cook]
Drs_startup + drs_lock - continue to test the locking mechanism. [Neil Cook]
Drs_startup + drs_lock - continue to test the locking mechanism. [Neil Cook]
Drs_startup + drs_lock - continue to test the locking mechanism. [Neil Cook]
Drs_startup + drs_lock - continue to test the locking mechanism. [Neil Cook]
Drs_startup + drs_lock - continue to test the locking mechanism. [Neil Cook]
Core.core.drs_database.py - correct typo. [Neil Cook]

0.5.119 (2019-11-29)¶

Io.drs_lock.py - change name of function in @sync call. [Neil Cook]
Drs_startup + drs_lock - try to improve locking. [Neil Cook]
Core.core.drs_startup.py - correct name of function. [Neil Cook]
Io.drs_table.py - remove use of locking (for debug) [Neil Cook]
Io.drs_lock.py - add a randomisation to the wait time (so multiple hits don’t start at the same time) [Neil Cook]
Add to readme. [Neil Cook]
Test out new lock. [Neil Cook]
Add more readme.md. [Neil Cook]
Merge remote-tracking branch ‘origin/dev’ into dev. [Neil Cook]
Update README.md. [Neil Cook]
Update readme.md. [Neil Cook]
Update readme.md. [Neil Cook]
Io.drs_lock.py - add a printout when file unlocks (debug?) [Neil Cook]
Update language database. [Neil Cook]
Update the README.md with new installation instructions. [Neil Cook]
Tools.module.setup.drs_installation.py - add in skipping of reset if not clean_install (and print that we are doing reset) [Neil Cook]
Update data_example. [Neil Cook]
Science.calib.general.py shape.py - fix typo and remove breakpoint. [Neil Cook]
Scence.calib.general.py - remove unphysical pixel values (set to NaN) [Neil Cook]
Io.drs_image.py - fix for high bad pixels (clean with border) [Neil Cook]
Core.instruments.*.default_keywords.py - add frmtime and saturate + add comments for input header keys. [Neil Cook]
Io.drs_table.py - change the locking order. [Neil Cook]
Science.calib.shape.py - move breakpoint. [Neil Cook]
Update debug table. [Neil Cook]
Science.calib.shape.py - remove old breakpoint. [Neil Cook]
Add breakpoints and saving of fpcube for debug. [Neil Cook]
Science.calib.background.py - correct axis order in sz_small. [Neil Cook]
Add dark_fp_sky and lfc_lfc file types. [Neil Cook]
Core.core.drs_startup.py - fix for quiet always being found (even when None) [Neil Cook]
Core.instruments.spirou.default_config.py - remove INTROOT references. [Neil Cook]
Io.drs_table.py - try to add more informative error in write_table (index.fits is not saving every time in parallel) [Neil Cook]

0.5.118 (2019-11-27)¶

Etiennes speed up codes. [Neil Cook]
Tools.module.setup.drs_reset.py - update __NAME__ [Neil Cook]
Tools.module.setup.drs_installation.py - add print headers, add validation command, add quiet mode to reset, add paths before executing os.system commands. [Neil Cook]
Tools.dev.requirement_check.py - add code (from SpirouDRS) to check requirements. [Neil Cook]
Tools.bin.validate.py - add code to validate (for now just a splash screen) [Neil Cook]
Setup.install.py - add validation check for required/recommended modules. [Neil Cook]
Remove unused imports. [Neil Cook]
Misc.fast_convolve_correct_local_background.py - etiennes correct to add (speed up) [Neil Cook]
Remove unused imports. [Neil Cook]
Core.instruments.default.recipe_definitions.py - add required_check program (in tools) [Neil Cook]
Update permissions. [Neil Cook]
Update language database. [Neil Cook]
Core.core.*.py - add quiet option so setup info/splash is not displayed. [Neil Cook]
Core.constants.param_functions.py - add window size function. [Neil Cook]
Tools.resources.setup - rename from terrapipe –> apero. [Neil Cook]
Core.instruments.default.recipe_definitions.py - fix problem with listing.instrument name and add validate placeholder. [Neil Cook]
Update .gitignore. [Neil Cook]
Terrapipe –> apero, move INTROOT2 to .., move INTROOT to misc. [Neil Cook]
Terrapipe –> apero, move INTROOT2 to .., move INTROOT to misc. [Neil Cook]
Terrapipe –> apero, move INTROOT2 to .., move INTROOT to misc. [Neil Cook]
Core.instruments.spirou.file_definitions.py - correct out_dark_master (accept dark_dark_tel and dark_dark_int) [Neil Cook]
Setup.install.py - add a todo (need to make sym links) [Neil Cook]
Tools.module.setup.drs_reset.py - add functionality to skip warning if folder is empty (there is no point warning if we have an empty folder) [Neil Cook]
Tools.module.setup.drs_installation.py - add functionality to install drs. [Neil Cook]
Setup/install.py - fill out the installation code (formally in drs_installation.py) [Neil Cook]
Tools.bin.reset.py - add directory to reset_confirmation. [Neil Cook]
Tools.bin.validate.py - add placeholder (needs filling out) [Neil Cook]
Tools.resources.setup/* - add env setup codes. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.117 (2019-11-26)¶

Recipes.spirou.obj_fit_tellu_db_spirou.py + obj_mk_tellu_db_spirou.py + obj_spec_spirou.py - add global output list for displaying errors at the end. [Neil Cook]
Recipes.spirou.obj_fit_tellu_db_spirou.py + obj_mk_tellu_db_spirou.py + obj_spec_spirou.py - add global output list for displaying errors at the end. [Neil Cook]
Tools.module.setup.drs_processing.py - run_process and combine_outlist. [Neil Cook]
Tools.module.setup.drs_processing.py - add run_process function to run a recipe. [Neil Cook]
Science.extract.other.py - remove breakpoint. [Neil Cook]
Recipes.spirou - change pol_spirou name + add place holders for obj_spec_spirou and obj_pol_spirou. [Neil Cook]
Recipes.spirou.obj_fit_tellu_db_spirou.py obj_mk_tellu_db_spirou.py - add new functions to run_process. [Neil Cook]
Recipes.spirou.obj_fit_tellu_db_spirou.py obj_mk_tellu_db_spirou.py - add new functions to run_process. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add obj_spec_spirou and obj_pol_spirou. [Neil Cook]
Core.instruments.default.recipe_definitions.py - add white/black list kwarg to processing. [Neil Cook]
Core.core.drs_startup.py - Add a group title to header (if in group) [Neil Cook]
Core.constants.param_functions.py - if we have a list then just return (map_listparameter function) [Neil Cook]
Recipes.spirou.cal_thermal_spirou.py - add log message for writing thermal files. [Neil Cook]
Core.instruments.spirou.default_constants.py - set thermal_always_extract to False. [Neil Cook]
Tools.module.setup.drs_processing.py - move group_name to drs_startup. [Neil Cook]
Tools.bin.processing.py - update link to group_name (now in drs_startup) [Neil Cook]
Science.extract.other.py - add breakpoint to test code. [Neil Cook]
Recipes.spirou.cal_thermal_spirou.py - remove breakpoint. [Neil Cook]
Core.core.drs_startup.py - move group_name construct from processing to drs_startup. [Neil Cook]
Tools.module.setup.drs_processing.py - construct group name and pass it to recipe via linear_process. [Neil Cook]
Tools.bin.processing.py - generate group name. [Neil Cook]
Recipes.spirou.cal_thermal_spirou.py - add breakpoint for debugging. [Neil Cook]
Core.instruments.spirou.default_keywords.py - change order to reflect current and wanted input header keys. [Neil Cook]
Core.core.drs_log.py - add group handling. [Neil Cook]
Core.core.drs_startup.py - add group handling. [Neil Cook]
Core.instruments.default.recipe_definitions.py - update the dtype setting for –cores in processing recipe. [Neil Cook]
Core.instruments.default.recipe_definitions.py - update the default setting for –cores in processing recipe. [Neil Cook]
Tools.module.setup.drs_processing.py - add blacklist, whitelist, cores and test run arguments from user input. [Neil Cook]
Tools.bins.processing.py - update instrument name. [Neil Cook]
Core.instruments.default.recipe_definitions.py - add arguments to processing recipe. [Neil Cook]
Update language database. [Neil Cook]
Science.calib.wave.py - correct input to get_input_files. [Neil Cook]
Core.core.drs_database.py - add in debug function names to find problem. [Neil Cook]
Science.calib.dark.py - add dprtype to dprtypes for dark master table. [Neil Cook]
Recipes.spirou.cal_dark_master_spirou.py - get allowed types as a list. [Neil Cook]
Core.instruments.spirou.default_constants.py - add DARK_DARK_INT to dark master allowed types. [Neil Cook]
Science.calib.dark.py - add dprtype to dark table. [Neil Cook]
Recipes.spirou.cal_dark_master_spirou.py - allow dark master to use multiple dark_dark types. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - allow cal_badpix to use dark_dark_tel and dark_dark_int. [Neil Cook]
Io.drs_fits.py - improve id file error. [Neil Cook]
Update language database. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.116 (2019-11-15)¶

Tools.module.setup.drs_processing.py - remove breakpoint. [Neil Cook]
Science.extract.general.py - fix input to get_input_files. [Neil Cook]
Science.extract.berv.py - remove breakpoint. [Neil Cook]
Science.calib.wave.py - correct pep8. [Neil Cook]
Science.calib.general.py - add darkfile, abdpixfile, backfile from kwargs. [Neil Cook]
Core.constants.param_functions.py - disable the Ctrl+C –> breakpoint functionality it doesn’t work well. [Neil Cook]
Tools.module.setup.drs_processing.py - deal with optional file args being requested. [Neil Cook]
Tools.module.setup.drs_processing.py - add extra keys to default run keys. [Neil Cook]
Core.core.drs_startup.py - set the source when debug mode taken from arguments. [Neil Cook]
Core.constants.param_functions.py - add info and history functions to ParamDict and cache some settings for immediate use. [Neil Cook]
Science.preprocessing.identification.py - fix return to fix_header (for case where we have an input infile) [Neil Cook]
Tools.module.setup.drs_processing.py - add defaults after only if not found and warn user. [Neil Cook]
Update language database. [Neil Cook]
Tools.module.setup.drs_processing.py - add default run keys (for when values are not in files) [Neil Cook]
Science.velocity.general.py - add ccf mask to suffix of output file. [Neil Cook]
Science.velocity.general.py - add ccf mask to suffix of output file. [Neil Cook]
Add masks from Andres. [Neil Cook]
Science.prprocessing.identification.py - fix_header: fix return when no infile given. [Neil Cook]
Tools.module.setup.drs_processing.py - fix_header make sure header comes in as keyword argument. [Neil Cook]
Science.preprocessing - add recipe as arg in fix_header (and push to pseudo_const.py) [Neil Cook]
Update date/version/changelog. [Neil Cook]
Science.velocity.general.py - make sure users input of ccf step and width is good (ccfstep < ccfwidth / 10) [Neil Cook]
Core.instruments.default.*.default_constants.py - add CCF_MAX_CCF_WID_STEP_RATIO. [Neil Cook]

0.5.115 (2019-11-14)¶

Update language database. [Neil Cook]
Science.velocity.general.py - add break point to test crash. [Neil Cook]
Update language database. [Neil Cook]
Io.drs_lock.py - add way to get out of lock loop (Ctrl + C) will now delete file - elsewise Ctrl + C goes to debugger (and then exits) [Neil Cook]
Core.core.drs_database.py - deal with not having a night name. [Neil Cook]
Core.core.drs_database.py - make sure all strings are stripped of whitespaces (before and after) [Neil Cook]
Add new ccf mask. [Neil Cook]
Rename error.py –> language_db.py. [Neil Cook]
Tools.bin.remake_db.py -fix db_time. [Neil Cook]
Tools.bin.remake_db.py - do not open all files at once (save to master one by one) [Neil Cook]
Tools.modeul.setup.drs_reset.py - split reset_dbdir to allow accessing copy_default_db. [Neil Cook]
Tools.dev.error.py - add a TODO here. [Neil Cook]
Tools.bin.remake_db.py - add code to remake databases. [Neil Cook]
Science.preprocessing.py - replace drs_infile_id with call to fits.drs_fits. [Neil Cook]
Science.extract.general.py - add fiber. [Neil Cook]
Science.calib.flat_blaze.py + localisation + wave - add fiber to outputs. [Neil Cook]
Update language database. [Neil Cook]
Io.drs_fits.py - add id_drs_file to identify any filename in a drs_file_set (and return its DrsInputFile/DrsFitsFile instance) [Neil Cook]
Core.instruments.default.recipe_definitions.py - add remake_db (generalised remake_cdb) [Neil Cook]
Core.instruments.default.default_constants.py - remake_database_default. [Neil Cook]
Core.instruments.spirou.pseudo_const.py - pep8 clean up. [Neil Cook]
Core.instruments.default.recipe_definitions.py - add remake_cdb recipe definition. [Neil Cook]
Core.instruments.*.file_definitions.py - add calib_file set and clean up (pep8 wise) [Neil Cook]
Core.core.drs_file.py - check if drsfile has recipe (and if not set it to self.recipe) [Neil Cook]
Core.core.drs_database.py - make _get_time more specific to using header/hdict. [Neil Cook]
Core.instrument.spirou.default_constants.py - change to gl581. [Neil Cook]
Science.velocity.general.py - correct plot keyword found_rv –> rv. [Neil Cook]

0.5.114 (2019-11-14)¶

Science.preprocessing.identification - add the fix_headers wrapper (passes it to instrument pseudo constants) + add a debug in id process to show which drs file we are currently looking at. [Neil Cook]
Tools.module.setup.drs_processing - add header keys via fix_header (non-instrument specific) [Neil Cook]
Science.calib.dark.py - make sure get dark is getting dark master only (dark master is DARK_DARK_TEL by default) [Neil Cook]
Cal_thermal_spirou.py - deal with different types of darks (OBJ –> dark_tel, HC,FP–> dark_int) + add switch to turn off thermal correction. [Neil Cook]
Recipe.spirou.cal_loc_spirou.py - add center_fits to qc (diff of order cols must be positive) [Neil Cook]
Recipe.spirou.cal_preprocessing.py - add fix_header to fix keys before drs_infile_id. [Neil Cook]
Io.drs_fits.py - change get_mid_obs_time assuming it is now always present in header. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.spirou.file_definitions + recipe_definitions - split dark_dark in to dark_dark_int, dark_dark_tel, dark_dark_sky. [Neil Cook]
Core.instruments.*.pseudo_const.py - add HEADER_FIXES (to control instrument specific header fixes required) [Neil Cook]
Core.instruments.*.default_keywords.py - add calibwh and target_type keywords. [Neil Cook]
Core.core.drs_file.py - fix how we check read before copying. [Neil Cook]
Core.instruments.*.default_constants.py - remove skydark references and update references to DARK_DARK –> DARK_DARK_INT, DARK_DARK_TEL, DARK_DARK_SKY. [Neil Cook]

0.5.113 (2019-11-12)¶

Core.instruments.spirou.recipe_defintions.py - add blazefile, flatfile and thermal file arguments to required recipes. [Neil Cook]
Science.calib.flat_blaze.py - allow user to set flat and blaze file. [Neil Cook]
Calib.general.py - allow user defined thermal file to come from calibDB. [Neil Cook]
Calib.general.py - allow user defined file to come from calibDB. [Neil Cook]
Calib.wave.py - allow user defined file to come from calibDB. [Neil Cook]
Calib.shape.py - allow user defined file to come from calibDB. [Neil Cook]
Calib.localisation.py - allow user defined file to come from calibDB. [Neil Cook]
Calib.dark.py - allow user defined file to come from calibDB. [Neil Cook]
Calib.badpix.py - allow user defined file to come from calibDB. [Neil Cook]
Calib.background.py - allow user defined file to come from calibDB. [Neil Cook]

0.5.112 (2019-11-12)¶

Recipes/spirou/obj_pol_spirou.py and science/polar/general.py - add polar s1d (calculation, file writing and plotting) [Neil Cook]
Core.instruments.spirou.py - add s1d plotting. [Neil Cook]
Plotting.plot_functions.py - allow s1d plot to not have fiber argument. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.spirou.file_definitions.py recipe_definitions.py - add polar s1d outputs. [Neil Cook]
Core.instruments.default.default_config.py - update author list. [Neil Cook]
Misc/dispatch_object.py - add argparse arguments. [Neil Cook]

0.5.111 (2019-11-09)¶

Tools.module.setup.drs_installation.py - add user_interface, copy_configs and update_configs. [njcuk9999]
Core.constants.constant_functions.py - add get_constants_from_file and update_file functions. [njcuk9999]
Core.instruments.default.pseudo_const.py - add print function to Color class (to print in colour) [njcuk9999]
Tools.module.setup.drs_installation.py - first commit of the installation script. [njcuk9999]

0.5.110 (2019-11-09)¶

Obj_pol_spirou.py - add generate stats + plotting + writing of files. [Neil Cook]
Science.calib.dark.py - add text entry for error 40-011-00006. [Neil Cook]
Recipe.spirou.cal_shape_spirou.py - add recipe to args + add new debug plot. [Neil Cook]
Plotting.plot_functions.py - add polar plots. [Neil Cook]
Update language database. [Neil Cook]
Io.drs_text.py - add text entry for error 00-008-00020. [Neil Cook]
Io.drs_fits.py - add text entry for error 00-008-00019. [Neil Cook]
Io.drs_data.py - add text entry for error 09-021-00009. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py + file_definitions.py - add plot and file definitions for polar + extra debug plot for shape/shape_master. [Neil Cook]
Core.instruments.spirou.py - add file_definitions for polar outputs. [Neil Cook]
Core.core.drs_startup.py - remove input params from plotter.close_plots. [Neil Cook]
Core.core.drs_file.py - make sure all filenames in add_hkey_1d and 2d are basenames only. [Neil Cook]
Instruments.*.default_constants.py and default_keywords.py - add polar keywords/constants/plot constants. [Neil Cook]
Core.constants.param_functions.py - ParamDict.copy - add doc string (with return type) [Neil Cook]
Misc.dispatch_object.py - code to process tar of objects. [Neil Cook]
Misc.dispatch_object.py - code to process tar of objects. [Neil Cook]
Recipes/spirou/cal_ccf_spirou.py - fix that we need to check whether wprops[‘WFP_DRIFT’] is None. [Neil Cook]
Science.velocity.general.py - fix bug in plotting. [Neil Cook]
Recipes/spirou/cal_ccf_spirou.py - fix bug with compute_ccf_fp. [Neil Cook]
Recipes/spirou/cal_ccf_spirou.py - fix bug with compute_ccf_fp. [Neil Cook]
Science.polar.general.py - update polar class. [Neil Cook]

0.5.109 (2019-11-07)¶

Update construct_filename –> construct_path. [Neil Cook]
Tools.module.setup.drs_reset.py - change call to construct_filename –> construct_path. [Neil Cook]
Science.polar.* - add whole lsd module. [Neil Cook]
Recipes/spirou/obj_pol_spirou.py - add call to lsd analysis wrapper. [Neil Cook]
Io.drs_data.py - add lsd mask getting. [Neil Cook]
Data/spirou/lsd/lsd_order_mask.dat - add order wavelength file for lsd. [Neil Cook]
Core.instruments.*.default_constants.py - add polar lsd constants. [Neil Cook]
Data/spirou/lsd - add lsd masks and meta data. [Neil Cook]

0.5.108 (2019-11-07)¶

Science.telluric.general.py - curve fit forces floats - cast kp as bool after it was forced to floats. [Neil Cook]
Science.telluric.general.py - add breakpoint to investigate bug. [Neil Cook]
Tools.dev.cal_update_berv.py - re-fix erv measurement - group all files by odometer code. [Neil Cook]
Tools.dev.cal_update_berv.py - need to group files to make this quicker + skip those that use barycorrpy already. [Neil Cook]

0.5.107 (2019-11-06)¶

Recipe/spirou/obj_pol_spirou.py - continue adding to polar recipe. [Neil Cook]
Update language database. [Neil Cook]
Core.maths.*.py - add continuum calculation function. [Neil Cook]
Core.instruments.*.default_constants.py - add polar constants. [Neil Cook]

0.5.106 (2019-11-05)¶

Berv.py - set leap_update to False, add file update to cal_update_berv.py. [njcuk9999]
Update object_query_list. [njcuk9999]
Cal_update_berv.py - print filename processing. [njcuk9999]
Science.extract.berv.py - catch iers warning and display. [njcuk9999]
Science.extract.berv.py - split exception in barycorrpy and iers. [njcuk9999]
Science.extract.berv.py - add force=False (force recalculation of berv) [njcuk9999]
Science.extract.berv.py - add warn=False (when True prints exception when barycorrpy fails) [njcuk9999]
Merge remote-tracking branch ‘origin/dev’ into dev. [njcuk9999]

pirou_py3 into dev

# Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with ‘#’ will be ignored, and an empty message aborts # the commit.
Add cal_update_berv.py - to update bervs. [njcuk9999]
Add gui stuff. [njcuk9999]

0.5.105 (2019-11-03)¶

First commit of a gui module. [njcuk9999]
Add trigger place-holders. [njcuk9999]
Rename drs_reprocess –> drs_processing. [njcuk9999]
Rename drs_reprocess –> drs_processing. [njcuk9999]
Plotting.core.py - fix __NAME__ [njcuk9999]
Core.instruments.default.recipe_definitions.py - rename reprocess.py to processing.py. [njcuk9999]

0.5.104 (2019-11-01)¶

Science.calib.dark.py - rearrange steps. [njcuk9999]
Science.calib.dark.py - clean out data. [njcuk9999]
Science.calib.dark.py - replace median with a smart median (smaller) [njcuk9999]

0.5.103 (2019-11-01)¶

Io.drs_table.py - fix problem with hdu lists. [njcuk9999]
Tools.modules.setup.drs_reprocess.py - fix bug in keepmask for engineering files. [njcuk9999]
Drs_reprocess.py - fix error in remove engineering (fdata–>ftable) [Neil Cook]
Add option to listing code to regenerate rawindex.fits (for all raw files) [Neil Cook]
Add PI_NAME to raw columns in index files. [Neil Cook]

0.5.102 (2019-10-30)¶

Merge remote-tracking branch ‘origin/dev’ into dev. [njcuk9999]
Module.setup.drs_reprocess.py - add _remove_engineering option. [njcuk9999]
Core.core.drs_recipe.py - change break for continue if DrsRecipeException. [njcuk9999]

0.5.101 (2019-10-29)¶

Science.calib.localisation.py - remove break point. [Neil Cook]
Science.calib.localisation.py - pep8 add second blank line. [Neil Cook]
Test changes to localisation. [njcuk9999]
Update date/version/changelog. [Neil Cook]

0.5.100 (2019-10-28)¶

Science.telluric.general.py - catch all berv = nan (not allowed) [Neil Cook]
Science.telluric.general.py - should be using USE_BERV not BERV. [Neil Cook]
Berv update - add in additional barycorrpy parameters. [Neil Cook]
Update language database. [Neil Cook]
Science.telluric.general.py - catch bad berv value. [Neil Cook]
Update language database. [Neil Cook]
Science.extract.berv.py - correct setting use_berv from estimate. [Neil Cook]
Science.telluric.general.py - add break point to identify bug in _wave_to_wave. [Neil Cook]
Science.calib.wave.py - hc only solution has no CCF –> set CCF used keys to None. [Neil Cook]
Science.calib.wave.py - deal with header not having fiber kwarg (is a pp file header) [Neil Cook]
Science.calib.wave.py - need to add more empty constants for hc only wave sol. [Neil Cook]
Obj_pol_spirou.py - start filling out polarisation code (from SPIRou DRS) [Neil Cook]
Update language database. [Neil Cook]
Science.calib.wave.py - fix differing fiber values from header vs usefiber. [Neil Cook]
Plot_functions.py - only add suffix if kind is not None. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.099 (2019-10-25)¶

Science.polar.general.py - add PolarObj class and validate_polar_files + valid_polar_file functions. [Neil Cook]
Recipes.spirou.obj_pol_spirou.py - first commit - start filling out polar recipe. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add obj_pol_spirou. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.*.default_constants.py - add polar constants. [Neil Cook]
Plotting - fix loop_allowed switch. [Neil Cook]
Plotting.* - fix summary plots using plotloop. [Neil Cook]
Plotting.plot_functions.py - make sure all plots in loops update the filename. [Neil Cook]
Plotting.plot_functions.py - fix generators in plot_shape_angle_offset. [Neil Cook]
Flat_blaze - fix problem with SHAPE_ANGLE_OFFSET_ALL arguments. [Neil Cook]
Flat_blaze - make threshold for scut = 0.1 + add a cubic term to sinc function + adjust the flat/blaze rms calculation. [Neil Cook]
Science.calib.shape.py - try to fix bug with corr_dx_from_fp. [Neil Cook]
Science.calib.shape.py - remove breakpoint for lin_mini. [Neil Cook]
Cal_shape_master_spirou.py - add in breakpoint to address bug. [Neil Cook]
Core.math.general.py - fix linear_minimization (need to re-calculate shapes after masking) [Neil Cook]
Recipe.spirou.cal_shape_master_spirou.py + science.calib.shape.py - add breakpoint to identify crash. [Neil Cook]
Plotting.core.py - do not clean html warning messages and add text in one paragraph. [Neil Cook]
Science.calib.wave.py and plotting.plot_functions.py - add fiber to WAVE_FP_IPT_CWD_LLHC and SUM_WAVE_FP_IPT_CWID_LLHC plots. [Neil Cook]
Science.calib.wave.py and plotting.plot_functions.py - add fiber to WAVE_FP_IPT_CWD_LLHC and SUM_WAVE_FP_IPT_CWID_LLHC plots. [Neil Cook]
Cal_wave_spirou.py - fix hcprops not having fpprops values (for summary) + don’t base summary plot on pass/fail just fp_e2ds_file being set. [Neil Cook]
Core.math.fast.py - fix and catch jit (numba) [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.098 (2019-10-24)¶

Recipe.spirou.cal_wave_spirou.py + sciecne.calib.wave.py - add summary plot functionality. [Neil Cook]
Plotting.* - add summary plots. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add wave solution summary plots. [Neil Cook]
Flat_blaze.py and extraction.py - add sloping sinc fit for blaze and move summary/qc to modules. [Neil Cook]
Obj_fit_tellu_spirou, obj_mk_tellu_spirou and obj_mk_template_spirou - add telluric plotting. [Neil Cook]
Move summary + qc + writing to modules (not in main recipes) [Neil Cook]
Plotting.* - add telluric plots. [Neil Cook]
Update language database. [Neil Cook]
Core.math.general.py - add sloped sinc function. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add fit_tellu plots and mk_template plots. [Neil Cook]
Core.instruments.*.default_*.py - add blaze sinc constants + plotting constants for fit_tellu. [Neil Cook]
Misc - copy of Etiennes sinc function for blaze correction. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.097 (2019-10-23)¶

Science.velocity.general.py - change arguments (found_rv –> rv) [Neil Cook]
Science.telluric.general.py - add recipe to inputs (for plotting) [Neil Cook]
Science.calib.wave.py - fix plots + force wave modes to ints (were strings) [Neil Cook]
Recipe.obj_mk_tellu_spirou.py - add debug and summary plots. [Neil Cook]
Recipe.spirou.cal_loc_spirou.py - fix check coeffs (Etiennes fix) [Neil Cook]
Plotting.*.py - add mktellu plots, fix ioff in pdb, fix mask order in html, add warnings to summary document. [Neil Cook]
Plotting.*.py - add mktellu plots, fix ioff in pdb, fix mask order in html, add warnings to summary document. [Neil Cook]
Update the language database. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add mktellu plot outputs. [Neil Cook]
Core.instruments.*.default_constants.py - add wave and mktellu plot constants. [Neil Cook]
Drs_log.py - allow use of output_param_dict without updating parameter dictionary. [Neil Cook]

0.5.096 (2019-10-17)¶

Update language database. [Neil Cook]
Science.velocity.general.py - add rv_fit plot. [Neil Cook]
Science.calib.wave.py - add plotting. [Neil Cook]
Plotting.plot_functions.py - add wave plotting functions. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add wave plots (and a ccf plot) [Neil Cook]
Core.instruments.*.default_constants.py - add WAVE plot constants. [Neil Cook]
SpirouWAVE2.py - remove todo statement. [Neil Cook]

0.5.095 (2019-10-16)¶

Math.fast.py - rearrange imports. [Neil Cook]
Recipes/spirou/cal_loc_spirou.py - fix problems with clean loc coeffs. [Neil Cook]
Lin_mini_upgrade.py - raw source code from Etienne. [Neil Cook]
Plotting.plot_functions.py - close plots if we have an open (before plot loop) + fix loc ceoff plot. [Neil Cook]
Plotting.py - add self.plots_active (flag that is true when we have plots open in interactive mode) [Neil Cook]
Core.math.fast.py + general.py - add linear minimisation speed up using numba (if present on system) [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add master_run, calib_run and science_run (for trigger?) [Neil Cook]
Core.instruments.*.default_constants.py - add loc plot/clean up coeff constants. [Neil Cook]
Core.core.drs_recipe.py - in add_extras value can now be objects other than string –> re-test instance. [Neil Cook]
Core.core.drs_recipe.py - fix how we identify special list keys (arguments that come from params but are lists) [Neil Cook]
Core.core.drs_recipe.py - fix new_runs in _gen_run. [Neil Cook]
Core.core.drs_recipe.py + tools.module.setup.drs_reprocess.py - deal with multiple extra arguments better (from sequences) [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - obj_mk_template need objname arguments. [Neil Cook]

0.5.094 (2019-10-15)¶

Core.instruemnts.spirou.recipe_definitions.py - fix the full run and remove science run sequences. [Neil Cook]
Core.instruemnts.spirou.recipe_definitions.py - add back mk and fit tellu limited run individual commands (for object specific) [Neil Cook]
Science.calib.wave.py - remove interactive plot sections and add WAVE_HC_GUESS plot. [Neil Cook]
Science.calib.shape.py - deal with norm_fp being zero (skip) [Neil Cook]
Science.calib.localisation.py - add check_coeffs function. [Neil Cook]
Recipe.spirou.cal_loc_spirou.py - check coefficient and sigma clip / smooth them between orders. [Neil Cook]
Plotting.plot_functions.py - add plot_loc_check_coeffs and plot_wave_hc_guess. [Neil Cook]
Core.math.general.py - add robust_polyfit. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add loc and wave plots. [Neil Cook]
Core.instruments.*.default_constants.py - add loc and wave plot constants. [Neil Cook]
Plotting - make sure location is set in all recipes. [Neil Cook]

0.5.093 (2019-10-14)¶

Core.instruments.spirou.recipe_definitions.py + recipes.spirou.obj_fit_tellu_spirou.py - must add s1d plot args to fit_tellu. [njcuk9999]

0.5.092 (2019-10-13)¶

Plotting.core.py + latex.py - update layout for stat + qc tables + try to latex floating orders. [Neil Cook]
Update language database. [Neil Cook]
Science.extract.general.py - add fiber to e2ds_to_s1d inputs (for plotting) [Neil Cook]
Plotting.*.py - continue work on plotting. [Neil Cook]
Core.instruments.spirou.default_constants.py - adjust extract s1d zoom parameters. [Neil Cook]
Recipe.spirou.*.py - add recipe.plot.set_location (need iterator) [Neil Cook]
Plotting.plot_functions.py - remove full spectrum plot (too big) [Neil Cook]
Science.extract.general.py - move qc and file writing to functions. [Neil Cook]
Cal_extract_spirou.py - add plots + summary document. [Neil Cook]
Plotting.plot_functions.py - add extraction plots. [Neil Cook]
Plotter.core.py - update test case. [Neil Cook]
Update object query list file. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add plot definitions to recipe. [Neil Cook]
Core.instruments.*.default_constants.py - add extract plot constants. [Neil Cook]
Core.core.drs_recipe.py - correct problem with recipes that have no file arguments (were just being skipped) [Neil Cook]
Core.core.drs_file.py - correct a problem with using fibers = [None] [Neil Cook]
Plotting.core.py - fix the addition of fibers to qc_params and stat table. [Neil Cook]

0.5.091 (2019-10-11)¶

Add a section to how to (to fill in later) [Neil Cook]
Science.calib.shape.py - move qc and file writing to module + todo identified problem. [Neil Cook]
Science.calib.localisation.py - move qc and file writing to module. [Neil Cook]
Science.calib.flat_blaze.py - move qc and file writing to module. [Neil Cook]
Recipe.spirou. badpix, dark, flat, loc, shape, shape_master - add plotting. [Neil Cook]
Plotting.*.py - continue adding plotting functionality. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add plots to shape and flat recipes. [Neil Cook]
Core.math.general.py - fix sigfig (deal with zero and non-finites) [Neil Cook]
Core.instruments.*.default_constants.py - add plotting constants. [Neil Cook]

0.5.090 (2019-10-10)¶

Recipe.spirou.cal_shape_master_spirou.py + science.calib.shape.py - add plots. [Neil Cook]
Recipe.spirou.cal_loc_spirou.py - fix typo in qc. [Neil Cook]
Plotting.*.py - continue work on plotting functionality. [Neil Cook]
Core.math.general.py - add the sigfig function. [Neil Cook]
Update the language database. [Neil Cook]
Core.instruments.spirou.recipe_defintions.py - add some plots to cal_shape_master. [Neil Cook]
Core.instruments.*.default_constants.py - add plot constants. [Neil Cook]

0.5.089 (2019-10-10)¶

Continue adding plotting. [Neil Cook]
Update how to terrapipe guide. [Neil Cook]
Update language database. [Neil Cook]
Data.core..pdbrc - need to go up two levels (up via exception) [Neil Cook]
Core.isntruments.spirou.recipe_definitions.py - add loc graphs. [Neil Cook]
Core.instruments.*.default_constants.py - add plot constants. [Neil Cook]
Core.core.drs_startup.py - change plotter –> plot, move end plotting to plotter. [Neil Cook]
Core.core.drs_recipe.py - change plotter –> plot. [Neil Cook]
Core.constants.param_functions.py - fix ipdb exception on exit. [Neil Cook]

0.5.088 (2019-10-08)¶

Tools.module.setup.drs_reprocess.py - add plot closing and fix bugs with nightname/str_arg_list and self.recipe.args. [Neil Cook]
Reprocess.py + telluric_db recipes - change how process_run_list works (now needs recipe) [Neil Cook]
Recipe.spirou.cal_dark_spirou.py - add plots. [Neil Cook]
Recipe.spirou.cal_badpix_spirou.py - add plots. [Neil Cook]
Plotting.*.py - add html, fix some latex issues and add dark/badpix plot definitions. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add debug/summary plot definitions to cal_dark and cal_badpix. [Neil Cook]
Core.instruments.default.pseudo_const.py - fix night name in index_lock_filename definition. [Neil Cook]
Core.instruments.output_filenames.py - fix nightname. [Neil Cook]
Core.instruments.*.defaul_* - add plotting constants. [Neil Cook]
How_to_terrapipe.md - add readme file on how to develop using terrapipe. [Neil Cook]
Core.core.drs_recipe.py add set_debug_plots and set_summary_plots. [Neil Cook]

0.5.087 (2019-10-07)¶

Core.constants.param_functions.py - if breakpoints does not have params force allow_breakpoints. [Neil Cook]

0.5.086 (2019-10-06)¶

Tools.module.setup.drs_reprocess.py - deal with input nightname and filename. [njcuk9999]
Science.calib.wave.py - change ‘night_name’ to nightname. [njcuk9999]
Update language database. [njcuk9999]
Core.core.drs_recipe.py - remove breakpoint. [njcuk9999]
Core.instruments.default.default_config.py - add allow_breakpoints constant. [njcuk9999]
Core.core.drs_recipe.py + drs_startup.py - add breakpoint special argument. [njcuk9999]
Core.core.drs_argument.py - add breakpoint special argument. [njcuk9999]
Core.constants.constant_functions.py - add break point to allow stopping at certain point in the code easily. [njcuk9999]
Core.constants.__init__.py - add break point to aliases. [njcuk9999]

0.5.085 (2019-10-05)¶

Tools.module.setup.drs_reprocess.py - add filename and nightname from inputs. [njcuk9999]
Replace . imports with terrapipe imports. [njcuk9999]
Plotting.core.py - replace . imports with terrapipe + store debug plots. [njcuk9999]
Locale.core.*.py - replace . imports with terrapipe imports. [njcuk9999]
Update language database. [njcuk9999]
Io.*.py - replace . imports with terrapipe imports. [njcuk9999]
Core.__init__.py - replace . imports with terrapipe imports. [njcuk9999]
Core.math.* - replace . imports with terrapipe imports. [njcuk9999]
Core.instruments.default.file_definitions.py - remove call to output_filenames. [njcuk9999]
Core.instruments.*.recipe_definitions.py - remove drs_interactive and add filename to reprocess definition. [njcuk9999]
Core.instruments.*.default_config - remove drs_interactive and add drs_plot_ext and drs_summary_ext. [njcuk9999]
Core.core.* - remove . imports and add plotter to drs_startup. [njcuk9999]
Core.core.__init__.py - remove imports. [njcuk9999]
Core.constants - move . imports to terrapipe imports. [njcuk9999]

0.5.084 (2019-10-04)¶

Update language database. [Neil Cook]
Core.core.drs_recipe.py - record sys.argv to self.str_arg_list if not from fkwargs. [Neil Cook]
Plotting - add in latex functions and summary plot. [Neil Cook]

0.5.083 (2019-10-03)¶

Tools.modules.setup.drs_reprocess.py - change closeall (now in plotter) [Neil Cook]
Modify inputs to core.post_main (tools) [Neil Cook]
Modify inputs to core.post_main (tools) [Neil Cook]
Continue work on plotting functions. [Neil Cook]
Update language database. [Neil Cook]
Io.drs_path.py - add makedirs function. [Neil Cook]
Core.core.drs_startup.py - remove call to plotter module (and get via recipe) [Neil Cook]
Change inputs to core.post_main() [Neil Cook]
Start work on plotting. [Neil Cook]
Update the language database. [Neil Cook]
Core.instruments.spirou.py - only calculate ccf for science targets. [Neil Cook]
Core.core.drs_file.py - fix type keyword in check_table_filename should be “allowedfibers” not “fiber” [Neil Cook]
Core.instruments.spirou.default_constants.py - change default ccf width to 300 km/s. [Neil Cook]
Update object list. [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - add ccf to limited run. [Neil Cook]
Core.instruments.default.output_filenames.py - need to re-get insuffix in fiber loop. [Neil Cook]
Core.core.drs_file.py - fix adding fiber to historic files. [Neil Cook]
Update changelog/version/date. [Neil Cook]
Update object list. [njcuk9999]

0.5.082 (2019-10-02)¶

Tools.module.setup.drs_reprocess.py - deal with traceback as a list or string. [Neil Cook]
Science.telluric.general.py - fix bug if we have template must divide image by it! [Neil Cook]
Science.calib.wave.py - check for empty wfp variables and set to None. [Neil Cook]
Recipe.spirou.cal_extract_spirou.py - correct typo in text entry. [Neil Cook]
Recipe.spirou.cal_ccf_spirou.py - add saving of files (via write_ccf) [Neil Cook]
Update language database. [Neil Cook]
Update object list. [Neil Cook]
Core.instruments.spirou.file_definitions.py + recipe_defintions.py - add out_ccf_fits. [Neil Cook]
Core.instruments.*.default_keywords.py - add CCF keywords. [Neil Cook]
Core.constants.param_functions.py - correct typo in merge function “source” –> “sources” [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.081 (2019-10-01)¶

Science.velocity.general.py - add locate_reference_file function and work on calculating ccf (now combining with nanmean) [Neil Cook]
Science.telluric.general.py - add make_1d_template_cube and mk_1d_template_write functions. [Neil Cook]
Science.extract.berv.py - add option not to log obtaining berv (log=True/False) [Neil Cook]
Science.calib.wave.py - get wave time in wprops. [Neil Cook]
Recipe.spirou.obj_mk_template_spirou.py - add s1d template code to mk_template. [Neil Cook]
Recipe.spirou.cal_ccf_spirou.py - start adding in ccf fp stuff. [Neil Cook]
Update language database. [Neil Cook]
Io.drs_fits.py - correct typo “fornat” –> “format” [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add s1d files to set outputs. [Neil Cook]
Core.instruments.spirou.file_definitions.py - add the s1d template files + s1d lists for e2ds files. [Neil Cook]
Core.instruments.*.default_constants.py - add new mk_template constants. [Neil Cook]
Core.core.drs_file.py - add s1d property and fix shape for table. [Neil Cook]

0.5.080 (2019-09-30)¶

Tools.module.setup.drs_reprocess.py - fix error in printing errors at end (and add these errors to the log properly) [Neil Cook]
Core.core.drs_log.py - add wlog.logmessage (to manually add a message to the log file) [Neil Cook]
Neil_TODO.md - update list. [Neil Cook]
Terrapipe.science.velocity.general.py - add test plots while ccf is not working. [Neil Cook]
Terrapipe.recipes.spirou.py - add TEST_RUN to obj_fit_tellu_db_spirou and obj_mk_tellu_db_spirou and uncomment mk_obj_template. [Neil Cook]
Update language database. [Neil Cook]
Terrapipe.io.drs_fits.py - make sure values are striped of whitespaces before comparison. [Neil Cook]
Core.core.recipe_definition.py - add obj_mk_telludb and obj_fit_telludb instead of obj_mk_tellu/obj_fit_tellu and obj_mk_template. [Neil Cook]
Tools.module.setup.drs_reprocess.py - deal with adding extra arguments to reprocessing recipes. [Neil Cook]
Science.calib.wave.py - remove maxcpp references. [Neil Cook]
Core.core.drs_recipe.py - add extras to recipe (to overwrite arguments from reprocessing) [Neil Cook]
Core.core.drs_log.py - update debugging in print function mode. [Neil Cook]
Core.core.drs_file.py - do not continue if not valid. [Neil Cook]
Update language database. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.079 (2019-09-26)¶

Tools.module.setup.drs_reprocess.py - take out pushing skip to recipes and add in pushing debug to recipes, rename DEBUG –> TEST_RUN to do a test run. [Neil Cook]
Sciecne.velocity.general.py - new ccf calculation functions + work on ccf for science/fp. [Neil Cook]
Science.preprocessing.detectory.py - remove unused functions/imports. [Neil Cook]
Science.calib.wave.py - clean up and move ccf stuff to velocity module. [Neil Cook]
Cal_preprocess_spirou.py - pep8 empty line clean up. [Neil Cook]
Cal_ccf_spirou.py - remove nan filling and copy image from infile when tellurics are not removed. [Neil Cook]
Update language database. [Neil Cook]
Add Etiennes ccf mask for Gl699. [Neil Cook]
Update run files. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add mask file definition and add path in –mask kwarg. [Neil Cook]
Core.instruments.*.pseudo_const.py - add FIBER_CCF (defines what is a science fiber and what is a reference fiber for CCF calculation. [Neil Cook]
Core.instruments.*.default_constants.py + default_keywords.py - fix/modify constants/keywords for wavecff/ccf. [Neil Cook]
Core.core.drs_startup.py - _get_arg_strval: deal with DrsInputFile as well as DrsFitsFile. [Neil Cook]
Core.core.drs_recipe.py - add display_func and deal with no drs_files added to files when dtype=file/files, add function _check_arg_path. [Neil Cook]
Core.core.drs_log.py - find_param: add required and default inputs (and allow them to return without error) [Neil Cook]
Core.core.drs_file.py - add methods has_correct_extension, header_keys_exist, has_correct_header_keys, read, write for DrsInputFile. [Neil Cook]
Core.core.drs_argument.py - need to deal with drsfiles being a single drsfile + add attribute “path” [Neil Cook]
Core.instruments.spirou.default_constants.py - do not force get the wave solution from the calibDB (use header) [Neil Cook]
Core.instruments.spirou.default_constants.py - default wave mode now C Lovis method. [Neil Cook]
Science.telluric.general.py - for drs_data.load_text_file must define dtype. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.078 (2019-09-25)¶

Misc.mk_template_s1d.py - etiennes code to be added to mk_template. [Neil Cook]
Recipe_definitions.py - only process e2dsff files for obj_mk_tellu and obj_fit_tellu. [Neil Cook]
Core.drs_file.py - make sure tested keys have no white spaces at start/end and all are upper case (case insensitive) [Neil Cook]
Science.velocity.general.py - coravelation - fix reporting of number of lines found. [Neil Cook]
Science.calib.wave.py - change name of fp_wavelength_sol_new to add_fpline_calc_cwid, remove unused outputs of assign_abs_fp_numbers, make two method consistent with FP equation d = m * ll/2, fix no_overlap_match_calc, and try to fix NaNs in fp e2ds for ccf calculation. [Neil Cook]
Add cavity length ll and m fit files to data. [Neil Cook]
Update language database. [Neil Cook]
Recipes.spirou.cal_wave_spirou.py - print that we are updating hc/fp files with new wave solution. [Neil Cook]
Io.drs_data.py - load text file needs to default to floats in an array. [Neil Cook]
Core.instruments.spirou.default_keywords.py - correct typos in keywords. [Neil Cook]
Core.instrument.*.default_constants.py - cavity_length_m_fit.dat. [Neil Cook]

0.5.077 (2019-09-24)¶

Science.velocity.general.py - add compute_ccf_sciecne and fill_e2ds_nans functions (continued work on cal_ccf_spirou) [Neil Cook]
Science.calib.wave.py - add some extra wave keys (from ccf process) [Neil Cook]
Cal_wave_spirou.py - add a TODO for cal_wave_spirou. [Neil Cook]
Recipe.spirou.cal_ccf_spirou.py - continue to port code from SpirouDRS –> terrapipe. [Neil Cook]
Update language database. [Neil Cook]
Core.isntruments.spirou.recipe_definitions.py - correct typo in cal_wave -fpmode definitions (found by @melissa-hobson) [Neil Cook]
Core.instruments.*.default_constants.py + default_keywords.py - add CCF/RV keys. [Neil Cook]
Core.core.drs_file.py - add option in read_header_key_1d_list to try to guess dim1 (if manually set to None) [Neil Cook]
Core.constants.param_functions.py - add merge function (to merge one param dict into another) [Neil Cook]
Tools.module.setup.drs_reprocess.py - fix how we set infile.filetype (look at output.intype and deal with None/list/str) [Neil Cook]

0.5.076 (2019-09-23)¶

Science.telluric.general.py - re calculate tapas_water and tapas_other after shift. [Neil Cook]
Science.extract.general.py - fix s1d how we interpolate over NaN gaps. [Neil Cook]
Core.instruments.spirou.file_definitions.py/recipe_definitions.py - fix intypes for file definitions and tellu default_refs. [Neil Cook]
Udpate object list. [Neil Cook]
Core.instruments.spirou.default_keywords.py - fix KW_MKTELL_AIRMASS/WATER values. [Neil Cook]
Core.instruments.*.default_constants - change telluric filetype/dprtype/fiber type definitions. [Neil Cook]
Core.core.drs_log.py - always have log file (put it in home directory) [Neil Cook]
Update changelog/date/version. [Neil Cook]

0.5.075 (2019-09-20)¶

Tools.module.setup.drs_reprocess.py - set filemod and recipemod for srecipes that do not have them set. [Neil Cook]
Science.telluric.general.py - guess the sed that goes in (not just ones) + sigma clip around fit_dd + add a bad mask for sp2 (set to NaN) [Neil Cook]
Drs_recipe.py - for process adds method (in DrsRunSequence) add filemod and recipemod is frecipe does not have them set. [Neil Cook]
Update object_query_list. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.074 (2019-09-19)¶

Science.telluric.general.py - add an upper and lower limit to keep for the pca fit. [Neil Cook]
Science.extract.general.py - fix some minor bugs + pep8 correction. [Neil Cook]
Calib.wave.py, velocity module - change module rv–> velocity, add remove_telluric_domain function. [Neil Cook]
Recipe.spirou.cal_extract_spirou.py - add KW_EXT_TYPE. [Neil Cook]
Recipe.spirou.cal_ccf_spirou.py - first commit + testing of inputs. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - change –add2calib to –database, add cal_ccf definition. [Neil Cook]
Core.instruments.*.default_constants.py + default_keywords.py - add first CCF constants. [Neil Cook]
Core.core.drs_startup - change p to param. [Neil Cook]
Core.core.drs_database.py - add a check for params[‘INPUTS’][‘DATABASE’] to check whether we should save to database when add_file is used. [Neil Cook]
Core.constants.param_functions.py - deal with copying ParamDict inside ParamDict. [Neil Cook]
Update language database. [Neil Cook]
Io.drs_lock.py - add debug printout for locking. [Neil Cook]
Core.math.fast.py - bn.nansum return bool arrays as bools we don’t want this. [Neil Cook]
Core.core.drs_log.py - only turn off wrapping for debug wlog entries. [Neil Cook]
Core.core.drs_database.py - move locking/checking into copy db file function. [Neil Cook]
Update changelog.md. [Neil Cook]
Tools.module.setup.drs_reprocess.py - add shortname to Run class, check that all recipes in run table are valid, print group name (recipe short name) on group print out. [Neil Cook]
Update language database. [Neil Cook]
Core.math.gauss.py - mp references should be “fast” references within math module. [Neil Cook]
Core.instruments.spirou.py - remove unused recipes + give names to wavehc and wavefp. [Neil Cook]
Core.core.drs_recipe.py - process_adds should look for [‘files’, ‘file’] in arg dtype. [Neil Cook]
Core.core.drs_log.py - params may be None - deal with this. [Neil Cook]
Drs_database.py - lock the input and output files before copying to database. [Neil Cook]
Recipes.spirou.cal_loc_spirou.py - need to import math as mp. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.073 (2019-09-18)¶

Core.math - add a fast medfilt_1d function. [Neil Cook]
Core.math.fast.py - first commit numpy nan functions from bottleneck if available. [Neil Cook]
Change nan numpy functions to mp.nan functions (use bottleneck if available for speed up) [Neil Cook]
Science.calib.shape.py - test cube as array. [Neil Cook]
Science.calib.shape.py - add length of cube for printout. [Neil Cook]
Science.calib.shape.py - add printouts to check. [Neil Cook]
Science.calib.shape.py - set transforms/xres/yres to zero. [Neil Cook]
Science.calib.shape.py - test the fpmaster loop (without long parts) [Neil Cook]
Update date/changelog/version. [Neil Cook]

0.5.072 (2019-09-17)¶

Tools.bin.reset.py - remove instrument re-definition (now done in core.setup) [Neil Cook]
Science.telluric.general.py - change KW_DPRTYPES –> KW_DPRTYPE. [Neil Cook]
Science.calib.shape.py - add filename and basename (just for printing/logging) [Neil Cook]
Recipes.spirou.obj_fit_tellu_db_spirou.py - fix inputs. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - fix kwargs –objname. [Neil Cook]
Core.core.drs_argument.py - checks for arg/kwarg/special arg on naming - kwarg and special should have ‘-’ positional should not. [Neil Cook]
Science.core.shape.py - correct type fpfile_it.image –> fpfile_it.data. [Neil Cook]
Correct vstack_cols (needs to handle single row as well as astropy table) [Neil Cook]
Science.telluric.general.py - change function get_objects to get_non_tellu_objs and generalise. [Neil Cook]
Recipes.spirou.obj_fit_tellu_db_spirou.py - get dprtypes and robjnames in main code. [Neil Cook]
Science.calib.shape.py - calibrate after combining group of FPs. [Neil Cook]
Core.insturments.spirou.recipe_definitions.py - change default to None. [Neil Cook]
Science.telluric.general.py - add function get_objects to get non telluric objects. [Neil Cook]
Recipe.spirou.obj_fit_tellu_db_spirou.py - first commit (mostly just copy of obj_mk_tellu_db_spirou) but does fit_tellu, mk_template, fit_tellu on all objects except telluric stars) [Neil Cook]
Recipe.spirou.obj_mk_template_spirou.py - add ending script when files are skipped. [Neil Cook]
Recipes.spirou.obj_mk_tellu_db_spirou.py - remove todo (dealt with internally) [Neil Cook]
Update the language database. [Neil Cook]
Core.io.drs_table.py - lock the index file when reading (and don’t try to open when closing) [Neil Cook]
Io.drs_fits.py - update find_files to allow returning of a astropy table for all files found (a stack of the valid entries in the index files) [Neil Cook]
Core.instruments.spirou.recipe_deinfitoins.py - fix help files + add obj_fit_tellu_db + add options to feiltypes and fiber arguments. [Neil Cook]
Cpre.instruments.default.pseudo_const.py - remove EXT_TYPE (and add DPRTYPE) to list of indexing columns. [Neil Cook]
Core.instruments.*.default_* - add telluric db keys. [Neil Cook]
Core.core.drs_recipe.py - make vstack a public function and change how coluns are added (via list comprehension) [Neil Cook]

0.5.071 (2019-09-16)¶

Tools.module.setup.drs_reprocess.py - add generate_run_table to generate run_table from a set of args/kwargs. [Neil Cook]
Tools.module.listing.general.py - functions for listing.py. [Neil Cook]
Tools.bin.listing.py - first commit - code to re-index directories. [Neil Cook]
Recipes.spirou.obj_mk_template_spirou.py - correct typo (get filetype and fiber from inputs) [Neil Cook]
Recipe.spirou.obj_mk_tellu_db_spirou.py - first commit. [Neil Cook]
Io.drs_fits.py - correct typo and add required switch to get_index_files. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.spirou.recipe_defintions.py - add mk_tellu_db and obj_fit_tellu_db. [Neil Cook]
Core.instruments.default.recipe_definitions.py - add listing recipe. [Neil Cook]
Core.core.drs_startup.py - make indexing and save_index_file non private functions. [Neil Cook]
Core.core.drs_recipe.py - test log message in group_run_files + remove old olg test message. [Neil Cook]
Core.core.drs_recipe.py - change how we stack tablelist. [Neil Cook]
Core.core.drs_recipe.py - test wlog statements. [Neil Cook]
Core.core.drs_recipe.py - test wlog statements. [Neil Cook]
Core.core.drs_recipe.py - add print statements. [Neil Cook]
Tools.module.setup.drs_reprocess.py - add nightname for all (for when ftable is empty) [Neil Cook]
Tools.module.listing.file_explorer.py - change where params comes from. [Neil Cook]
Io.drs_table.py - try to fix index file error. [Neil Cook]
Core.core.drs_startup.py - remove unused import. [Neil Cook]
Core.core.drs_recipe.py - clear printer after printing filenames. [Neil Cook]
Science.preprocessing.identification.py - need kind to be set (even if file not found) for error message. [Neil Cook]
Science.calib.shape.py - need to only copy extract parameters for those that are not skiped. [Neil Cook]
Io.drs_table.py - remove table before writing it (to try to get rid of “file exists” error) [Neil Cook]
Add “runs” folder to data. [Neil Cook]
Update date/version/changelog. [Neil Cook]
Science.extract.berv.py - fix bug that berv will be set to NaN if coming from header (need to check both key and output[0] for kwargs) [Neil Cook]
Core.instruments.default.pseudo_const.py - fix bug that p is locked (so set manually) [Neil Cook]
Drs_changelog.py - fix bug in updating version/date. [Neil Cook]

0.5.070 (2019-09-13)¶

Tools.bin.reprocess.py - change how master table is defined (keys ‘KW_MID_OBS_TIME’ and ‘KW_DPRTYPE’ need values creating as not in raw file headers), filters need to check for lists. [Neil Cook]
Science.telluric.general.py - add some new logging. [Neil Cook]
Sciecne.calib.dark.py - add some new logging for dark master creation. [Neil Cook]
Recipes.spirou.obj_fit_tellu_spirou.py - change how image2 is normalised by blaze (not the same as mk_tellu) [Neil Cook]
Update language database. [Neil Cook]
Io.drs_fits.py - add get_dprtype. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - move filemod to pseudo consts + add KW_DPRTYPE to limited run for fit_tellu/mk_tellu. [Neil Cook]
Core.instruments.spirou.py - add some new intypes. [Neil Cook]
Core.instruments.*.pseudo_const.py - add FILEMOD and RECIPEMOD definitions. [Neil Cook]
Core.instruments.*.default* - add end of file and debug constants. [Neil Cook]
Core.core.drs_startup.py - get filemod and recipemod from pseudo constants (and re-get them if we change instrument) [Neil Cook]
Core.core.drs_recipe.py - add some display_func, and debug logging + add params to check_table_keys. [Neil Cook]
Core.core.drs_log.py - add display_func and put debug numbers into params (not hard coded) [Neil Cook]
Core.core.drs_file.py - add generate_reqfiles (for checking infile name in construct_filename) [Neil Cook]
Science.calib.dark.py - add some extra print outs. [Neil Cook]
Core.instruments.spirou.file_definitions.py - fix bad shape intypes (some should be hc1_hc1 not fp_fp) [Neil Cook]
Core.core.drs_recipe.py - when running a master recipe only do one run (multiple are not needed) [Neil Cook]
Tools.module.setup.drs_reprocess.py - add changes to generate_runs and add allowed fibers getting. [Neil Cook]
Sciecne.telluric.general.py - change message in recon s1d writing. [Neil Cook]
Sciecne.extract.berv.py - fix berv - properties weren’t copying. [Neil Cook]
Sciecne.calib.background.py - do not check file for debug (could be any input file and we don’t care here) [Neil Cook]
Update language database. [Neil Cook]
Io.drs_fits.py - add changes to RAW_OUTPUT_KEYS/REDUC_OUTPUT_KEYS. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - change sequences (must start with full preprocess - master dark + master shape wont work otherwise) [Neil Cook]
Core.instruments.spirou.file_definitions.py - add intypes to all out files (for file history lookup) [Neil Cook]
Core.instruments.spirou.default_keywords.py - KW_OBJNAME from OBJNAME –> OBJECT. [Neil Cook]
Core.instruments.default.pseudo_const.py - re-work output columns (now only output_keys) [Neil Cook]
Core.instruments.default.py - add additional features to general output file (infile suffix removal) [Neil Cook]
Core.core.drs_startup.py - change how we index using raw and reduc output columns –> keys (allows more flexible changing of header keys without rewriting full index) [Neil Cook]
Core.core.drs_recipe.py - fix how we generate file names for runs (follow file history) [Neil Cook]
Core.core.drs_file.py - add remove insuffix, control better construct filename. [Neil Cook]
Recipes.spirou.cal_extract_spirou.py + cal_flat_spirou.py - transform localisation coefficients to master grid. [Neil Cook]
Science.calib.shape.py - add ea_transform_coeff function to transform per night localisation coefficients to master grid. [Neil Cook]
Science.extract.berv.py - fix problem when we don’t have BERV variables (set header keys to None) [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - update shortname of fit_tellu. [Neil Cook]
Update language database. [Neil Cook]
Toolts.module.setup.drs_reprocess.py - deal with fact RunSequence recipes are lost after generation (run must take inrecipe when recipe is given) [Neil Cook]
Toolts.module.setup.drs_reprocess.py - deal with fact RunSequence recipes are lost after generation (run must take inrecipe when recipe is given) [Neil Cook]
Toolts.module.setup.drs_reprocess.py - take out stop just use event.is_set. [Neil Cook]
Toolts.module.setup.drs_reprocess.py - deal with recipe finishing (but not successfully) [Neil Cook]
Toolts.module.setup.drs_reprocess.py - extra stopping criteria added. [Neil Cook]
Toolts.module.setup.drs_reprocess.py - extra stopping criteria added. [Neil Cook]
Toolts.module.setup.drs_reprocess.py - make master stop at exception always. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.069 (2019-09-11)¶

Science.extract.general.py - fix loading of tapas (in thermal correction 1) [Neil Cook]
Science.extract.berv.py - fix how berv is obtained from header. [Neil Cook]
Science.calib.wave.py - add a way to get dimensions from header (NAXIS2 and NAXIS1) if image (via infile) is not defined. [Neil Cook]
Recipe.spirou.obj_fit_tellu_spirou.py + obj_mk_tellu_spirou.py + obj_mk_template_spirou.py - continue work on telluric functions (SpirouDRS –> terrapipe) [Neil Cook]
Recipe.spirou.cal_extract_spirou.py - add fiber key to header. [Neil Cook]
Locale.core.drs_text.py - add way to deal with TextEntry args being a int/float/bool (still not a list)–> list. [Neil Cook]
Update language database. [Neil Cook]
Io.drs_fits.py - fix find_files (now deals with having a fiber filter as well) [Neil Cook]
Io.drs_data.py - return both table and outfilename in load_tapas function. [Neil Cook]
Data.spirou.reset.telludb.master_tellu_SPIROU.txt - add objname to default telluDB entries. [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add outputs to telluric recipes. [Neil Cook]
Core.instruments.spirou.pseduo_const.py - fix typo in bervmaxest key. [Neil Cook]
Core.instruments.spirou.file_definitions.py - make adjustments to telluric files. [Neil Cook]
Core.instruments.default.output_filenames.py - allow suffix to be added to set_file. [Neil Cook]
Core.instruments.*.default_constants/default_keywords - add missing make_tellu, fit_tellu and make_template constants/keywords. [Neil Cook]
Core.core.drs_file.py - by default overwrite data if already read in DrsFitsFile.read() [Neil Cook]
Core.core.drs_database.py - add objname to telludb column. [Neil Cook]
Tools.module.setup.drs_reprocess.py = add total time calculation. [Neil Cook]
Science.telluric.general.py - add make_template_cubes placeholder. [Neil Cook]
Recipe.spirou.obj_mk_template_spirou.py - first commit - port from SpirouDRS. [Neil Cook]
Recipe.spirou.cal_dark_master/cal_spirou_master - update call to find_files. [Neil Cook]
Recipe.spirou - add KW_OUTPUT (needs to be added everywhere we copy_hdict to separate different files) [Neil Cook]
Update language database. [Neil Cook]
Io.drs_fits.py - remove find_filetypes and add (more generic) find_files function. [Neil Cook]
Core.instrumets.spirou.py - add in obj_mk_template. [Neil Cook]
Core.instruments.*.default_constants.py - add in mk_template constants. [Neil Cook]
Core.core.drs_database.py - add in default mode (CALIB_DB_MATCH) [Neil Cook]
Core.constants.constant_functions.py - for bool arguments make sure they are strings to do .lower and change second if to elif. [Neil Cook]
Core.core.drs_file.py - update pep8 remove redundant lines. [Neil Cook]
Update version/date/changelog. [Neil Cook]

0.5.068 (2019-09-10)¶

Tools.modlue.setup.drs_reprocess.py - load “adds” when checking sequences (taken out of recipe init) [Neil Cook]
Science.extract.berv.py - do not report estimate used when we are meant to be return no berv. [Neil Cook]
Science.calib.general.py + science.telluric.general.py - need to enumerate around entries. [Neil Cook]
Locale.core.drs_text.py - cache data - do not load a textdict again for an instrument (now cached) [Neil Cook]
Core.math.gauss.py - import general (for fwhm) [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add obj_mk_temp. [Neil Cook]
Drs_recipe.py - remove second deep copy (now copied internally to constants.load) [Neil Cook]
Core.core.drs_file.py - replace KW_DRS_QC with params[‘KW_DRS_QC’][0] [Neil Cook]
Core.core.drs_argument.py - move textdict loading to error handling (only needed here) [Neil Cook]
Core.constants.param_functions.py - add caches to speed up loading. [Neil Cook]
Update language database. [Neil Cook]
Rename obj_mk_tellu and obj_fit_tellu (add _spirou suffix) [Neil Cook]
Make recipes executable. [Neil Cook]
Update language database. [Neil Cook]
Obj_fit_tellu.py + obj_mk_tellu.py - keep porting telluric code from SpirouDRS. [Neil Cook]
Recipe.spirou - pep8 changes. [Neil Cook]
Core.math.__init__.py - add fwhm alias. [Neil Cook]
Core.instruments - add telluric constants/keywords/definitions. [Neil Cook]

0.5.067 (2019-09-06)¶

Science.extract.berv.py - add additional flag for when estiamte is used/not used. [njcuk9999]
Extract.berv.py - add USE_BERV, USE_BJD and USE_BERV_MAX to berv props (these are the ones that should be used and will be either estimate or barycorrpy values. [njcuk9999]
Science.telluric.general.py - add gen_abso_pca_calc, shift_all_to_frame and calc_recon_and_correct functions. [njcuk9999]
Obj_fit_tellu.py - continue porting content from SpirouDRS to terrapipe. [njcuk9999]
Update language database. [njcuk9999]
Core.core.drs_database.py - add default parameters to get_db_file. [njcuk9999]

0.5.066 (2019-09-05)¶

Obj_fit_tellu.py - update how far we have got. [njcuk9999]
Update language database. [njcuk9999]
Science.calib and science.extract - fix calls to load_calib_file. [njcuk9999]
Obj_fit_tellu.py/obj_mk_tellu.py - continue to port from SpirouDRS to terrapipe. [njcuk9999]
Core.io.drs_path.py - add ‘get_most_recent’ function. [njcuk9999]
Core.instruments - add mk_tellu constants/keywords. [njcuk9999]
Core.core.drs_database.py - change how loading works (rearrange functionality) [njcuk9999]
Obj_fit_tellu.py - start to copy over code from SpirouDRS to terrapipe. [njcuk9999]

0.5.065 (2019-09-04)¶

Update language database. [njcuk9999]
Core.core.drs_file.py - add overall pass/fail QC key. [njcuk9999]
Obj_mk_tellu.py - continue work on adding SpirouDRS code to terrapipe. [njcuk9999]
Cal_loc_spirou.py - remove blank space. [njcuk9999]
Core.instruments - add mk_tellu constants. [njcuk9999]
Update language database. [njcuk9999]
Science.rv.general.py - remove empty lines. [njcuk9999]
Recipe.spirou.obj_mk_tellu.py - continue copying over SpirouDRS code (obj_mk_tellu) [njcuk9999]
Core.maths - split out some functions into own scripts (separate from general.py) [njcuk9999]
Core.instruments.spirou.py - add obj_mk_tellu an obj_fit_tellu as DrsRecipes. [njcuk9999]
Core.core.drs_database.py - add option to get header from database file. [njcuk9999]

0.5.064 (2019-09-02)¶

Science.calib.wave.py - add NBPIX to wprops. [njcuk9999]
Core.core.drs_startup.py - add success and passed to outdict. [njcuk9999]
Fix end_main calls. [njcuk9999]
Tools.module.setup - fix some small bugs. [njcuk9999]
Obj_mk_tellu.py - first commit and functions ported from SpirouDrs. [njcuk9999]
Science.extract - add fiber key and fix orderp logging in npy read/write functions. [njcuk9999]
Science.calib.wave.py - allow get_wavelength solution to force to master. [njcuk9999]
Science.calib.general.py - move load_calib_file to drs_database. [njcuk9999]
Update language database. [njcuk9999]
Data.core..pdbrc - update pdb rc file (print out) [njcuk9999]
Core.core.recipe_definitions.py - add reprocess=True to cal_wave + add wave to limited_run. [njcuk9999]
Core.instruments.*.default_keywords - add fiber and KW_MID_OBS_TIME. [njcuk9999]
Core.core.drs_startup.py - fixes to indexing + pdb debug mode and exit functionality. [njcuk9999]
Core.core.drs_recipe.py - add_output_file method and remove params[‘OUTPUTS’] [njcuk9999]
Core.core.drs_file.py - add get_fiber method. [njcuk9999]
Core.core.drs_database.py - load_db_file load_db_file_from_filename functions. [njcuk9999]
Core.core.drs_argument.py - add a reprocess key as well as required key. [njcuk9999]
Recipes.spirou.* - add_output_file to allow indexing to work. [njcuk9999]

0.5.063 (2019-08-31)¶

Data.core..pdbrc - add pdb/ipdb script to run on execution (after copying to working directory) [njcuk9999]
Tools.module.error.find_error.py tools.module.listing.file_explorer.py - change exit/cleanup function calls. [njcuk9999]
Tools.dev.changelog.py - change exit/cleanup function calls. [njcuk9999]
Science.extract.other.py - fix problem with thermal (was returning e2ds instance not thermal e2ds instance) [njcuk9999]
Update the exit/clean up function calls in main and __main__ functions. [njcuk9999]
Update language database. [njcuk9999]
Update object query list. [njcuk9999]
Core.__init__.py - add aliases to new exit/cleanup functions. [njcuk9999]
Core.instruments.default.default_config.py - add idebug constants. [njcuk9999]
Core.core.drs_startup.py - change the way ending is cleared up (ipdb + ll redo + locals sorting) [njcuk9999]
Core.core.drs_recipe.py - add special set_ipython_return (for idebug mode) [njcuk9999]
Core.core.drs_argument.py - add SetIpythonReturn class (for idebug mode) [njcuk9999]
Core.constants.param_functions.py - add get_relative_folder and. [njcuk9999]
Tools.module.setup.drs_reprocess.py - change when to lock/unlock params + handle deep copying / deletion better. [njcuk9999]
Tools.dev.* - change call to core.end_main. [njcuk9999]
Tools.bin.* - change call to core.end_main. [njcuk9999]
Science.calib.localisation.py - use fiber params to get some parameters. [njcuk9999]
Science.calib.dark.py - change where filetype comes from (not params) [njcuk9999]
Receipes.spirou.* - change call to core.end_main. [njcuk9999]
Core.instruments.*.pseudo_const.py - fix writing to params (now fiber_params) [njcuk9999]
Drs_startup.py - get params from llmain. [njcuk9999]
Param_functions.py - add a way to set while being locked (only for use when really know what you are doing) [njcuk9999]

0.5.062 (2019-08-30)¶

Tools.module.setup.drs_reprocess.py - fix copying (deep copy) [njcuk9999]
Tools.dev.changelog.py - fix end_main and get_locals() [njcuk9999]
Tools.bin.* - fix main function (end_main + get_locals) [njcuk9999]
Science.extract.other.py - remove params[‘QC’] –> passed. [njcuk9999]
Science.extract.general.py - fix order_profiles (must be DrsNpyFile) [njcuk9999]
Science.calib.wave,py - continue work to get cal_wave_spirou.py to work. [njcuk9999]
Science.calib.shape.py - fix spelling in comment. [njcuk9999]
Recipe.spirou.* - remove params[‘QC’] –> passed, fix core.end_main params call. [njcuk9999]
Update the language database. [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - add a hcmode and fpmode (for changing the WAVE_MODE_HC and WAVE_MODE_FP) [njcuk9999]
Output_filenames.py - add output function to func_name (for error printing - need to locate the problem better) [njcuk9999]
Core.core.instruments - deal with copying better (deep copies) + check used/unused keys. [njcuk9999]
Core.core.drs_startup.py - deal with copying params better + lock after copies. [njcuk9999]
Core.core.* - deal with deep copying better. [njcuk9999]
Core.constants.param_functions.py - add locking/unlocking function - stop setting keys to params. [njcuk9999]

0.5.061 (2019-08-29)¶

Science.rv.general.py - fix tabbing typo + other fixes (found after first run) [njcuk9999]
Science.calib.shape.py - fix error in log args (C pos 3 –> 4 ) [njcuk9999]
Cal_wave_spirou.py + science.calib.wave.py - continue work on converting spiroudrs to terrapipe. [njcuk9999]
Recipes.spirou.cal_shape_spirou.py - add shape keywords. [njcuk9999]
Recipes.spirou.cal_extract_spirou.py - add shape keywords. [njcuk9999]
Update language database. [njcuk9999]
Io.drs_data.py - add colnames to ccf mask data function. [njcuk9999]
Core.__init__.py - add fiber_processing_update. [njcuk9999]
Core.math.general.py - fix nanpolyfit (if kwargs[‘w’] is None it breaks) [njcuk9999]
Core.instruments.spirou.recipe_definitions.py - add new wave fp outputs. [njcuk9999]
Core.instruments.spirou.file_definitions.py - add wave definitions and make sure name == KW_OUTPUT. [njcuk9999]
Data.spirou.ccf - add CCF masks. [njcuk9999]
Core.instruments.*.output_filenames.py - add set_file function. [njcuk9999]
Core.instruments.* - add wave constants/keyword args. [njcuk9999]
Core.core.drs_startup.py - get_file_definition needs to remove fiber if present + add function ‘fiber_processing_update’ [njcuk9999]
Core.core.drs_file.py - add group option to copy_original_keys (including checking _check_keyworddict) [njcuk9999]
Core.constants.param_functions.py - add get_keyword_instances (for obtaining dictionary of header keys linked to params + their instances) [njcuk9999]
Core.constants.constant_functions.py - add group. [njcuk9999]
Cal_wave_spirou.py - corrections from Melissa commit + nanpolyfit change. [njcuk9999]

0.5.060 (2019-08-28)¶

Tools.module.setup.drs_reprocess.py - fix updating keys in Run (runstring/args/kwargs), deal with wrong nightname. [njcuk9999]
Update language database. [njcuk9999]
Io.drs_fits.py - correct formatting of Time (need to use dtype) [njcuk9999]
Core.instruments.spirou.default_keywords.py - correct typo in constants. [njcuk9999]

0.5.059 (2019-08-27)¶

Science.rv.general - add get_ccf_mask, coravelation, delta_v_rms_2d calculate_ccf correlbin and fit_ccf functions. [njcuk9999]
Cal_wave_spirou.py - continue updating from SpirouDRS –> terrapipe. [njcuk9999]
Update language database. [njcuk9999]
Update language database. [njcuk9999]
Drs_data.py - add load_ccf_mask function. [njcuk9999]
Core.math.* - add fitgauss, get_dll and get_ll functions. [njcuk9999]
Core.instruments.*.py - continue adding wave constants/keywords. [njcuk9999]
Drs_reprocess.py - fix the return to self.find_recipe. [njcuk9999]
Drs_reprocess.py - fix the return to self.find_recipe. [njcuk9999]

0.5.058 (2019-08-22)¶

Neil_TODO.md - currently needed before release of terrapipe. [Neil Cook]
Tools.module.setup.drs_reprocess.py - change SystemExit to LogExit. [Neil Cook]
Science.calib.wave.py - continue convert spiroudrs wave fp solution to terrapipe. [Neil Cook]
Update test files with new __main__ and exception handling (from default and spirou) [Neil Cook]
Update language database. [Neil Cook]
Drs_exceptions.py - add LogExit and Exit classes. [Neil Cook]
Io.drs_text.py - add save text file. [Neil Cook]
Terrapipe.io.drs_data.py - add load + save cavity files. [Neil Cook]
Core.instruments.* - add WAVE_FP constants. [Neil Cook]
Core.core.drs_startup.py - change SystemExit catch to LogExit catch. [Neil Cook]
Core.core.drs_log.py - change exit system (now via LogExit) [Neil Cook]
SpirouWAVE2.py - another question for Melissa. [Neil Cook]

0.5.057 (2019-08-21)¶

Science.calib.wave.py - continue to add wave fp code. [Neil Cook]
Update language database. [Neil Cook]
SpirouWAVE2.py - add a todo on progress of terrapipe adding. [Neil Cook]
Cal_wave_spirou.py - continue adapting SpirouDRS wave codes to terrapipe. [Neil Cook]
Science.rv.general.py - add measure_fp_peaks (create_drift_file) and remove_wide_peaks. [Neil Cook]
Core.math.general.py - add gauss_function. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.* - continue to add wave_fp constants. [Neil Cook]

0.5.056 (2019-08-21)¶

Constants_SPIROU_H4RG.py - add comments for @melissa-hobson to try to explain. [Neil Cook]
Cal_wave_spirou.py and science.calib.wave.py - continue work on converting from SpirouDRS. [Neil Cook]
Cal_loc_spirou.py - fix comment indentation. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.spirou.file_definitions.py - add out_wave_hc, out_wave_fp, out_wave_hcline, out_wave_hcres and update recipe definitions accordingly. [Neil Cook]
Core.instruments.* - continue adding wave constants + keywords. [Neil Cook]
Core.core.drs_file.py - fix add_hkey_1d function (no longer using kwstore in same way) [Neil Cook]

0.5.055 (2019-08-19)¶

Science.calib.wave.py - continued integration of wave from SpirouDRS. [Neil Cook]
Cal_wave_spirou.py - update call to wave.hc_wavesol. [Neil Cook]
Core.math.general.py - add fit_gauss_with_slope function. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments - add wave constants. [Neil Cook]
Core.constants.param_functions.py - _map_listparameter and _map_dictparameter - deal with value == ‘’ [Neil Cook]
SpirouWAVE2.py - clean up (for integration into terrapipe) [Neil Cook]

0.5.054 (2019-08-16)¶

Tools.module.setup.drs_reprocess.py - change how find_recipe works. [Neil Cook]
Science.extract.other.py - add other extraction functions (specifically for extracting files in recipes) [Neil Cook]
Recipe.spirou.cal_wave_spirou.py - start conversion of cal_wave / wave.py. [Neil Cook]
Recipes.spirou.*.py - add DATA_DICT and change average/sum to median for combining. [Neil Cook]
Udpate language database. [Neil Cook]
Io.drs_image.py - only check fiber in params[‘inputs’] if it is in inputs. [Neil Cook]
Core.instruments.recipe_definitions.py - add cal_wave. [Neil Cook]
Core.instruments.file_definitions.py - add out_hcline. [Neil Cook]
Core.instruments.*.default_constants.py - add wave constants. [Neil Cook]
Core.core.drs_startup.py - add DATA_DICT functionality + recipemod saving. [Neil Cook]
Core.core.drs_recipe.py - add unset recipemod to recipe class. [Neil Cook]
Core.core.drs_file.py - change combine to include median. [Neil Cook]
Merge branch ‘melissa’ into dev. [Neil Cook]

Conflicts:
INTROOT/config/constants_SPIROU_H4RG.py INTROOT/misc/cal_HC_E2DS_spirou.py
Cal_wave_spirou: new QC: consecutive pixels along an order must have increasing wavelengths. [melissa-hobson]
Merge remote-tracking branch ‘origin/melissa’ into melissa. [Melissa Hobson]

Conflicts:
INTROOT/bin/cal_CCF_E2DS_FP_spirou.py INTROOT/misc/cal_CCF_wrap_MH.py
SpirouWAVE2 - bug fixes. [melissa-hobson]
SpirouWAVE2.py - implementation of fit_1d_solution method for wave_new. [melissa-hobson]
SpirouWAVE2.py - move polynomial fitting to function. [melissa-hobson]
SpirouWAVE2 - corrections to saves for line list table. [melissa- hobson]
Cal_wave_spirou, spirouWAVE2.py - fixed line list table for wave_new method. [melissa-hobson]
Cal_wave_spirou, spirouWAVE2.py - fixed results table for wave_new method. [melissa-hobson]
SpirouPlot, spirouWAVE2 - plot fixes. [melissa-hobson]
Merge branch ‘melissa’ of https://github.com/njcuk9999/spirou_py3 into melissa. [melissa-hobson]
Constants_SPIROU_H4RG: added wave constants spirouPlot.py: added plots for cal_wave_new spirouWAVE2.py - cal_wave_new adaptation - update_cavity switch and proper paths, plots moved to spirouPlot, fitting cleaned up. [melissa-hobson]
Cal_wave_new_final save. [melissa-hobson]
Cal_HC_E2DS_EA - corrected QC mistake. [melissa-hobson]
Constants_SPIROU_H4RG: added wave constants spirouPlot.py: added plots for cal_wave_new spirouWAVE2.py - cal_wave_new adaptation - update_cavity switch and proper paths, plots moved to spirouPlot. [melissa-hobson]
Constants_SPIROU_H4RG: added wave constants for FP peak ID spirouWAVE2.py - cal_wave_new adaptation - FP peak ID. [melissa- hobson]
Constants_SPIROU_H4RG: added wave constants spirouWAVE2.py - cal_wave_new adaptation. [melissa-hobson]
SpirouWAVE2.py - clarification of all_lines creation; fix of start and end orders for FP method 0; common parts of FP solution (Littrow, CCF) moved outside if loop. [melissa-hobson]
Cal_wave_spirou.py, spirouWAVE2 - cleanup. [melissa-hobson]
Cal_wave_spirou.py - bug fixes. [melissa-hobson]
Cal_wave_spirou.py, spirouWAVE2.py - C Lovis method incorporation. [melissa-hobson]
Cal_wave_spirou.py, spirouWAVE2.py - creation of single unified wavelength solution codes. [melissa-hobson]
Cal_WAVE_NEW_E2DS_spirou_2.py - fixes to correctly handle NaNs. [melissa-hobson]
Cal_HC_E2DS_EA, cal_WAVE_E2DS_EA: New QC that verifies that the difference in wavelength fits between consecutive orders is positive. [melissa-hobson]
SpirouWAVE.py, spirouRV.py - fixes to correctly deal with NaN warnings. [melissa-hobson]
SpirouWAVE.py - in find_hc_gauss_peaks, segments with fewer not-nan values than gaussian parameters + 1 are ignored. [melissa-hobson]
Merge branch ‘master’ into melissa. [melissa-hobson]

# Conflicts: # INTROOT/bin/cal_CCF_E2DS_FP_MH_spirou.py # INTROOT/bin/cal_CCF_E2DS_FP_spirou.py # INTROOT/misc/cal_CCF_wrap_MH.py # INTROOT/misc/cal_WAVE_NEW_E2DS_spirou_2.py
Merge remote-tracking branch ‘origin/melissa’ into melissa. [melissa- hobson]

# Conflicts: # INTROOT/bin/cal_CCF_E2DS_FP_spirou.py # INTROOT/misc/cal_CCF_wrap_MH.py
Cal CCF bla. [melissa-hobson]
Merge branch ‘master’ into melissa. [Melissa Hobson]

Conflicts:
INTROOT/bin/cal_CCF_E2DS_FP_MH_spirou.py INTROOT/bin/cal_CCF_E2DS_FP_spirou.py INTROOT/misc/cal_CCF_wrap_MH.py INTROOT/misc/cal_WAVE_NEW_E2DS_spirou_2.py
Cal_HC function updates cal_WAVE_NEW save all input files. [melissa- hobson]
Cal_CCF_MH: allows wavesols as arguments cal_CCF_wrap: calls all CCFs. [melissa-hobson]
Cal_WAVE_E2DS_EA: fix wave file reading. [melissa-hobson]
Recipes.spirou.cal_wave_spirou.py - first commit. [Neil Cook]

0.5.053 (2019-08-15)¶

Tools.module.setup.drs_reprocess.py - correct how we determine whether we have errors in odict. [Neil Cook]
Core.instruments.spirou.py - add hc_run. [Neil Cook]
Update object list. [Neil Cook]
Tools.module.setup.drs_reprocess.py - add shortname to processing list and skip RUN=False before generation (speed up) [Neil Cook]
Science.extract.berv.py - make columns lower case (to fix table) [Neil Cook]
Core.core.drs_startup.py - lock before making directories (for parallisation) [Neil Cook]
Update language database. [Neil Cook]
Science.preprocessing.identification.py - fix problem shallow copying fileset instance (use completecopy) [Neil Cook]
Science.preprocessing.detector.py - add dx/dy and suppress warnings for nan problems in pp functions. [Neil Cook]
Science.calib.* - change times to mid_obs_time + change debug_back to recipe.outputs definition. [Neil Cook]
Berv - shift around berv code + make time used come from mid_obs_time. [Neil Cook]
Cal_preprocess_spirou.py - add in fix for 1 pixel shift + add in calculation of mid observation time. [Neil Cook]
Update language database. [Neil Cook]
Drs_fits.py - add header_end_time and get_mid_obs_time functions. [Neil Cook]
Core.instrument.spirou.recipe_definitions.py - add debug_back to outputs. [Neil Cook]
Core.instruments.*.file_defintions.py - move debug_back to instrument setup. [Neil Cook]
Drs_database.py - correct typo need to return t for get_mid_obs_time call. [Neil Cook]
Core.instruments.*.py - add new time constants. [Neil Cook]
Drs_database.py - go from start_time –> mid_obs_time. [Neil Cook]

0.5.052 (2019-08-14)¶

Update object query list. [Neil Cook]
Update language database. [Neil Cook]
Reprocessing fix - continue work. [Neil Cook]

0.5.051 (2019-08-13)¶

Reprocessing - continue work on reprocessing. [Neil Cook]
Reprocessing - continue work on reprocessing. [Neil Cook]
Recipe.spirou.cal_thermal_spirou.py - fix bug with THERMAL_E2DS_FILE –> recipe.outputs[‘THERMAL_E2DS_FILE’] [Neil Cook]
Data.core.object_query_list.fits - update query list. [Neil Cook]
Core.instruemnts.spirou.recipe_definitions.py - update shortnames + add science run. [Neil Cook]
Core.core.drs_recipe.py - copy arguments/files properly (avoid shallow copying) [Neil Cook]
Core.core.drs_log.py - add printmessage to WLOG. [Neil Cook]
Core.core.drs_file.py - allow copying of drsfiles (required to allow recipe copying) [Neil Cook]
Core.core.drs_argument.py - add changes to allow copying of arguments (needed for new recipe copies) [Neil Cook]
Drs_reprocess.py - fix problems with modulemain. [Neil Cook]
Recipes.spirou.cal_extract_spirou - remove unused imports. [Neil Cook]
Core.instrument.* - add reprocessing constants. [Neil Cook]
Drs_startup.py - every call to import_module should call func_name (so we know where they come from) [Neil Cook]
Drs_recipe.py - remove _import_module without path. [Neil Cook]
Core.constants.param_functions.py - every call to import_module should have func_name as argument (so we know where it came from) [Neil Cook]
Core.constants.constant_functions.py - every use of import_module should have ‘func_name’ as argument (so we know where it came from) [Neil Cook]
Recipes.spirou.cal_badpix_spirou.py - fix bug BACKMAP –> recipe.outputs[‘BACKMAP’] [Neil Cook]
Update old version file. [Neil Cook]
Update changelog/version/date. [Neil Cook]

0.5.050 (2019-08-12)¶

Tools.reprocess - add processing (linear/parallel) functionality. [Neil Cook]
Science.telluric.general.py - first commit - add get_whitelist and get_blacklist functions. [Neil Cook]
Update language database. [Neil Cook]
Drs_text.py - first commit - add text reading functionality. [Neil Cook]
Io.drs_data.py - add load_text_file functionality. [Neil Cook]
Data.spirou.tellu_*list.txt - add telluric black/white list. [Neil Cook]
Core.instruments - add white/black list for tellurics (needed for reprocessing) [Neil Cook]
Core.core.drs_startup.py - get recipe definitions module from call. [Neil Cook]
Drs_recipe.py - changes to generate_runs. [Neil Cook]
Core.core.drs_file.py - outfile should just be the basename. [Neil Cook]

0.5.049 (2019-08-10)¶

Drs_reprocess.py - address new bugs. [Neil Cook]
Drs_reprocess.py - address new bugs. [Neil Cook]
Core.instruments - add outfunc=out.blank (and blank description) [Neil Cook]
Drs_recipe.py - add return of runs. [Neil Cook]
Drs_reprocessing.py - update for continued work on reprocessing. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments - add repreocessing constants. [Neil Cook]
Drs_file.py - add functionality for reprocessing. [Neil Cook]

0.5.048 (2019-08-08)¶

Tools.reset.py - remove update_params and set __INSTRUMENT__ from recipe update. [Neil Cook]
Reprocess.py/drs_reprocess.py - continue work on reprocessing (unfinished) [Neil Cook]
Cal_preprocess_spirou.py - allow skipping of files if done and –skip=True. [Neil Cook]
Update language database. [Neil Cook]
Core.__init__.py - remove update_params (now done in setup) [Neil Cook]
Core.instruments.spirou.recipe_definitions.py - add file module to DrsRecipe calls, add shortname and master to master recipes, add section defining run sequences (run order + filters) [Neil Cook]
Core.instruments.spirou.py - add outfunc for pp_file. [Neil Cook]
Core.instruments.*.output_filenames.py - fix how _calibration_prefix works and add an error if “outpath” is None. [Neil Cook]
Core.instruments.*.default_constants.py - add and update constants. [Neil Cook]
Drs_startup.py - update parameters if instrument is in inputs (go from no instrument to using an instrument) [Neil Cook]
Drs_recipe.py - add copy function to DrsRecipe add DrsRunSequence class. [Neil Cook]
Drs_argument.py - remove debug print statement. [Neil Cook]

0.5.047 (2019-08-07)¶

Drs_reprocess.py - add RUN and SKIP names (unfinished) [Neil Cook]
Add outfiles from recipe.outputs. [Neil Cook]
Recipe_definitions.py - add set_outputs and outputs to all recipes. [Neil Cook]
Drs_recipe.py - add set_outputs method and outputs attribute (for adding output file definitions to files) [Neil Cook]

0.5.046 (2019-08-06)¶

Tools.bin - first commit of reprocessing (not finished) [Neil Cook]
Update language database. [Neil Cook]
Io.drs_table.py - fix problem with no data_start keyword in fmt=’fits’ [Neil Cook]
Core.instruments - add in reprocessing constants. [Neil Cook]
Core.core.drs_startup.py - allow find_recipe not be non-private. [Neil Cook]
Core.core.drs_recipe.py - add a way to skip checks (for getting arg list from runlist) [Neil Cook]
Core.core.drs_argument.py - add a way to skip checks (for getting arg list from runlist) [Neil Cook]
Core.constants.constant_functions.py - modify import_module to have quiet mode. [Neil Cook]
Update todo statements (more specific) [Neil Cook]

0.5.045 (2019-07-27)¶

Sciecne.extract.extraction.py - remove use of params[‘FIBER’] [Neil Cook]
Sciecne.extract.berv.py - fix assign_properties. [Neil Cook]
Science.calib.* - add in the option to get filename from call and from params[‘INPUTS’] [Neil Cook]
Cal_thermal_spirou.py - check if cal_extract (for the DARK_DARK) failed before continuing. [Neil Cook]
Cal_shape_master_spirou.py - remove use of params[‘FIBER’] [Neil Cook]
Cal_loc_spirou.py - remove use of params[‘FIBER’] [Neil Cook]
Cal_flat_spirou.py - remove use of params[‘FIBER’] [Neil Cook]
Cal_extract_spirou.py - add options to skip on DPRTYPE and OBJNAME. [Neil Cook]
Update language database. [Neil Cook]
Io.drs_image.py - remove use of params[‘FIBER’] [Neil Cook]
Recipe_definitions.py - add more options (calibration files) [Neil Cook]
Pseduo_const.py - remove use of params[‘FIBER’] [Neil Cook]
File_definitions.py - add KW_OBSTYPE to raw files. [Neil Cook]
Pseudo_const.py - remove use of params[‘FIBER’] [Neil Cook]
Recipe_definition - replace kwarg –> set_kwarg and arg –> set_arg. [Neil Cook]
Update language database. [Neil Cook]
Berv.py - add things left to do. [Neil Cook]
Update example_run_list.txt. [Neil Cook]
Update example_run_list.txt. [Neil Cook]
Core.instruments.spirou.file_defintions.py - correct suffix for out_shape_debug_ihc. [Neil Cook]
Cal_flat_spirou.py - correct order call. [Neil Cook]
Misc.update_wave_header.py - script to update master_wave header with new keys. [Neil Cook]
Misc.example_run_list.txt - list of test codes to run (while reprocessing script is being built) [Neil Cook]
Tools.bin - add reset code (formally cal_reset.py) [Neil Cook]
Identification.py - fix drs_outfile_id to find files with a different prefix. [Neil Cook]
Science.calib - get_file_definition must specify kind (raw/tmp/red) [Neil Cook]
Cal_preprocess_spirou.py - correct problems with drs_outfile_id. [Neil Cook]
Cal_dark_master_spirou.py - deal with no dark files being found. [Neil Cook]
Drs_data.py - construct_filename function all filename/directory name to be unset. [Neil Cook]
Data.spirou.reset - update MASTER_WAVE.fits (new header keys) [Neil Cook]
Core.__init__.py - add some new aliases and rearrange order. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments - add reset functionality + small fixes to run codes. [Neil Cook]
Core.core.drs_startup.py - pipe errors in main end script to WLOG (were just raising) + add function update_params (to update param with instrument params) [Neil Cook]
Core.core.drs_recipe.py - add exceptions for bad sys.argv and misbehaving parsing to argparse. [Neil Cook]
Core.core.drs_file.py - fix error message (should be the drs file not just the name) [Neil Cook]
Data.spirou.reset - add reset files for calibdb and telludb. [Neil Cook]
Reorganisation of the tools folder. [Neil Cook]
Tools - update tools now have bin folder and dev folder (rest are modules) [Neil Cook]
Science.calib.shape.py - add log for ea_transform. [Neil Cook]
Update language database. [Neil Cook]
Object_query_list.fits - first commit - the gaia query database (so we don’t have to query online every time) [Neil Cook]
Science.extract.general.py - fix problems with thermal. [Neil Cook]
Science.extract.crossmatch.py - correction to new berv functionality including plx limit and mag limit. [Neil Cook]
Science.extract.berv.py - correction to new berv functionality (including dberv and rv when present) [Neil Cook]
Cal_loc_spirou.py - add calibs to header. [Neil Cook]
Cal_extract_spirou.py - add rest of the cdb keywords. [Neil Cook]
Drs_data.py - correct problems with construct_filename and add unique error message for obj_list function. [Neil Cook]
Core.math.general.py - apply fix #567 by @melissa-hobson. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.* - added calibration and extraction (berv) keyword defintions. [Neil Cook]
SpirouMath.py - correct issue #567 (fix by @melissa-hobson) [Neil Cook]

0.5.043 (2019-07-25)¶

Science.extract.berv.py - add features to query gaia / lookup table. [Neil Cook]
.gitignore - add .lock to ignore list. [Neil Cook]
Science.extract.crossmatch.py - first commit – adding to query gaia/lookup table. [Neil Cook]
Science.extract.extraction.py - change warning keys 0016 –> 016. [Neil Cook]
Cal_extract_spirou.py - fix typo add_berv_keys requires params. [Neil Cook]
Drs_data.py - add return file option to data functions. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments - add obj_list constants (for gaia crossmatch) [Neil Cook]
Param_functions.py - add set_instance and set_instances. [Neil Cook]

0.5.042 (2019-07-23)¶

Science.extract.berv.py - continue work on adding berv calculation. [Neil Cook]
Cal_extract_spirou.py - add header to get_berv. [Neil Cook]
Dsr_fits.py - use param.instances to get fmt and dtype for KW_ACQTIME. [Neil Cook]
Core.constants - add instance dictionary (like source dictionary) for ParamDict. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.* - add constants for berv. [Neil Cook]
Changelog.md: refractor header_time –> header_start_time. [Neil Cook]
Science.extract - add berv functionality. [Neil Cook]
Science.extract.wave.py - add function add_wave_keys. [Neil Cook]
Science.calib.dark/shape - refractor header_time–>header_start_time. [Neil Cook]
Cal_extract_spirou.py - add berv stuff. [Neil Cook]
Update language database. [Neil Cook]
Io.drs_fits.py - rename header_time –> header_start_time. [Neil Cook]
Drs_database.py - rename header_time –> header_start_time. [Neil Cook]

0.5.041 (2019-07-19)¶

Science.extract.general.py - correct typo: red_limt –> red_limit. [Neil Cook]
Science.extract.general.py - correct corrtype2 type: THERMAL_CORRETION_TYPE1 –> THERMAL_CORRETION_TYPE2. [Neil Cook]
Cal_extract_spirou.py - print process of extraction fiber {0} of [{0} {1} {2}] [Neil Cook]
Update language database. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.040 (2019-07-19)¶

Science.extract.general.py - add s1d funtionality and add log message to thermal correction. [Neil Cook]
Science.calib.wave.py - get the wfp keys and store in wprops. [Neil Cook]
Science.calib.localisation.py - return locofile instance with localisation properties. [Neil Cook]
Science.calib.flat_blaze.py - correct blaze getting function (was set to get flat) [Neil Cook]
Cal_extract_spirou.py - add s1d functionality. [Neil Cook]
Update language database. [Neil Cook]
Drs_fits.py - fix problem that table cannot be primary hdu (start from ext=1 in these cases) [Neil Cook]
Core.instruments - add s1d constants. [Neil Cook]
Drs_file.py - fix hdict copying header cards, make sure header keys only copy basename for paths, add key formating for 1d and 2d keys. [Neil Cook]

0.5.039 (2019-07-18)¶

Science.extract.general.py - fix typo “red_limt” –> “red_limit” [Neil Cook]
Wave.py - make wave master use specific fibers and search for file defintion. [Neil Cook]
Shape.py - correct program with shape finding (dymap y0[:, ix] –> y0[:, dim2//2]) [Neil Cook]
Cal_thermal_spirou.py - add program name for when cal_thermal uses cal_extract (thermal_extract), make sure header is added to outfile before adding to calibDB. [Neil Cook]
Cal_flat_spirou.py - add textentry for qc fail message (missed before) [Neil Cook]
Cal_extract_spirou.py - update QC should just check for NaN image. [Neil Cook]
Drs_table.py - remove “data_start” for fits files (in read_table) [Neil Cook]
File_definitions.py - add wavem file and correct thermal file (should be a general_file not a calib_file) [Neil Cook]
Drs_startup.py - always plot the header line before file processing message. [Neil Cook]
Drs_database.py - update the error when there is not hdict or header present (must be one or the other) [Neil Cook]
Drs_argument.py - make debug message a text entry. [Neil Cook]
Update language database. [Neil Cook]
SpirouImage.py - fix the shape problem with dymap bending (fit y0 for center pixel not ix’th pixel) [Neil Cook]
Data.core - add tapas_all_sp.fits. [Neil Cook]
Extract.general.py - continue to port thermal correction code. [Neil Cook]
Shape.py - remove test cases for dymap generation (still unfixed/unworking) [Neil Cook]
General.py - reorganise load_calib_file (no load_calib_table) [Neil Cook]
Drs_image.py - allow fiber type “ALL” [Neil Cook]
Drs_data.py - add load_tapas. [Neil Cook]
Core.__init__.py - copy_kwargs alias. [Neil Cook]
Cal_extract/cal_thermal - continue work on porting from spirou drs. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments - add constanst for extraction (thermal mostly) [Neil Cook]
Drs_startup.py - add copy_kwargs function. [Neil Cook]
Drs_recipe.py - add set_program special argument. [Neil Cook]
Drs_log.py - set default values for params. [Neil Cook]
Drs_argument.py - correct how to handle string instead of list for files. [Neil Cook]
SpirouImage.py - remove test cases. [Neil Cook]
Constants_SPIROU_H4RG.py - correct comment. [Neil Cook]

0.5.037 (2019-07-10)¶

Extraction/flat/blaze - continue work to port changes from spiroudrs. [Neil Cook]
Extraction/flat/blaze - continue work to port changes from spiroudrs. [Neil Cook]
Update language database. [Neil Cook]
Recipe_definitions.py - change –extfiber to –fiber. [Neil Cook]
Pseudo_const.py - update constants (add FIBER_DATA_TYPE) [Neil Cook]
SpirouMath.py - pep8 change. [Neil Cook]
Cal_shape_master_spirou.py - fix problem FP file should be FPfiles. [Neil Cook]
Science.extract.py - work on completing the extraction functions (for cal_flat) [Neil Cook]
Science.calib.shape.py - fix getting the calibration files (don’t want to use file_definitons for specific instrument) [Neil Cook]
Science.calib.localisation.py - fix load_orderp. [Neil Cook]
Science.calib.general.py - check dtype in add_calibs_to_header. [Neil Cook]
Cal_flat_spirou.py - continue porting over code from spiroudrs. [Neil Cook]
Recipes.spirou.py - add missing keywords to header. [Neil Cook]
Update language database. [Neil Cook]
Drs_image.py - fix get_fiber_types. [Neil Cook]
Drs_fits.py - add check_dtype_for_header function. [Neil Cook]
Recipe_definitions.py - remove extract method. [Neil Cook]
Pseudo_const.py - add FIBER_WAVE_TYPES. [Neil Cook]
Core.instruments.spirou.file_definitions.py - fix types in calls. [Neil Cook]
Core.instruments..output_filenames.py - tweak npy_file. [Neil Cook]
Core.instruments.py - add cal_flat constants/keywords. [Neil Cook]
Drs_startup.py - make sure name == file.name if we aren’t returning all files. [Neil Cook]
Drs_log.py - add dtype to allow listp/dictp to test/convert elements before returning. [Neil Cook]
Drs_file.py - fix NpyFile to overwrite needed functions of InputFile. [Neil Cook]
Core.constants.param_function.py - modify params.listp and params.dictp to add a dtype for list/dict elements. [Neil Cook]

0.5.035 (2019-07-08)¶

Update language database. [Neil Cook]
Science.extraction.py - first commit (port from spiroudrs) [Neil Cook]
Science.calib.shape.py - change shape files to load from general.load_calib_file. [Neil Cook]
Science.calib.localisation.py - add load_orderp. [Neil Cook]
Science.calib.general.py - add load_calib_file and load_calib_table. [Neil Cook]
Cal_extract_spirou.py/cal_flat_spirou.py - start porting code. [Neil Cook]
Drs_image.py - add function get_fiber_types. [Neil Cook]
Drs_data.py - change error code. [Neil Cook]
File_definitions.py - add drs_ninput and out_orderp_straight. [Neil Cook]
Output_filenames.py - add npy_file. [Neil Cook]
Drs_log.py - allow find_param (pcheck) to get listp or dictp as well as constant. [Neil Cook]
Drs_file.py - add DrsNpyFile and move some functionality to DrsInputFit. [Neil Cook]
Param_functions.py - add _map_dictparameter and redefine _map_listparameter. [Neil Cook]
Science.calib.shape.py - update how shape files are obtained from calibDB (including new function get_shapelocal) [Neil Cook]
Science.calib.localisation.py - update how we get loco files from calibDB. [Neil Cook]
Recipes.spirou.cal_loc_spirou.py - change outfile definiton (and how we identify which fiber file is for) [Neil Cook]
Cal_extract/cal_flat – continue porting functionality from spiroudrs. [Neil Cook]
Update language database. [Neil Cook]
Drs_path.py - correct __NAME__ [Neil Cook]
Drs_fits.py - allow read function to take function name as argument + correct pep8. [Neil Cook]
Drs_data.py - correct typoe in relfolder and filename for load_full_flat_pp() [Neil Cook]
Recipe_defintions.py - update filetypes (no need to distiguish fiber files) [Neil Cook]
File_defintions.py - update all filedefinitions with prefix, suffix, filetype where needed. [Neil Cook]
Output_filenames.py - change how getting filenames work (now uses prefix/suffix/filetype and deal with having a fiber defined) [Neil Cook]
Drs_startup.py - allow get_file_definition to return all files found (and name to be a string within drs file instance name) [Neil Cook]
Drs_recipe.py - change variable index –> indextable. [Neil Cook]
Drs_file.py - add suffix, prefix, fiber, fibers and rename ext –>filetype, index –> indextable, add method get_dbkey (adding use for fibers) [Neil Cook]
Drs_database.py - change how dbkey is obtained. [Neil Cook]

0.5.034 (2019-07-05)¶

README.md - move from recipes to terrapipe.recipes. [Neil Cook]
README.md - move from recipes to terrapipe.recipes. [Neil Cook]
File_definitions.py - remove slit_shape. [Neil Cook]
Constants - add FIBER_TYPES. [Neil Cook]
Param_functions.py - add listp method (to turn a string list into a list) [Neil Cook]
Cal_thermal_spirou.py - get the nightname from parameter dict. [Neil Cook]
Science.calib.shape.py - test how to deal with out of bounds coefficients in dymap [UNFINISHED + NOT WORKING] [Neil Cook]
Science.calib.general.py - get number of files (from DrsFitsFile instance) and push this into dark correction (for average) [Neil Cook]
Science.calib.dark.py - DARK key should be DARKM. [Neil Cook]
Core.instruments.spirou.pseduo_const.py = flip A and B coefficients to match spiroudrs. [Neil Cook]
Update language database. [Neil Cook]
Drs_file.py - add and set numfiles constant (for use when combining files to know how many files were combined) [Neil Cook]
Cal_shape_master_spirou.py [terrapipe] - sum files don’t average them, do not correct background (to make similar to spiroudrs code) and fix typo for dxmap0. [Neil Cook]
SpirouStartup.py - only return unique files when returning multiple files. [Neil Cook]
SpirouImage.py - fpdata1 –> masterfp, test how to deal with bounds in dymap. [Neil Cook]
Cal_shape_master_spirou.py - change fpfile to fpfiles, set frames to use all fp files, make fpdata1 not masterfp. [Neil Cook]
Science.calib.shape.py - add shape_local functions. [Neil Cook]
Science.calib.localisation.py - change where we add one to the coefficient numbers. [Neil Cook]
Science.calib.general.py - add calibration log message. [Neil Cook]
Update language database. [Neil Cook]
Core.instruments.spirou.file_definitions.py/rcipe_defintions - add shape outputs/shape_local recipe definition. [Neil Cook]
Cal_shape_spirou.py - first commit - push over code from spiroudrs. [Neil Cook]
Cal_shape_master_spirou.py - fix bugs with saving. [Neil Cook]
Cal_loc_spirou.py - change math from average to sum. [Neil Cook]

0.5.032 (2019-07-03)¶

Science.calib.wave.py - correct bug in loading keys from wave header. [Neil Cook]
Science.calib.shape.py - add dymap functionality + correct some dxmap bugs. [Neil Cook]
Science.calib.localisation.py - correct get_coefficients function. [Neil Cook]
Science.calib.general.py - add add_calibs_to_header function. [Neil Cook]
Update language database. [Neil Cook]
Constants - continue adding shape constants + add pseudo constant functions. [Neil Cook]
Drs_log.py - find_param function: function call takes prescendence over params[key] [Neil Cook]
Cal_shape_master_spirou.py - continue work on adding spiroudrs code (file saving) [Neil Cook]
Cal_loc_spirou.py - change the way calibration files are added to header. [Neil Cook]
Cal_dark_master_spirou.py - fix comment. [Neil Cook]
SpirouBERV.py - replace “t” with “jdutc” so all bjds returned. [Neil Cook]
Calib.science.preprocessing.detector.py - move loading of full flat to drs_data.py. [Neil Cook]
Calib.science.shape.py - continue to add functionality from SpirouDRS. [Neil Cook]
Calib.science.localisation.py - fix getting localisation coefficients. [Neil Cook]
Calib.science.badpix.py - move loading of full flat to drs_data.py. [Neil Cook]
Core.math.general.py - fix when there are no NaNs (don’t interpolate linearly) [Neil Cook]
Drs_data.py - first commit: module to control loading of internal drs data. [Neil Cook]
Update language database. [Neil Cook]
Add line lists and cavity length file. [Neil Cook]
Add to config parameters. [Neil Cook]
Cal_shape_master_spirou.py - add dxmap and start dymap conversion. [Neil Cook]
Calib.science.shape.py - continue to add functionality from SpirouDRS. [Neil Cook]
Localisation.py/wave.py - change output return (props only) [Neil Cook]
Core.math.py - add fwhm, iuv_spline, median_filter_ea, gaussian_function_nn, gauss_fit_nn, gauss_fit_s. [Neil Cook]
Default_constants.py - add shape constants. [Neil Cook]
Cal_shape_master_spirou.py - change the get_coefficients, get_wavesolution. [Neil Cook]
Science.calib.shape.py - start adding constants for shape master dxmap. [Neil Cook]
Default_constants.py - start adding constants for shape master dxmap. [Neil Cook]
Cal_shape_master_spirou.py - placeholder for calculate_dxmap. [Neil Cook]
Reprocess.py - do not scan tmp and reduced files. [Neil Cook]
Reprocess.py - pep8 - remove extra blank space. [Neil Cook]
SpirouBACK.py - correct typo th_blue_limit = p[‘THERMAL_RED_LIMIT’] –> th_blue_limit = p[‘THERMAL_BLUE_LIMIT’] [Neil Cook]
Constants_SPIROU_H4RG.py - correct typo THERMAL_BLUE_LIMIT = 24580 –> THERMAL_BLUE_LIMIT = 2450 and add ALLOWED_TELLURIC_DPRTYPES. [Neil Cook]
Obj_fit_tellu.py obj_mk_tellu.py - should only process files if DPRTPYE is correct, QC should fail if transmission map is all NaNs. [Neil Cook]
Cal_extract_RAW_spirou.py - QC should fail if file is all NaNs. [Neil Cook]

0.5.029 (2019-06-27)¶

Update date/version/changelog. [Neil Cook]
Science.calib.shape.py - fix rows missing from fp_table. [Neil Cook]

0.5.028 (2019-06-27)¶

Science.calib.shape.py - fix construct_master_fp (add fp_table results) + place holder for calculate_dxmap. [Neil Cook]
Science.calib.localisation.py - add get_coefficients function. [Neil Cook]
Science.calib.general.py - add logging to various steps of calibrate_ppfile. [Neil Cook]
Science.calib.badpix.py - fix a comment. [Neil Cook]
Science.calib.wave.py - first commit add get_masterwave_filename and get_wavesolution functions. [Neil Cook]
Update language database. [Neil Cook]
File_definitions.py - add more files to out_file file set. [Neil Cook]
Recipe_definitions.py - remove instances of tilt file. [Neil Cook]
Add default constants/keywords for shape_master. [Neil Cook]
Drs_startup.py - fix error reporting in get_file_definition and fix found_file when file not found. [Neil Cook]
Drs_file.py - fix the way keys are read in read/read1d and read2d keys. [Neil Cook]
Cal_shape_master_spirou.py - add plan for rest of code add localisation and wave files. [Neil Cook]
Science.calib.shape.py - first commit add fp_master functions - construct_fp_table, construct_master_fp, get_linear_transform_params, ea_transform, _max_neighbour_mask and _xy_acc_peak. [Neil Cook]
Science.calib.general.py - first commit add calibrate_ppfile function. [Neil Cook]
Science.calib.background/badpix/dark - change the return of calib correction functions - now returns fileused + corrected image. [Neil Cook]
Update language database. [Neil Cook]
Drs_image.py - add clean_hotpix function. [Neil Cook]
Core.math.py - add fit2dpoly, linear_minimization functions. [Neil Cook]
Recipe_definitions.py - add cal_shape_master and remove cal_slit. [Neil Cook]
Default_constants.py - add shape master (fp_master) constant definitions. [Neil Cook]
Cal_shape_master_spirou.py - add master fp generation (untested) [Neil Cook]
Cal_loc_spirou.py - update cal_loc with changes to how we calibrate ppfiles. [Neil Cook]
Cal_shape_master_spirou.py - first commit (placeholder that needs filling) [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.5.027 (2019-06-26)¶

Drs_path.py - make sure night_name does not start with a separator in “get_nightname” function. [Neil Cook]
Drs_database.py - allow the addition of the night name to “add_file” function. [Neil Cook]
Cal_dark_master_spirou.py - add nightname from reference file. [Neil Cook]
SpirouStartup.py - remove unused import. [Neil Cook]
Update language database. [Neil Cook]
Drs_fits.py - integrate _get_time functionality into header_time. [Neil Cook]
Pseudo_const.py - add back nirps logo. [Neil Cook]
Drs_database.py - update _get_time to use drs_fits.header_time. [Neil Cook]
Reorganize config and constants (now all in core sub-module) - update module order. [Neil Cook]
Reorganize config and constants (now all in core sub-module) [Neil Cook]
Reorganize where default settings are kept (now in config.instruments.default) – modifications to fix bugs. [Neil Cook]
Reorganize where default settings are kept (now in config.instruments.default) – modifications to fix bugs. [Neil Cook]
Reorganize where default settings are kept (now in config.instruments.default) [Neil Cook]
Science.calib.dark.py - correct dark_master functionality including setup to infile. [Neil Cook]
Background.py - update how debug file is made (with updates to write_multi) [Neil Cook]
Update language database. [Neil Cook]
Drs_path.py - change conditions on finding time_unit to be astropy unit/quantity. [Neil Cook]
Drs_fits.py - update Header class (from @cusher work) [Neil Cook]
Constants/keywords - add/update values for dark_master. [Neil Cook]
Drs_startup.py - fix get_drs_params inputs and make warning that code did not complete successfully red. [Neil Cook]
Drs_file.py - make corrections to write_multi (including new update_header_with_hdict function) [Neil Cook]
Cal_dark_master_spirou.py - finish converting dark_master to terrapipe. [Neil Cook]

0.5.026 (2019-06-25)¶

Science.calib.dark.py - add dark master functionality. [Neil Cook]
Update language database. [Neil Cook]
Terrapipe.io - add find_filetypes, get_index_files and header_time functions. [Neil Cook]
Constants - add dark master constant definitions. [Neil Cook]
Drs_startup.py - add function get_file_definition and update pid getting (to add htime) [Neil Cook]
File_definitions - add dark_master file definition. [Neil Cook]
Cal_dark_master_spirou.py - first commit and transfer from SpirouDRS. [Neil Cook]
Remove old drsmodule files. [Neil Cook]
Update version/changelog and date. [Neil Cook]

0.5.025 (2019-06-24)¶

Obj_mk_obj_template.py + spirouTelluric - move location of GetBERV. [njcuk9999]
SpirouTable.py - change order of backup operations (always close lock file last) [njcuk9999]
SpirouTable.py - fix problem with closing/replacing index.fits. [njcuk9999]

0.5.024 (2019-06-24)¶

SpirouTable.py - remove the index file before writing it. [Neil Cook]
SpirouRfiles.py - if reset is true make user confirm it. [Neil Cook]
SpirouRfiles.py - add a raw index file that should save time opening already read headers. [Neil Cook]

0.5.023 (2019-06-23)¶

SpirouRgen.py - fix problem when two independent file types defined (i.e. DARK_FLAT and FLAT_DARK) [Neil Cook]
SpirouRgen.py - check that master night name exists (raise error if it doesn’t) [Neil Cook]

0.5.022 (2019-06-21)¶

SpirouRgen.py - rename obj_mk_tellu_new –> obj_mk_tellu. [Neil Cook]
SpirouFITS.py - try to create lock directory. [Neil Cook]
SpirouBERV.py - add keys for processing. [Neil Cook]
SpirouDB.py - try to create lock folder if needed. [Neil Cook]
SpirouMath.py - linear bad pix must have at least two non-NaN pixels. [Neil Cook]
SpirouBACK.py - deal with thermal being empty or NaN filled entirely. [Neil Cook]
Obj_mk_tellu_db.py - renamed obj_mk_tellu_new to obj_mk_tellu. [Neil Cook]
Obj_mk_tellu.py - renamed from obj_mk_tellu_new.py. [Neil Cook]
Constants_SPIROU_H4RG.py - add berv dtypes. [Neil Cook]
Cal_dark_master_spirou.py - fix type dark_cube –> dark_cube1. [Neil Cook]

0.5.021 (2019-06-20)¶

SpirouBERV.py - update comments to be more specific about inputs. [njcuk9999]
SpirouBERV.py - update berv codes to be more specific about units etc. [njcuk9999]
Update berv tests. [njcuk9999]
Constants_SPIROU_H4RG.py - update observatory location. [njcuk9999]

0.5.020 (2019-06-19)¶

SpirouKeywords.py - add keywords to list. [njcuk9999]
Berv_error_test.py - continue testing of berv. [njcuk9999]
Reprocess.py - add back main function. [njcuk9999]
SpirouBERVest.py - degtorad –> deg2rad. [njcuk9999]
SpirouBERV - testing berv calculation. [njcuk9999]
SpirouImage/spirouStartup - make sure files is a list (if string make a list) [njcuk9999]
SpirouLog.py - add colour option in wlog.printmessage. [njcuk9999]

0.5.019 (2019-06-18)¶

SpirouImage.py - add warning capture for oweight (divide by NaNs okay) [njcuk9999]
SpirouRfiles.py - add run directory from param dict. [njcuk9999]
Config.py - add run directory. [njcuk9999]

0.5.018 (2019-06-17)¶

SpirouTelluric.py - add tau_h20 and tau_rest to code. [Neil Cook]
SpirouReprocess.py - add skipping into code. [Neil Cook]
SpirouLog.py - add method: “print message” [Neil Cook]
SpirouKeywords.py - add tau_h20 and tau_rest header keys. [Neil Cook]
SpirouConst.py - update file name function defintions. [Neil Cook]
SpirouBACK.py - correct typo dim2 –> dim1. [Neil Cook]
Obj_fit_tellu.py - add tau_h20 and tau_rest to header. [Neil Cook]
Cal_shape_spirou.py - change debug file defintions (need filename defined) [Neil Cook]
Cal_preprocess_spirou.py - make file name come from definition. [Neil Cook]

0.5.017 (2019-06-14)¶

SpirouReprocess - update the reprocessing codes. [Neil Cook]
Recipe_defintions.py - fix some recipe definitions. [Neil Cook]
File_definitions.py - update file definitions. [Neil Cook]

0.5.016 (2019-06-13)¶

SpirouReprocessing - continue work. [Neil Cook]
Correct recipe and file definitions for non-input-redo. [Neil Cook]
Obj_fit_tellu_db.py - correct number of required arguments. [Neil Cook]

0.5.015 (2019-06-12)¶

SpirouReprocess.py - continue writing code. [Neil Cook]
SpirouBACK.py - fix a problem with one of the returns in correction_thermal. [Neil Cook]
Multiprocess_test.py - add an event (to terminate all current and future jobs on crash) [Neil Cook]
Constants_SPIROU_H4RG.py - update a comment. [Neil Cook]
Merge branch ‘input_redo’ into dev. [Neil Cook]
Merge branch ‘dev’ into input_redo. [njcuk9999]
Merge branch ‘dev’ into input_redo. [njcuk9999]
Merge branch ‘dev’ into input_redo. [njcuk9999]

# Conflicts: # INTROOT2/drsmodule/io/drs_lock.py
Drs_lock.py - Merged 10b82f1 from @cusher into input_redo. [njcuk9999]
Localisation - update parameters for @melissa-hobson. [njcuk9999]
Merge branch ‘master’ into input_redo. [Neil Cook]
Localisation.py - continue work for cal_loc. [Neil Cook]
Background.py - fix backfile. [Neil Cook]
Update language database. [Neil Cook]
Drs_fits.py - fix write function having no dtype. [Neil Cook]
Constants.default.default_constants.py - add fiber_set_num key. [Neil Cook]
Config.instruments.spirou.*.py - add/correct loc keys. [Neil Cook]
Drs_file.py - correct problems with add_hkeys_2d. [Neil Cook]
Cal_loc_spirou.py - continue work on input redo cal_loc. [Neil Cook]
Background.py - change key for add_hkey. [Neil Cook]
Update language database. [Neil Cook]
Drs_fits.py - fix import of drs_log. [Neil Cook]
General.py - fix imports. [Neil Cook]
Config.instruments.spirou.*.py - correct keys and constants. [Neil Cook]
Drs_log.py - correct the find_param function. [Neil Cook]
Drs_file.py - fix when key = keywordstore. [Neil Cook]
Drs_database.py - correct call to find_param. [Neil Cook]
File_definitions.py - correct bad extension. [Neil Cook]
Cal_loc_spirou.py - continue fixes to input_redo changes. [Neil Cook]
Update language database. [Neil Cook]
Localisation.py - add image_superimp function. [Neil Cook]
Drs_fits.py - move the resize/flip images add convert functions. [Neil Cook]
Constants.defaults.*.py - add constants/headers from localisation. [Neil Cook]
Config.math - add calculate_polyvals function. [Neil Cook]
Instruments.spirou.*.py - add constants/keywords for localisation. [Neil Cook]
Drs_file.py - add method ‘copy_hdict’ [Neil Cook]
Cal_loc_spirou.py - continue work on adapting recipe for terrapipe. [Neil Cook]
Cal_loc_spirou.py - continue work on adapting recipe for terrapipe. [Neil Cook]
Recipes.spirou - move flip/resize functions. [Neil Cook]
Update language database. [Neil Cook]
Science.calib.localisation.py - continue work on localisation functions. [Neil Cook]
Constants.default.*.py - add localisation constant defintions. [Neil Cook]
Config.math.general.py - add measure_box_min_max, nanpolyfit. [Neil Cook]
Config.instruments.spirou.*.py - add localisation constants. [Neil Cook]
Output_filenames.py - make output file function generic. [Neil Cook]
File_definitions.py - make debug_back output generic to debug outputs. [Neil Cook]
Cal_loc_spirou.py - continue work on porting over cal_loc. [Neil Cook]
Cal_dark_spirou.py - modify how combine works for header input files. [Neil Cook]
Cal_badpix_spirou.py - modify how combine works for header input files. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Localisation.py - continue development from cal_loc. [Neil Cook]
Dark.py - continue development from cal_loc. [Neil Cook]
Badpix.py - continue development from cal_loc. [Neil Cook]
Background.py - continue development from cal_loc. [Neil Cook]
Update the language database. [Neil Cook]
Drs_fits.py - work on read/write single and multi functions (should be universal) + use @cusher Header class. [njcuk9999]
Constants.defaults.*.py - add cal_loc constants. [Neil Cook]
Config.__init__.py - add find_param (aliased to pcheck) to __init__ [Neil Cook]
Config.math - add a general math functions module (and nanpad/killnan functions) [Neil Cook]
Config.instruments.spirou.*.py - add cal_loc constants and definitions. [Neil Cook]
Drs_log.py - upgrade the find_param function to look in kwargs if definied. [Neil Cook]
Drs_file.py - move read and write to io module. [Neil Cook]
Config.core.default.*.py - add loc constants and definitions. [Neil Cook]
Cal_loc_spirou.py - continuing copying over and converting code. [Neil Cook]
Cal_badpix_spirou.py - make sure images are np.array copies. [Neil Cook]
Science/calib/dark.py - add dark correction function. [Neil Cook]
Drs_table.py - generalise lock functions. [Neil Cook]
Drs_path.py - pep8 corrections. [Neil Cook]
Drs_lock.py - generalise lock functions. [Neil Cook]
Constants/default - add initial cal_loc constants. [Neil Cook]
Config/instruments/spirou - add initial cal_loc constants. [Neil Cook]
Drs_startup.py - make lock functions more general and only index if recipe was successful. [Neil Cook]
Drs_database.py - add first methods for new Database class. [Neil Cook]
Update language database. [Neil Cook]
Cal_loc_spirou.py - first commit [unfinished] [Neil Cook]
Badpix.py - fix bugs with conversion. [Neil Cook]
Update language database. [Neil Cook]
Default_keywords - add default badpix keyword definitions. [Neil Cook]
Default_constant.py - add input kwargs. [Neil Cook]
Recipe_definitions.py - finalise cal_badpix definition. [Neil Cook]
Output_filenames.py - add badpix_file and backmap_file. [Neil Cook]
File_definitions.py - add out_badpix and out_backmap output files. [Neil Cook]
Default_keywords.py - add badpix header keywords. [Neil Cook]
Default_constants.py - add input kwargs. [Neil Cook]
Cal_preprocess_spirou.py - add dimanme for header of KW_INFILE1. [Neil Cook]
Cal_dark_spirou.py - change __NAME__ to all lower case. [Neil Cook]
Cal_badpix_spirou.py - update and finish first test. [Neil Cook]
Badpix.py - first commit - space for bad pixel map functions. [Neil Cook]
Background.py - first commit space for background functions. [Neil Cook]
Update language database. [Neil Cook]
Drs_fits.py - add flip_image function. [Neil Cook]
Default_config.py - add badpix values. [Neil Cook]
Default_config.py - add badpix values. [Neil Cook]
Cal_dark_spirou.py - change name of parmeter for combining files on input. [Neil Cook]
Cal_badpix_spirou.py - first commit [UNFINISHED] [Neil Cook]
Default_config.py - update version. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Drs_reset.py - first commit of reset code. [Neil Cook]
Drs_changelog.py - add comments and move text to language database. [Neil Cook]
Update language database. [Neil Cook]
Update language database. [Neil Cook]
Default_config.py - update version and date. [Neil Cook]
Drs_changelog.py - make sure we define outputs=None for recipe without outputs. [Neil Cook]
Psuedo_const.py - deal with DRS_DATA_MSG being None. [Neil Cook]
Drs_changelog.py - preview is in params[‘INPUT’] [Neil Cook]
Recipe_definitions.py - add definition for drs_changelog. [Neil Cook]
Drs_startup.py - allow no instrument to search for recipe name. [Neil Cook]
Update language database. [Neil Cook]
Param_functions.py - force printing to string. [Neil Cook]
Drs_changelog.py - update with new locations. [Neil Cook]
Default_config.py - give more space for version. [Neil Cook]
Drs_changelog.py - correct number of arguments for get_relative_folder. [Neil Cook]
Recipe_definitions.py - add change log definition. [Neil Cook]
Update database. [Neil Cook]
Drs_changelog.py - first commit of drs changelog for input redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Drs_startup.py - end with header. [Neil Cook]
Drs_log.py - tidy up logging messages. [Neil Cook]
Drs_log.py - tidy up logging messages. [Neil Cook]
Drs_file.py - remove references to hdict comments (now in fits.Header) [Neil Cook]
Drs_argument.py - do not print info. [Neil Cook]
Change text message. [Neil Cook]
Change text message. [Neil Cook]
Drs_startup.py - edit title. [Neil Cook]
Dark.py - remove warning about NaNs. [Neil Cook]
Drs_database.py - change how we access hdict. [Neil Cook]
Drs_file.py - deal with how to access hdict. [Neil Cook]
Drs_startup.py - edit logo. [Neil Cook]
Drs_startup.py - edit logo. [Neil Cook]
Drs_startup.py - edit logo. [Neil Cook]
Drs_startup.py - edit logo. [Neil Cook]
Drs_startup.py - edit logo. [Neil Cook]
Drs_startup.py - edit logo. [Neil Cook]
Drs_startup.py - edit logo. [Neil Cook]
Drs_startup.py - edit logo. [Neil Cook]
Drs_startup.py - edit logo. [Neil Cook]
Drs_startup.py - edit logo. [Neil Cook]
Drs_startup.py - edit logo. [Neil Cook]
Drs_file.py - header is now fits.Header not OrderedDict. [Neil Cook]
Rename drs to terrapipe. [Neil Cook]
Rename drs to terrapipe. [Neil Cook]
Merge branch ‘dev2’ into input_redo. [Neil Cook]
Merge branch ‘dev2’ into input_redo. [Neil Cook]
Recipes.spirou.cal_preprocess_spirou.py - chmod +x. [njcuk9999]
Recipes.spirou.cal_dark_spirou.py - chmod +x. [njcuk9999]
Config.instruments.spirou.default_keywords.py - correct KW_EXT_TYPE value (was a typo) [njcuk9999]
Drs_startup.py - don’t try to create folders when we don’t have nightname. [njcuk9999]
File_explorer.py - define a path for ds9 (will need moving to some installation specific place) and better deal with index col differences in error report. [njcuk9999]
Constants.default.pseudo_const.py - add changes from old code (version and pversion in index.fits) [njcuk9999]
Config.core.drs_file.py - fix bug “copy” –> “copyother” [njcuk9999]
Refactor new –> newcopy and copy –> copyother. [Neil Cook]
Update datacutmask. [Neil Cook]
Update language database. [Neil Cook]
Update constants/config/keywords. [Neil Cook]
Drs_recipe.py - update functions after run through. [Neil Cook]
Drs_file.py - update functions after run through. [Neil Cook]
Drs_database.py - update functions after run through. [Neil Cook]
Channge ErrorEntry and ErrorText to TextEntry and TextDict. [Neil Cook]
Drs_fits.py - deal with zero and one infiles separately. [Neil Cook]
Update language database. [Neil Cook]
Update constants files. [Neil Cook]
Delete drsmodule.config.database (moved to core in single .py file) [Neil Cook]
Drs_startup.py - add run function (to keep recipes clean) [Neil Cook]
Drs_database.py - update datebase setting (combine calib and telluric) [Neil Cook]
Cal_preprocess_spirou.py - update qc to match cal_dark. [Neil Cook]
Cal_dark_spirou.py - flesh out functionality. [Neil Cook]
Drsmodule.science.calib.dark.py - add measure_dark_badpix function. [Neil Cook]
Update language database. [Neil Cook]
Drsmodule.constants.default - add dark keys. [Neil Cook]
Drsmodule.config.instrument.spirou - add dark keys. [Neil Cook]
Drsmodule.config.database - first commit of database.py, calibdb.py, telludb.py. [Neil Cook]
Cal_dark_spirou.py - fill out more of the sections. [Neil Cook]
Dark.py - first commit add measure_dark function. [Neil Cook]
Drs_fits.py - add combine and resize functions. [Neil Cook]
Update language database. [Neil Cook]
Add new constants to constants/keyword files. [Neil Cook]
Drs_log.py - add find_param logger function. [Neil Cook]
Drs_file.py - add combine and get_key functions. [Neil Cook]
Blank_spirou.py - update the blank example script. [Neil Cook]
Cal_preprocess_spirou.py - move file processing to config.file_processing_update. [Neil Cook]
Cal_dark_spirou.py - start filling out code. [Neil Cook]
Update language database. [Neil Cook]
Drs_fits.py - add skeleton for combine function. [Neil Cook]
Drsmodule.constants.default.default_constants.py - add COMBINE_IMAGES constant. [Neil Cook]
Drsmodule.config.__init__.py - link to file_processing_update. [Neil Cook]
Instruments.spirou.recipe_definitions.py - add default value for combine option. [Neil Cook]
Instruments.spirou.default_constants.py - add combine_images constant. [Neil Cook]
Drs_startup.py - add general file processing logger. [Neil Cook]
Recipes.spirou.cal_preprocessing_spirou - continue input_redo. [Neil Cook]
Drsmodule.science.preprocessing - continue input_redo. [Neil Cook]
Drsmodule.locale - continue input_redo. [Neil Cook]
Drsmodule.io - continue input_redo. [Neil Cook]
Drsmodule.constants.default - continue input_redo. [Neil Cook]
Drsmodule.config.instruments - continue input_redo. [Neil Cook]
Drsmodule.config.core - continue input_redo. [Neil Cook]
Drsmodule.science.preprocessing - continue input_redo. [Neil Cook]
Drsmodule.locale - continue input_redo. [Neil Cook]
Drsmodule.io - continue input_redo. [Neil Cook]
Drsmodule.data - continue input_redo. [Neil Cook]
Drsmodule.constants.default - continue input_redo. [Neil Cook]
Drsmodule.constants.core - continue input_redo. [Neil Cook]
Drsmodule.config.instruments.spirou - continue input_redo. [Neil Cook]
Drsmodule.config.core - continue input_redo. [Neil Cook]
SpirouRecipe.py - continue input_redo. [Neil Cook]
Test_spirou.py - remove bad code (test to crash) [Neil Cook]
Identification.py - check file by copying drs_file over given_drs_file and then use self.check_file() [Neil Cook]
Drs_recipe.py - move checking functionality to drs_file. [Neil Cook]
Dsr_file.py - add copy function to drs_file. [Neil Cook]
Update language file. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Identification.py - start writing code to identify drs file. [Neil Cook]
File_definitions - change append to addset. [Neil Cook]
Drs_file.py - addset functions and plan new checking functions. [Neil Cook]
Update input redo - work on cal_preprocess. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Continue working on upgrade. [Neil Cook]
Continue working on upgrade. [Neil Cook]
Update language database. [njcuk9999]
Add placeholders for preprocessing functions. [njcuk9999]
Add spirou preprocessing recipe. [njcuk9999]
Update test recipes. [njcuk9999]
Fix module pathing system. [njcuk9999]
Config.__init__.py - add alias to get_locals. [njcuk9999]
Recipe_definitions - update preprocessing defintion. [njcuk9999]
Default_config.py - make plot variables an int. [njcuk9999]
Drs_startup.py - add temp messgae for loading arguments + add a code unsuccessful message. [njcuk9999]
Drs_recipe.py - change INPUT –> INTPUTS + make param dict. [njcuk9999]
Drs_log.py - sort out LOGGER_ERROR etc (now stored per PID + add Printer class (TLOG) to print temporary messages which disappear if no other text inbetween. [njcuk9999]
Drs_argument.py - add a new line in the debug messages (for Printer to be on new line) [njcuk9999]
Add __init__.py files to new folders. [njcuk9999]
Port_database.py - output more log messages. [njcuk9999]
Test_spirou.py - fix function call. [njcuk9999]
Update language database. [njcuk9999]
Constants_functions.py - fix problem with relative imports. [njcuk9999]
Recipe_definitions.py - make plot and integer and only allow values 0, 1, 2. [njcuk9999]
Drs_startup.py - fix the printing of arg log strings (arguments used) [njcuk9999]
Drs_recipe.py - fix missed error (should be from database) [njcuk9999]
Drs_arguemnt.py - allow arguments to specify a min and max value (and check for it) [njcuk9999]
Attempt to remove relative imports. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
File_explorer.py - move data loading / mask applying to different threads. [Neil Cook]
*.__init__.py - fix imports (should be empty) [Neil Cook]
Locale.core.__init__.py - fix imports (should be empty) [Neil Cook]
File_explorer.py - update length and add new instrument box. [Neil Cook]
File_explorer.py - update about statement. [Neil Cook]
File_explorer.py - continue upgrade. [Neil Cook]
File_explorer.py - continue upgrade. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
File_explorer.py - continue to write code. [Neil Cook]
File_explorer.py - add table. [Neil Cook]
Config.__init__.py: add aliases to __all__ [Neil Cook]
Drsmodule.io - need to import drs_log separately (drs_startup uses drs_table) [Neil Cook]
Find_error - change comment to better represent section. [Neil Cook]
Combine_index_files.py - pep8 changes. [Neil Cook]
File_explorer.py - app to find drs files. [Neil Cook]
Drs_table.py - update doc strings. [Neil Cook]
Drs_table.py - update doc strings. [Neil Cook]
Drs_lock.py - update doc strings. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Added a misc folder and a first misc script. [Neil Cook]
Recipes/test/* - update paths to drs_setup (via config) [Neil Cook]
__init__.py - add a functions section (currently blank) [Neil Cook]
Tools.* - update paths to drs_setup (via config) [Neil Cook]
Plotting.* - update paths to drs_setup (via config) [Neil Cook]
Io.* - update paths to drs_setup (via config) [Neil Cook]
Config.__init__.py - add aliases to functions that will be used lots. [Neil Cook]
Drs_startup.py - continue improvements to documentation. [Neil Cook]
User_config.ini[NIRPS] - update DRS_PLOT value and comment (now an int [0, 1, 2]) [Neil Cook]
Drs_text.py - make get_relative_folder a public function. [Neil Cook]
Find_error.py - update doc strings to pep8 standards. [Neil Cook]
Find_error.py - update comments. [Neil Cook]
Find_error.py - add drop down instrument box. [Neil Cook]
Find_error.py - improve gui. [Neil Cook]
Drs_setup - add better doc strings. [Neil Cook]
Find_error.py - continued to work on application. [njcuk9999]
Drs_text.py - got args for language database reads. [njcuk9999]
Constant_functions.py - added the source to dtype errors in config files. [njcuk9999]
Drs_startup.py - allowed instrument to be None. [njcuk9999]
Tool to find error codes in database/code. [njcuk9999]
Drs general - initialise new sub package folders. [Neil Cook]
Drs general - initialise new sub package folders. [Neil Cook]
Merge remote-tracking branch ‘origin/input_redo’ into input_redo. [Neil Cook]

Conflicts:
INTROOT2/drsmodule/config/core/drs_startup.py
Default_config.py - add DRS_DATA_PLOT. [Neil Cook]
Add drs_data_plot to start up parameters. [Neil Cook]
Drs_recipe.py - change plotting mode - only if drs_plot is 1 (to screen) [Neil Cook]
User_config.ini - add plot modes (instead of bool) [Neil Cook]

0.5.014 (2019-06-11)¶

SpirouReprocess.py - add processing (parallalised) to reprocess. [Neil Cook]
SpirouImage.py - fix small bug with position of log message. [Neil Cook]
Multiprocess_test.py - test of multiple. [Neil Cook]

0.5.013 (2019-06-10)¶

SpirouReprocess.py - first commit reworking of reprocessing script and run files (works for unit test and any/all reprocessing) [Neil Cook]
Correct names. [Neil Cook]
Bin folder - add __args__ and __required__ [Neil Cook]
SpirouImage.py - add in shape qc. [Neil Cook]
Constants_SPIROU_H4RG.py - add in shape qc. [Neil Cook]
Cal_shape_master_spirou.py - add in QC (std of shape map) [Neil Cook]
SpirouConst.py - remove overlap file and add SLIT_SHAPE_BDXMAP_FILE debug file. [Neil Cook]
Cal_shape_spirou.py - produce debug plots to check transform for the input fp file + save master shape (x/y) files to header. [Neil Cook]
Cal_shape_master_spirou.py - straighten the dxmap (using dymap) and save the bent dxmap as debug product. [Neil Cook]
SpirouBACK.py - add correction_thermal2 functionality. [Neil Cook]
Recipe_control.txt - add new name for cal_shape_master (cal_shape_master_spirou) [Neil Cook]
Constants_SPIROU_H4RG.py - add more thermal constants and correct thermal correction types to single fiber values. [Neil Cook]
Cal_shape_master_spirou.py - correct both dx and dy maps. [Neil Cook]
Cal_extract_RAW_spirou.py - thermal correction must be based on individual fiber type not DPRTYPE. [Neil Cook]

0.5.012 (2019-06-08)¶

SpirouUnitRecipes.py - remove cal_SHAPE_spirou and add cal_shape_spirou. [Neil Cook]
SpirouImage.py - add new loading functions (for new calibDB files) [Neil Cook]
SpirouPlot.py - add new thermal_background_debug_plot function. [Neil Cook]
SpirouKeywords.py - add shape and new cdb keys. [Neil Cook]
SpirouConst.py - add SLIT_SHAPE_LOCAL_FILE + fix slit_SHAPE functions. [Neil Cook]
SpirouBACK.py - add correction_thermal, correction_thermal1 and correction_thermal2. [Neil Cook]
Reset_calibDB - add tapas_all_sp.fits.gz to calibDB. [Neil Cook]
Recipe_control.txt - add cal_shape_spirou.py. [Neil Cook]
Output_keys.py - add local shape to tags. [Neil Cook]
Cal_SHAPE_spirou.py - moved from bin folder (now old code) [Neil Cook]
Constants_SPIROU_H4RG.py - add thermal constants. [Neil Cook]
Cal_shape_spirou.py - first commit new local shape recipe. [Neil Cook]
Cal_shape_master_spirou.py - put FPMASTER in calibDB. [Neil Cook]
Cal_FF_RAW_spirou.py - add FP master file getting. [Neil Cook]
Cal_extract_RAW_spirou.py - add thermal correction (untested) [Neil Cook]

0.5.011 (2019-06-07)¶

Cal_shape_master.py - apply dxmap and dymap + remove reference to FPFILES (–> FPFILE) [Neil Cook]
SpirouLOCOR.py - add modifications for new shape parameters. [Neil Cook]
SpirouImage.py - continue working on new shape functionality. [Neil Cook]
SpirouEXTOR.__init__.py - add alias to CleanHotpix. [Neil Cook]
SpirouMath.py - change how IUVSpline deals with NaNs (full set of NaNs and group of Nans –> fill with linear interp) [Neil Cook]
SpirouKeywords.py - add backgroun key and new shape header keys. [Neil Cook]
SpirouBACK.py - return background filename for adding to header. [Neil Cook]
Cal_shape_master.py - correct change to table (needed extra term) [Neil Cook]
Cal_SHAPE_spirou_old.py - add changes for background file loading. [Neil Cook]
Constants_SPIROU_H4RG.py - add shape master/local qc parameters. [Neil Cook]
Cal_SLIT_spirou.py - add changes for background file loading. [Neil Cook]
Cal_shape_master.py - add changes from Etiennes redo. [Neil Cook]
Cal_loc_RAW_spirou.py - add changes for background file getting. [Neil Cook]
Cal_ff_raw_spirou.py - add changes for new shape files. [Neil Cook]
Cal_extract_RAW_spirou.py - add changes for new shape files. [Neil Cook]

0.5.010 (2019-06-06)¶

SpirouImage.py - add get_x_shape_map and get_y_shape_map functions and aliases. [Neil Cook]
SpirouPlot.py - add shape_linear_trans_param_plot debug plot. [Neil Cook]
SpirouConst.py - add dxmap, dymap and fpmaster file defintions. [Neil Cook]
Output_keys.py - add dxmap, dymap and fpmaster file tags. [Neil Cook]
Register_fp_2.py - add etiennes additional changes. [Neil Cook]
Cal_SHAPE_spirou_old.py - refractor file name. [Neil Cook]
Constants_SPIROU_H4RG.py - add new shape_master constants. [Neil Cook]
Cal_shape_master.py - continue adapting cal_shape_master to handle dxmap and dymap. [Neil Cook]
Cal_SHAPE_spirou.py - refractor filename (now need sape x and shape y) [Neil Cook]
Cal_shape_master.py - continue adding etiennes changes. [Neil Cook]
Cal_extract_RAW_spirou.py - write todos. [Neil Cook]

0.5.009 (2019-06-05)¶

SpirouImage.py - start adding etiennes new adaptations to register_fp_2. [Neil Cook]
Register_fp_2.py - add etiennes new register fp code. [Neil Cook]
Calc_berv.py - add berv source / berv est. [Neil Cook]
SpirouTelluric.py - move get_berv_value to spirouImage(spirouBERV) [Neil Cook]
SpirouBERV.py - add get_berv_value and modify current functions to add berv estimate + lock berv while calculating barycorrpy. [Neil Cook]
SpirouTDB.py - correct pep8. [Neil Cook]
SpirouKeywords.py - add berv est and berv source. [Neil Cook]
Test_bigcube_berv.py - add berv/berv_est test. [Neil Cook]
Obj_mk_tellu_new.py - change how berv is obtained. [Neil Cook]
Obj_fit_tellu.py - change how berv is obtained. [Neil Cook]
Cal_extract_RAW_spirou.py - add berv estimate and berv source. [Neil Cook]
Cal_CCF_E2DS_spirou.py - add berv estimate and berv source. [Neil Cook]
Berv_estimate_comparison.py - test and compare berv estimate to barycorrpy. [Neil Cook]

0.5.008 (2019-06-04)¶

SpirouImage.py - correction to register_fp. [Neil Cook]
SpirouKeywords.py - estimated BERV keys added. [Neil Cook]
Cal_extract_RAW_spirou.py - estimated BERV keys added to hdict. [Neil Cook]
SpirouBERV.py - add implementation of BERV_EST and use lock file to only open one BERV instance. [Neil Cook]
SpirouEXTOR.py - add quick mode for clean_hotpix. [Neil Cook]
Merge_fp_fp.py - correct typo for print statement. [Neil Cook]
Constants_SPIROU_H4RG.py - add a way to turn off certain features that slow down the code (not to be used for science data) [Neil Cook]
SpirouImage.py - correct construct_master_fp. [njcuk9999]

0.5.007 (2019-06-03)¶

Cal_shape_master.py - continued work integrating fp master function. [njcuk9999]
SpirouImage.py - continued work on FP master functions. [njcuk9999]
Cal_shape_master.py - change input to 1 hchc and 1 fpfp. [njcuk9999]
SpirouImage.py - add construct_master_fp, group_files_by_time and register_fp functions (for cal_shape_master and cal_dark_master) [njcuk9999]
Recipe_control.txt - add cal_shape_master.py to recipe control. [njcuk9999]
Merge_fp_fp.py - etiennes merge fp code. [njcuk9999]
Constants_SPIROU_H4RG.py - add the cal_shape_master constants. [njcuk9999]
Cal_shape_master.py - first commit - copy of cal_SHAPE_spirou.py - with additions from Etienne for making the fp master file. [njcuk9999]
Cal_dark_master_spirou.py - remove code in common with shape master into function. [njcuk9999]
Merge branch ‘neil’ into dev. [njcuk9999]
Merge pull request #566 from njcuk9999/header-copy-exact. [Neil Cook]

Header Copy Exact – also implemented into INTROOT2 in input_redo branch
Merge pull request #565 from njcuk9999/db-lock-fix. [Neil Cook]

DB lock check retry bug - Okay this one I can merge with both INTROOT and INTROOT2!
Fixed a bug with db locking check. [Chris Usher]

0.5.006 (2019-06-01)¶

Updated to match changes on dev. [Chris Usher]
Reworked how fits headers are used. [Chris Usher]
Update test.run. [Neil Cook]
SpirouImage.py - change dark calibration to dark_master calibration, make sure read_raw_data loading primary data array. [Neil Cook]
SpirouFITS.py - adjust read_raw_data to add an imageext (otherwise defaults 0) [Neil Cook]
Recipe_control.txt - add cal_dark_master and cal_thermal_spirou. [Neil Cook]
Cal_thermal_spirou.py - renamed from cal_thermal2_spirou.py. [Neil Cook]

0.5.005 (2019-05-30)¶

SpirouBERVest.py - first commit (test of berv estimate) [Neil Cook]
SpirouConst.py - add filename to EXTRACT_E2DS_FILE. [Neil Cook]
Constants_SPIROU_H4RG.py - add always_extract. [Neil Cook]
Cal_thermal_spirou.py - continue work. [Neil Cook]
Cal_thermal2_spirou.py - extraction of darks (using cal_extract) [Neil Cook]
Merge branch ‘thermal’ into dev. [Neil Cook]
Merge branch ‘master’ into thermal. [njcuk9999]
First commit of thermal recipe for Low pass dark/thermal calibration. [njcuk9999]
Add fiber to header. [Neil Cook]
Add “DRS_DATE” and “DATE_NOW” to all recipes. [Neil Cook]
Cal_dark_master_spirou.py - fix bugs in while loop. [Neil Cook]

0.5.004 (2019-05-29)¶

SpirouImage.py - correct get_files function. [Neil Cook]
SpirouEXTOR.py - fix comment typos. [Neil Cook]
SpirouKeywords.py - add dark master keys. [Neil Cook]
SpirouConst.py - add DARK_FILE_MASTER function. [Neil Cook]
Output_keys.py - add dark_master_file tag. [Neil Cook]
Constants_SPIROU_H4RG.py - add cal_dark_master constants. [Neil Cook]
Cal_DARK_spirou.py - correct typo. [Neil Cook]
Cal_dark_master_spirou.py - continue adapting new recipe. [Neil Cook]

0.5.003 (2019-05-28)¶

SpirouImage.py - add get_files function. [njcuk9999]
SpirouImage.py - add get_files function. [njcuk9999]
Hp_dark.py - store EA cal_dark_master code (raw) [njcuk9999]
Constants_SPIROU_H4RG.py - add dark_master constant to constants. [njcuk9999]
Cal_dark_master_spirou.py - first commit - first integration of EA code. [njcuk9999]
SpirouKeywords.py - INFILE should be INF1, INF2, INF3. [njcuk9999]
Update date/version/changelog. [njcuk9999]
Cal_HC_E2DS_EA_spirou.py - CDBBAD –> CDBLAZE. [njcuk9999]

0.5.002 (2019-05-27)¶

SpirouPlot.py - add output_rv to ccf_rv_ccf_plot. [njcuk9999]
SpirouKeywords.py - add new CCF keyword defintions. [njcuk9999]
Cal_CCF_E2DS_spirou.py - renamed from cal_CCF_E2DS_FP_spirou.py. [njcuk9999]
Deal with move of cal_CCF_E2DS_FP_spirou.py. [njcuk9999]
Move older CCF recipes to misc folder. [njcuk9999]
Removed old cal_CCF_E2DS_spirou.py. [njcuk9999]
Cal_CCF_E2DS_spirou.py - from cal_CCF_E2DS_FP.py + cosmetic changes. [njcuk9999]
Cal_CCF_E2DS_FP_spirou.py - add changes to allow science without FP. [njcuk9999]
Cal_FF_RAW_spirou.py - IC_EXTRACT_TYPE –> IC_FF_EXTRACT_TYPE (always for cal_FF) [njcuk9999]
SpirouTelluric.py - change parameter name MKTELLU_MED_SAMPLING –> IMAGE_PIXEL_SIZE. [njcuk9999]
SpirouLOCOR.py - add curve drop parameter. [njcuk9999]
Constants_SPIROU_H4RG.py - change loc threshold. [njcuk9999]
SpirouKeyword.py - Add key word for CCF (telluric cut) [njcuk9999]
Constants_SPIROU_H4RG.py - add new constants for CCF. [njcuk9999]
Cal_loc_RAW_spirou.py - correct a bug in DEBUG (should be > 0) [njcuk9999]
Cal_CCF_E2DS_FP_spirou.py - add changes from @Francois for CCF masked by tellurics. [njcuk9999]
Cal_CCF_E2DS_FP_spirou_new.py - modify line endings. [njcuk9999]
Cal_CCF_E2DS_FP_spirou_new.py - francois changes to cal ccf (to be integrated into cal_CCF actual) [njcuk9999]

0.5.001 (2019-05-27)¶

Merge branch ‘master’ into neil. [Neil Cook]
SpirouConst.py - fix s1d names. [Neil Cook]
SpirouStartup.py - fix the windows/unix night_name bug. [Neil Cook]
SpirouFITS.py, spirouDB.py - reset. [Neil Cook]
SpirouFITS.py, spirouDB.py - fix problem with windows and lock file including paths that do not exist (i.e. when using night names with sub-directories) [Neil Cook]
SpirouFITS.py, spirouDB.py - fix problem with windows and lock file including paths that do not exist (i.e. when using night names with sub-directories) [Neil Cook]
SpirouFITS.py, spirouDB.py - fix problem with windows and lock file including paths that do not exist (i.e. when using night names with sub-directories) [Neil Cook]
Extract_trigger.py - update run. [Neil Cook]
SpirouConst.py - _w_ –> _v_ [Neil Cook]
Update settings for reprocess extract tellu/obj run for May pernight/perrun runs. [Neil Cook]
Move unused test modules to misc. [Neil Cook]
Drs_dependencies.py - add a debug mode. [Neil Cook]
Select_per_tc_per_night_calibs.py - add Feb and April runs to the per run selection. [Neil Cook]
Update date/version/update notes/changelog. [Neil Cook]

0.5.000 (2019-05-10)¶

SpirouDB.py - add lock file in waiting printout. [Neil Cook]
SpirouPlot.py - attempt to setup_figure a second time before crashing. [Neil Cook]
SpirouPlot.py - attempt to setup_figure a second time before crashing. [Neil Cook]
Update test.run. [Neil Cook]
SpirouPlot.py - fix to plot crash. [Neil Cook]
Update changelog.md. [Neil Cook]
Extract_trigger.py - modify extract trigger. [Neil Cook]
SpirouTDB.py - add locking of file in put_file. [Neil Cook]
SpirouCDB.py - add locking of file in put_file. [Neil Cook]
Update date and changelog. [Neil Cook]
SpirouCDB.py - fix calibDB file copy in parallisation. [Neil Cook]
Extract_trigger.py - note problem with parallisation. [Neil Cook]
Update changelog.md. [Neil Cook]
Extract_trigger.py - update comments. [Neil Cook]
Changelog.md - update the change log with new commits. [Neil Cook]
Update test.run. [Neil Cook]
Extract_trigger.py - add email option (start + end) [Neil Cook]
SpirouPlot.py - add fix for large files saved to disk (should be temporary fix) [Neil Cook]
SpirouLOG.py - clear out logs after run. [Neil Cook]
SpirouImage.py - replace IC_S1D_BLAZE_MIN with TELLU_CUT_BLAZE_NORM. [Neil Cook]
SpirouConst.py - update version/changelog/constants file. [Neil Cook]
Comp_s1d_to_s2d.py - add a normalised blaze cut. [Neil Cook]
Constants_SPIROU_H4RG.py - change the blaze min value. [Neil Cook]
Comp_s1d_to_s2d.py - compare the output of s1d to s2d. [Neil Cook]
Test.run - update text.run. [Neil Cook]
Time_log_file.py - code to measure timing of log printouts. [Neil Cook]
Constnats_SPIROU_H4RG.py - update s1d starting wavelength from 980 to 965. [Neil Cook]
Changed permissions on new tools in spirouTools. [Neil Cook]
SpirouMath.py - add nanpad and killnan functions. [Neil Cook]
SpirouBACK.py - re-add warning around backmask condition. [Neil Cook]
Constants_SPIROU_H4RG.py - chagne IC_BKGR_BOXSIZE from 64 to 128. [Neil Cook]
Drs_local_background.py - first commit - code to find amplitude scale for local background (using DARK_FLAT) [Neil Cook]
SpirouPlot.py - add local_scattered_light_plot. [Neil Cook]
SpirouBACK.py - add function make_local_background_map and measure_local_background. [Neil Cook]
Recipe_control.txt - add drs_local_background to valid receipes. [Neil Cook]
Constants_SPIROU_H4RG.py - add constants for drs_local_background.py. [Neil Cook]
Constants_SPIROU_H4RG.py - update ic_bkgr_percent value. [Neil Cook]
SpirouBACK.py - add adjustments to background correction. [Neil Cook]
SpirouBACK.py - fix some bugs with measure background from map function. [Neil Cook]
Update test.run. [Neil Cook]
Cal_BADPIX_spirou.py - background addition - fix typo in new file upload to calibDB. [Neil Cook]
SpirouBACK.py - return background image only. [Neil Cook]
Cal_extract,FF,loc,SHAPE,slit - replace old background measurement with new one. [Neil Cook]
SpirouBACK.py - correct bug in new function. [Neil Cook]
Constants_SPIROU_H4RG.py - change background from 5 to 10. [Neil Cook]
Cal_BADPIX_spirou.py - resize flat as well as bad pixel. [Neil Cook]
SpirouImage.py - add function get_background_map. [Neil Cook]
SpirouConst.py - add function BKGD_MAP_FILE. [Neil Cook]
SpirouBACK.py - add functions: make_background_map and measure_background_from_map. [Neil Cook]
Output_keys.py - add background map tag. [Neil Cook]
Constants_SPIROU_H4RG.py - add new background map constants. [Neil Cook]
Cal_BADPIX_spirou.py - add the background map making and save to calibDB. [Neil Cook]
Merge branch ‘dev2’ [Neil Cook]

Conflicts:
INTROOT/SpirouDRS/spirouUnitTests/Runs/test.run
Remove CHANGELOG.md. [Neil Cook]
Update changelog. [Neil Cook]
Test.run. [Neil Cook]

0.4.123 (2019-05-03)¶

Drs_changelog_2.py - update comments for new changelogger. [Neil Cook]
Extract_trigger.py - update bugs. [Neil Cook]
SpirouUnitRecipes.py - update for fit_tellu_db. [Neil Cook]
Extract_trigger.py - update for fit_tellu_db. [Neil Cook]
SpirouTelluric.py - remove the print statement. [Neil Cook]
Obj_fit_tellu_db.py - add in second making of the target template. [Neil Cook]
Update date/version/changelog. [Neil Cook]
Drs_changelog_2.py - add changes to allow preview mode. [Neil Cook]
Obj_fit_tellu_db.py - correct type in wlog message. [Neil Cook]
SpirouTelluric.py - p[‘OBJECTS’] when None will be a string. [Neil Cook]
Obj_fit_tellu_db.py - add full run through 1. fit_tellu 2. mk_template 3. fit_tellu. [Neil Cook]
SpirouTelluric.py - need to clean out sys.argv before running codes. [Neil Cook]
SpirouDB.py - need to make sure folder exists otherwise lock will persist. [Neil Cook]
Obj_fit_tellu_db.py - correct bug in writing code. [Neil Cook]
SpirouTelluric.py - add find_objects function and alias. [Neil Cook]
Constants_SPIROU_H4RG.py - correction to comments. [Neil Cook]
Obj_fit_tellu_db.py - first commit of fit tellu db redo. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.4.122 (2019-05-02)¶

Drs_changelog_2.py - add updating of drs files. [Neil Cook]
Drs_changelog_2.py - add updating of drs files. [Neil Cook]
Update_fileversion.py - add extra code to fix the fix. [Neil Cook]
Drs_changelog_2.py - update new change log code. [Neil Cook]
Add git tools to replace drs_changelog. [Neil Cook]
Add git tools to replace drs_changelog. [Neil Cook]
Update_fileversion.py - remove skip file check. [Neil Cook]
SpirouConst.py - add new filenames. [Neil Cook]
Output_keys.py - add tellu s1d keys. [Neil Cook]
Update_fileversion.py - first commit fix code for bad header keys. [Neil Cook]
Obj_fit_tellu.py - remove old header keys. [Neil Cook]
Cal_extract_RAW_spirou.py - remove old header keys. [Neil Cook]
Update version. [Neil Cook]

0.4.121 (2019-04-30)¶

Update trigger. [Neil Cook]
Obj_fit_tellu.py - fix NBLAZE to BLAZE in uniform velocity s1d. [Neil Cook]

0.4.120 (2019-04-29)¶

Compare_outputs.py - change paths. [Neil Cook]

0.4.119 (2019-04-26)¶

Extract_trigger.py - correct mistake with extraction trigger. [Neil Cook]
Update test.run. [Neil Cook]
SpirouTable.py - fix problem with NaNs in header (make string) [Neil Cook]
SpirouTable.py - fix problem with NaNs in header (make string) [Neil Cook]
Extract_trigger.py - should use DRS_DATA_RAW in preprocessing. [Neil Cook]
Obj_fit_tellu.py - add s1d telluric corrected files. [Neil Cook]
SpirouImage.py - correct s1d ith telluric NaNs. [Neil Cook]
Obj_fit_tellu.py - change to NBLAZE. [Neil Cook]
SpirouImage.py - new s1d - deal with full order being NaNs (for telluric) [Neil Cook]
Obj_fit_tellu.py - save s1d for corrected spectrum. [Neil Cook]
Constants_SPIROU_H4RG.py - increase edge smoothing size. [Neil Cook]
Constants_SPIROU_H4RG.py - increase edge smoothing size. [Neil Cook]
Constants_SPIROU_H4RG.py - increase edge smoothing size. [Neil Cook]
Cal_extract_RAW_spirou.py - s1d fix problems with adding new s1d code. [Neil Cook]
Cal_extract_RAW_spirou.py - s1d fix problems with adding new s1d code. [Neil Cook]
SpirouImage.py - new s1d - iuv spline wrong. [Neil Cook]
SpirouImage.py - edges was wrong. [Neil Cook]
Cal_extract_RAW_spirou.py - correct s1d (now s1dw and s1dv) [Neil Cook]

0.4.118 (2019-04-25)¶

SpirouImage.py - write new s1d function. [Neil Cook]
SpirouPlot.py - add ext_1d_spectrum_debug_plot plot for debugging s1d plot. [Neil Cook]
Constants_SPIROU_H4RG.py - add new s1d constants. [Neil Cook]
Cal_extract_RAW_spirou.py - added new s1d code (not finished) [Neil Cook]
SpirouRV.py - update pearson r test for NaNs. [Neil Cook]
Update test.run. [Neil Cook]
SpirouRV.py - catch NaN warnings that are valid. [Neil Cook]
SpirouRV.py - catch NaN warnings that are valid. [Neil Cook]
SpirouRV.py - catch NaN warnings that are valid. [Neil Cook]
SpirouRV.py - catch NaN warnings that are valid. [Neil Cook]
SpirouRV.py - looking for NaN warnings. [Neil Cook]
SpirouRV.py - looking for NaN warnings. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - looking for NaN warnings. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - looking for NaN warnings. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - looking for NaN warnings. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - looking for NaN warnings. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - looking for NaN warnings. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - looking for NaN warnings. [Neil Cook]
SpirouTelluric.py - catch warnings from less than for NaNs. [Neil Cook]
Compare_outputs.py - script to difference all outputs in two folders with files of the same name (output difference) [Neil Cook]
Constants_SPIROU_H4RG.py - turn off plotting all fit_tellu orders. [Neil Cook]
Obj_mk_tellu_new.py - add warning around less than (for NaNs) [Neil Cook]
Obj_fit_tellu.py - remove a NaN sum. [Neil Cook]
Test.run - update just mk_tellu/fit_tellu to test. [Neil Cook]
Test.run - update just fit_tellu to test. [Neil Cook]
Change np.sum –> np.nansum, np.mean –> np.nanmean, np.median –> np.nanmedian etc. [Neil Cook]

0.4.117 (2019-04-24)¶

Change all np.polyfit to SpirouDRS.spirouCore.spirouMath.nanpolyfit. [Neil Cook]
Change all np.polyfit to SpirouDRS.spirouCore.spirouMath.nanpolyfit. [Neil Cook]
Change all np.polyfit to SpirouDRS.spirouCore.spirouMath.nanpolyfit. [Neil Cook]
Change all np.polyfit to SpirouDRS.spirouCore.spirouMath.nanpolyfit. [Neil Cook]
Change all np.polyfit to SpirouDRS.spirouCore.spirouMath.nanpolyfit. [Neil Cook]
Change all np.polyfit to SpirouDRS.spirouCore.spirouMath.nanpolyfit. [Neil Cook]
Change all np.polyfit to SpirouDRS.spirouCore.spirouMath.nanpolyfit. [Neil Cook]
Change the way InterpolatedUnivariateSpline works. [Neil Cook]
Update test.run. [Neil Cook]
Update test.run. [Neil Cook]

0.4.116 (2019-04-10)¶

Update test.run. [njcuk9999]
SpirouRV.py - deal with NaNs. [njcuk9999]
SpirouLOCOR.py - deal with NaNs. [njcuk9999]
SpirouImage.py - deal with NaNs. [njcuk9999]
SpirouPlot.py - convert zeros to NaNs. [njcuk9999]
See_shift.py - test for pixel shifting by different amounts. [njcuk9999]
Cal_WAVE_E2DS_EA_spirou.py - convert zeros to NaNs. [njcuk9999]
Cal_SLIT_spirou.py - change zeros to NaNs. [njcuk9999]
Cal_loc_RAW_spirou.py - change zeros to NaNs. [njcuk9999]
Cal_extract_RAW_spirou.py - change zeros to NaN. [njcuk9999]

0.4.115 (2019-04-08)¶

SpirouEXTOR.py - add options in extraction method to test different weighting systems. [njcuk9999]
SpirouImage.py - replace zeros with NaNs. [njcuk9999]
SpirouFLAT.py - replace zero’s with NaNs. [njcuk9999]
SpirouEXTOR.py - replace zeros with NaNs. [njcuk9999]
SpirouPlot.py - replace zeros with NaNs. [njcuk9999]
SpirouBACK.py - replace zeros with NaNs. [njcuk9999]
Cal_FF_RAW_spirou.py - replace zeros with nans. [njcuk9999]
SpirouEXTOR.py - readd raw_weights. [njcuk9999]

0.4.114 (2019-04-07)¶

Cal_FF_RAW_spirou.py - re-add in new background subtraction. [Neil Cook]
SpirouEXTOR.py - reset raw_weights. [Neil Cook]
SpirouEXTOR.py - reset raw_weights. [Neil Cook]
Cal_FF_RAW_spirou.py - try to match neil branch. [Neil Cook]
Cal_FF_RAW_spirou.py - try to match master. [Neil Cook]
Cal_FF_RAW_spirou.py - test force extractff type to 3c. [Neil Cook]
SpirouBACK.py - add in old measure background function (as test) [Neil Cook]
Cal_FF_RAW_spirou.py - redo debananafication. [Neil Cook]
Cal_FF_RAW_spirou.py - undo debananafication. [Neil Cook]
Reset cal_loc (no background) for test. [Neil Cook]
Reset cal_loc (no background) for test. [Neil Cook]
Cal_FF_RAW_spirou.py - remove background subtraction (for test) [Neil Cook]

0.4.113 (2019-04-06)¶

Cal_FF_RAW_spirou.py - remove background subtraction (for test) [Neil Cook]
Test.run - update test.run. [Neil Cook]
Cal_FF_RAW_spirou.py - unfix negative values set to zero. [Neil Cook]

0.4.112 (2019-04-05)¶

SpirouEXTOR.py - remove weighting of raw pixels less than zero to very low value. [njcuk9999]
SpirouConst.py - update date and version. [njcuk9999]
Cal_SHAPE_spirou_old.py - edit background correction. [njcuk9999]
Cal_SLIT_spirou.py - do not mask out the zeros. [njcuk9999]
Caal_loc_RAW_spirou.py - do not mask out the zeros. [njcuk9999]
Cal_FF_RAW_spirou.py - do not mask out the zeros. [njcuk9999]
Cal_extract_RAW_spirou.py - do not mask out the zeros. [njcuk9999]
Merge branch ‘neil’ into dev. [njcuk9999]
SpirouBACK.py - add background debug plot to background finding function. [njcuk9999]
Cal_SLIT_spirou.py - add hdr and cdr to background correction (to save debug file) [njcuk9999]
Cal_loc_RAW_spirou.py - add hdr and cdr to background correction (to save debug file) [njcuk9999]
Cal_extract_RAW_spirou.py - add hdr and cdr to background correction (to save debug file) [njcuk9999]
Cal_FF_RAW_spirou.py - add hdr and cdr to background correction (to save debug file) [njcuk9999]
Misc/cal_SHAPE_spirou_old.py - add changes to background subtraction. [njcuk9999]
Cal_low_RAW_spirou.py - add changes to background subtraction. [njcuk9999]
Cal_FF_RAW_spirou.py - add changes to background subtraction. [njcuk9999]
SpirouWAVE.py - add initial keep parameter for line width. [njcuk9999]
SpirouBACK.py - add Etienne’s changes into measure_background_flatfield. [njcuk9999]
Cal_WAVE_NEW_E2DS_spirou_2.py - add fix for updating the HC/Fp header for wave solution. [njcuk9999]
Constants_SPIROU_H4RG.py - change background correction constants. [njcuk9999]
Cal_extract_RAW_spirou.py - change background correction to Etienne’s new method! [njcuk9999]

0.4.111 (2019-04-04)¶

Cal_SHAPE_spirou.py - fix typo in output filenames (only affected debug outputs) [njcuk9999]
Cal_CCF_wrap_MH.py - fix typo in return table values ‘cloc’ –> ‘loc’ [njcuk9999]
Cal_CCF_wrap_MH.py - call from command line was missing. [njcuk9999]
Cal_CCF_wrapper changes for Melissa (temporary addition of cal_CCF_E2DS_FP_MH_spirou.py) [njcuk9999]

0.4.108 (2019-04-03)¶

SpirouPlot.py - allow all orders to be plot in tellu plot. [Neil Cook]

0.4.109 (2019-04-03)¶

Update test.run. [njcuk9999]
SpirouWAVE.py - comment out non-used line. [njcuk9999]
SpirouDrs.data - undo changes from Melissa Branch. [njcuk9999]
Config.py - undo changes from Melissa Branch. [njcuk9999]
Cal_WAVE_E2DS_EA_spirou.py - undo changes from Melissa branch. [njcuk9999]
Cal_extract_RAW_spirou.py - add WFP keys to cal extract and deal with not having values. [njcuk9999]
Merge branch ‘neil’ into dev. [njcuk9999]
SpirouEXTOR.py - fix normalisation of spelong (E2DSLL) [njcuk9999]
Cal_extract_RAW_spirou.py - add WFP keys to cal extract. [njcuk9999]
Cal_CCF_E2DS_FP_spirou.py - replace manual call to filename. [njcuk9999]

0.4.110 (2019-04-03)¶

Cal_WAVE_NEW: fixes to m(x) residuals plot. [melissa-hobson]
Cal_CCF_E2DS_FP: keeps base name only for WFP file. [melissa-hobson]
Cal_WAVE_E2DS_EA: save wave FP CCF keys. [melissa-hobson]
Cal_WAVE_NEW: save wave FP CCF target RV and width. [melissa-hobson]
Cal_CCF_E2DS_FP: writes WFP keys to CCF headers properly. [melissa- hobson]
Cal_CCF_E2DS_FP: read correct keyword for drift. [melissa-hobson]
Cal_CCF_E2DS_FP: reads correct keyword for wave sol drift, writes WFP keys to CCF headers spirouKeywords: added unique WFP file source keyword. [melissa-hobson]
SpirouKeywords: add wave FP CCF keys to list. [melissa-hobson]

0.4.107 (2019-04-02)¶

Cal_WAVE_NEW: modified FP CCF keywords spirouKeywords: added unique WFP keywords for wave FP CCF keys. [melissa-hobson]
Merge branch ‘melissa’ of https://github.com/njcuk9999/spirou_py3 into melissa. [melissa-hobson]
Merge branch ‘master’ into melissa. [Melissa Hobson]

Conflicts:
INTROOT/SpirouDRS/spirouTHORCA/spirouWAVE.py INTROOT/bin/cal_WAVE_E2DS_EA_spirou.py INTROOT/misc/cal_HC_E2DS_spirou.py INTROOT/misc/wave_comp_night.py
Merge branch ‘melissa’ of https://github.com/njcuk9999/spirou_py3 into melissa. [melissa-hobson]
Config save. [melissa-hobson]

0.4.106 (2019-03-29)¶

Github backup before merging with master. [melissa-hobson]
Cal_WAVE_NEW improved cross-order matching. [melissa-hobson]

0.4.104 (2019-03-28)¶

Fix bug in extraction modes for cal_exposure_meter and cal_wave_mapper. [Neil Cook]
Cal_FF_RAW_spirou.py - missed the debananafication. [Neil Cook]
Cal_extract/cal_ff - fix mode extract_shape/ll. [Neil Cook]
Cal_extract/cal_FF - fix mode selection. [Neil Cook]
SpirouImage.py - DeBananafication needs ParamDict in function call. [Neil Cook]
Make_1ds_etienne_new.py - new s1d code to integrate into the drs. [Neil Cook]
SpirouImage.py - fix for use of DeBananafication since change to function (for cal_SHAPE here) [Neil Cook]
Update date/version/changelog/update_notes. [Neil Cook]

0.4.102 (2019-03-28)¶

Cal_extract_RAW_spirou.py - turn off ic_extract debug. [Neil Cook]
Merge branch ‘extract_issue555’ into neil. [Neil Cook]
SpirouEXTOR.py - do not round in dy statement. [Neil Cook]

0.4.105 (2019-03-28)¶

Cal_HC_E2DS_EA: log statistics cal_WAVE_NEW: improved cross-order FP peak matching, store m(x) fits, remove modulo-1-pixel line center errors. [melissa-hobson]

0.4.101 (2019-03-25)¶

SpirouPlot.py - add the debanana plot in. [Neil Cook]
Misc/new_plot_test.py - test of plotting fixes. [Neil Cook]
Qc_examples.py - add code to document qc parameters for each output in reduced. [Neil Cook]

0.4.100 (2019-03-22)¶

SpirouLOCOR.py - add get_fiber_data function and get_straightened_orderprofile function. [Neil Cook]
SpirouEXTOR.py - fix bug in modes which don’t use pos_a. [Neil Cook]
SpirouImage (spirouFile/spirouFITS/spirouImage) - add changes for new extraction mode. [Neil Cook]
SpirouEXTOR.py - add etienne’s changes to debananafication. [Neil Cook]
SpirouPlot.py - add ext_debanana_plot to show straightened image. [Neil Cook]
SpirouConfig.py - fix ParamDict copy function. [Neil Cook]
Constants_SPIROU_H4RG.py - change mode to ‘5b’ and ‘5a’ [Neil Cook]
Cal_extract_RAW_spirou.py - add changes to all modes ‘5a’ and ‘5b’ to work. [Neil Cook]
Merge branch ‘master’ into extract_issue555. [Neil Cook]
Extract_test_5a_5b.py - want a and b and c separately. [Neil Cook]
Cal_extract_RAW_spirou.py - fix bug in width getting. [Neil Cook]
SpirouLOCOR.py - add function required to get AB + C fiber coefficients when needed. [Neil Cook]
SpirouEXTOR.py - add changes required for extract mode 5a/5b. [Neil Cook]
Test of extract mode 5a/5b. [Neil Cook]
Cal_extract_RAW_spirou.py - add code required for mode 5a/5b. [Neil Cook]

0.4.099 (2019-03-20)¶

Tellu_file_number_test.py - distinguish between TELL_OBJ and TELL_MAP in counting from telluDB. [Neil Cook]
Merge pull request #557 from njcuk9999/neil. [Neil Cook]

Neil –> Master. Confirmed successful unit tests.

0.4.098 (2019-03-19)¶

Cal_extract_RAW_spirou.py - fix problem with width getting for fiber A. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.4.097 (2019-03-19)¶

SpirouKeywords.py - remove the “1” suffix (no longer needed) [Neil Cook]
SpirouEXTOR.py - set up two new extract functions to test adding of fractional contributions of pixels. [Neil Cook]
Update test.run. [Neil Cook]
Update test.run. [Neil Cook]
SpirouFITS.py - fix bug with index lock file (when path does not exist) [Neil Cook]
SpirouFITS.py - add lock file descriptions for print message. [Neil Cook]
SpirouStartup.py - allow main_end script to be used not at the end. [Neil Cook]
SpirouFITS.py - modify open/close lock file functions. [Neil Cook]
Constants_SPIROU_H4RG.py - reduced max db wait time to 10 minutes. [Neil Cook]
Cal_preprocess_spirou.py - index files separately. [Neil Cook]
Update extract_trigger to be able to extract darks. [Neil Cook]
Merge branch ‘sky_dark_fix’ into neil. [Neil Cook]

Conflicts:
INTROOT/SpirouDRS/spirouImage/spirouImage.py UPDATE_NOTES.txt
Update notes. [Neil Cook]
SpirouImage.py - re-add skydark in. [Neil Cook]
Constants_SPIROU_H4RG.py - add option to switch between SKYDARK only and “DARK or SKYDARK” (depending which is closest) [Neil Cook]
SpirouImage.py - correct bug in sky dark. [Neil Cook]
Update extract_trigger.py. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.4.096 (2019-03-18)¶

Tellu_file_number_test.py - update the paths. [Neil Cook]
SpirouConst.py - fix bug with INDEX_LOCK_FILENAME - must not use PID (must be unique to night name not individual process otherwise does not lock out other pids) [Neil Cook]
Update extract_trigger.py. [Neil Cook]
SpirouTelluric.py - remove extract_file. [Neil Cook]

0.4.095 (2019-03-16)¶

Obj_mk_obj_template.py - copy all cdb from other outputs. [Neil Cook]
SpirouFITS.py - separate forbidden keys into absolutely don’t copy and drs don’t copy (that will be copied for updating current files) [Neil Cook]
SpirouFITS.py - separate forbidden keys into absolutely don’t copy and drs don’t copy (that will be copied for updating current files) [Neil Cook]
SpirouFITS.py - need to copy all keys when updating wave solutions. [Neil Cook]
Fix the references to old values of fp_rv. [Neil Cook]
Update date/version/changelog. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - plot duplicate plot correctly. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - correct typo in WMREF. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - correct typo in WSOURCE (was WAVESOURCE) [Neil Cook]
SpirouConst.py - correct typo. [Neil Cook]

0.4.094 (2019-03-15)¶

SpirouConst.py - remove DRS_EOUT from forbidden keys (it should follow extracted file) [Neil Cook]
Calc_berv.py - make sure CopyOriginalKeys comes first before other calls to hdict. [Neil Cook]
SpirouFITS.py - change QC_HEADER_KEYS to FORBIDDEN_HEADER_PREFIXES. [Neil Cook]
SpirouKeywords.py - change some keyword to make them unique (thus can remove them) [Neil Cook]
SpirouConst.py - add more forbidden keys, change qc_keys to any prefix that shouldn’t be copied. [Neil Cook]
Obj_fit_tellu.py - CopyOriginalKeys should be called before other hdict commands. [Neil Cook]
Update unit test scripts. [Neil Cook]
SpirouRV.py - fix problem with getting C file from header. [Neil Cook]
SpirouConst.py - add CCF_FP_TABLE1 and 2. [Neil Cook]
Recipe_control.txt - do not allow OBJ_DARK files - only OBJ_FP. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - add a C table as well as a fits table. [Neil Cook]
Extract_trigger.py - update settings. [Neil Cook]
SpirouKeywords.py - remove unused keywords. [Neil Cook]
SpirouConst.py - add AB and C files for CCF_FP. [Neil Cook]
Tellu_file_number_test.py - change path (for new test) [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - separate AB and C files for output. [Neil Cook]
SpirouTelluric.py - fix list of col names for bigcube (only one bad file now) [Neil Cook]
Extract_trigger - update trigger. [Neil Cook]
SpirouLOCOR.py - fix localisation error - should be a median not an average (option was there but not used) [Neil Cook]
SpirouFITS.py - remove a HUGE BUG - eval(‘2018-08-05’) –> 2005 (as date is interpreted as a subtraction)!!!!! [Neil Cook]
Tellu_file_number_test.py - add raw files and disk vs index.fits. [Neil Cook]
Log_analyser.py - code to look for errors in set of log files. [Neil Cook]
Cal_DRIFT_E2DS_spirou.py - fix typo in get wave sol return. [Neil Cook]
Cal_SHAPE_spirou.py - fix typo in cdbbad value name. [Neil Cook]
Cal_SHAPE_spirou.py - fix typo in cdbbad value name. [Neil Cook]

0.4.093 (2019-03-14)¶

Cal_preprocess_spirou.py - fix filename (should only be filename not path) [Neil Cook]
Update date/version/changelog/notes. [Neil Cook]

0.4.092 (2019-03-14)¶

Make sure all input files are added to header in form: INF#### where the first digit shows the file-set and the other three the position i.e. for recipe.py night_name file1 file2 file3 file4 where inputs expected are 1 flat and multiple darks header would add INF1001 INF2001 INF2002 INF2003. [Neil Cook]
Add header keys for calibration files used to create outputs (CDBDARK, CDBWAVE) etc, also add a source for the wave solution (WAVELOC) [Neil Cook]
SpirouImage.py - correct the rms percentile to allow more darks to pass the rms test. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.4.091 (2019-03-13)¶

Cal_DARK_spirou.py and spirouImage.py - tweak changes to all SKYDARK files to be used. [Neil Cook]
Extract_trigger.py - readd the “skip” criteria. [Neil Cook]
Drs_reset.py - skip the log file for this instance of drs_reset (otherwise can get stuck) [Neil Cook]
Drs_reset.py - fix removal of files when in dir (if still present) [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - correct bad qc parameters. [Neil Cook]
Obj_mk_tellu_new.py - fix typo in qc parameters. [Neil Cook]
Obj_mk_tellu_new.py - fix typo in qc parameters. [Neil Cook]
Drs_reset.py - fix typo in reset1. [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - fix bug with new qc_pass criteria. [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - fix bug with new qc_pass criteria. [Neil Cook]
Unit_test.py - update logging (log all) [Neil Cook]
SpirouFITS.py - add function “add_qc_keys” to take the keys and push them into hdict correctly. [Neil Cook]
SpirouConst.py - change PPVERSION to VERSION for reduced index.fits. [Neil Cook]
Update QC parameters (to store in order) [Neil Cook]
Update changelog. [Neil Cook]
Drs_reset.py - set DEBUG = False in reset, add the removal of all sub- directories in drs folders. [Neil Cook]
SpirouStartup.py - fix bug that we only need lock file is outputs is not None. [Neil Cook]
Update changelog. [Neil Cook]
SpirouConst.py - add version to the index files. [Neil Cook]
Update extraction trigger. [Neil Cook]

0.4.090 (2019-03-12)¶

Update extraction trigger. [Neil Cook]
SpirouPOLAR.py - add qc_pass. [Neil Cook]
SpirouFITS.py - add a test for formatting defined in the keyword (for 1d and 2d lists only) [Neil Cook]
SpirouKeywords.py - add KW_DRS_QC_PASS + change position of number in QCV, QCN, QCL. [Neil Cook]
SpirouConst.py - change the qc_keys to look for. [Neil Cook]
Add qc_pass parameter (flag for each qc parameter) [Neil Cook]

0.4.103 (2019-03-12)¶

Updates to cal_WAVE_NEW_2. [melissa-hobson]
Updated to cal_HC, cal_WAVE_NEW. [melissa-hobson]

0.4.089 (2019-03-11)¶

Extract_trigger.py - update the settings ready for re-runs of extractions. [Neil Cook]
SpirouStartup.py - fix where we lock the index file. [Neil Cook]
SpirouConst.py - add an INDEX_LOCK_FILENAME to lock the indexing in parallel processes. [Neil Cook]
Tellu_file_number_test.py - code to test the number of telluric files at difference stages of the DRS. [Neil Cook]
Merge pull request #553 from njcuk9999/dev. [Neil Cook]

cfht/melissa_fix–>Dev–>master. confirm unti test completed
Update date/version/changelog. [Neil Cook]

0.4.088 (2019-03-09)¶

SpirouLSD.py - fix str to float bug. [Neil Cook]
Test.run - update. [Neil Cook]
SpirouPOLAR.py - fix string - float bug. [Neil Cook]
SpirouTelluric.py -fix berv from string. [Neil Cook]
SpirouRV - must have finite BERV value – but should this be set to zero? [Neil Cook]
SpirouFITS.py - undo hdr type fix. [Neil Cook]
Update test.run. [Neil Cook]
SpirouBERV.py - correct strings coming from header (BERV, BJD, BERV_MAX) [Neil Cook]
Update test.run. [Neil Cook]
Update test.run. [Neil Cook]
SpirouLOCOR.py - fix bug with strings not being ints. [Neil Cook]
SpirouFITS.py - fix problem with changing output type (should not change) [Neil Cook]
Cal_HC_E2DS_EA_spirou.py - fix typo in updatewavesolution. [Neil Cook]
SpirouWAVE.py - fix typo in new masknaems ordermask–>omask. [Neil Cook]
SpirouFITS.py - fix values now as strings –> cast to ints/floats. [Neil Cook]
Fix problem with mjd being a string. [Neil Cook]
Fix problem with mjd being a string. [Neil Cook]
SpirouFITS.py - allow NaNs into header by converting to string. [Neil Cook]
SpirouFITS.py - allow NaNs into header by converting to string. [Neil Cook]
SpirouFITS.py - allow NaNs into header by converting to string. [Neil Cook]
SpirouFITS.py - allow NaNs into header by converting to string. [Neil Cook]
SpirouFITS.py - allow NaNs into header by converting to string. [Neil Cook]
SpirouBERV.py - fix bug when we don’t need a BERV still need BERVHOUR in loc. [Neil Cook]
Cal_extract_RAW_spirou.py - fix typo BCHOUR –> BERVHOUR. [Neil Cook]
Cal_loc_RAW_spirou.py - fix mistake in assigned QCV value. [Neil Cook]
Cal_loc_RAW_spirou.py - fix mistake in assigned QCV value. [Neil Cook]

0.4.087 (2019-03-08)¶

Change AddKey –> AddKey1DList for QC names/values/logic. [Neil Cook]
Cal_preprocess_spirou.py - correct qc missing from param dict. [Neil Cook]
SpirouKeywords.py - fix missed comma in list. [Neil Cook]
SpirouBERV.py - add BERVHOUR to loc (for saving to header) [Neil Cook]
SpirouBERV.py - add BERVHOUR to loc (for saving to header) [Neil Cook]

0.4.086 (2019-03-08)¶

SpirouBERV.py - add BERVHOUR to loc (for saving to header) [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - add some more TODO’s for sections that need work. [Neil Cook]
Cal_HC - allow multiple files (need to update all files + add files to header) [Neil Cook]
Add WMEANREF for AB and C to header. [Neil Cook]
Add PID to output header files (so one can find the log file for each) [Neil Cook]
Add Quality control header keys QC, QCV# (value), QCN# (name), QCL# (name) - and make sure these are not copied over from inputs + some pep8 fixes. [Neil Cook]
SpirouWAVE.py - clean up the code (pep8) [Neil Cook]
SpirouFITS.py - clean up the code (pep8) [Neil Cook]
SpirouBERV.py - clean up the code (pep8) [Neil Cook]
SpirouPlot.py - clean up the code (pep8) [Neil Cook]
SpirouConst.py - clean up the code (pep8) [Neil Cook]
Cal_WAVE_NEW_E2DS_spirou.py - clean up the code (pep8) [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - clean up the code (pep8) [Neil Cook]
Merge branch ‘melissa_fixes’ into dev. [Neil Cook]
Merge pull request #551 from njcuk9999/cfht. [Neil Cook]

Fixed lock timer bug and added barycorr retry.

0.4.085 (2019-03-07)¶

Fixed lock timer bug and added barycorr retry. [Chris Usher]

0.4.084 (2019-03-05)¶

Delete wave_comp_night.py. [melissa-hobson]
Update cal_WAVE_E2DS_EA_spirou.py. [melissa-hobson]
Merge pull request #547 from njcuk9999/melissa. [melissa-hobson]

Melissa

0.4.083 (2019-02-28)¶

SPlt.debug_locplot_finding_orders pauses correctly after each plot; plot limit modified to improve visualization. [melissa-hobson]
SpirouBACK.measure_background_and_get_central_pixels: removed duplicate call to locplot_y_miny_maxy. [melissa-hobson]

0.4.081 (2019-02-22)¶

Littrow check plot: ylimits added based on QCs and results. [melissa- hobson]
Cal_WAVE_NEW gets HC catalog lines correctly. [melissa-hobson]
Merge pull request #542 from njcuk9999/master. [melissa-hobson]

update
Merge pull request #541 from njcuk9999/dev. [Neil Cook]

Dev –> Master
Update date/version/changelog. [Neil Cook]
Correct error estimation for cal_WAVE_NEW. [melissa-hobson]
Merge pull request #538 from njcuk9999/master. [melissa-hobson]

update

0.4.076 (2019-02-22)¶

SpirouLOCOR.py - fix problem with locplot_im_sat_threshold plot. [Neil Cook]

0.4.082 (2019-02-22)¶

SpirouPlot.py - fix problem with locplot_im_sat_threshold plot. [Neil Cook]
Cal_loc_RAW_spirou.py - fix problem with locplot_im_sat_threshold plot. [Neil Cook]
Merge remote-tracking branch ‘origin/dev’ into dev. [Neil Cook]
Merge pull request #537 from njcuk9999/neil. [Neil Cook]

Neil
Update date/version/changelog. [Neil Cook]

0.4.075 (2019-02-21)¶

SpirouTelluric.py - need to stop if not index files found. [Neil Cook]

0.4.073 (2019-02-19)¶

Cal_validate_spirou.py - fix bug it version checking (found by Melissa) [Neil Cook]
Merge branch ‘dev’ into neil. [Neil Cook]
Cal_validate_spirou.py - fix bug it version checking (found by Melissa) [Neil Cook]
SpirouWAVE.py - add some more comments for resolution map. [Neil Cook]

0.4.074 (2019-02-19)¶

SpirouTelluric.py - remove hard coded number of orders. [njcuk9999]
Obj_mk_tellu_new.py - comment out unused lines. [njcuk9999]

0.4.080 (2019-02-18)¶

Testing linear minimization FP wave sol fitting. [melissa-hobson]
Merge branch ‘master’ into melissa. [Melissa Hobson]
Merge pull request #536 from njcuk9999/neil. [Neil Cook]

Neil –> Master. Confirm full tests complete.
Update date/version/changelog/update_notes. [Neil Cook]
Tests: -new version of Lovis method (fit n(x) for all lines, rather than linear interpolation) - wave sol comparison. [melissa-hobson]

0.4.072 (2019-02-13)¶

Obj_mk_tellu_db.py - need to only print errors if we have errors. [Neil Cook]
Obj_mk_tellu_db.py - need to only print errors if we have errors. [Neil Cook]

0.4.071 (2019-02-12)¶

Extract_trigger.py - make sure obj_fit_tellu errors are stored. [Neil Cook]
Obj_mk_tellu_db.py - keep track of errors and exceptions - only print at end. [Neil Cook]
Obj_mk_obj_template.py - fix bug when filtering by snr (all columns of fits table must be same length) [Neil Cook]
SpirouPlot.py - fix bug with HC plot (from added save of plotting) [Neil Cook]
Cal_preprocess_spirou.py - remove rms printout and add values to QC errors. [Neil Cook]
SpirouPlot.py - deal with TclError (with new call for setup_figure) [Neil Cook]
Cal_loc_RAW_spirou.py - add p to call to plotting function. [Neil Cook]
SpirouPlot.py - modify figure setup to try to catch TclError’s and deal with them. [Neil Cook]
Extract_trigger.py - modify printing to logfile (print input args) [Neil Cook]
Obj_mk_obj_template.py - change number of tell files to info. [Neil Cook]
Obj_mk_obj_template.py - fix typo in new snr constraint. [Neil Cook]
Obj_mk_obj_template.py - fix typo in new snr constraint. [Neil Cook]
Obj_mk_obj_template.py - fix typo in new snr constraint. [Neil Cook]
Obj_mk_obj_template.py - fix typo in new snr constraint. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.4.070 (2019-02-12)¶

SpirouFITS.py - add UpdateWaveSolution (update_wave_sol) function to update correctly the HC and FP files. [Neil Cook]
Obj_mk_obj_template.py - add criteria to check median SNR and remove any below half the median SNR (in specific order) [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - BUG FIX - hc and fp files have wrong headers when updating wave solution. [Neil Cook]

0.4.069 (2019-02-11)¶

Cal_WAVE_E2DS_EA_spirou.py - Big Bug FIX ASAP. [Neil Cook]
SpirouPlot.py - update wave_ea_plot_line_profiles fig size. [Neil Cook]
SpirouImage.py - pep8 correction to corruption test. [Neil Cook]
Constants_SPIROU_H4RG.py - add second criteria for corrupt files. [Neil Cook]
Cal_preprocess_spirou.py - update corruption tests. [Neil Cook]
SpirouImage.py - adjust rms values (scaled by percentile) [Neil Cook]
Cal_preprocess_spirou.py - move qc cuts to main code (from function) [Neil Cook]
SpirouImage.py - update corruption test. [Neil Cook]
SpirouPlot.py - update some plot parameters. [Neil Cook]
SpirouPlot.py - enforce a default fig size on all plots + only save in png and pdf. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]

Conflicts:
INTROOT/SpirouDRS/spirouStartup/spirouStartup.py
Merge remote-tracking branch ‘origin/input_redo’ into neil. [Neil Cook]

Conflicts:
.gitignore
DRS startup - need to make data/msg etc folders if they don’t exist. [njcuk9999]

0.4.068 (2019-02-10)¶

SpirouPlot.py - make sure plots are unique. [njcuk9999]
Cal_DRIFTPEAK_E2DS_spirou.py - modifications to plotting changes. [njcuk9999]
Drs_reset.py - add option to reset plot folder. [njcuk9999]
SpirouStartup.py - deal with getting / setting / displaying plot level. [njcuk9999]
SpirouPlot.py - add all functionality to support plotting to file. [njcuk9999]
SpirouConst.py - add plot extensions and plot figsize to constants (for saving plots to file) [njcuk9999]
Spirou modules - make all plot calls compatible with saving to file. [njcuk9999]
Misc - make all plot calls compatible with saving to file. [njcuk9999]
Config.py - make DRS_PLOT an int and change description of DRS_INTERACTIVE. [njcuk9999]
Bin folder - modify all calls to plot to allow saving to file (all calls require “p” as an argument) [njcuk9999]

0.4.067 (2019-02-08)¶

Cal_preprocess_spirou.py - print out the corruption check value. [Neil Cook]
Cal_preprocess_spirou.py - print out the corruption check value. [Neil Cook]
Cal_preprocess_spirou.py - better message for corrupt file. [Neil Cook]
Cal_preprocess_spirou.py - better message for corrupt file. [Neil Cook]
SpirouImage.py - catch warning “RuntimeWarning: All-NaN slice encountered r = func(a, **kwargs)” [Neil Cook]
Cal_preprocess_spirou.py - pep8 tidy up of QC. [Neil Cook]
SpirouImage.py - add get_full_flat, get_hot_pixels, test_for_corrupt_files functions (for checking corruption in preprocessing) [Neil Cook]
Constants_SPIROU_H4RG.py - add corrupt file constants. [Neil Cook]
Cal_preprocess_spirou.py - add QC for corrupt files. [Neil Cook]
Extract_trigger.py - update conditions for mk_tellu and fit_tellu. [Neil Cook]
Extract_trigger.py - update conditions for mk_tellu and fit_tellu. [Neil Cook]
Obj_mk_obj_template.py - make sure BigCube table in both BigCube and BigCube0. [Neil Cook]
Obj_mk_obj_tempalte.py - fit BADFILE –> BADPFILE keyword. [Neil Cook]
SpirouKeywords.py - update KW_OBJECT (was a typo) [Neil Cook]
Obj_mk_obj_template.py - add the data type to ReadParams (otherwise tries to make them floats) [Neil Cook]
SpirouImage.py - deal with keylook up and report better error (via keylookup) [Neil Cook]
Obj_mk_obj_template.py - fix another typo since last update. [Neil Cook]
SpirouKeywords.py - add keyword KW_OBJECT. [Neil Cook]
Obj_mk_obj_template.py - fix type in previous changes. [Neil Cook]
Check_for_corrupt_files.py - add an extra fix from Etienne. [Neil Cook]
Obj_mk_tellu_db.py - fix typo in printout text. [Neil Cook]
Obj_mk_obj_template.py - correct mistake in calling ReadParams (from most recent edit) [Neil Cook]
SpirouTelluric.py - add a function to construct the big cube table (added as a second import to BigCube) [Neil Cook]
SpirouFITS.py - add a write_image_table function to write a image and a table to single fits file. [Neil Cook]
Check_for_corrupt_files.py - adjust with Etiennes changes. [Neil Cook]
Obj_mk_obj_template.py - add fits table to big table with rows of file parameters (used in the big cube) [Neil Cook]
Check_for_corrupt_files.py - fix bugs in the test. [Neil Cook]

0.4.066 (2019-02-07)¶

Update the leapseconds. [Neil Cook]
Check_for_corrupt_files.py - worker code to check corrupt files functionality (before implementing into preprocessing) [Neil Cook]
Update to only do mk_tellu and fit_tellu. [Neil Cook]
Add / get functions for recon file. [Neil Cook]
Constants_SPIROU_H4RG.py - qc snr for mk_tellu and fit_tellu. [Neil Cook]
Obj_mk_tellu_*.py - distinguish between SNR cut in fit_tellu and mk_tellu. [Neil Cook]
Obj_fit_tellu.py - add qc of SNR > 100 for order 33. [Neil Cook]
Check_objname.py - pep9 remove blank lines. [Neil Cook]
Check_objname.py - check objnames and dprtype for preprocessed files in a given directory. [Neil Cook]
Update extract_trigger settings. [Neil Cook]
Update telluric white/black lists. [Neil Cook]
Extract_trigger.py - add a comment. [Neil Cook]
Check_calibdb_2.py - check calibdb and sort and make “pernight” and “pertc” calibdb entries. [Neil Cook]
SpirouTelluric.__init__.py - Add aliases to blacklist and whitelist functions. [Neil Cook]
Extract_trigger.py - get whitelist from file. [Neil Cook]

0.4.065 (2019-02-06)¶

Add a note to locale README.md. [Neil Cook]
Update language database. [Neil Cook]
Drs_table.py - remove text to language database. [Neil Cook]

0.4.079 (2019-02-06)¶

Cal_WAVE_NEW corrected Littrow extrapolation for reddest orders. [melissa-hobson]

0.4.064 (2019-02-05)¶

Drs_startup.py - tweak display settings for interactive + debug mode in drs setup text. [Neil Cook]
Update language database. [Neil Cook]
Drs_text.py - tweak short codes and how length works with Entry(None) [Neil Cook]
Drs_exceptions.py - tweak how exception work (and add string representation) [Neil Cook]
Update language database. [Neil Cook]
Pseudo_const.py - do not automatically write debug message language codes (only when debug >= 100) [Neil Cook]
Drs_startup.py - continue editing how errors work. [Neil Cook]
Drs_recipe.py - continue update to errors. [Neil Cook]
Drs_log.py - do not use ‘p’ use params, update reporting (report all if debug >= 100) [Neil Cook]
Drs_file.py - add extra param (pep8) [Neil Cook]
Drs_argument.py - redo DrsArgument.exception and update _display_info. [Neil Cook]
Drs_text.py - expand functionality of Entry classes (__add__, __radd__, __len__, __iter__, __next__, __eq__, __ne__, __contains__) and how .get() works. [Neil Cook]
Drs_exception.py - add ArgumentException/Error/Warning. [Neil Cook]
Update language database. [Neil Cook]
Param_functions.py - get ArgumentError/Warning. [Neil Cook]
Drs_startup.py - deal with changes to ErrorEntry (no “n” automatically added now) [Neil Cook]
Drs_recipe.py - move argument classes/functions to separate script + continue string moving to language database. [Neil Cook]
Drs_loy.py - add comment that some strings cannot be moved to language database. [Neil Cook]
Drs_argument.py - move argument classes/function to separate script. [Neil Cook]

0.4.063 (2019-02-04)¶

Obj_mk_tellu_db.py - do not reset tellu db in code (do it manually before) [Neil Cook]
Update extract_trigger.py for obj_mk_tellu_db.py. [Neil Cook]
Merge branch ‘master’ into neil. [Neil Cook]
Merge branch ‘master’ into neil. [Neil Cook]
Extract_trigger.py - add obj_mk_tellu_db to triggered files. [Neil Cook]
Unit test runs - add obj_mk_tellu_db to runs. [Neil Cook]
SpirouTelluric.py - fix bugs after moving functions here. [Neil Cook]
Code to check the calibdb entries vs files. [Neil Cook]
Add obj_mk_tellu_db to list of available unit tests. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.4.078 (2019-02-04)¶

Cal_WAVE_NEW update: no longer breaks if FP peak(s) next to reference line are missing. [melissa-hobson]

0.4.062 (2019-02-03)¶

Port_database.py - just try to open csv files as they are done in the drs – hits problems here and not later. [njcuk9999]
Drs_text.py - edit the way csv databases are loaded (to avoid encoding errors) [njcuk9999]
Drs_exceptions.py - add errorobj as possible input to exceptions (and exctract message/level accordingly) [njcuk9999]
Update language database. [njcuk9999]
Drs_recipe.py - continue moving errors to database. [njcuk9999]
Drs_log.py - continue moving errors to database. [njcuk9999]
Drs_file.py - continue moving errors to database. [njcuk9999]

0.4.061 (2019-02-01)¶

Update language database. [Neil Cook]
Drs_file.py - continue taking out error messages. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Add wiki plots. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Update langauge databases. [Neil Cook]
Drs_file.py - continued error movement to database. [Neil Cook]

0.4.077 (2019-02-01)¶

Cal_WAVE_NEW_E2DS attempt to fix issues with FP line adjacent to reference peak being missing. [melissa-hobson]
Merge branch ‘master’ into melissa. [Melissa Hobson]
Merge pull request #534 from njcuk9999/dev. [Neil Cook]

Dev –> Master
SpirouWAVE.py - fix a deprecated WLOG message (found by Melissa) [Neil Cook]
SpirouLog.py - must catch WLOG error before trying to do anything with p. [Neil Cook]
Cal_WAVE_NEW_E2DS: added plot axis titles, littrow check and extrapolation, saving to files spirouConst: added functions for cal_WAVE_NEW spirouWAVE: corrected logging error. [melissa-hobson]
Merge pull request #533 from njcuk9999/master. [melissa-hobson]

update
Merge pull request #531 from njcuk9999/master. [melissa-hobson]

update melissa

0.4.060 (2019-01-31)¶

Update langauge databases. [Neil Cook]
Drs_file.py - continue to take out error messages. [Neil Cook]
Recipe_definitions.py - update location of locale module. [Neil Cook]

0.4.021 (2019-01-30)¶

SpirouTelluric.py - continue to write/upgrade new mk_tellu functions and functions for mk_tellu_db. [Neil Cook]
SpirouPlot.py - add new mk_tellu plot. [Neil Cook]
SpirouConst.py - add definition of whitelist file. [Neil Cook]
Tellu_whitelist.txt - add a white list of all possible telluric star names. [Neil Cook]
Constants_SPIROU_H4RG.py - add constants from new recipes. [Neil Cook]
Obj_mk_tellu_db.py - move constants to constants files and functions to spirouTelluric. [Neil Cook]
Obj_mk_tellu_new.py - move constants to constants file. [Neil Cook]

0.4.059 (2019-01-30)¶

Obj_mk_tellu_new.py - update code with Etienne’s changes. [Neil Cook]
Obj_mk_tellu_db.py - new wrapper script for mk_tellu + fit_tellu on tellurics – creates the telluric database. [Neil Cook]

0.4.020 (2019-01-29)¶

Update .gitignore to ignore .npy files. [Neil Cook]
SpirouTelluric.py - added aliases to two new mk_tellu functions. [Neil Cook]
SpirouTelluric.__init__.py - added aliases to two new mk_tellu functions. [Neil Cook]
SpirouKeywords.py - added two new keywords for new mk_tellu recipe. [Neil Cook]
SpirouConfig.py - update bug in ConfigError (forced list) [Neil Cook]
Combine_tapas.py - new mk_tellu recipe (original code from E.A.) [Neil Cook]
Obj_mk_tellu_new.py - new mk_tellu recipe. [Neil Cook]

0.4.058 (2019-01-28)¶

Upgrade of language database. [Neil Cook]
Drs_lock.py - continued upgrade of error entry. [Neil Cook]
Drs_recipe.py - continued upgrade of error entry. [Neil Cook]
Drs_log.py - continued upgrade of error entry. [Neil Cook]
Drs_file.py - continued upgrade of error entry. [Neil Cook]
Drs_log.py - fix bug in log and how exceptions are handled. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge pull request #532 from njcuk9999/neil. [Neil Cook]

Neil -> Master
Update date/version/changelog. [Neil Cook]

0.4.017 (2019-01-28)¶

SpirouLog.py - fix a bug in logger (only a problem when log breaks) [Neil Cook]

0.4.057 (2019-01-26)¶

Modify test recipes with upgrades. [Neil Cook]
Drsmodule.plotting - moved from drsmodule.plot. [Neil Cook]
Drsmodule.locale - continue upgrade. [Neil Cook]
Drsmodule.constants.io - continue upgrade. [Neil Cook]
Drsmodule.constants.default - continue upgrade. [Neil Cook]
Drsmodule.constants.core - continue upgrade. [Neil Cook]
Drsmodule.config.instruments - continue upgrade. [Neil Cook]
Drsmodule.config.core - continue upgrade. [Neil Cook]
Update DRS_VERSION / DRS_DATE / DRS_RELEASE. [Neil Cook]
Update user_config.ini. [Neil Cook]
Update user_config.ini. [Neil Cook]

0.4.056 (2019-01-25)¶

Drs_startup.py - tweak the system information display section. [Neil Cook]
Drs_log.py - separate print and log (and use default language for log) [Neil Cook]
Backup language database. [Neil Cook]
Drs_text.py - fill language database empty with ‘N/A’ [Neil Cook]
Update language databases. [Neil Cook]

0.4.055 (2019-01-24)¶

Add READMEs to explain empty directories. [Neil Cook]
Add instrument language packs and backup folder for language database. [Neil Cook]
Drsmodule.locale - construct a readme. [Neil Cook]
Drsmodule.locale.__init__.py - add drs_exceptions to internal imported modules. [Neil Cook]
Drsmodule.locale.databases - update language databases. [Neil Cook]
Drmodule.locale.core - move exceptions and make sure all are using basiclogger. [Neil Cook]
Drsmodule.constants - update readme. [Neil Cook]
Constants.default - make Const and Keywords have a source argument. [Neil Cook]
Constants.core - change how exceptions work and where they are sourced from. [Neil Cook]
Config.instruments.spirou - make copy have a source argument. [Neil Cook]
Config.instruments.nirps - make copy have a source argument. [Neil Cook]
Drs_setup.py - change how the exceptions work and where they are sourced from + continue to replace hard-coded text to text from database. [Neil Cook]
Drs_recipe.py - carryon replacing text hard-coded to text in database. [Neil Cook]
Drs_log.py - change how the exceptions work and where they are sourced from. [Neil Cook]

0.4.054 (2019-01-23)¶

Moved locale module to drsmodule root. [Neil Cook]
Locale.databases - continued to add to databases. [Neil Cook]
Locale.databases - continued to add to databases. [Neil Cook]
.gitignore - added ignoring of .npy files and .~lock files. [Neil Cook]
Constants.default.pseudo_const.py - added REPORT_KEYS method. [Neil Cook]
Constants.core.param_functions.py - started added language / basic log functionality. [Neil Cook]
Constants.core.constants_functions.py - added tracking of warnings (so they only print once) [Neil Cook]
Config.math.time.py - added get_hhmmss_now function (for log) [Neil Cook]
Removed locale folder from config folder to separate sub-module directory. [Neil Cook]
Instruments.spirou.recipe_definitions.py - language implementation. [Neil Cook]
Instruments.nirps.recipe_definitions.py - language implementation. [Neil Cook]
Instruments.nirps.pseudo_const.py - format change. [Neil Cook]
Drs_startup.py - language implementation. [Neil Cook]
Drs_recipe.py - language implementation. [Neil Cook]
Drs_log.py - language implementation. [Neil Cook]

0.4.053 (2019-01-22)¶

Added error.csv and “language.xls” - use language.xls to edit strings for each language (given a specific key) [Neil Cook]
Default_config.py - updated options (now with ENG and FR allowed - ENG as default) [Neil Cook]
Updated help.csv. [Neil Cook]
Removed recipe_descriptions.py from config.locale.core. [Neil Cook]
Drs_text.py - (formally text.py) - continued work on upgrade. [Neil Cook]
Recipe_definitions.py - use HelpText to define strings (language support) [Neil Cook]
Drs_recipe.py - COLOURED_LOG –> DRS_COLOURED_LOG. [Neil Cook]
Drs_log.py - update WLOG to deal with ErrorEntry objects as WLOG messages. [Neil Cook]
Use HelpText to define strings (language support) [Neil Cook]
Update user_config.ini file. [Neil Cook]
Update user_config.ini file. [Neil Cook]
Add default help file. [Neil Cook]
Change from ./configuration –> ./config. [Neil Cook]
Change from ./configuration –> ./config. [Neil Cook]
Added alias to new function “get_file_names” [Neil Cook]
Adjusted path name ./configuration –> ./config. [Neil Cook]
Started adding language support. [Neil Cook]
Renamed drsmodule.configuration to drsmodule.config. [Neil Cook]

0.4.052 (2019-01-21)¶

Add source config file to error messages. [Neil Cook]
Fixed printing of config errors in constants file. [Neil Cook]
Added a test recipe for spirou and nirps. [Neil Cook]
Added lock and table to drsmodule.io package. [Neil Cook]
Added “getmodnames” to drsmodule.constants.__init__ file. [Neil Cook]
Continued upgrade to drsmodule.constants.default. [Neil Cook]
Continued upgrade to drsmodule.constants.core. [Neil Cook]
Added __init__ file to drsmodule.configuration. [Neil Cook]
Continued upgrade to drsmodule.configuration.instruments.spirou. [Neil Cook]
Added a drsmodule.configuration.core.default folder (for default file/recipe descriptions) [Neil Cook]
Continued upgrade to drsmodule.configuration.core. [Neil Cook]
Default file definitions and recipe defintions. [Neil Cook]
Add test default config for NIRPS. [Neil Cook]
Add test user config for NIRPS. [Neil Cook]

0.4.051 (2019-01-19)¶

Add minor changes to drs_recipe.py and drs_startup.py. [Neil Cook]
Add a test recipe to recipes.test. [Neil Cook]
Added a plot module. [Neil Cook]
Continued upgrade of constants.default packages. [Neil Cook]
Added locale package. [Neil Cook]
Continued update of instruments.spirou defintions. [Neil Cook]
Adding drs_recipe + drs_file to configuration.core modules. [Neil Cook]

0.4.050 (2019-01-18)¶

Move constants functions from package –> core (remove package module) [Neil Cook]
Add init file for drsmodule (to be named something else eventually) [Neil Cook]
Add configuration.instruments.spirou files. [Neil Cook]
Remove the core.general package. [Neil Cook]
Add init and README.md to constants module. [Neil Cook]
Add a defaults folder (this has definitions of constants as well as default values) - sets up the classes for instruments to overwrite. [Neil Cook]
Remove the const package (now “constants”) [Neil Cook]
Add a time module to the configurations.math module. [Neil Cook]
Add a init file to configuration.instruments. [Neil Cook]
Add spirou config files to configuration.instruments. [Neil Cook]
Add logging to configuration.core. [Neil Cook]
Add default user config files (will be commented out in future) [Neil Cook]
SpirouRecipe.py - add “instrument” to attributes of spirouRecipe.py. [Neil Cook]
Files_spirou.py - modify name and description docstring. [Neil Cook]
SpirouConst.py - fix a bug in exit definition. [Neil Cook]

0.4.049 (2019-01-17)¶

Added additional file to INTROOT 2 (remanage) [Neil Cook]
Test_processing.py - remove need for replacing ‘.py’ [Neil Cook]
Recipes_spirou.py - added instrument name (will be needed in the future) [Neil Cook]
First draft of INTROOT remanage. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge pull request #529 from njcuk9999/neil. [Neil Cook]

Neil –> Master
Update date/version/changelog. [Neil Cook]
Test_processing.py - modify code to return errors and timings (via multiprocessing.Manager) [Neil Cook]
SpirouRecipe.py - modified the generate_runs_from_filelist function to fix when there is no directory from pos args. [Neil Cook]
SpirouFile.py - added read_header/read_data functions and optimized (with todo comment) the read function. [Neil Cook]
Wavecompy.py - added some comments. [Neil Cook]

0.4.048 (2019-01-16)¶

Test_processing.py - for now comment out main call (while testing) [Neil Cook]
SpirouRecipe.py - reformat help printing, add required option to optional arguments (for when we do not have positional arguments) and rework the generation of runs from files (especially when we only have optional arguments) [Neil Cook]
Recipe_spirou.py - add required keyword (for testing) [Neil Cook]
Wavecomp.py - code to compare wavelength solutions (misc) [Neil Cook]

0.4.047 (2019-01-15)¶

Drs_dependencies.py - remove looking in the /misc/ folder for dependecies/code stats. [Neil Cook]
Test_recipe.py - test self. [Neil Cook]
Test_processing.py - upgrade to allow execution of recipes (in single and in parallel) [Neil Cook]
SpirouStartup2.py - allow overwriting of drs_params when they are obtained via kwargs (get_params) [Neil Cook]
SpirouRecipe.py - continued upgrade of input_redo. [Neil Cook]
Recipe_spirou.py - continued upgrade of input_redo. [Neil Cook]

0.4.016 (2019-01-15)¶

SpirouLog.py - fixed an error with logging (if p not set crashes because there was no DRS_DEBUG key – fixed now) [Neil Cook]
SpirouRV.py - fixed bug found with part of correlbin - only affects spectra which have peaks with start/end different by +2 (rare?) but for now using the old correlbin which works for these. [Neil Cook]

0.4.046 (2019-01-11)¶

Recipe_spirou.py - change nomenclature require kwarg arguments have ‘-’ optional have ‘–’ [Neil Cook]
Test_recipe.py - change comment to make clearer. [Neil Cook]
SpirouStartup2.py - remove ‘-’ in specials to allow them to work. [Neil Cook]
SpirouRecipe.py - modify _parse_args to take into that we don’t wont the ‘-’ [Neil Cook]
Recipes_spirou.py - testing file list as keyword arguments. [Neil Cook]
SpirouStartup2.py - changed order of functions, modified display order, added functionality to deal with debug mode and other special keys. [Neil Cook]
SpirouRecipe.py - continued upgrade (changes to parser handling of special arguments, check files + added debug as special argument) [Neil Cook]
SpirouFile.py - small formatting changes in continued input redo. [Neil Cook]
Recipe_spirou.py - remove references to debug (now a special command added to all recipes) [Neil Cook]
Recipe_descriptions.py - remove unused help. [Neil Cook]
Files_spirou.py - modify names to better suit input redo. [Neil Cook]

0.4.045 (2019-01-09)¶

Test_recipe.py - test on cal_HC_E2DS_spirou.py. [Neil Cook]
SpirouStartup2.py - modified which argument display on setup (now only those that were entered at run time) [Neil Cook]
SpirouRecipe.py - redone error reporting on header check. [Neil Cook]
SpirouFile.py - continued upgrade of input redo. [Neil Cook]
Recipes_spirou.py - added cal_hc definition. [Neil Cook]
Recipe_descriptions.py - added cal_hc text. [Neil Cook]
Files_spirou.py - updated names to better represent files (i.e. added fiber name) [Neil Cook]
SpirouRecipe.py - make some methods/function private (protected) using the “_” character as a prefix. [Neil Cook]
Recipe_spirou.py - add more argument defintions (blazefile/flatfile/wavefile), add cal_hc test. [Neil Cook]
Recipe_descriptions - fix imports and define language in constants file. [Neil Cook]
SpirouConst.py - add language constant (Not used yet) [Neil Cook]
SpirouStartup2.py - modify special_keys_present function to look at altnames as well as names (i.e. DrsArgument.names instead of DrsArgument.name) [Neil Cook]
SpirouRecipe.py - modify and add special actions (now: –help, –listing, –listall, –version, –info) [Neil Cook]
Recipe_spirou.py - convert remaining descriptions/help to recipe_descriptions calls. [Neil Cook]
Recipe_descriptions.py - continue to fill out recipe descriptions/examples/help. [Neil Cook]

0.4.044 (2019-01-08)¶

SpirouConst.py, spirouRecipe, spirouStartup2.py - move around the header –> into spirouConst.py. [Neil Cook]
SpirouStartup2.py - add a check for special keys and do not display normal “splash” if found. [Neil Cook]
SpirouRecipe.py - update listing, add version/ epilog and other small fixes to input redo. [Neil Cook]
Recipe_spirou.py - continued work on recipe definitions (including references to recipe_descriptions) [Neil Cook]
Recipe_descriptions.py - storage for longer text (allowing possibility of language support later) [Neil Cook]
SpirouConst.py - added constant to define the maximum display limit for files/directorys (when showing an argument error) [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge pull request #528 from njcuk9999/neil. [Neil Cook]

Neil –> Master
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Update the reset files for the calibDB and telluDB. [Neil Cook]
Update date/version/changelog. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]

Conflicts:
INTROOT/SpirouDRS/spirouCore/spirouLog.py
Merge pull request #527 from njcuk9999/neil. [Neil Cook]

Neil –> Master. Confirmed unit tests completed successfully.

0.4.015 (2019-01-08)¶

SpirouPOLAR.py - fix dependence on KW_ACQTIME_KEY_JUL –> KW_ACQTIME. [Neil Cook]
SpirouCDB.py/spirouDB.py - change all human times to be in format YYYY-mm-dd_HH:MM:SS.f for consistency. [Neil Cook]
Test.run - update test.run to finish testing (start before last failure) [Neil Cook]
SpirouDB.py - fix database definitions in modified “get_database” function. [Neil Cook]
Updated version/date/changelog. [Neil Cook]
Move old tests to spirouUnitTests/old_tests. [Neil Cook]

0.4.014 (2019-01-07)¶

SpirouDB.py - changed from reading human date to reading julian date, changed to use astropy.timea. [Neil Cook]
SpirouCDB.py - reformatted calibDB functions to use spirouDB wherever possible, changed from reading human date to reading julian date, changed to use astropy.time. [Neil Cook]
SpirouDB.__init__.py - moved location of get_acqtime (moved to spirouDB) [Neil Cook]
SpirouKeywords.py - removed KW_ACQTIME_KEY and KW_ACQTIME_KEY_JUL in place of KW_ACQTIME (which is the modified julian date) - with supporting format in case of change (uses astropy.time) [Neil Cook]
SpirouConst.py - removed the use of ACQTIME_KEY_JUL now uses KW_ACQTIME (which is the modified julian date by definition) [Neil Cook]
Cal_HC_E2DS_EA_spirou.py - changed acqtime to ACQTIME (for consistency) [Neil Cook]

0.4.043 (2018-12-21)¶

Test_processing.py - continued work on input_redo. [Neil Cook]
SpirouRecipe.py - continued work on input_redo. [Neil Cook]
Recipes_spirou.py - continued work on input_redo. [Neil Cook]

0.4.013 (2018-12-19)¶

SpirouLog.py - fix for printlogandcmd now having argument “colour” [Neil Cook]
SpirouLog.py - update of ipdb to allow magic commands. [Neil Cook]

0.4.042 (2018-12-19)¶

SpirouRecipe.py - continue input redo upgrade. [Neil Cook]
SpirouFile.py - add some extra empty attributes to DrsInputFile and DrsFitsFile. [Neil Cook]
SpirouLog.py - alias for embeded ipython (in ipdb type “ipython()”) [Neil Cook]
Recipes_spirou.py - update values during input_redo upgrade. [Neil Cook]
Test_processing.py - script to test input_redo with processing. [Neil Cook]

0.4.041 (2018-12-18)¶

Test_recipe.py - continued update of input redo. [Neil Cook]
SpirouStartup2.py - continued update of input redo. [Neil Cook]
SpirouStartup.py - update from spirouStartup2.py. [Neil Cook]
SpirouRecipe.py - continued update of input redo. [Neil Cook]
SpirouFile.py - continued update of input redo. [Neil Cook]
Merge branch ‘neil’ into input_redo. [Neil Cook]

0.4.012 (2018-12-18)¶

SpirouStartup.py - update display. [Neil Cook]
SpirouConst.py - update colours and themes and Color Class. [Neil Cook]
SpirouLog.py - add debug and custom colour modes to log messages. [Neil Cook]
SpirouLog.py - add debug and custom colour modes to log messages. [Neil Cook]
SpirouConst.py - update log constants. [Neil Cook]
Obj_mk_obj_template.py - adjust log message to be more clear. [Neil Cook]
Test codes for testing bug in BigCube/telluDB. [Neil Cook]
SpirouFile.sort_by_name - return sort indices not array (so we can sort multiple arrays) [Neil Cook]
Obj_mk_obj_template.py - fix bug in sorting files (wrong OBJNAME for filename) [Neil Cook]

0.4.040 (2018-12-17)¶

SpirouRecipe.py - continued work on input redo. [Neil Cook]
SpirouStartup2.py - continued work on input redo. [Neil Cook]
SpirouRecipe.py - continued work on input redo. [Neil Cook]
SpirouFile.py - continued work on input redo. [Neil Cook]
Test_recipe.py - continued update for input_redo. [Neil Cook]
SpirouRecipe.py - continued update for input_redo. [Neil Cook]
SpirouFile.py - continued update for input_redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]

Conflicts:
INTROOT/SpirouDRS/spirouUnitTests/extract_trigger.py

0.4.011 (2018-12-17)¶

Obj_mk_obj_template.py - fix bug when forcing calibDB from wave solution (calibDB needs to be re-read each time) [Neil Cook]
Obj_mk_obj_template.py - fix bug when forcing calibDB from wave solution (calibDB needs to be re-read each time) [Neil Cook]
Obj_mk_obj_template.py - fix bug when forcing calibDB from wave solution (calibDB needs to be re-read each time) [Neil Cook]
SpirouLog.py - update log to allow option to be added (by default uses “RECIPE” or “LOG_OPT” or ‘’) [Neil Cook]

0.4.010 (2018-12-16)¶

Wave_sol_to_header.py - code to update header of all e2ds/e2dsff (object and fpfps) in a night_name or all files. [Neil Cook]
Merge pull request #525 from njcuk9999/dev. [Neil Cook]

Melissa –> Dev –> Master. Confirm tested.
Update date/version/changelog/update_notes. [Neil Cook]

0.4.039 (2018-12-15)¶

SpirouFile.py - continued work on input redo. [Neil Cook]
SpirouRecipe.py - continued work on input redo. [Neil Cook]

0.4.009 (2018-12-14)¶

Cal_CCF_E2DS_FP_spirou.py - fix if CCF_RV2 not in whdr. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - fix if CCF_RV2 not in whdr. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - fix if CCF_RV2 not in whdr. [Neil Cook]
Test.run - update for current testing. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - fix crash bug Exception –> SystemExit. [Neil Cook]
Test.run - change for continued test. [Neil Cook]
Test.run - change for continued test. [Neil Cook]
SpirouTHORCA.py - fudge factor fix –> n_order_init = p[‘IC_LITTROW_ORDER_INIT_{0}’.format(1)] [Neil Cook]
SpirouTHORCA.py - test fix. [Neil Cook]
SpirouTHORCA.py - fix for n_order_init (from init –> init_1/init_2) [Neil Cook]
Update test.run - cal_test.run (from cal_WAVE) onwards. [Neil Cook]
Merge branch ‘melissa’ into dev. [Neil Cook]
SpirouConst.py - pep8 changes to WAVE_FILE_EA_2. [Neil Cook]
Cal_WAVE_NEW_E2DS_spirou.py - pep8 changes. [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - few logic checks and pep8 changes. [Neil Cook]
Extract_trigger.py - update run time parameters. [Neil Cook]
Extract_trigger.py - fix incompatible version of cal_shape in reprocessing code. [Neil Cook]

0.4.038 (2018-12-14)¶

SpirouRecipe.py and spirouStartup2.py - continued update to input redo. [Neil Cook]
Extract_trigger.py - fix incompatible version of cal_shape in reprocessing code. [Neil Cook]

0.4.037 (2018-12-13)¶

SpirouRecipe.py - update to check code (put into DrsRecipe class as methods) [Neil Cook]
SpirouRecipe.py - update to check code (put into DrsRecipe class as methods) [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]

0.4.008 (2018-12-13)¶

Constants_SPIROU_H4RG: new constants for start/end littrow orders. [melissa-hobson]
Cal_WAVE_E2DS_EA: littrow can now start and end at any order. Recalculation of littrow sigma handled for all cases. [melissa-hobson]
Extrapolate_littrow_sol: correct initial littrow order. [melissa- hobson]
WAVE_FILE_EA_2 function adds fp filename to wavefilename. [melissa- hobson]
Cal_WAVE_NEW shifted plots. [melissa-hobson]
Merge pull request #523 from njcuk9999/master. [melissa-hobson]

update
Merge pull request #522 from njcuk9999/dev. [Neil Cook]

Francois –> Dev –> Master
Update date/version/changelog. [Neil Cook]
Update date/version/changelog. [Neil Cook]
Merge pull request #521 from njcuk9999/francois. [melissa-hobson]

Francois
Merge branch ‘master’ into francois. [Neil Cook]
Merge pull request #520 from njcuk9999/master. [melissa-hobson]

Update melissa from master

0.4.007 (2018-12-13)¶

Extract_trigger.py - changes to reprocessing code (correct order) [Neil Cook]
Merge branch ‘master’ into dev. [Neil Cook]
Merge pull request #519 from njcuk9999/neil. [Neil Cook]

Neil
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Code to check the telluric corrections. [Neil Cook]

0.4.006 (2018-12-12)¶

Add .idea to .gitignore. [Neil Cook]
Re-do requirements files. [njcuk9999]
Merge branch ‘francois’ into dev. [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - pep8 clean up of Francois branch. [Neil Cook]
Cal_DRIFTPEAK_E2DS_spirou.py - pep8 clean up of Francois branch. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - pep8 clean up of Francois branch. [Neil Cook]
Format of flux ratio set to .3f. [FrancoisBouchy]
Compute the absolute CCF drift of the FP and save it in the wavelength solution file as CCFRV2. [FrancoisBouchy]
Absolute CCF drift of FP is read from the wavelength solution file. The relative CCF drift takes into account this Absolute drift. [FrancoisBouchy]
Merge remote-tracking branch ‘origin/master’ [Neil Cook]
Update README.md. [Neil Cook]

Update with recent changes
Update requirements (barycorrpy required) [Neil Cook]
Add a minimum requirements and current requirements (as .txt files) [Neil Cook]
Merge pull request #518 from njcuk9999/neil. [Neil Cook]

Neil
Update date/version/changelog/ update notes. [Neil Cook]

0.4.005 (2018-12-11)¶

SpirouTable.py - fix an error with missing end card. [Neil Cook]
Update extraction_trigger.py run time parameters. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Cal_validate_spirou.py - correct cal_validate for new wlog. [Neil Cook]

0.4.036 (2018-12-11)¶

Cal_validate_spirou.py - correct cal_validate for new wlog. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]

0.4.004 (2018-12-10)¶

SpirouConst.py - undo change to global file. [Neil Cook]
SpirouFITS.py - fix for lock file on non-fits files. [Neil Cook]

0.4.035 (2018-12-10)¶

SpirouStartup2.py - upgrade WLOG (requires drs_params to track pid) [Neil Cook]
SpirouRecipe.py - upgrade WLOG (requires drs_params to track pid) [Neil Cook]
SpirouFile.py - upgrade WLOG function (requires drs_params to track pid) [Neil Cook]
Recipes_spirou.py - fix pep8 in helpstr. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge pull request #516 from njcuk9999/dev_shape_redo. [Neil Cook]

Dev shape redo (confirmed testing on cal_test, tellu_test and pol_test)
Update date/version/changelog. [Neil Cook]
Merge branch ‘master’ into input_redo. [njcuk9999]

0.4.003 (2018-12-10)¶

Cal_WAVE_E2DS_EA_spirou.py - correct pep8 and add TODO’s for problems. [Neil Cook]
Cal_WAVE_NEW_E2DS_spirou.py - correct pep8 and WLOG changes. [Neil Cook]
Merge branch ‘dev’ into dev_shape_redo. [Neil Cook]

Conflicts:
INTROOT/misc/cal_WAVE_NEW_E2DS_spirou.py
Remove hard-coded initial wavelenth solution. [melissa-hobson]
Merge pull request #515 from njcuk9999/master. [melissa-hobson]

update melissa from master
Add new CCF mask (masque_sept18.mas) [njcuk9999]
Improvements to fp_wavelength_sol_new fp m value determination correction to fp line insertion into all_lines assorted tests for fitting HC lines. [melissa-hobson]
Littrow: get total orders from echelle_orders, not all_lines; save orders of min/max deviation. [melissa-hobson]
SpirouMath: calculates wave coeff from chebyshev polynomials spirouPlot: correct wavelengths for fitted lines in wave_ea_plot_single_order. [melissa-hobson]
Cal_WAVE_NEW_E2DS_EA update (calculates wave sol, does Littrow) [melissa-hobson]
Cal_WAVE_EA order information on Littrow QC fail. [melissa-hobson]
Update timings for V0.4.001. [Neil Cook]
SpirouRV.py - change an info log message to general log message (too many for CCF) [Neil Cook]
SpirouLSD.py - remove some of the info logs and make them general logs. [Neil Cook]
Pol_spirou.py - remove some of the info logs and make them general logs. [Neil Cook]
Update date/version/changelog. [Neil Cook]

0.4.001 (2018-12-08)¶

Unit_Test runs - update test for run. [Neil Cook]
Extract_trigger.py - update values for run time. [Neil Cook]
SpirouStartup.py - define initial values for log_opt and program in Begin() [Neil Cook]

0.4.002 (2018-12-08)¶

Constants_SPIROU_H4RG.py - add “fitsopen_max_wait” time. [Neil Cook]
Cal_reset.py - fix fake p (with real p) [Neil Cook]

0.3.077 (2018-12-07)¶

SpirouTable.py - add lock files around writing to fits file (avoids writing at the same time) [Neil Cook]
SpirouImage.__init__.py - add links to check/close/open fits lock file. [Neil Cook]
SpirouFITS.py - add fits file lock file (to avoid writing to same fits file at same time) [Neil Cook]
SpirouDB.py - edit message and sleep time for waiting lock file. [Neil Cook]
Extract_trigger - update to allow skipping of mk_tellu and fit_tellu files. [Neil Cook]
Obj_fit_tellu.py - fix problems with WLOG update. [Neil Cook]
SpirouStartup.py - add telluDB info to the start up printout/log. [Neil Cook]

0.3.076 (2018-12-05)¶

SpirouDRS/spirouUnitTest folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouUnitTest folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouTools folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouTHORCA folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouTelluric folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouStartup folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouRV folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouPOLAR folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouLOCOR folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouImage folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouFLAT folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouEXTOR folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouDB folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouCore folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouConfig folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
SpirouDRS/spirouBACK folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
Spirou_drs/misc folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
Spirou_drs/bin folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
Spirou_drs/bin folder - major redo of logging system (to allow passing of process-id) [Neil Cook]
Cal_extract_RAW_spirou.py - remove the need to a TILT file is mode == ‘4a’ or ‘4b’ [Neil Cook]
Cal_extract_RAW_spirou.py - remove the need to a TILT file is mode == ‘4a’ or ‘4b’ [Neil Cook]
SpirouConfigFile.py - update comment to make it clear why two tests are needed. [Neil Cook]

0.3.075 (2018-12-04)¶

SpirouImage.py - adjust warning for getting unix_time from string (where time is not valid) - warning or error? [Neil Cook]

0.3.074 (2018-12-03)¶

SpirouConst.py - modify colour for white screen people. [Neil Cook]
SpirouKeywords.py - update keys (must be shorter with addition of numbers) [Neil Cook]
SpirouKeywords.py - update keys (must be shorter) [Neil Cook]
SpirouUnitRecipes.py - remove cal_SHAPE_spirou2. [Neil Cook]
Extract_trigger.py - update run arguments. [Neil Cook]
Unit_tests - update test.run and Pol_Test.run. [Neil Cook]
SpirouStartup.py - add functionality to assign process id (on begin) –> timestamp. [Neil Cook]
SpirouTable.py - update comment to give some idea of the IDL command to open table. [Neil Cook]
SpirouLog.py - start process of having individual logs for each instance. [Neil Cook]
Recipe control - adjust inputs to cal_SHAPE_spirou. [Neil Cook]
Cal_SHAPE_spirou.py - change name of cal_SHAPE_spirou2.py –> cal_SHAPE_spirou.py. [Neil Cook]
SpirouLSD.py - modify output of LSD table to be a FIT BINARY Table. [Neil Cook]

Note to open fits tables in IDL see here:
https://idlastro.gsfc.nasa.gov/ftp/pro/fits_table/aaareadme.txt

lookup:
ftab_print, ‘file.fits’

read:
tab = readfits(‘file.fits’, hdr, /EXTEN) col1 = tbget(hdr, tab, ‘COLUMN1’)
Extract_trigger.py - update extract_trigger run constants. [Neil Cook]
SpirouLSD.py - change format of output to FITS table. [Neil Cook]
SpirouTable.py - add option in write_table to accept header (hdict) [Neil Cook]
SpirouUnitRecipes.py - remove reference to cal_SHAPE_spirou2.py. [Neil Cook]
Extract_trigger.py - update run parameters (and slightly change order of constants) [Neil Cook]
Cal_SHAPE_spirou.py - change reference to GetShapeMap2 –> GetShapeMap. [Neil Cook]
SpirouImage.py - change get_shape_map2 –> get_shape_map (change old get_shape_map –> get_shape_map_old) [Neil Cook]
Recipe_control.txt - change cal_SHAPE_spirou2 –> cal_SHAPE_spirou (remove old one) [Neil Cook]
Cal_SHAPE_spirou.py - renamed from cal_SHAPE_spirou2.py (old code moved to ./misc) [Neil Cook]

0.3.073 (2018-11-30)¶

Update test.run. [njcuk9999]

0.3.072 (2018-11-28)¶

Changes to parallelisation (test) [njcuk9999]
Extract_trigger.py - updates to extraction trigger. [njcuk9999]
Tellu_whitelist.txt - a white list of telluric stars. [njcuk9999]

0.3.071 (2018-11-27)¶

Extract_trigger.py - correct problems with pre-processing automation. [njcuk9999]
Recipe_control.txt - add some more options for POL_STOKES_I. [njcuk9999]
Merge pull request #514 from njcuk9999/dev_shape_redo. [Neil Cook]

Dev shape redo - tested on Cal_test.run and Tellu_Test.run

0.3.070 (2018-11-26)¶

Update test.run. [njcuk9999]
Run_off_listing.py - fix errors in code. [njcuk9999]
Update date/version/changelog. [njcuk9999]

0.3.069 (2018-11-26)¶

Run_off_listing.py - correct to try/except in run_off_listing.py. [njcuk9999]
Extract_trigger.py - upgrades to extract trigger just do extractions. [njcuk9999]
Run_off_listing.py - code to redo indexing. [njcuk9999]
SpirouStartup.py - fix error with change to indexing (and old index files) [njcuk9999]
SpirouConst.py - change func_name for REDUC_OUTPUT_COLUMNS. [njcuk9999]

0.3.068 (2018-11-24)¶

Update extraction trigger. [njcuk9999]
SpirouConst.py - add MJDATE to index.fit. [njcuk9999]
Merge branch ‘master’ into dev_shape_redo. [njcuk9999]

Conflicts:
INTROOT/SpirouDRS/spirouImage/spirouBERV.py
Update spirouBERV.py. [Neil Cook]

Correct error with spriouBerv.get_earth_velocity_correction - only calculate BERV for OBSTYPE = ‘OBJECT’ (an do not look for ra/dec etc in the headers - it wont be there for lab files)
Cal_SHAPE_spirou/spirou2 - correct mistakes found by unit test run. [njcuk9999]
Update date/version/changelog. [njcuk9999]

0.3.067 (2018-11-24)¶

Cal_Test.run - add cal_SHAPE_spirou2 to Cal_Test.run. [njcuk9999]
Unit tests: add cal_SHAPE_spirou2 to unit test definition. [njcuk9999]
SpirouImage.py - update get_shape_map2 and get_offset_sp in-line with Etienne’s changes. [njcuk9999]
SpirouPlot.py - update new shape plots in-ilne with Etiennes changes. [njcuk9999]
SpirouMath.py - update “gauss_fit_s” (Etienne updated it) [njcuk9999]
SpirouKeywords.py - add extra keys (for index.fits) and for wave-list in bigcubes. [njcuk9999]
SpirouConst.py - update acquisition of filenames now we have “HCFILE” and “FPFILES” (not “HCFILES” and “FPFILE”) [njcuk9999]
Constants_SPIROU_H4RG.py - update constants inline with Etiennes changes. [njcuk9999]
Obj_mk_obj_template.py - list wave files in header (along with file name and berv) for big cube. [njcuk9999]
Cal_SHAPE_spirou2.py - continued work on shape upgrade + now 1 hcfile and multiple fp files. [njcuk9999]

0.3.066 (2018-11-23)¶

SpirouFits.py - fix bug with hdict being empty (possible on some writes) [njcuk9999]

0.3.065 (2018-11-22)¶

SpirouTable.py - updated the error outputs to include filename. [njcuk9999]
SpirouImage.py - continued to modify get_offset_sp and get_shape_file2 (for new SHAPE code) [njcuk9999]
SpirouPlot.py - adjusted slit_shape_angle_plot and added slit_shape_offset_plot (for new SHAPE recipe) [njcuk9999]
SpirouMath.py - adjusted problem in gauss_fit_s file “correction = (x - np.mean(x)) * slope” –> “correction = (x - x0) * slope” [njcuk9999]
Updated the catalogue_UNe.dat file and added cavity_length.dat file (for new SHAPE code) [njcuk9999]
Master_tellu_SPIROU.txt - updated the master calibdb with the new MASTER_WAVE.fits. [njcuk9999]
Master_calib_SPIROU.txt - updated the master calibdb with the new MASTER_WAVE.fits. [njcuk9999]
Recipe_control.txt - added cal_SHAPE_spirou2 to the recipe control (with two arguments for FP_FP and HC_HC files - pp fits not e2ds!) [njcuk9999]
Constants_SPIROU_H4RG.py - added new constants and modified constants changed by Etienne. [njcuk9999]
Cal_SHAPE_spirou2.py - continued work on adapting Etiennes changes into cal_SHAPE. [njcuk9999]

0.3.064 (2018-11-21)¶

Add copy of old xt code (to compare with new one for changes) [njcuk9999]
Add function: read_cavity_length, get_shape_map2, get_offset_sp for new shape code. [njcuk9999]
SpirouConst.py - add new file definitions. [njcuk9999]
Output_keys.py - add defintions for shape sanity check debug files. [njcuk9999]
Notes on etiennes codes - no real changes just comments. [njcuk9999]
Constants_SPIROU_H4RG.py - modify SHAPE constants to for new shape code. [njcuk9999]
Obj_mk_tellu.py - fix copy of code - redundant. [njcuk9999]
Cal_SHAPE_spirou2.py - modification of cal_SHAPE_spirou.py with changes to cal_shape needed. [njcuk9999]
SpirouBERV.py - fix bug in berv code - non-objects should not look for star parameters. [njcuk9999]
Update version/dates/changelog.txt. [njcuk9999]

0.3.063 (2018-11-20)¶

Add test files to misc. [njcuk9999]
Add Etiennes files in misc folder. [njcuk9999]
Runs - update the unit tests. [njcuk9999]

0.4.034 (2018-11-14)¶

Test_recipe.py - change permissions for file. [njcuk9999]

0.3.062 (2018-11-14)¶

Fit_triplets sigma-clip change. [melissa-hobson]
Cal_WAVE_E2DS_EA - fix HC file being overwritten with FP data (fixes #513) [melissa-hobson]
Merge pull request #512 from njcuk9999/master. [melissa-hobson]

update Melissa
Merge remote-tracking branch ‘origin/melissa’ into melissa. [Melissa Hobson]

Conflicts:
INTROOT/bin/cal_WAVE_E2DS_EA_spirou.py
Merge pull request #509 from njcuk9999/master_copy. [melissa-hobson]

update melissa
Merge branch ‘melissa’ into master_copy. [melissa-hobson]
Bug fix for fit_gaussian triplet (fixes #507) [melissa-hobson]

0.4.033 (2018-11-09)¶

Continued work on input redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge pull request #511 from njcuk9999/dev. [Neil Cook]

Francois –> Dev, Neil–> Dev, Dev –> master

0.3.060 (2018-11-08)¶

Cal_WAVE_EA match to master. [melissa-hobson]

0.3.061 (2018-11-08)¶

Update date/version/changelog. [Neil Cook]

0.3.056 (2018-11-08)¶

SpirouWAVE.py - Melissa’s fix for Issue #507 -> “<” needs to be “<=” [Neil Cook]
Merge branch ‘neil’ into dev. [Neil Cook]
Add hcone files for the cal_DRIFTCCF_E2DS recipe. [FrancoisBouchy]

0.4.032 (2018-11-07)¶

SpirouFile.py - continue to fill out drs file fits methods. [Neil Cook]

0.3.055 (2018-11-07)¶

New UrNe CCF mask based on lines used for the wavelength solution and to be used to compute DRIFT on hcone files. [FrancoisBouchy]

0.4.031 (2018-11-06)¶

Test_recipe.py - tested cal_badpix_spirou.py. [Neil Cook]
SpirouStartup2.py - continue work on inputs update. [Neil Cook]
SpirouRecipe.py - continue work on inputs update. [Neil Cook]
SpirouFile.py - allow filename to be set in construction (via kwargs) [Neil Cook]
Recipes_spirou.py - add and reformat options to set/take defaults. [Neil Cook]
SpirouConst.py - add a variable that can globally update pp (for use when we don’t have p) [Neil Cook]

0.4.030 (2018-11-05)¶

Test_recipe.py - tested cal_FF_RAW_spirou.py inputs. [Neil Cook]
SpirouStartup2.py - modified code to line up with continued work on spirouRecipe. [Neil Cook]
SpirouRecipe.py - continued to develop new recipe class. [Neil Cook]
SpirouFile.py - filled out some attributes/methods. [Neil Cook]
Recipe_spirou.py - added more definitions and started to fill out drs recipes (badpix –> extract) [Neil Cook]
Files_spirou.py - updated call to spirouFile.DrsInput –> spirouFile.DrsInputFile. [Neil Cook]

0.4.029 (2018-11-04)¶

SpirouRecipe.py - move DrsInputs from here to spirouFile.py. [njcuk9999]
SpirouFile.py - move DrsInputs from spirouRecipes to here. [njcuk9999]
Files_spirou.py - update links to DrsInput: spirouRecipe –> spirouFile. [njcuk9999]

0.4.028 (2018-11-02)¶

SpirouRecipes.py - add todo. [Neil Cook]
SpirouStartup2.py - pushed renaming of recipes –> recipes_spirou into code. [Neil Cook]
Recipes_spirou.py - renamed from recipes.py. [Neil Cook]
Files_spirou.py - renamed from spirouFiles.py. [Neil Cook]
SpirouRecipe.py - add doc strings for new classes (DrsArgument/DrsRecipe/DrsInputFile/DrsFitsFile) [Neil Cook]
Test_receip.py - update with new name for “ufiles”–>”filelist” [Neil Cook]
SpirouStartup2.py - continue work on input code - update with changes to spirouRecipe.py. [Neil Cook]
SpirouRecipe.py - define how DrsArgument, DrsRecipe and DrsInput (+DrsFitsFile) interact - continued testing of input redo. [Neil Cook]
SpirouFiles.py - define all raw/pp/out files as instances of DrsFitsFile. [Neil Cook]
Recipes.py - continue to test new inputs with test_recipe definition. [Neil Cook]

0.3.059 (2018-11-01)¶

Test of not using Littrow sols for cal_WAVE_EA. [melissa-hobson]

0.4.027 (2018-11-01)¶

SpirouStartup2.py - continue work on input code. [Neil Cook]
SpirouRecipe.py - continue work on input code. [Neil Cook]
SpirouFiles.py - define file types using new classes. [Neil Cook]
Recipe.py - update recipe definitions based on changes. [Neil Cook]

0.3.058 (2018-10-31)¶

Cal_WAVE_NEW update. [melissa-hobson]

0.4.026 (2018-10-31)¶

Recipe.py - add new comment. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]

0.3.054 (2018-10-30)¶

Test_wavsol.py - fixed bugs and added STD for H band. [Neil Cook]
Test_wavsol.py - added code to compare wave solutions from a calibDB (defined manually in the code) [Neil Cook]
HC_Test.run - added run 47 back in (had been missed) [Neil Cook]

0.3.057 (2018-10-30)¶

Cal_WAVE_NEW update. [melissa-hobson]
Updates to C. Lovis method. [melissa-hobson]
Merge pull request #500 from njcuk9999/master. [melissa-hobson]

update melissa

0.3.053 (2018-10-29)¶

Add hc_test.run back to unit tests. [Neil Cook]
Merge pull request #501 from njcuk9999/neil. [Neil Cook]

Neil –> Master - confirm unit tests
Update date/version/changelog. [Neil Cook]

0.3.052 (2018-10-29)¶

Pep8 clean up. [Neil Cook]

0.3.051 (2018-10-26)¶

Pep8 clean up. [Neil Cook]
Update TODO’s, remove old H3RG dependencies and clean up. [Neil Cook]
Merge pull request #497 from njcuk9999/dev. [Neil Cook]

Dev –> Master (tested on Cal_Test.run)
Update date/version/changelog/update-notes. [Neil Cook]

0.3.050 (2018-10-26)¶

SpirouKeywords.py - add separate set of header keys for the FP analysis. [Neil Cook]
SpirouConst.py - add CCF_FP versions so files are separate (for now) [Neil Cook]
Output_keys.py - add new keys for CCF_FP. [Neil Cook]
SpirouConfig.py - define a copy function for ParamDict - copy all keys into new ParamDict. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - separate and keep separate the FP analysis (cp and cloc) - including header keys. [Neil Cook]
Merge pull request #495 from njcuk9999/dev. [Neil Cook]

Neil –> Dev, Francois –> Dev, Dev –> Master. Confirm unit tested
Update test files - mistake in run018b. [Neil Cook]
Gl699_Aug05-A_B.run - unit test run for A and B files. [Neil Cook]
Update date/version/update notes/changelog. [Neil Cook]

0.3.049 (2018-10-25)¶

Tellurics2.run - add a second telluric run - to preprocess, extract and mk_tellu missed tellurics. [Neil Cook]
Update test - only 1 telluric test + move others to old_tests. [Neil Cook]
SpirouTelluric.py - template should be in MASTERWAVE frame not WAVE_IT frame. [Neil Cook]
SpirouPlot.py - modify tellu_fit_debug_shift_plot to only plot one order. [Neil Cook]
Recipe_control.txt - allow cal_CCF_E2DS_FP_spirou to use A, B files and TELLU_CORRECTED/POL_ files. [Neil Cook]
Update unit tests. [Neil Cook]
Obj_fit_telluy.py - todo question about possibly broken plot. [Neil Cook]
SpirouFile.py - better error message when wrong directory used for input files. [Neil Cook]
New unit_test runs for maestria with missed Gl699 targets. [Neil Cook]

0.3.048 (2018-10-24)¶

SpirouRV.py - need to deal with the differing fibers (for now manually) [Neil Cook]
SpirouRV.py - added function “get_foberc_e2ds_name” to deal with the different file types expected –> need E2DS AB file for C fiber. [Neil Cook]
SpirouPOLAR.py - adjusted calls to headers to not be hard coded (should have been called from p –> spirouKeywords.py) [Neil Cook]
SpirouKeywords.py - add MJEND keyword (for pol_spirou.py) - also changed naming to all upper case. [Neil Cook]
Obj_mk_tellu.py - turn off debug plot. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - get correct filename for fiber C (E2DS file only) [Neil Cook]
Cal_validate_spirou.py - add option to check (check=0 just prints paths) [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - correct imports and catch warnings (As with cal_CCF_E2DS_spirou) [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - correct link to header key in p. [Neil Cook]
SpirouKeywords.py - make tellu header keys shorter. [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - load file C not from a telluric corrected spectrum but from the E2DS itself (using header) [Neil Cook]
SpirouExposeMeter.py - fix some pep8 issues. [Neil Cook]
SpirouKeywords.py - add header key definitions for options input in tellu. [Neil Cook]
Obj_fit_tellu.py - add extra header keys to know how many components were fit in PCA etc. [Neil Cook]
Cal_CCF_E2DS_spirou.py - fix some pep8 convension. [Neil Cook]
Merge branch ‘neil’ into dev. [Neil Cook]
Update unit test runs. [Neil Cook]
SpirouUnitRecipes.py - update input name for cal_exposure_meter and cal_wave_mapper. [Neil Cook]
Cal_exposure_meter.py - correct input name: “reffile” –> “flatfile” [Neil Cook]
Cal_CCF_E2DS_spirou.py + spirouRV.py - catch warnings for NaNs in mean and divide. [Neil Cook]
SpirouUnitRecipes.py - add cal_CCF_E2DS_FP_spirou to unit tests. [Neil Cook]
Update date/version/update_notes/changelog. [Neil Cook]

0.3.047 (2018-10-23)¶

Cal_Test.run - add cal_wave_mapper to tested recipes. [Neil Cook]
SpirouExoposureMeter.py - use wave parameters instead of wave map + add normalisation option. [Neil Cook]
Constants_SPIROU_H4RG.py - add constants for normalisation and flat_correction. [Neil Cook]
Cal_exposure_meter.py - try rescale for the flux (Issue #490) [Neil Cook]
Cal_wave_mapper.py - divide through by flat field (on request) and attempt to rescale flux (Issue #490) [Neil Cook]
SpirouExoposeMeter.py - Issue #490 - add ability to not re-calculate order profile image (if already processed) + add shape as well as tilt (use shape if in calibDB) [Neil Cook]
SpirouKeywords.py - add infilelist as keyword (For use for pushing input file list to header) [Neil Cook]
SpirouConst.py - define a tmp file for the order profile map (Issue #490) [Neil Cook]
Cal_wave_mapper.py - Issue #490 - add shape + fix badpixel function returns. [Neil Cook]
Cal_exposure_meter.py - fix Issue #490 - use shape file + correct output of badpix mask. [Neil Cook]

0.3.046 (2018-10-22)¶

Obj_mk_tellu.py - make sure the NaNs do not propagate through to the convolution (NaN * 0.0 = NaN —> need 0.0) [Neil Cook]
Obj_mk_tellu.py - make sure the NaNs do not propagate through to the convolution (NaN * 0.0 = NaN —> need 0.0) [Neil Cook]
Obj_mk_tellu.py - catch warnings as sp now can have nans. [Neil Cook]
Obj_mk_obj_template.py - change median to nan median and catch warnings with nanmedian of empty stack (all nans) [Neil Cook]
Obj_mk_tellu.py - catch warnings in dev (nans allowed) [Neil Cook]
SpirouTelluric.py - kernal resize. [Neil Cook]
Obj_mk_tellu.py - shift data to master before (to match tapas) - instead of shifting transmission after. [Neil Cook]

0.3.045 (2018-10-22)¶

Updated permissions on spirouUnitTest files (chmod +x) [Neil Cook]
Tellu_Test.run - added a test of cal_CCF_E2DS_FP_spirou.py (currently not working) [Neil Cook]
SpirouKeywords.py - added kw_DRIFT_RV definition to keywords files (for use in cal_CCF_E2DS_FP_spirou.py) [Neil Cook]
Recipe_control.txt - added cal_CCF_E2DS_FP_spirou to recipe_control - for fiber AB only (will only work with fiber AB) [Neil Cook]
Cal_CCF_E2DS_FP_spirou.py - added changes to integrate into DRS. [Neil Cook]
Merge branch ‘francois’ into dev. [Neil Cook]
Cal_CCF_E2DS with simultaneous CCFDrift on FP fiber C. [FrancoisBouchy]
Merge remote-tracking branch ‘origin/francois’ into francois. [FrancoisBouchy]
New CCF mask for FP. [FrancoisBouchy]
Merge pull request #491 from njcuk9999/neil. [Neil Cook]

Melissa –> Neil –> Master (confirm unit tests)
Update tests. [Neil Cook]
Update date/version/changelog/update notes. [Neil Cook]

0.3.043 (2018-10-19)¶

Unit_test runs - add maestria tests. [Neil Cook]
Update triggers/unit_tests to catch and handle errors better. [Neil Cook]
Update triggers/unit_tests to catch and handle errors better. [Neil Cook]
Redo tests - comments where broken. [Neil Cook]
SpirouStartup.py - remove print statement (was there to debug) [Neil Cook]
SpirouLog.py - return useful message on sys.exit (after error log) [Neil Cook]
Error_test.py - test catching errors for trigger/unit_tests. [Neil Cook]
SpirouWAVE.py - make debug plot only show in debug mode (even with plotting on) [Neil Cook]
Merge branch ‘melissa’ into neil. [Neil Cook]
Merge branch ‘master’ into melissa. [Neil Cook]
SpirouWAVE: plots will now appear in interactive mode only. [melissa- hobson]
Merge pull request #487 from njcuk9999/master. [melissa-hobson]

update melissa from master
Update HC/WAVE test. [Neil Cook]
Unit_test.py - better catching/recording of errors (for batch run that doesn’t crash out) [Neil Cook]
Update HC/WAVE test. [Neil Cook]
Update HC/WAVE test. [Neil Cook]
Update HC/WAVE test. [Neil Cook]
Update HC/WAVE test. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Merge pull request #489 from njcuk9999/dev. [Neil Cook]

Francois –> Dev, Neil –> Dev, Dev –> Master
Update date/version/changelog. [Neil Cook]
Update date/version/changelog. [Neil Cook]
Cal_DRIFTCCF_E2DS_spirou.py - comment out saving of fits file - no loc[‘DRIFT’] defined. [Neil Cook]
Update date/version/changelog. [Neil Cook]
Merge branch ‘neil’ into dev. [Neil Cook]

Conflicts:
CHANGELOG.md INTROOT/SpirouDRS/spirouConfig/spirouConst.py VERSION.txt
Fp.mas - added the fp mask to the ccf_masks folder (for cal_driftccf) [Neil Cook]
Update HC/WAVE test. [Neil Cook]

0.3.042 (2018-10-18)¶

Update date/version/changelog. [Neil Cook]
Unit_test.py - fix comment. [Neil Cook]
TelluricsAll.run - add a list of all tellurics for maestria. [Neil Cook]
Constants_SPIROU_H4RG.py - add quality control parameters for mk_tellu (RMS) [Neil Cook]
Obj_mk_tellu.py - add an RMS cut to the QC parameters checked. [Neil Cook]
Obj_mk_obj_template.py - turn multi fits into fits cubes. [Neil Cook]
Unit_test_parallel.py - test of multiprocessing on unit tests - DRS not stable to use this yet! [Neil Cook]
Extract_trigger.py - for now only do up to extraction of HC_HC and FP_FP. [Neil Cook]
Gl699_small.run - just extract and fit those across one glitch. [Neil Cook]
Cal_HC/cal_WAVE only copy over original file parameters if QC passed. [Neil Cook]
SpirouFITS.py - fix bug in check_wave_sol_consistency. [Neil Cook]
Obj_mk_tellu.py - add notes for new QC check (TODO’s) [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - remove print statement. [Neil Cook]
Cal_SHAPE_spirou.py - update permissions on cal_SHAPE. [Neil Cook]
Update run list (for maestria runs) [Neil Cook]
Extract_trigger.py - full calibration trigger test. [Neil Cook]
Extract_trigger.py - update imports. [Neil Cook]
Extract_trigger.py - use spirouUnitRecipes to run recipes. [Neil Cook]
Extract_trigger.py - print the error. [Neil Cook]
Extract_trigger.py - print output before running. [Neil Cook]
Extract_trigger.py - changes to test run printing. [Neil Cook]
Extract_trigger.py - fix for when there are no files found. [Neil Cook]
Extract_trigger.py - turn off test run. [Neil Cook]
Extract_trigger.py - add options to combine all files from a night and to limit the number of files used for a recipe. [Neil Cook]
Recipe_control.txt - do not support FLAT_DARK and DARK_FLAT in cal_FF. [Neil Cook]

0.3.040 (2018-10-17)¶

Extract_trigger.py - add filters to allow only certain files to be process based on DPRTYPE. [Neil Cook]
Clean_calibDB - custom script to remove all unwanted keys (set in the code) and remove files not in the calibDB and move all good files to new folder with a new master calibDB file. [Neil Cook]
Reset the calibDB and telluDB with new MASTER wave solutions. [Neil Cook]
Extract_trigger.py - make test run - with printing/storing of commands only and add/modify printing/logging statements. [Neil Cook]
Extract_trigger.py - correct problem with preprocess trig. [Neil Cook]
Extract_trigger - fix bugs. [Neil Cook]
Extract_trigger - fix mistake. [Neil Cook]
Extract_trigger - correct mistake in ask function. [Neil Cook]
Extract_trigger.py - allow to skip pp and make function. [Neil Cook]
Extract_trigger.py - first working version. [Neil Cook]
SpirouStartup.py - fix bug with inputs (numpy array not allowed) [Neil Cook]
Extract_trigger.py - start work on a simple calibration trigger (upto and including extraction) [Neil Cook]

0.3.041 (2018-10-17)¶

SpirouStartup.py - fixed problem when no column is present (set to None) [Neil Cook]
Extract_trigger.py - start of a trigger that goes from pp –> extraction (including all calibrations) - [NOT FINISHED] [Neil Cook]
SpirouConst.py - add DPRTYPE to index file for raw outputs. [Neil Cook]
SpirouFITS.py - added “check_wave_sol_consistency” function to check and remap coefficients if incorrect from constants file (IC_LL_DEGR_FIT) [Neil Cook]
Cal_HC/ cal_WAVE - added check for consistent number of coefficients in wave solution - if wrong refitted onto new coefficients with correct number. [Neil Cook]
SpirouFile.py - add function to sort by base name (sort_by_name) with alias SortByName. [Neil Cook]
Explore_headers.py - code to explore headers of all files in given dir string (with wild cards) [Neil Cook]
Obj_mk_obj_stack.py - for making stacks of images (Nobs x Nb_xpix x Nbo) [Neil Cook]
SpirouKeywords.py - add new header keys to list + define them as keywordstores. [Neil Cook]
Obj_mk_obj_template.py - sort template files by base file name. [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - add some header keys to help identify the source of output. [Neil Cook]
Cal_HC_E2DS_EA_spirou.py - add some more header keys to enable identifying source of output files. [Neil Cook]

0.3.038 (2018-10-16)¶

Update version/date/changelog/update notes. [Neil Cook]
Cal_Test.run - add cal_DRIFTCCF_E2DS_spirou to tested codes. [Neil Cook]
SpirouUnitRecipes.py - add cal_DRIFTCCF_E2DS_spirou to unit recipe definitions. [Neil Cook]
SpirouKeywords.py - add reference rv keyword and keywordstore definition. [Neil Cook]
SpirouConst.py - fix tags in new DRIFTCCF file name definitions. [Neil Cook]
Recipe_control.txt - add cal_DRIFTCCF_E2DS_spiour to the runable codes - for FP only. [Neil Cook]
Output_keys.py - add DRIFTCCF_E2DS_FITS_FILE to output keys. [Neil Cook]
Constants_SPIROU_H4RG.py - add driftccf constants to constants file. [Neil Cook]
Cal_DRIFTCCF_E2DS_spirou.py - re-save driftfits to file. [Neil Cook]
Cal_DRIFTCCF_E2DS_spirou.py - pep8 changes + load constants from file + add flux ratio + save reference RV to header. [Neil Cook]
Merge branch ‘francois’ into dev. [Neil Cook]
Merge pull request #488 from njcuk9999/dev. [Neil Cook]

spirouEXTOR.py - undo debananafication all zeros check - does not work
SpirouEXTOR.py - undo debananafication all zeros check - does not work. [Neil Cook]

0.3.039 (2018-10-16)¶

New recipe to compute the drift of simultaneous FP on Fiber C with fp.mas. [FrancoisBouchy]

0.3.044 (2018-10-16)¶

New function DRIFTCCF_E2DS_TBL_FILE to save driftccf file DRIFTCCF_E2DS_FITS_FILE still to be adapted. [FrancoisBouchy]

0.3.037 (2018-10-15)¶

SpirouKeywords.py - add the two new header keys for bigcube list. [Neil Cook]
Obj_mk_obj_template.py - add file names and bervs for input files to big cube header. [Neil Cook]
Update_note.txt - update with telluric changes. [Neil Cook]
SpirouConst.py - add prefix and change filename. [Neil Cook]
Obj_fit_tellu.py - save and remove abso save files - massive speed up. [Neil Cook]
SpirouTelluric.py - catch more NaN warnings from order_tapas. [Neil Cook]
SpirouFile.py - add get_most_recent function to get most recent unix time of list of files. [Neil Cook]
SpirouConst.py - add TELLU_ABSO_SAVE file (for saving loaded trans files) [Neil Cook]
Obj_fit_tellu.py - store abso unless there are new trans_files. [Neil Cook]
SpirouTelluric.py - swap sign on dv. [Neil Cook]
SpirouFITS.py - fix for new output of read_tilt_file. [Neil Cook]
SpirouFITS.py - add reading a key 1D list from header. [Neil Cook]
Constants_SPIROU_H4RG.py - add constants for quality control in obj_mk_tellu. [Neil Cook]
Obj_mk_tellu.py - quality control SNR in order QC_TELLU_SNR_ORDER greater than QC_TELLU_SNR_MIN. [Neil Cook]
Obj_mk_obj_tellu.py - only use unique filenames for tellu files. [Neil Cook]
Obj_fit_tellu.py - only use unique filenames from trans files. [Neil Cook]

0.3.036 (2018-10-14)¶

SpirouEXTOR.py - fix bug where whole order is zeros - will break spline. [Neil Cook]
Merge pull request #486 from njcuk9999/dev. [Neil Cook]

Melissa –> Dev –> Master (Confirm test on Cal_Test.run, Tellu_Test.run, Tellu_Test2.run, Pol_Test.run)
Update changelog and test.run. [Neil Cook]
SpirouTelluric.py - catch known warnings and disregard. [Neil Cook]
Update notes and changelog. [Neil Cook]

0.3.035 (2018-10-12)¶

Update unit test runs. [Neil Cook]
SpirouTelluric.py - modify get_molecular_tell_lines to use master wavelength solution, rename functions to better describe functionality, use relativistic dv correction function. [Neil Cook]
SpirouTDB.py - rename functions to better describe functionality. [Neil Cook]
SpirouDB.__init__.py - rename aliases to better describe functions. [Neil Cook]
SpirouPlot.py - add tellu_fit_debug_shift_plot - Issue #478. [Neil Cook]
SpirouMath.py - add relativistic_waveshift function. [Neil Cook]
Constants_SPIROU_H4RG.py - turn off the fit derviative part for principle components - Issue #478. [Neil Cook]
Obj_mk_obj_template.py - further fixes for wavelength shift addition - Issue #478. [Neil Cook]
Obj_fit_tellu.py - further fixes for wavelength shift addition - Issue #478. [Neil Cook]
Obj_fit_tellu.py - fix bugs in shifting wavelength (Issue #478) [Neil Cook]
Cal_extract/FF_RAW_spirou.py - catch warnings from extraction process. [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - currently only supports one FP_FP and one HC_HC (due to file updating) - added check to error if more used. [Neil Cook]
Cal_HC_E2DS_EA_spirou.py - currently only supports one FP_FP and one HC_HC (due to file updating) - added check to error if more used. [Neil Cook]
SpirouTelluric.py - change bad mask from 0.999 to 0.5 to avoid NaN fringing - Issue #478. [Neil Cook]
Update date/version/changelog/update notes. [Neil Cook]
SpirouWAVE.py - small pep8 and visual changes / simplifications. [Neil Cook]
SpirouPlot.py - bring new plot in-line with other plots + pep8 changes. [Neil Cook]
Constants_SPIROU_H4RG.py - small pep8 fixes to constants. [Neil Cook]
Merge branch ‘master’ into melissa. [Melissa Hobson]
Merge pull request #485 from njcuk9999/dev. [Neil Cook]

Eder –> Dev –> Master
Update unit_tests. [Neil Cook]
Unit_test.py - make sure all plots are closed. [Neil Cook]
Cal_WAVE_EA: moved plot of single HC order + fitted lines to spirouPlot constants: added cal_WAVE_EA constants spirouWAVE: improvements to FP line identification. [melissa-hobson]
SpirouPlot: moved plot of single HC order + fitted lines here from cal_WAVE_EA. [melissa-hobson]
Merge remote-tracking branch ‘origin/melissa’ into melissa. [Melissa Hobson]
Find_hc_gauss_peaks: added log message when found lines are read from table, reporting the table file. [melissa-hobson]

0.3.034 (2018-10-11)¶

Unit_test.py - make sure all plots are closed. [Neil Cook]
SpirouEXTOR.__init__.py - add alias for compare_extraction_modes (CompareExtMethod) - Issue #481. [Neil Cook]
SpirouEXTOR.py - add compare_extraction_mode function to test difference between flat and e2ds extraction modes (#481) [Neil Cook]
Cal_FF_RAW_spirou.py - save extraction method to header (like cal_extract) [Neil Cook]
Cal_extract_RAW_spirou.py - get flat header, compare flat extraction to extraction type (Issue #481) [Neil Cook]
SpirouFITS.py - return header for flat file so we can get extraction type for the flat (Issue #481) [Neil Cook]
Unit_tests - do not currently test cal_WAVE_E2DS_EA_spirou.py - comment out. [Neil Cook]
Update date/version/changelog/update notes. [Neil Cook]
SpirouLSD.py - add a few outstanding TODO comments and fix error print (filename may not be defined) [Neil Cook]
SpirouPOLAR.__init__.py - chagen polarHeader –> PolarHeader (for convention) [Neil Cook]
Pol_spirou.py - Update to alias for convention polarHeader –> PolarHeader. [Neil Cook]
Merge branch ‘master’ into eder. [Neil Cook]
Merge pull request #484 from njcuk9999/neil. [Neil Cook]

Neil –> Master (confirm test on Cal_Test.run, Tellu_Test.run and Tellu_Test2.run)
Update date/version/timings/changelog/update notes. [Neil Cook]
Merge branch ‘master’ into eder. [Eder]
Changed parameters for LSD analysis. [Eder]
Implemented selection of CCFFILE in LSD analysis matching closest temperature to source observed. [Eder]
Updated keyworks BERV, BJD, and MJD of polar products by central values calculated in the module. Also updated keyword EXPTIME by the sum of all EXPTIME values from individual exposures. [Eder]
Updated keyworks BERV, BJD, and MJD of polar products by central values calculated in the module. Also updated keyword EXPTIME by the sum of all EXPTIME values from individual exposures. [Eder]
Merge branch ‘master’ into eder. [Eder]
Tuned parameters to improve LSD analaysis and added new statistical quantities calculated from LSD analysis. [Eder]
Added new keywords in polar products, mainly the BJD time calculated at center of observations. Also fixed small bugs. [Eder]
Added new keywords in polar products, mainly the BJD time calculated at center of observations. Also fixed small bugs. [Eder]
Added new keywords in polar products, mainly the BJD time calculated at center of observations. Also fixed small bugs. [Eder]
Added new keywords in polar products, mainly the BJD time calculated at center of observations. Also fixed small bugs. [Eder]
Added new keywords in polar products, mainly the BJD time calculated at center of observations. Also fixed small bugs. [Eder]
Merge branch ‘master’ into eder. [Eder]
Merge branch ‘master’ into eder. [Eder]
Resolved merging conflicts. [Eder]

0.3.032 (2018-10-11)¶

Unit_tests - update tellu_test2 and test. [Neil Cook]
SpirouFITS.py - fix output of wavelength solution - Issue #483. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Merge pull request #482 from njcuk9999/neil. [Neil Cook]

Neil –> master - tested on Cal_Test.run, Tellu_Test.run, Tellu_Test2.run
SpirouConst.py - after reading default config file must look for a user config file (parameters depend on it) [Neil Cook]
SpirouConfigFile.py - moved get_user_config to here (to allow accessing from spirouConst.py) [Neil Cook]
SpirouConfig.py - move get_user_config to spirouConfigFile.py - (needed to fix not obtaining constants from user config file) [Neil Cook]
SpirouLog.py - add a possibility to debug in ipython. [Neil Cook]
SpirouFITS.py - fix error - now if image is not defined tries to get dimensions from header before giving error - Issue #483. [Neil Cook]
Update date/version/update notes and changelog. [Neil Cook]

0.3.031 (2018-10-10)¶

Tellu_Test2.run - add additional test to test different wavelength solutions in telluric recipes. [Neil Cook]
SpirouUnitTests/Runs - fix the units test with new recipes/names. [Neil Cook]
SpirouUnitRecipes.py - fix for the change of name of obj_mk_tell_template –> obj_mk_obj_template. [Neil Cook]
SpirouWAVE.py - Etienne’s fix for cal_HC stability in “fit_gaussian_triplets” [Neil Cook]
SpirouFITS.py - add a quiet mode (to not duplicate log) and fix bug in getting wavemap from header (from wave params) [Neil Cook]
SpirouConst.py - add filenames for obj_mk_obj_template. [Neil Cook]
Master_calibDB_SPIROU.txt - no longer need AB wave solutions and shape - only AB and C needed / shape generated online. [Neil Cook]
Output_keys.py - add obj_mk_obj_template filenames to output keys + recipe_control. [Neil Cook]
Constnats_SPIROU_H4RG.py - turn off force calibDB for wave solution + add HC parameters (Etienne’s fix) [Neil Cook]
Obj_mk_obj_template - renamed from obj_mk_tell_template.py + fixed for wavelength grid shift - Issue #478. [Neil Cook]
Obj_mk_tell_template.py - update with shifted wavelength grid - Issue #478. [Neil Cook]
Cal_HC_E2DS_EA_spirou.py - correct bug that wavelength solution parameters were not saved to header correctly. [Neil Cook]
Recipe_control.txt - add DARK_FP to drift and driftpeak allowed inputs - Issue #475. [Neil Cook]
Constants_SPIROU_H4RG.py - add dark_fp to the drift peak allowed constants (to all in use for drift/driftpeak) - Issue #475. [Neil Cook]
Recipe_control.txt - add OBJ_DARK to allowed files used in cal_DARK_spirou.py (Issue #479) [Neil Cook]
Cal_DARK_spirou.py - all use of skydarks and push SKYDARK to calibDB if used (Issue #479) [Neil Cook]
Constants_SPIROU_H4RG.py - add key “use_skydark_correction” to allow SKYDARKs to be use (and take presence over DARK in calibDB) [Neil Cook]
SpirouTelluric.py - shift templates if they are not created at runtime from mastergrid to current wavelength grid - Issue #478. [Neil Cook]
SpirouTelluric.py - fix bug with convolve_files (should not be re- copied into telluDB) [Neil Cook]
SpirouImage.py - allow SKYDARK to be used (if present in calibDB) if USE_SKYDARK_CORRECTION = True - Issue #479. [Neil Cook]
Obj_mk_tellu.py - fix headers in saved file (now wavelength is shifted) - Issue #478. [Neil Cook]
Obj_fit_tellu.py - fix bug with shifting PCA components (Issue #478) [Neil Cook]
Pol_spirou.py + all recipes use GetWaveSolution - force fiber A and B to use wave solution AB (Issue #480) [Neil Cook]
All recipes using GetWaveSolution - force fiber A and B to use AB wave solution. [Neil Cook]

0.3.030 (2018-10-09)¶

SpirouUnitRecipes.py - remove the moved HC/WAVE recipes from import (no longer in bin folder) [Neil Cook]
SpirouTelluric - add function wave2wave to shift an image from one wavelength grid to another (Issue #478) [Neil Cook]
SpirouFITS.py - allow wave solution to be obtained quietly. [Neil Cook]
SpirouTDB - add get_database_master_wave to get the master wavelength grid from TelluDB (Issue #478) [Neil Cook]
Recipe_control.txt - Allow sky objects for cal_DARK_spirou (Issue #479) [Neil Cook]
Master_tellu_SPIROU.py + file - modify master telluric database to have a MASTER_WAVE key - containing the master wavelength grid [unfinished] - Issue #478. [Neil Cook]
Wave2wave.py - backup of Etiennes function to shift images from one wavelength grid to another - Issue #478. [Neil Cook]
HC/WAVE recipes - move all (older) recipes to misc folder - can still be used when in this directory - cannot currently be used with unit tests. [Neil Cook]
Obj_mk_tellu.py - add code to shift transmission map [unfinished] - Issue #478. [Neil Cook]
Obj_fit_tellu.py - add code to shift pca components and template components [unfinished] - Issue #478. [Neil Cook]
Cal_extract_RAW_spirou.py - fix bug with extraction method 4a and 4b - data2 shallow copied - shouldn’t be! (Issue #477) [Neil Cook]
Update date/version/changelog/update notes. [Neil Cook]

0.4.025 (2018-10-06)¶

Input_file.txt - update list of inputs (Issue #475) [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]

0.3.029 (2018-10-06)¶

Cal_FF_RAW_spirou.py - update extraction to deal with different outputs. [Neil Cook]
SpirouFile.py - made sure pre-procesing always adds DPRTYPE even if file not recognised (#Issue 475) [Neil Cook]
SpirouEXTOR.py - for modes 3c, 3d, 4a, 4b add the e2dsll extraction type. [Neil Cook]
SpirouConst.py - add file definition for e2dsll. [Neil Cook]
Recipe_control.txt - added and corrected dark_fp, dark_flat and obj_obj. [Neil Cook]
Output_keys.py - added output type extract_e2dsll_file. [Neil Cook]
Cal_extract_RAW_spirou.py - added “un-sum” extraction output (E2DSLL) to see what the extraction is doing. [Neil Cook]
Merge pull request #476 from njcuk9999/extract_redo. [Neil Cook]

Extract redo –> Merge (cal_WAVE_E2DS_EA_spirou not working with new extraction)

0.3.028 (2018-10-05)¶

Update_note.txt - update with note about setting extraction to 4b (default = 3d) [Neil Cook]
Constants_SPIROU_H4RG.py - set extraction_type back to 3d for now - until 4a/4b tested. [Neil Cook]
Update - version/date/changelog/update notes. [Neil Cook]

0.3.027 (2018-10-05)¶

Timings.txt - update timings with new runs. [Neil Cook]
Cal_Test.run - comment out cal_WAVE_E2DS_EA_spirou - not working with extraction 4b? [Neil Cook]
SpirouTHORCA.__init__.py - add alias to generate_res_files (GenerateResFiles) [Neil Cook]
SpirouWAVE.py - add generate_res_files functions to generate arrays/header dictionary in correct format for wave resolution line profile map file. [Neil Cook]
SpirouConst.py - add WAVE_RES_FILE_EA to file definitions. [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - add saving of wavelength resolution line profiles to file. [Neil Cook]
Output_keys.py - added “WAVE_RES” to output keys (for wave solution res map) [Neil Cook]
Cal_HC_E2DS_EA_spirou.py - added saving of resolution map and line profiles to file. [Neil Cook]
SpirouUnitTest.py - up date title of log timings. [Neil Cook]
Recipe_control.txt - hide dark_fp dark_flat for now (test later) [Neil Cook]
SpirouFITS.py - allow fiber-forcing in getting wave solution (otherwise when calibDB is used, uses p[‘FIBER’]) [Neil Cook]
Off_listing_RAW_spirou.py - correct mistake with off_listing (rawloc should be a list) [Neil Cook]
SpirouFITS.py - make sure the source of the wavelength solution is reported (Issue #468) [Neil Cook]
Update date/version/update notes and changelog. [Neil Cook]

0.3.026 (2018-10-05)¶

Cal_Test.run - add cal_SHAPE_spirou.py to unit test. [Neil Cook]
SpirouUnitsRecipes.py - add cal_HC_E2DS_EA_spirou, cal_SHAPE_spirou, cal_WAVE_E2DS_EA_spirou to unit tests. [Neil Cook]
Recipe_control.txt - add cal_SHAPE_spirou (copy of cal_SLIT_spirou) [Neil Cook]
Cal_SHAPE_spirou.py - change __NAME__ (after recipe control integration) [Neil Cook]
SpirouImage.py - optimisation - moved a few things out of loop to speed up process. [Neil Cook]
SpirouPlot.py - corrected type in constant name (slit_shape_angle_plot) [Neil Cook]
Constants_SPIROU_H4RG.py - move cal_SHAPE_spirou.py constants to constants file. [Neil Cook]
Cal_SHAPE_spirou.py - move constants to constants file. [Neil Cook]

0.3.025 (2018-10-04)¶

SpirouFITS.py - get shape file from header. [Neil Cook]
Cal_extract_RAW_spirou.py - add shape file to header (if mode 4a/4b) [Neil Cook]
Cal_SHAPE_spirou.py - fix type - should be SHAPE file not TILT file. [Neil Cook]
SpirouImage.__init__.py - add alias to get_shape_map (GetShapeMap) [Neil Cook]
SpirouImage.py - move get_shape_map to spirouImage functions (And add imports as required) [Neil Cook]
SpirouPlot.py - add slit shape plot. [Neil Cook]
SpirouKeywords.py - add kw_SHAPEFILE to output keys. [Neil Cook]
SpirouConst.py - add SLIT_SHAPE_FILE filename definition. [Neil Cook]
Output_keys.py - add slit_shape_file output key. [Neil Cook]
New_bananarama.py - fix to work with DRS. [Neil Cook]
Cal_SLIT_spirou.py - replace old path function with new and correct small typo. [Neil Cook]
Cal_SHAPE_spirou.py - add plotting, filesaving, calibDB movement and move functions to spirouImage (finally runs) [Neil Cook]
Cal_SHAPE_spirou.py - added plotting, file saving and adding to calibDB. [Neil Cook]
Cal_SHAPE_spirou.py - fix bugs that now produce identical results to new_bananarama code. [Neil Cook]

0.3.024 (2018-10-03)¶

Cal_SHAPE_spirou.py - fix typo dx[iw] = coeffs[1] –> dx[iw] = gcoeffs[1] [Neil Cook]
New_bananarama.py - added TODO questions for Etienne. [Neil Cook]
Cal_SHAPE_spirou.py - more changes to update with Etiennes new_bananarama code. [Neil Cook]
Merge branch ‘master’ into extract_redo. [Neil Cook]
Cal_Test.run - must test HC/WAVE EA recipes - added to runs. [Neil Cook]
Cal_HC_E2DS_EA_spirou.py - fix bug flatfile in header should be blazefile. [Neil Cook]
Cal_SHAPE_spirou.py - updated code [unfinished/not working] [Neil Cook]
Copy of etiennes shap finding code. [Neil Cook]
Merge branch ‘master’ into extract_redo. [Neil Cook]

Conflicts:
.gitignore INTROOT/SpirouDRS/spirouImage/spirouFITS.py
Merge pull request #473 from njcuk9999/neil. [Neil Cook]

Neil –> Master
Update timings and update notes. [Neil Cook]
Test code for one target. [Neil Cook]
Update version/date/changelog/update notes. [Neil Cook]
Unit tests - remove some extractions (not needed for minimum test) [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Unit tests - add full telluric test for TC3. [Neil Cook]
SpirouImage.py - WAVE_FILE is now WAVEFILE. [Neil Cook]
Dark_test.py - test of the values supplied in the dark header file (for specific files + night_name) [Neil Cook]
Visu_E2DS_spirou.py - readblazefile now need p returned. [Neil Cook]
Obj_fit_tellu.py - re-add loc[‘WAVE’] (used for plotting) + loc[‘WAVE_IT’] need filename returned. [Neil Cook]
Cal_wave_mapper.py - remove flat file (not used or obtained) from header. [Neil Cook]
Cal_exposure_meter.py - remove flatfile (not used or obtained) [Neil Cook]
Update spirouImage.py. [Neil Cook]

spirouImage.py - fix for bug in itable dtype being bytes not string (certain python installations only)
Merge pull request #470 from njcuk9999/neil. [Neil Cook]

Neil –> master
Cal_SHAPE_spirou.py - working on integrating nuxtract from EA. [Neil Cook]
Update gitignore to ignore misc folder. [Neil Cook]
Sync file - not used. [Neil Cook]
Cal_SHAPE_spirou.py - first commit [unfinished] [Neil Cook]
Reset_calibDB file - add shape map file (placeholder - will be generated in new cal_SLIT code) [Neil Cook]
.gitignore - remove unneeded ignore. [Neil Cook]
SpirouUnitRecipes.py - remove references to cal_extract_RAW_spirouAB and C. [Neil Cook]
SpirouFITS.py - add read_shape_file function to get shape file from calibDB. [Neil Cook]
SpirouEXTOR.__init__.py - add aliases and remove old commented aliases. [Neil Cook]
SpirouEXTOR.py - modify extraction wrapper function to accept new arguments of shape extraction functions, fill out shape extraction functions and add “debananafication” function. [Neil Cook]
SpirouCDB.py - fix typo in error message. [Neil Cook]
Master_calib_SPIROU.txt - add SHAPE file for reset (until new cal_SLIT code is running) [Neil Cook]
Constants_SPIROU_H4RG.py - update normal method to 4b. [Neil Cook]
Cal_extract_RAW_spirou: add modifications required for extraction methods 4a and 4b. [Neil Cook]
Cal_extract_EA_test: update test for EA changes 2018-09-20. [Neil Cook]
Misc - backup old files. [Neil Cook]
SpirouEXTOR.py - add todo and comment to remind to move afterwards. [Neil Cook]
SpirouEXTOR.py - add shape extract method to test methods. [Neil Cook]
Cal_Extract_EA_test.py: add test code to experiment with extraction methods. [Neil Cook]
Constants_SPIROU_H4RG: add extra extraction types to allowed types. [Neil Cook]

0.3.023 (2018-10-02)¶

Cal_CCF_E2DS_spirou.py - fix order out GetWaveSolution outputs (Issue #464) [Neil Cook]
Cal_Test.run - change over (cal_exposure_meter last) [Neil Cook]
SpirouTelluric.py - modify functions to allow filename saved to p - for insertion into header at hdict creation (Issue #471) [Neil Cook]
SpirouLOCOR.py - modify functions to allow filename save to p - for insertion into header at hdict creation (Issue #471) [Neil Cook]
SpirouImage.py - modify functions to allow filename to be saved to p - to insert into header at hdict creation (Issue #471) - fix bug with mask2 (in getting drift files function) [Neil Cook]
SpirouFITS.py - mmodify read functions to save the filename to p - to inject into header at hdict creation (Issue #471) [Neil Cook]
SpirouFLAT - add filenames to headers (Issue #471) [Neil Cook]
SpirouKeywords.py - add the keywords for each file (that will go in the header) - Issue #471. [Neil Cook]
Obj_mk_tellu.py - add filenames to headers (Issue #471) [Neil Cook]
Obj_mk_tellu_template.py - add filenames to headers (Issue #471) [Neil Cook]
Obj_fit_tellu.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_wavE_mapper.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_[WAVE_E2DS]_spirou.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_SLIT_spirou.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_loc_RAW_spirou.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_HC_E2DS_spirou.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_HC_E2DS_EA_spirou.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_FF_RAW_spirou.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_extract_RAW_spirou.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_exposure_meter.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_DRIFTPEAK_E2DS_spirou.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_DRIFT_E2D.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_DARK_spirou.py - add filenames to headers (Issue #471) [Neil Cook]
Cal_BADPIX_spirou.py - add filenames to headers (Issue #471) [Neil Cook]
Update date/version/changelog. [Neil Cook]
SpirouWAVE - replace get_e2ds_ll (Issue #468) [Neil Cook]
SpirouFITS.py - allow header return. [Neil Cook]
SpirouPlot.py - fix bug plot_style cannot be None - now ‘’ when empty. [Neil Cook]
Cal_CCF_E2DS_spirou.py - fix bug - swap wave and param. [Neil Cook]
Cal_extract_RAW_spirou.py - add header to wave solution returns. [Neil Cook]

0.3.022 (2018-10-01)¶

SpirouTHORCA.__init__.py - remove use of GetE2DSll - use GetWaveSolution (Issue #468) [Neil Cook]
SpirouTHORCA.py - remove use of GetE2DSll - use GetWaveSolution (Issue #468) [Neil Cook]
Cal_CCF_E2DS_spirou.py - remove use of GetE2DSll - use GetWaveSolution (Issue #468) [Neil Cook]
SpirouTHORCA.py - re-work the obtaining of wave solution (Issue #468) [Neil Cook]
SpirouFITS.py - re work wave solution functions (Issue #468) [Neil Cook]
SpirouImage.__init__.py - remove old wave sol functions (Issue #468) [Neil Cook]
Cal_DRIFT_RAW_spirou.py - work on wave solution functions (Issue #468) [Neil Cook]
Pol_spirou.py - work on wave solution functions (Issue #468) [Neil Cook]
Cal_extract_RAW_spirou.py - work on wave solution functions (Issue #468) [Neil Cook]
Visu_[ALL]_spirou.py - work on wave solution functions (Issue #468) [Neil Cook]
Obj_[fit/mk]_tellu.py - work on wave solution functions (Issue #468) [Neil Cook]
Cal_wave_mapper.py - work on wave solution functions (Issue #468) [Neil Cook]
Cal_HC_E2DS_EA_spirou.py - work on wave solution functions (Issue #468) [Neil Cook]
Cal_WAVE_[ALL].py - work on wave solution functions (Issue #468) [Neil Cook]
Cal_exposure_meter.py - work on wave solution functions (Issue #468) [Neil Cook]
Cal_DRIFTPEAK_E2DS_spirou.py - work on wave solution functions (Issue #468) [Neil Cook]
Cal_DRIFT_E2DS_spirou.py - work on wave solution functions (Issue #468) [Neil Cook]
SpirouImage.py - modify get_all_similar_files to add check of fiber for OBJ_FP OBJ_HCONE etc (i.e. only allow on fiber C) and return filetype to show user which DRS_EXTOUT were allowed (Issue #464) [Neil Cook]
SpirouImage.__init__.py - update alias to better represent what we are doing get_all_similar_files –> GetSimilarDriftFiles. [Neil Cook]
Constants_SPIROU_H4RG.py - add constant to check which fiber is being used (for OBJ_FP and OBJ_HCONE etc should only work on fiber C) - Issue #464. [Neil Cook]
Cal_DRIFTPEAK_E2DS_spirou.py - fix code to allow FP_FP and OBB_FP (and report back on allowed types) - Issue #464. [Neil Cook]
Cal_DRIFT_E2DS_spirou.py - fix code to allow FP_FP and OBB_FP (and report back on allowed types) - Issue #464. [Neil Cook]
Teset.run - update tested files. [Neil Cook]
Re-add misc folder to github sync. [Neil Cook]
SpirouImage.py - change how get_all_similar_files works (now look for kw_OUTPUT based on “DRIFT_PEAK_ALLOWED_OUTPUT” - Issue #464. [Neil Cook]
Constnats_SPIROU_H4RG.py - Issue #464 - add definitions for which outputs are allowed for “fp” and “hc” [Neil Cook]
Add misc backup files. [Neil Cook]
Removed problematic fitgaus.py from fortran (conflicts with fitgaus.f) and removed fitgaus.f from spirouTHORCA. [Neil Cook]
SpirouImage.py - Issue #464 - get_all_similar_files - modify to run indexing if no index.fits exists. [Neil Cook]
Off_listing_REDUC_spirou.py - Issue #464 - allow off_listing to run in quiet mode. [Neil Cook]

0.3.021 (2018-09-26)¶

SpirouWAVE.py - adapt to allow force creating of linelist. [Neil Cook]
SpirouPlot.py - adapt to be able to use different style. [Neil Cook]
SpirouConst.py - add plot style (for alternate plotting) [Neil Cook]
Constants_SPIROU_H4RG.py - add control to force linelist re- computation. [Neil Cook]

0.3.020 (2018-09-25)¶

SpirouPlot.py - pass font changes for all graphs (via matplotlib.rc) [Neil Cook]
SpirouConst - add descriptions for plot font functions. [Neil Cook]
SpirouConst.py - add plot pseudo constants (to enable changing plot fontsize easily - for all plots) [Neil Cook]
Cal_CCF_E2DS_spirou.py - add inputs for ccf_rv_ccf_plot (modified inputs for plot title) [Neil Cook]
Merge pull request #466 from njcuk9999/neil. [Neil Cook]

fix typo in last commit
Merge pull request #465 from njcuk9999/neil. [Neil Cook]

Neil –> Master (Fixes for issue #464)

0.3.019 (2018-09-24)¶

Cal_DRIFTPEAK_E2DS_spirou.py - fix typo bug with drift_peak_allowed_types. [Neil Cook]
Recipe_control.txt - add HCTWO_HCTWO and OBJ_FP to cal_DRIFT and cal_DRIFTPEAK recipes - Issue #464. [Neil Cook]
Constnats_SPIROU_H4RG.py - added new constant to control with files (with header key KW_EXT_TYPE) are associated with fp and hc (for setting other constants) - Issue #464. [Neil Cook]
Cal_extract_RAW_spirou.py - note from Etienne to Francois re: negative fluxes to zero after background correction. [Neil Cook]
Cal_DRIFTPEAK_E2DS_spirou.py - modified the lamp parameter to get from constants (for easier addition of different types) - Issue #464. [Neil Cook]
Merge pull request #463 from njcuk9999/dev. [Neil Cook]

Dev

0.3.018 (2018-09-21)¶

Update timings. [Neil Cook]
Update date/version/changelog/timings. [Neil Cook]

0.3.017 (2018-09-21)¶

SpirouTHORCA.py - fix code to not have min/max of HC/FP_N_ORD START/FINAL for cal WAVE/cal HC. [Neil Cook]
Cal_WAVE_E2DS_spirou.py - fix code to not have min/max of HC/FP_N_ORD START/FINAL for cal WAVE. [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - fix code to not have min/max of HC/FP_N_ORD START/FINAL for cal WAVE. [Neil Cook]
Cal_HC_E2DS_spirou.py - fix code to not have min/max of HC/FP_N_ORD START/FINAL for cal HC. [Neil Cook]

0.3.016 (2018-09-21)¶

Remove user specific ignore (should not be needed) [Neil Cook]
Update .gitignore to ignore misc folder. [Neil Cook]
SpirouWAVE.py - Merge changes from Dev into Melissa. [Neil Cook]
SpirouTHORCA.py - Merge changes from Dev into Melissa. [Neil Cook]
SpirouRV.py - Merge changes from Dev into Melissa. [Neil Cook]
SpirouPlot.py - Merge changes from Dev into Melissa (Issue #460) [Neil Cook]
Constants_SPIROU_H4RG.py - Merge changes from Dev into Melissa. [Neil Cook]
Cal_WAVE_E2DS_EA_spirou.py - Merge changes from Melissa. [Neil Cook]
Cal_CCF_E2DS_spirou.py - full header added to “CCF_FITS_FILE” [Neil Cook]
Merge pull request #459 from njcuk9999/dev. [Neil Cook]

Dev –> master
Update version/changelog/date/update notes. [Neil Cook]

0.3.015 (2018-09-19)¶

Unit_tests: fix bug in run names. [Neil Cook]

0.3.012 (2018-09-19)¶

Unit_tests: add cal_CCF test to Tellu_Test.run. [Neil Cook]
Unit_tests: update unit test with new hc files (from 2018-08-05) [Neil Cook]
Recipe_control.txt - remove duplicate line in cal_CCF definition. [Neil Cook]
Cal_CCF_E2DS_spirou.py - update comments and remove extra spaces. [Neil Cook]
Merge remote-tracking branch ‘origin/francois’ into francois. [FrancoisBouchy]
Update date/version/changelog. [Neil Cook]

0.3.013 (2018-09-19)¶

New CCF mask provided by Xavier on 2018 Sept 19. [FrancoisBouchy]
Add E2DS_FF for cal_CCF_E2DS recipe. [FrancoisBouchy]
Adaptation for telluric corrected spectra. [FrancoisBouchy]

0.3.011 (2018-09-19)¶

Recipe_control.txt - add e2dsff files to cal_drift codes and cal_ccf. [Neil Cook]
Cal_DRIFTPEAK_E2DS_spirou: fix obtaining of lamp type with hc_hc (ext_type == “HCONE_HCONE” or “HCTWO_HCTWO”) [Neil Cook]
Cal_extract_RAW_spirou.py: better error message for no DPRTYPE in header (Issue #456) [Neil Cook]

0.4.024 (2018-09-18)¶

Test_recipe.py - continue work on getting new input method to work. [Neil Cook]
SpirouStartup2.py - continue work on getting new input method to work. [Neil Cook]
SpirouRecipe.py - continue work on getting new input method to work. [Neil Cook]
Recipes.py - add test recipe to test new definition method. [Neil Cook]
SpirouConst.py: fix pep8 issue - brackets not needed. [Neil Cook]
Merge branch ‘master’ into input_redo. [Neil Cook]

0.3.010 (2018-09-18)¶

Tellu_test.run: add actual non-hot stars to telluric test. [Neil Cook]
Tellu_test.run: add actual non-hot stars to telluric test. [Neil Cook]
Tellu_test.run: reset for full test. [Neil Cook]

0.3.009 (2018-09-17)¶

Test runs: update tellu_test.run. [Neil Cook]
Update cal_test.run. [Neil Cook]
SpirouStartup.py: extra check for no outputs in indexing (fixes crash) [Neil Cook]
SpirouPlot: fix telluric plots (labels, titles, limits) [Neil Cook]
Obj_mk_tellu: save SP to loc. [Neil Cook]
Obj_fit_tellu: fix bug (blaze must be normalised to fit telluric) [Neil Cook]

0.4.023 (2018-09-17)¶

Test_recipe: todo’s added. [Neil Cook]

0.4.022 (2018-09-14)¶

Input update: spirouStartup.__init__.py aliases / imports to spirouStartup2 (temporary) [Neil Cook]
Input update: recipes.py - holder for recipe definitions. [Neil Cook]
Input update: spirouRecipe.py - holder for new recipe classes. [Neil Cook]
Input update: spirouStartup2.py - holder for new spirouStartup. [Neil Cook]
Input update: test_recipe.py - test recipe to test new input functions. [Neil Cook]
Input update: add input_files.txt - definition of input files. [Neil Cook]
Merge pull request #453 from njcuk9999/V0.3_Cand. [Neil Cook]

V0.3 cand –> master. Confirm unit tests successful.

0.3.008 (2018-09-13)¶

Version.txt: update/check dependencies. [Neil Cook]
Drs_dependencies.py: fix for python 2 path. [Neil Cook]
Update date/version/changelog. [Neil Cook]
Timings.txt: For Neil reference only unit_test timings. [Neil Cook]

0.3.007 (2018-09-13)¶

Drs_changelog.py: undo pep8 name change (and redo properly) [Neil Cook]
Update_notes.txt: add unit tests to update (files and some explanation) [Neil Cook]
Pol_spirou.py: fix error with new input/output to WriteImageMulti. [Neil Cook]
SpirouWAVE.py: hide testing “print” statements. [Neil Cook]
Unit_tests: update unit test + add polarisation test. [Neil Cook]
SpirouCDB.py: fix bad call to DATE_FMT_HEADER (p not required) [Neil Cook]
Cal_reset.py: exit script has_plots=False. [Neil Cook]
SpirouWAVE.py: fix issue with pep8 update (ll_prev defined in wrong place) [Neil Cook]
SpirouWAVE.py (Issue #452): wave_catalog is now initialised as a NaN array (instead of an array of zeros) [Neil Cook]

0.3.006 (2018-09-12)¶

Off_listing.py: fix bug and add to index (if prompted by user) [Neil Cook]
SpirouStartup.py: added Y/N question function. [Neil Cook]
Off_listing.py: fix to bug in code (rawloc –> list) [Neil Cook]
Off_listing.py: generic off listing that takes any directory as only input (no night name) and read’s index.fits / _pp fits file headers to get off listing for that directory. [Neil Cook]
SpirouStartup.py: fix for not requiring night name in load_arguments. [Neil Cook]
SpirouConst.py: Added general off listing columns. [Neil Cook]
Made spirouTools executable. [Neil Cook]
Fix bad pep8 updates. [Neil Cook]
Pep8 updates. [Neil Cook]

0.3.005 (2018-09-11)¶

Pep8 updates. [Neil Cook]
Update_notes.txt: update with new unit tests. [Neil Cook]
Unit tests: update unit test –> add “Tellu_Test.run” and modify “Cal_Test.run”, remove test_tellu.run. [Neil Cook]
Recipe_control.txt –> add telluric and polarisation cases for visu_E2DS_spirou. [Neil Cook]
Obj_fit_tellu, obj_mk_tell_template, obj_mk_tellu: fix writing outputs to file. [Neil Cook]
Update date/version/changelog/update notes. [Neil Cook]

0.3.033 (2018-09-11)¶

Added BJD# and MEANBJD to header of polar products. [Eder]
Minor changes. [Eder]
Minor changes. [Eder]
Minor changes. [Eder]

0.3.004 (2018-09-11)¶

Recipe_control.txt –> add cases (for fiber) for visu_E2DS_spirou. [Neil Cook]
SpirouFile.py - fix bad error output {0} –> {1} [Neil Cook]
Cal_test.run: fix errors (typos …f –> …a) [Neil Cook]
Update recipe control for visu_RAW and visu_E2DS recipes. [Neil Cook]
Update notes with not done/finished. [Neil Cook]
SpirouWAVE - re-add dict() –> OrderedDict() [Neil Cook]
Config - merge fix - do NOT upload own config! [Neil Cook]
Cal_WAVE_E2DS_EA - extra imports. [Neil Cook]
Merge branch ‘dev2’ into melissa2. [Neil Cook]

Conflicts:
INTROOT/SpirouDRS/data/constants/recipe_control.txt INTROOT/SpirouDRS/spirouConfig/spirouConst.py INTROOT/SpirouDRS/spirouTHORCA/spirouWAVE.py INTROOT/bin/cal_WAVE_E2DS_EA_spirou.py
Cal_exposure_meter.py: fix bad call to get_telluric (p, loc –> loc) [Neil Cook]
Updated changelog/date/version/update notes. [Neil Cook]
Update unit tests. [Neil Cook]
SpirouUnitTests: fix outputs of manage_run (post H2RG removal) [Neil Cook]
SpirouTelluric.py: fix kind when reading TAPAS file (was FLAT now TAPAS) [Neil Cook]
SpirouStartup.py: fix indexing of files (add “LAST_MODIFIED” column) [Neil Cook]
SpirouStartup.__init__.py: fix aliases. [Neil Cook]
SpirouTable - increase width of table (now 9999) [Neil Cook]
SpirouExoposeMeter.py: update where TAPAS file is taken from (now from telluDB) [Neil Cook]
SpirouConst.py: update reduced output columns (need date and utc for drift) [Neil Cook]
Update master_calib_SPIROU.txt for reset - now we don’t need H2RG or TAPAS input. [Neil Cook]
Off_listing_RAW/REDUC_spirou - fix bug in adding unix time - now called “last_modified” (to be more specific) [Neil Cook]
Cal_FF_RAW_spirou: fix bug in H2RG removal. [Neil Cook]
Cal_exposure_meter/cal_wave_mapper - update location of telluric ref file (TAPAS) now via telluDB. [Neil Cook]

0.3.003 (2018-09-10)¶

Update notes - update. [Neil Cook]
Unit test .run files - update after removing H2RG dependency. [Neil Cook]
SpirouUnitTests.py: remove H2RG dependency (comparison not needed) [Neil Cook]
Unit_test.py: replace dict() –> OrderedDict() + remove H2RG dependency. [Neil Cook]
SpirouUnitTests.py: replace dict() –> OrderedDict() + remove H2RG dependency. [Neil Cook]
SpirouUnitRecipes.py: remove H2RG dependency (no comparison needed) + replace dict() –> OrderedDict() [Neil Cook]
SpirouUnitTests.__init__.py: remove H2RG dependency (remove check_type and set_comp) [Neil Cook]
Drs_tools: replace dict() –> OrderedDict() [Neil Cook]
Drs_documentation: replace dict() –> OrderedDict() [Neil Cook]
Drs_dependencies: replace dict() –> OrderedDict() [Neil Cook]
Drs_changelog: replace dict() –> OrderedDict() [Neil Cook]
Calc_berv: replace dict() –> OrderedDict() and remove H2RG dependency. [Neil Cook]
SpirouWAVE: replace dict() –> OrderedDict() [Neil Cook]
SpirouTHORCA.py: remove H2RG dependency. [Neil Cook]
SpirouTelluric.py: remove unused line (norm) [Neil Cook]
SpirouStartup.py: remove H2RG dependency and add “UNIX” file column. [Neil Cook]
SpirouRV.py: remove H2RG dependency. [Neil Cook]
SpirouPOLAR.py: replace dict() –> OrderedDict() [Neil Cook]
SpirouLOCOR.py: remove H2RG dependency. [Neil Cook]
SpirouImage.py: remove H2RG dependency. [Neil Cook]
SpirouFITS.py: remove H2RG dependency + replace dict() –> OrderedDict() [Neil Cook]
SpirouBERV.py: remove H2RG dependency. [Neil Cook]
SpirouEXTOR: replace dict() –> OrderedDict() [Neil Cook]
SpirouDB: replace dict() –> OrderedDict() [Neil Cook]
SpirouPlot.py: remove H2RG dependency. [Neil Cook]
SpirouConst.py: update reduced output columns (remove obs date and utc from reduced products) [Neil Cook]
SpirouConfig.py: replace dict() –> OrderedDict() [Neil Cook]
Main_drs_trigger: remove H2RG dependency. [Neil Cook]
Constants_SPIROU_H2RG: remove H2RG dependency (Delete file) [Neil Cook]
Off_listing_REDUC_spirou - add column for last modified (unix time) [Neil Cook]
Cal_wave_mapper: replace dict() –> OrderedDict() [Neil Cook]
Cal_SLIT_spirou: remove H2RG dependency. [Neil Cook]
Cal_preprocess_spirou: remove H2RG dependency. [Neil Cook]
Cal_loc_RAW_spirou: remove H2RG dependency. [Neil Cook]
Cal_FF_RAW_spirou: remove H2RG dependency. [Neil Cook]
Cal_extract_RAW_spirou: remove H2RG dependency. [Neil Cook]
Cal_exposure_meter: replace dict() –> OrderedDict() [Neil Cook]
Cal_DARK_spirou.py: remove H2RG dependency. [Neil Cook]
Cal_CCF_E2DS_spirou.py: replace dict() –> OrderedDict() [Neil Cook]

0.3.002 (2018-09-07)¶

Added an all_order plot of fitted gaussians (as discussed in #442) Saved additional values to loc in spirouWAVE functions that were required for cal_WAVE_E2DS_EA. [melissa-hobson]
Fit_emi_line: added check to not fit on lines with more than one zero- value (fix for #393) [melissa-hobson]

0.3.000 (2018-09-06)¶

Issue #418 spirouStartup.py - Make directory for NIGHT_NAME in TMP_DIR, index.fits saves to TMP_DIR, files are now checked for RAW in TMP_DIR. [Neil Cook]
Issue #418 spirouFile.py: obtaining tmppath and tmpfile to check for raw files (instead of rawpath which now throws error when used) [Neil Cook]
Issue #418 spirouConfig: added TMP_DIR definition (as DRS_DATA_WORKING dir) [Neil Cook]
Issue #418 cal_preprocess_spirou.py: made pp target raw folder but save to tmp dir. [Neil Cook]
Updated notes. [Neil Cook]
Updated the update notes. [Neil Cook]
Added Update Notes. [Neil Cook]
Update 20180805_test1.run to extract FP sequences and run DRIFT recipes (with extracted FPs) [Neil Cook]
Update 20180409 test to include off_listing_RAW/REDUC and not include pol_spirou (do not have the raw files needed) [Neil Cook]
Unit_test.py: Move Reset after set up (so errors reported before reset questions) [Neil Cook]
Issue #429: spirouUnitRecipes.py: modify the outputs of off_listing recipes (distinguish between RAW and REDUCED listing) [Neil Cook]
Issue #429: calc_berv - modify input/output of WriteImage (for handling p[‘OUTPUTS’]) [Neil Cook]
Issue #429: spirouStartup.py modify “main_end_script” to index outputs or pre-processing - via functions “index_pp”, “index_outputs”, “indexing” and “sort_and_save_outputs” [Neil Cook]
Issue #429: spirouStartup.__init__.py: alias sort_and_save_outputs to SortSaveOutputs. [Neil Cook]
Issue #429: spirouLSD - modify WriteImage to accept new input/output for writing p[‘OUTPUTS’] [Neil Cook]
Issue #429: spirouTable: Add ways of making, reading and writing fits table (via astropy.table.Table) - functions added = make_fits_table, read_fits_table, write_fits_table. [Neil Cook]
Issue #429: spirouImage.py: replace “get_all_similar_files” function to look at header keys instead of file name (for cal_DRIFT recipes) [Neil Cook]
SpirouFITS: modify write_image and write_image_multi to deal with writing output dict to p (via new function “write_output_dict”) [Neil Cook]
SpirouFile: add DRS_TYPE to identify RAW and REDUCED recipes (and pass to output processing later) [Neil Cook]
SpirouImage.__init__: add aliases for make_fits_table, read_fits_table and write_fits_table. [Neil Cook]
SpirouMath: reformat exception on timestamp (to print the input –> helps with debugging) [Neil Cook]
SpirouConst: add OFF_LISTING_RAW_FILE, OFF_LISTING_REDUC_FILE, INDEX_OUTPUT_FILENAME, OUTPUT_FILE_HEADER_KEYS, RAW_OUTPUT_COLUMNS, REDUC_OUTPUT_COLUMNS functions. [Neil Cook]
Modify unresize.py with the output to WriteImage (outputs management) [Neil Cook]
Update cal_drift_raw for outputs (but not file list) [Neil Cook]
Re-work off_listing recipes to look at the index files first (Much faster) - and to update the index files. [Neil Cook]
Modify cal_preprocess_spirou to sort out outputs and to skip index file. [Neil Cook]
Issue #429 - Re-work “listfiles” to get files from the headers (and index files) + deal with outputs. [Neil Cook]
Issue #429 - ReWork “WriteImage” to save to p[‘OUTPUTS’] and deal with spirouStartup.End dealing with outputs. [Neil Cook]

0.2.128 (2018-09-06)¶

SpirouPlot: updated wave_ea_plot_per_order_hcguess: - plots stay open until manually closed - each plot shows only the gaussian fits corresponding to the order (Fixes #442) [melissa-hobson]

0.2.124 (2018-09-05)¶

Issue #429 - add output header key to identify output files (KW_OUTPUT) - defined in output_keys.py (SpirouDRS/data), and added the obtaining of DPRTYPE to add EXT_TYPE key to header (extraction output id key –> giving DPRTYPE for extracted files) [Neil Cook]
Added a new log output to split up files to help see progress. [Neil Cook]
Issue #429 - add output header key to identify output files (KW_OUTPUT) - defined in output_keys.py (SpirouDRS/data) [Neil Cook]
Issue #429 - re-worked file identification only using header keys (no filename identification) [Neil Cook]
Issue #429 - added kw_OUTPUT and kw_EXT_TYPE definitions for saving output header id and extraction output header id. [Neil Cook]
Issue #429 - added TAGFOLDER and TAGFILE functions and modified all fits-file definition functions to accept tags. [Neil Cook]
Issue #429 - added get_tags function. [Neil Cook]
Pep8 fixes. [Neil Cook]
Issue #429 - re-work recipe_control.txt to take into account added output keys (and check keys on start up) [Neil Cook]
Issue #429 - definition of output header keys (based on output filename in spirouConst.py) [Neil Cook]
Issue #429 - add output header key to identify output files (KW_OUTPUT) - defined in output_keys.py (SpirouDRS/data) [Neil Cook]
Issue #429 - add output header key to identify output files (KW_OUTPUT) - defined in output_keys.py (SpirouDRS/data) [Neil Cook]
Issue #429 - add output header key to identify output files (KW_OUTPUT) - defined in output_keys.py (SpirouDRS/data) [Neil Cook]
Issue #429 - add output header key to identify output files (KW_OUTPUT) - defined in output_keys.py (SpirouDRS/data) [Neil Cook]
Issue #429 - add output header key to identify output files (KW_OUTPUT) - defined in output_keys.py (SpirouDRS/data) [Neil Cook]
Issue #429 - add output header key to identify output files (KW_OUTPUT) - defined in output_keys.py (SpirouDRS/data) [Neil Cook]
Issue #429 - add output header key to identify output files (KW_OUTPUT) - defined in output_keys.py (SpirouDRS/data) [Neil Cook]

0.2.125 (2018-09-05)¶

Cal_WAVE_E2DS_EA_spirou: updated HC section from cal_HC_E2DS_EA_spirou.py. [melissa-hobson]
Merge remote-tracking branch ‘origin/melissa’ into melissa. [Melissa Hobson]
Visu_E2DS_spirou, recipe_control: fiber is now obtained from file. [melissa-hobson]
Visu_E2DS_spirou, recipe_control: fiber is now obtained from file (Fixes #437) [melissa-hobson]
Commit local changes. [Melissa Hobson]
Merge pull request #441 from njcuk9999/master_copy. [melissa-hobson]

update melissa from Master copy
Merge branch ‘melissa’ into master_copy. [melissa-hobson]
Merge pull request #439 from njcuk9999/dev2. [Neil Cook]

Dev2
Merge remote-tracking branch ‘origin/dev2’ into dev2. [Neil Cook]
Merge pull request #438 from njcuk9999/dev2. [Neil Cook]

Dev2 –> Master (unit test complete and verified)
Update version/changelog and date. [Neil Cook]

0.2.126 (2018-09-05)¶

Commit local changes. [Melissa Hobson]

0.2.127 (2018-09-05)¶

SpirouRV (for cal_DRIFTPEAK_E2DS_spirou) - Fix repetition of warning messages in while loop. [njcuk9999]

0.2.123 (2018-09-04)¶

Move cal_HC_E2DS_EA constants to here. [Neil Cook]
Prep cal_HC_E2DS_EA for recipe run (add main function, move constants etc) [Neil Cook]
Updated date/version/changelog. [Neil Cook]

0.2.121 (2018-09-04)¶

Add placeholder marker for the new cal_HC_E2DS_EA_spirou work. [Neil Cook]
Modify generate_resolution_map –> fixes for integrating etiennes hcpeak functions. [Neil Cook]
Enter todo to rename variable. [Neil Cook]
Add plot for cal_HC_E2DS_EA_spirou (wave_ea_plot_line_profiles) and worker function (remove_first_last_ticks) [Neil Cook]
Modify the gauss_fit_s function (cal_HC_EA_E2DS usuage) [Neil Cook]
Separate input and output filename pseudo constant functions, added EA versions of cal_HC output filename definitions. [Neil Cook]
Update leapsec log. [Neil Cook]
Update to cal_HC_E2DS_EA_spirou - finish work on integrating Etienne’s work. [Neil Cook]
Fix for S1D spectra - there may be occasions when we cannot convert to S1D - print a warning if this is the case. [Neil Cook]
Merge pull request #434 from njcuk9999/neil. [Neil Cook]

Neil –> Dev 2

0.2.122 (2018-09-03)¶

Manually incorporated possibility to read wavelength solution from calibDB (from dev2) [melissa-hobson]
Cal_WAVE_E2DS_EA_spirou.py: incorporated FP lines into solution, corrected checks spirouWAVE.py: corrections to new FP functions. [melissa-hobson]

0.2.120 (2018-08-31)¶

Update date and version. [Neil Cook]
Script to manually add file to calibDB (from file in reduced folder) [Neil Cook]
Update change log/version and date. [Neil Cook]
Update master calibDB for reset. [Neil Cook]
Reset cal_CCF set NaNs to zeros (Issue #389) [Neil Cook]

0.2.117 (2018-08-31)¶

Added new wavelength solution and deleted files in data_example (not needed - run cal_reset or cal_validate) [Neil Cook]
Merge pull request #432 from njcuk9999/melissa-hobson-patch-1. [Neil Cook]

TC3 initial wavelength solution

0.2.116 (2018-08-30)¶

Add off_listing_REDUC_spirou to recipes available for testing. [Neil Cook]
Write a test for 18BQ01-Aug05 test files (20180805_test1.run) - Issue #400. [Neil Cook]
Fix micro seconds = 1e-6 not 1e-3. [Neil Cook]
Fix bug with PATH in bashrc file. [Neil Cook]
Add the resolution map (work-in-progress) [Neil Cook]
Fix bugs with cal_HC_E2DS_EA. [Neil Cook]
Fix bug with timestamp in logging. [Neil Cook]
Add writing of file for off_listing. [Neil Cook]

0.2.114 (2018-08-29)¶

Added fixes to triplet fitting function. [Neil Cook]
Added alias for the get_night_dirs function (GetNightDirs) [Neil Cook]
Fixed number of night_name dirs displayed on error. [Neil Cook]
Added night_name display limit (for when NIGHT_NAME is not an argument) [Neil Cook]
Fix to bad copy and paste in spirouPlot. [Neil Cook]
Improvements to having no FOLDER name - now displays all available folders. [Neil Cook]
Improvements to off_listing - having no night_name argument now displays all available night_names. [Neil Cook]
Improvements to off_listing - having no night_name argument now displays all available night_names. [Neil Cook]
Added off_listing_REDUC_spirou to allow listing of reduced folders. [Neil Cook]
Issue #428 - force calibDB wave solution - modify get_wave_keys. [Neil Cook]
Issue #428 - force calibDB wave solution - modify get_wave_solution. [Neil Cook]
Issue #428 - force calibDB wave solution - add constant switch. [Neil Cook]
Cal_HC_E2DS_EA - Set up for local running. [Neil Cook]

0.2.115 (2018-08-29)¶

TC3 initial wavelength solution. [melissa-hobson]

0.2.113 (2018-08-28)¶

First commit - Etienne’s cal_HC - added functions for cal_hc_ea. [Neil Cook]
First commit - Etienne’s cal_HC - added call to spirouMath. [Neil Cook]
First commit - Etienne’s cal_HC - moved lin_mini to spirouMath. [Neil Cook]
First commit - Etienne’s cal_HC - ReadTable/WriteTable/MakeTable correction when no formats. [Neil Cook]
First commit - Etienne’s cal_HC - wave_ea_plots. [Neil Cook]
First commit - Etienne’s cal_HC - gauss functions and lin_mini. [Neil Cook]
First commit - Etienne’s cal_HC - filename definition. [Neil Cook]
First commit - Etienne’s cal_HC. [Neil Cook]
Merge pull request #427 from njcuk9999/melissa. [Neil Cook]

Melissa –> Dev
Merge branch ‘dev2’ into melissa. [Neil Cook]
Merge remote-tracking branch ‘origin/melissa’ into melissa. [Neil Cook]
Set pixel_shift_inter and pixel_shift_slope back to zero (Issue #411) [Neil Cook]

0.2.118 (2018-08-27)¶

Issue #399 - copied in extra files (FILE_B and read me files) required by iers (but not currently linked to) [njcuk9999]
Issue #399 - modification to iers to make offline (hopefully) given testing offline. [njcuk9999]
Issue #399 - fix astropy_iers_dir to be the actual directory. [njcuk9999]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Merge pull request #426 from njcuk9999/neil. [Neil Cook]

Neil –> master (confirm tested on 20180409all.run and test_tellu.run)
Merge pull request #424 from njcuk9999/neil. [Neil Cook]

Neil –> Master

0.2.119 (2018-08-27)¶

Added location to save astropy iers file (Issue #389) [Neil Cook]
Possible fix for Issue #389: from @cusher - import astropy.utils.iers and set iers_table [Neil Cook]
Issue #399: barycorrpy offline file. [Neil Cook]

0.2.112 (2018-08-27)¶

Updated date, version and changelog. [Neil Cook]

0.2.107 (2018-08-27)¶

Updated date, version and changelog. [Neil Cook]
Issue with changelog (Version.txt not updating) –> corrected. [Neil Cook]

0.2.106 (2018-08-27)¶

Set pixel_shift_inter and pixel_shift_slope back to zero (Issue #411) [Neil Cook]

0.2.105 (2018-08-24)¶

Fix for Issue #406 - cal_CCF does not accept StokesI or e2dsff - fixed. [Neil Cook]
Fix for issue #406 - CCF recipe does not accept Stokes I spectra –> replace ‘_A.fits’ with ‘_AB_StokesI.fits’ [Neil Cook]
Fix for Issue #406 -CCF recipe does not accept stokes I spectra –> replace ‘_A.fits’ with ‘_AB_StokesI.fits’ [Neil Cook]
Fix for Issue #423 - cal_reset fails if folder does not exist. [Neil Cook]
Changed blacklist functino to look at objnames (Issue #419) [Neil Cook]
Changed blacklist file to object names (Issue #419) [Neil Cook]
Moved blacklist check to after we have the OBJNAME (Issue #419) [Neil Cook]

0.2.104 (2018-08-23)¶

Add check_blacklist and get_blacklist functions (Issue #419) [Neil Cook]
Add alias to check black list function (Issue #419) [Neil Cook]
Add alias to raw text file function (Issue #419) [Neil Cook]
Add blacklist filename (Issue #419) [Neil Cook]
Add code to read raw text file (Issue #419) [Neil Cook]
Add code to check for blacklisted file (Issue #419) [Neil Cook]
Add blacklist file (Issue #419) [Neil Cook]
Issue #389 - NaN values vauses error to be raised (Needs to be fixed properly) [Neil Cook]
Update date version and changelog. [Neil Cook]

0.2.110 (2018-08-23)¶

Update cal_HC_E2DS_spirou.py. [Neil Cook]

correct indentation error
Update spirouMath.py. [Neil Cook]

update pep8

0.2.103 (2018-08-23)¶

Re-write of median_one_over_f_noise function (Issue #420) [Neil Cook]
New alias for function re-write (Issue #420) [Neil Cook]
Using new function (re-write) from issue #420. [Neil Cook]

0.2.111 (2018-08-23)¶

Cal_WAVE_E2DS_EA_spirou.py update. [melissa-hobson]

0.2.109 (2018-08-22)¶

Cal_WAVE_E2DS_EA_spirou.py: moved FP solution to spirouWAVE. [melissa- hobson]

0.2.108 (2018-08-21)¶

Cal_WAVE_E2DS_EA_spirou.py: - check to remove double-fitted or spurious FP peaks - incorporation of FP lines (now working with no jumps) [melissa-hobson]
Merge remote-tracking branch ‘origin/melissa’ into melissa. [Melissa Hobson]
Removed test prints. [melissa-hobson]
SpirouMATH.py, spirouTHORCA.py: redo pixel shift implementation. [melissa-hobson]
Cal_HC_E2DS_spirou.py: changed start and end orders of second pass to be min (max) of FP and HC start (end) orders. spirouWAVE.py: correctly defined orders for inserting FP lines to all_lines_2 Fixes #411. [melissa-hobson]
Merge pull request #414 from njcuk9999/master. [melissa-hobson]

update melissa
Update changelog. [njcuk9999]

0.2.102 (2018-08-18)¶

Issue #411: reset cal_wave changes from Melissa (not working with unit_test 20180409all.run. [njcuk9999]
Merge pull request #413 from njcuk9999/dev. [Neil Cook]

Dev
Update version. [njcuk9999]
Update date version and changelog. [njcuk9999]

0.2.099 (2018-08-18)¶

Fix to file name (allow e2ds and e2dsff by only replaceing “_A.fits” [njcuk9999]
Allow LSD process (now it is fixed) [njcuk9999]
Merge remote-tracking branch ‘origin/dev’ into dev. [njcuk9999]
Merge pull request #412 from njcuk9999/eder. [Neil Cook]

Eder
Merge branch ‘master’ into eder. [Eder]
Merge pull request #410 from njcuk9999/melissa. [Neil Cook]

Merge Melissa’s branch with dev (for testing)
Merge pull request #409 from njcuk9999/neil. [Neil Cook]

Neil
Update date, version, changelog. [njcuk9999]

0.2.101 (2018-08-18)¶

Update spirouMath.py. [Neil Cook]

fix pep8

0.2.096 (2018-08-18)¶

Issue #382 - added a position to check for FLATFILE and DARKFILE (must agree with recipe_control.txt) [njcuk9999]

0.2.095 (2018-08-17)¶

Issue #401 - Added check that number of TELLU_MAP files > number of PCA components. [njcuk9999]
Issue #392 change “PPVERSION” to “PVERSION” - header key too long. [njcuk9999]
Issue #405 - add message when reset userinput is not “yes” [njcuk9999]

0.2.098 (2018-08-17)¶

Fixed memory issue by avoiding direct use of an nxn S^2 matrix. [Eder]

0.2.094 (2018-08-16)¶

Issue #392: added per-processed version keyword. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Issue #392: added version to outputs. [njcuk9999]
Entries prepared ready to fix issues #394 and #406. [njcuk9999]
Issue #407: fix bug where split lines not all printed to log file (only to screen) [njcuk9999]

0.2.097 (2018-08-16)¶

NaN-to-zero change moved from obj_fit_tellu to cal_CCF - warning printed if there are NaNs in the e2ds input to cal_CCF - Ref: #389, #390. [melissa-hobson]
Pixel shift incorporated to all wavelength solutions - added to constants file - read from constants for cal_WAVE_E2DS_EA_spirou.py - added to spirouMATH.get_ll_from_coefficients (and calls to it in spirouTHORCA) - warning is printed if the pixel shift is not zero. [melissa-hobson]
SpirouFITS.py: removed write_s1d. [melissa-hobson]
Merge pull request #408 from njcuk9999/master. [melissa-hobson]

update Melissa
Merge pull request #404 from njcuk9999/dev. [Neil Cook]

Dev - tested against unit tests 20180409all.run and test_tellu.run
Updated date, changelog and version. [njcuk9999]

0.2.093 (2018-08-15)¶

Update telluric unit test. [njcuk9999]
Add obj_mk_tellu and obj_fit_tellu to the unit tests. [njcuk9999]
Turn off the LSD analysis (until problem fixed) [njcuk9999]
Added a telluric test (based on Neil’s files) [njcuk9999]
Fix to issue #398: The first time running obj_mk_tellu fails with an I/O problem - convolve_file was being saved to the wrong location (and hence put_file was failing to copy it to telluDB) [njcuk9999]
Updated descriptions (from Etienne) [njcuk9999]
Updated date, changelog and version. [njcuk9999]
Fixed import issue. [njcuk9999]
Merge pull request #403 from njcuk9999/melissa. [Neil Cook]

Merge Melissa’s branch into Dev branch
Merge pull request #402 from njcuk9999/eder. [Neil Cook]

Merge Eder branch into Dev branch
Update spirouConst.py. [Neil Cook]

fix pep8 on doc string
Merge pull request #396 from njcuk9999/cfht. [Neil Cook]

Fixed __NAME__ of obj_fit_tellu

0.2.092 (2018-08-15)¶

Update config.py. [Neil Cook]

Revert config.py (Copying over a custom config.py file )
Update spirouFITS.py. [Neil Cook]

Todo added to remove write_s1d this should not be used - but keeps coming up in Melissa’s branch
Delete vcs.xml. [Neil Cook]

should be ignored by github

0.2.089 (2018-08-14)¶

Implemented Least Squares Deconvolution (LSD) Analysis to polar module. [Eder]
Merge branch ‘master’ into eder. [Eder]
Implemented Least Squares Deconvolution (LSD) Analysis to polar module. [Eder]

0.2.090 (2018-08-14)¶

Obj_fit_tellu.py: re-add blaze, set NaNs to zero in final e2ds (UNTESTED), as per #389, #390. [melissa-hobson]
SpirouLOCOR.py now prints name of localization file (Discussed in #387) [melissa-hobson]
SpirouStartup.py: removed lines that caused exit if DRS_PLOT was not set even when DRS_INTERACTIVE was set. Fixes #395. [melissa-hobson]

0.2.091 (2018-08-14)¶

Fixed __NAME__ of obj_fit_tellu. [Chris Usher]

0.2.088 (2018-08-13)¶

Cal_WAVE_E2DS_EA_spirou.py: began incorporation of FP lines (work in progress) [melissa-hobson]

0.2.087 (2018-08-09)¶

Cal_WAVE_E2DS_EA_spirou.py: incorporated extrapolation of Littrow solution for last two orders; added save to calibDB of good solutions. [Melissa Hobson]
Merge remote-tracking branch ‘origin/melissa’ into melissa. [Melissa Hobson]

Conflicts:
INTROOT/SpirouDRS/spirouCore/spirouPlot.py INTROOT/SpirouDRS/spirouImage/spirouBERV.py INTROOT/SpirouDRS/spirouImage/spirouImage.py INTROOT/SpirouDRS/spirouTHORCA/spirouWAVE.py INTROOT/bin/cal_FF_RAW_spirou.py INTROOT/bin/cal_SLIT_spirou.py INTROOT/bin/cal_WAVE_E2DS_EA_spirou.py INTROOT/bin/cal_extract_RAW_spirou.py INTROOT/bin/cal_loc_RAW_spirou.py INTROOT/config/constants_SPIROU_H4RG.py
Merge pull request #386 from njcuk9999/cfht. [Neil Cook]

Proposed fixes for minor issues
Merge pull request #388 from njcuk9999/neil. [Neil Cook]

Neil
Update date, version and change log. [njcuk9999]

0.2.083 (2018-08-08)¶

Update spirouFITS.py. [Neil Cook]

Made the warning handling more readable and added TODO, this should be handled properly not just ignored (i..e header cards should be corrected) - TODO will remind of this!

0.2.072 (2018-08-08)¶

Correctioned some constants and added value to loc. [njcuk9999]
Added definitions from FP files and EA wave files. [njcuk9999]
Updated cal_WAVE_E2DS files to check for. [njcuk9999]
Part2 test and updated/corrected some constants. [njcuk9999]
Added background subtraction. [njcuk9999]
Title to the plots + action TODO to find the right FIBER type. [njcuk9999]
Refinement of the cut of the left edge of blue orders for localisation - merge from @FrancoisBouchy. [njcuk9999]
Use only the part of E2DS > 0 to build the S1D spectra. [njcuk9999]
Read the OBSTYPE before computing BERV - OBSTYPE should be OBJECT to derive the BERV (i.e. not for calibrations) - merge from @FrancoisBouchy. [njcuk9999]
Some cosmetic / improvement for plot display - merged from @FrancoisBouchy. [njcuk9999]
Updated constants + new definition for the blue window on DARK - uc_fracminblaze = 16, new param to restrict the wings of spectral orders with flux lower than flux_at_blaze / 16, spectral order 0 is not taken into account. [njcuk9999]
Correction of center of the blaze window - put to zero edge of the spectra hwere flux is too low (less than flux_at_blaze/ IC_FRACMINBLAZE) - merged from @FrancoisBouchy. [njcuk9999]
Put to zero part of spectra where the blaze is not defined. [njcuk9999]
Add the background subtraction - from @FrancoisBouchy. [njcuk9999]
@melissa-hobson correct call to GetLampParams. [njcuk9999]

0.2.084 (2018-08-08)¶

Added fiber position identification from fiber type. [njcuk9999]
First version cal_WAVE developed by @eartigau, adapted to DRS format by @melissa-hobson added informational printouts - fixed figures - fixed asymmetry that allowed lines to be found in two windows - added all_lines data structure, Littrow check and uncertainty calclulation added possibility to set a pixel shift. [njcuk9999]

0.2.085 (2018-08-08)¶

Cal_WAVE_E2DS_EA_spirou.py: - added possibility to have a linear pixel shift when getting the initial wavelength solution (needed for TC2-TC3 change) - added QC - implemented storing of wavelength solution and tables (tables TBC) spirouConst.py: defined specific wave file names for outputs of cal_WAVE_E2DS_spirou.py and cal_WAVE_E2DS_EA_spirou.py. [Melissa Hobson]

0.2.086 (2018-08-08)¶

Suppress warnings about truncating FITS comments. [Chris Usher]
Prevent measure_background_flatfield from throwing error. [Chris Usher]
Fixed scrambled FITS headers. [Chris Usher]

0.2.082 (2018-08-07)¶

Cal_WAVE_E2DS_EA_spirou.py: added posibility to set a pixel shift recipe_control.txt: put correct DPRTYPE for cal_WAVE checks. [Melissa Hobson]

0.2.081 (2018-08-03)¶

Cal_WAVE_E2DS_EA_spirou.py: - added informational printouts - fixed figures - fixed asymmetry that allowed lines to be found in two windows - added all_lines data structure, Littrow check, and uncertainty calculation. [Melissa Hobson]

cal_WAVE_E2DS_spirou.py: test updates

visu_WAVE_spirou.py: lines in adjacent orders are now plotted alternately in magenta or purple for visibility

constants_SPIROU_H4RG.py: increased fit degrees, adjusted FP values

spirouPlot.py: changed Littrow plot to rainbow colours to improve distinguishing x cuts

spirouWAVE.py: small improvements
Merge pull request #381 from njcuk9999/francois. [melissa-hobson]

update Melissa from Francois

0.2.080 (2018-08-01)¶

Cal_WAVE_E2DS_EA_spirou.py: first version of cal_WAVE developed by @eartigau, adapted to DRS format. [Melissa Hobson]
Merge remote-tracking branch ‘origin/melissa’ into melissa. [Melissa Hobson]
Merge pull request #379 from njcuk9999/master. [melissa-hobson]

update melissa
Merge remote-tracking branch ‘origin/melissa’ into melissa. [Melissa Hobson]
Merge pull request #377 from njcuk9999/master. [melissa-hobson]

update melissa
Merge remote-tracking branch ‘origin/melissa’ into melissa. [Melissa Hobson]
Merge pull request #365 from njcuk9999/master. [melissa-hobson]

Melissa
Merge remote-tracking branch ‘origin/melissa’ into melissa. [Melissa Hobson]

Conflicts:
INTROOT/SpirouDRS/spirouTHORCA/spirouTHORCA.py

0.2.079 (2018-07-27)¶

Title to the plots + Action TODO to find the right FIBER type. [FrancoisBouchy]
Refinement of the Cut of the left edge of blue orders for localisation. [FrancoisBouchy]
Use only the part of E2DS > 0 to build the S1D spectra. [FrancoisBouchy]
Read the OBSTYPE Before computing BERV OBSTYPE should be OBJECT to derive the BERV (not for Calibrations) [FrancoisBouchy]
Some cosmetic / improvemtn for plot display. [FrancoisBouchy]
New definition for the blue window on DARK ic_fracminblaze = 16 –> New parameter to restrict the wings of spectral orders with flux lower than flux_at_blaze / 16 Spectral order 0 is not taken into account for QC of the Flat QC of Flat can be reduce to 5% [FrancoisBouchy]
Add the background correction. [FrancoisBouchy]
Correction of center of the blaze window Put to zero edge of the spectra where flux is too low (less than flux_at_blaze / IC_FRACMINBLAZE. [FrancoisBouchy]
Put to zero part of spectra where the blaze is not define. [FrancoisBouchy]

0.2.077 (2018-07-25)¶

Improvement for the localisation. [FrancoisBouchy]
Adaptation parameters for localisation. [FrancoisBouchy]
Add the background subtraction. [FrancoisBouchy]
Merge remote-tracking branch ‘origin/francois’ into francois. [FrancoisBouchy]

Conflicts:
INTROOT/SpirouDRS/data/ccf_masks/gl581_july18_clean_rec2.mas INTROOT/SpirouDRS/spirouBACK/spirouBACK.py INTROOT/SpirouDRS/spirouImage/__init__.py INTROOT/SpirouDRS/spirouImage/spirouImage.py INTROOT/bin/cal_FF_RAW_spirou.py INTROOT/bin/cal_extract_RAW_spirou.py INTROOT/bin/visu_WAVE_spirou.py INTROOT/config/constants_SPIROU_H4RG.py

0.2.078 (2018-07-25)¶

Inserted filename, MJD, and MJDEND keywords from expsoures in polar sequence to the header of polarimetry products. [Eder]
Merge branch ‘master’ into eder. [Eder]
Merge pull request #378 from njcuk9999/neil. [Neil Cook]

Neil
Update date/changelog/version. [njcuk9999]
Merge branch ‘master’ into eder. [Eder]
Merge branch ‘master’ into eder. [Eder]
Removed small comment – nothing really. [Eder]
Fixed formatting of doc strings. [Eder]
Merge branch ‘eder’ of https://github.com/njcuk9999/spirou_py3 into eder Removing function duplicated function calculate_stokes_I. [Eder]

0.2.071 (2018-07-20)¶

Update test run. [njcuk9999]
Misc functions. [njcuk9999]
Fixed call to earth velocity correction function. [njcuk9999]
Move get_good_object_name function. [njcuk9999]
Add aliases for getting obj name and airmass. [njcuk9999]
Fix acquisition time naming. [njcuk9999]
Added file iteration to plot. [njcuk9999]
Fix acquitision time naming (julian not unix) [njcuk9999]
Add tellu template file definition. [njcuk9999]
Remove extra recipe control key. [njcuk9999]
Move objname and airmass to functions. [njcuk9999]
Fix naming conversion time is julian not unix. [njcuk9999]
Correct filename bug. [njcuk9999]
Fixed bug with convolve file not being read correctly. [njcuk9999]
Fxied bug with get_param. [njcuk9999]
Fxied bug with get_param. [njcuk9999]
Fxied bug with get_param. [njcuk9999]
Fix bug in get_wave_solution. [njcuk9999]
Fixed but with header key too long (9 > 8) [njcuk9999]
Fix bug in assigned WAVEFILE. [njcuk9999]
Fix bug in get_param call. [njcuk9999]

0.2.070 (2018-07-19)¶

Add telluric database reset to cal_validate. [njcuk9999]
Tellu recipes - bug fix for plot. [njcuk9999]
Fix bug with timestamp (telluDB only) [njcuk9999]
Integrate telluric recipes with test runs: compressed + binned tapas_all_sp file. [njcuk9999]
Integrate telluric recipes with test runs: updated after test runs. [njcuk9999]
Integrate telluric recipes with test runs: updated error message in get_param. [njcuk9999]
Cal_preprocess - DPRTYPE = None rows of recipe_control should not be used to ID files. [njcuk9999]
Integrate telluric recipes with test runs: fixes afer test runs. [njcuk9999]
Integrate telluric recipes with test runs: updated aliases. [njcuk9999]
Integrate telluric recipes with test runs: updated TELL_MOLE file (.gz) [njcuk9999]
Integrate telluric recipes with test runs: fixes afer test runs. [njcuk9999]
Integrate telluric recipes with test runs: fixes afer test runs. [njcuk9999]
Integrate telluric recipes with test runs: fixes afer test runs. [njcuk9999]
Merge remote-tracking branch ‘origin/neil’ into neil. [njcuk9999]

0.2.069 (2018-07-18)¶

Integrate telluric recipes with test runs: updated after test runs. [njcuk9999]
Integrate telluric recipes with test runs: added get_wave_keys function. [njcuk9999]
Integrate telluric recipes with test runs: updated aliases. [njcuk9999]
Integrate telluric recipes with test runs: test run only. [njcuk9999]
Integrate telluric recipes with test runs: updated plots (corrected) [njcuk9999]
Integrate telluric recipes with test runs: resorted use_keys + added wave and telluric keys. [njcuk9999]
Updated filename (TELLU_FIT_OUT_FILE) [njcuk9999]
Integrate telluric recipes with test runs: added constants from Etienne and corrected bug in tell_lambda_max. [njcuk9999]
Integrate telluric recipes with test runs: update after running fit_tellu. [njcuk9999]
Integrate telluric recipes with test runs: update after running fit_tellu. [njcuk9999]
Integrate telluric recipes with test runs: test run only. [njcuk9999]
Modified cal_extract to save wavefile name and wave file dates (for telluric) [njcuk9999]

0.5.038 (2018-07-17)¶

Merge pull request #376 from njcuk9999/neil. [Neil Cook]

Neil
Update date/version/changelog. [njcuk9999]
Copy (same) [njcuk9999]
Update tellu recipes: fix bug with file name. [njcuk9999]
Update tellu recipes: drs telluDB reset now resets telluDB not calibDB (fix typos) [njcuk9999]
Update tellu recipes: fix after test run FWHM is function not object. [njcuk9999]
Update tellu recipes: fix after test run - telluDB get database values are already split on spaces. [njcuk9999]
Update tellu recipes: fix after test run - fix bug (needed enumerate(lines)) [njcuk9999]
Update tellu recipes: fix after test run - add alias to update_datebase_tell_temp. [njcuk9999]
Possible bug fix: tried to separate out interactive options in end_interactive_session function. [njcuk9999]
Possible bug fix: tried to reduce repetition of displayed warnings. [njcuk9999]
Update tellu recipes: added AIRMASS header key. [njcuk9999]
Bug fix: fix file name ‘_s1d_{0}.fits’ –> ‘_s1d_{0}.fits’.format(p[‘FIBER’]) [njcuk9999]
Update tellu recipes: add required line in master telluDB. [njcuk9999]
Update tellu recipes: add obj_mk_tell_template to recipe control. [njcuk9999]
Update tellu recipes: move obj_mk_tell_template constantsto here and correct some bugs after test run. [njcuk9999]
Update tellu recipes: fix after test run. [njcuk9999]
Update tellu recipes: fix after test run. [njcuk9999]
Updated date/changelog/version. [njcuk9999]
Merge remote-tracking branch ‘origin/neil’ into neil. [njcuk9999]
Merge pull request #375 from njcuk9999/neil. [Neil Cook]

Neil
Telluric integration: bug fixes (after move of functions) [njcuk9999]
Updated call to plot. [njcuk9999]
Moved debug plot back to main code. [njcuk9999]
Updating integration of tellu files: added functions - interp_at_shifted_wavelengths, calc_recon_abso, calc_molecular_absorption and lin_mini. [njcuk9999]
Updating integration of tellu files: added new function aliases. [njcuk9999]
Updating integration of tellu files: added plot function “tellu_fit_recon_abso_plot” [njcuk9999]
Updating integration of tellu files: Added abso output keyword. [njcuk9999]
Updating integration of tellu files; Added filename pseudo constants. [njcuk9999]
Updating integration of tellu files: added constants (need commenting!) [njcuk9999]
Updating integration of tellu files. [njcuk9999]
Updating integration of tellu files. [njcuk9999]
Merge remote-tracking branch ‘origin/neil’ into neil. [njcuk9999]
Merge pull request #374 from njcuk9999/neil. [Neil Cook]

add new mask from Xavier
Updated date and veresion and changelog. [njcuk9999]

0.2.066 (2018-07-15)¶

Add new mask from Xavier. [njcuk9999]
Merge pull request #373 from njcuk9999/neil. [Neil Cook]

Neil - runs with H4RG set up in data from 2018-04-09
Changed encoding (copy/paste/revert) – ignore. [njcuk9999]
Fixed log to not wrap this text - ONLY. [njcuk9999]
Changed name of sub-module. [njcuk9999]
Fixed cyclic imports (new sub-module - spirouBERV) [njcuk9999]
Fixed cyclic imports. [njcuk9999]
Added character_log_length pseudo constant. [njcuk9999]
Added maximum log length (wraps to new row with a tab) wraps words but still problem with long filenames. [njcuk9999]
Fixed typo in Merge from @FrancoisBouchy. [njcuk9999]
Fixed cyclic importing and typos in keyword assignment. [njcuk9999]
Fixed cyclic importing. [njcuk9999]
Bring S1D (cal_extract) in-line with rest of DRS (Fixing merges from @FrancoisBouchy) [njcuk9999]
Bring S1D (cal_extract) in-line with rest of DRS (Fixing merges from @FrancoisBouchy) [njcuk9999]
Bring S1D (cal_extract) in-line with rest of DRS (Fixing merges from @FrancoisBouchy) [njcuk9999]
Bring S1D (cal_extract) in-line with rest of DRS (Fixing merges from @FrancoisBouchy) [njcuk9999]
Bring S1D (cal_extract) in-line with rest of DRS (Fixing merges from @FrancoisBouchy) [njcuk9999]
Bring S1D (cal_extract) in-line with rest of DRS (Fixing merges from @FrancoisBouchy) [njcuk9999]
Bring S1D (cal_extract) in-line with rest of DRS (Fixing merges from @FrancoisBouchy) [njcuk9999]
Added spirouTelluric to modules list. [njcuk9999]
Fix pep8 issues (in-line comment should have at least two spaces between code and comment. [njcuk9999]
Merge @FrancoisBouchy changes - still need fixing (PEP8 and integration) [njcuk9999]
Merge @FrancoisBouchy changes - still need fixing (PEP8 and integration) [njcuk9999]
Merge @FrancoisBouchy changes - still need fixing (PEP8 and integration) [njcuk9999]
Merge @FrancoisBouchy changes - still need fixing (PEP8 and integration) [njcuk9999]
Merge @FrancoisBouchy changes - still need fixing (PEP8 and integration) [njcuk9999]
Merge @FrancoisBouchy changes - still need fixing (PEP8 and integration) [njcuk9999]
Merge @FrancoisBouchy changes - still need fixing (PEP8 and integration) [njcuk9999]
Fix needed commented code (commented for testing) –> uncommented now. [njcuk9999]
Updated construct_convolution_kernal2 function. [njcuk9999]
Added teullric aliases. [njcuk9999]
Added tellu_fit_tellu_spline_plot function. [njcuk9999]
Update ConstructConvKernel2 function. [njcuk9999]
Continued to merge Etiennes code. [njcuk9999]

0.2.065 (2018-07-13)¶

Add functions: calculate_absorption_pca, get_berv_value. [njcuk9999]
Add telluric aliases. [njcuk9999]
Add functions get_database_tell_template, update_database_tell_temp. [njcuk9999]
Continue to integrate functions. [njcuk9999]
Correct duplication of header is None. [njcuk9999]
Added telluric alias. [njcuk9999]
Added telluric pca plot. [njcuk9999]
Corrected bad function call to GetNormalizedBlaze and duplicated call to loc=ParamDict() [njcuk9999]
Moved getting berv to spirouTelluric. [njcuk9999]
First attempt at integrating code (unfinished) [njcuk9999]
Add keys defined in functions. [njcuk9999]
Add new TDB aliases. [njcuk9999]
Correct access to telluric database and update telluric database. [njcuk9999]
First commit - direct integration of mk_template.py from Etienne. [njcuk9999]
First commit - blank. [njcuk9999]
Updated where we get the telluric molecular file (now from database) [njcuk9999]
Added getting of absolute path for telluric files. [njcuk9999]
Added switch between telluricand calibration databases. [njcuk9999]
Added aliases from TDB. [njcuk9999]
Added get and update functions (wrapping generic functions in spirouDB) [njcuk9999]
Added todo’s to make general. [njcuk9999]
First commit - generic functions for database management. [njcuk9999]

0.2.076 (2018-07-13)¶

New correlation Mask made by XD. [FrancoisBouchy]
Background correction and set negative values to zero Read Blaze function Compute S1D spectra and archive it. [FrancoisBouchy]
Background correction and negative values set to zero. [FrancoisBouchy]
Typo correction to read the fitted lines. [FrancoisBouchy]
New constant parameters for background correction and e2dstos1d. [FrancoisBouchy]
Adaptation of function to measure the global background in the image. [FrancoisBouchy]
Add the two new functions e2dstos1d and write_s1d. [FrancoisBouchy]
New function to write S1D spectra with the same format than HARPS. [FrancoisBouchy]
New function to build S1D spectra. [FrancoisBouchy]

0.2.064 (2018-07-12)¶

First commit - added obj_mk_tellu functions. [njcuk9999]
Added spirouTelluric aliases. [njcuk9999]
Added wave param aliases. [njcuk9999]
Added read andget wave param functions. [njcuk9999]
Added plot for obj_mk_tellu. [njcuk9999]
Added file name definitions for obj_mk_tellu. [njcuk9999]
Added obj_mk_tellu to recipe control. [njcuk9999]
Added obj_mk_tellu constants. [njcuk9999]
Integrated obj_mmk_tellu into spirou drs (rea/write/constants etc) [njcuk9999]
Added saving of wave parameters to header of E2DS. [njcuk9999]
Remove. [njcuk9999]
Copy of etiennes raw mk_tellu code. [njcuk9999]
Added imports to python local namespace (for embeded run after code finish) [njcuk9999]
Blank files for telluric functions. [njcuk9999]
First commit of the spirou visu GUI. [njcuk9999]
First commit of obj_mk_tellu - processing the telluric files and adding them to telluDB. [njcuk9999]

0.2.063 (2018-07-11)¶

Add master_tellu_spirou file. [njcuk9999]
Add cal_wave_mapper to recipe control file. [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Add reset tellu to drs_reset functions. [njcuk9999]
Adde dcal_wave_mapper to recipe list (and unit recipe) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) + added printing of tilt/wave/blaze/flat file used. [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Fixed bug: hdr[‘KW_X’] –> hdr[p[‘KW_X’][0]] [njcuk9999]
Add telluDB constants. [njcuk9999]
Add telluDB (for now a copy of spirouCDB - but will change) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Update cal_wave_mapper (as main function with returns to local) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]
Rename calibDB module: spirouCDB –> spirouDB (to add telluric database) [njcuk9999]

0.2.062 (2018-07-10)¶

Added filename functions (WAVE_MAP_SPE_FILE and WAVE_MAP_SPE0_FILE) [njcuk9999]
Added filenames in spirouConfig. [njcuk9999]
Define todos. [njcuk9999]
Fix bug: night_name should only be a string (could be a int) [njcuk9999]
Update to accept multiple fibers AB and C or A B and C or any combination. [njcuk9999]
Change the files tested. [njcuk9999]
Fix to a bug ll_line_cat –> ll_line_fit. [njcuk9999]
E2ds back projection - first commit. [njcuk9999]
Fix for choice of fiber(s) [njcuk9999]

0.2.061 (2018-07-09)¶

Removed berv calculation from RV module. [njcuk9999]
Added print_full_table function. [njcuk9999]
Updated aliases and __all_ [njcuk9999]
Updated aliases and __all_ [njcuk9999]
Updated aliases and __all_ [njcuk9999]
Moved earth barycentric correction here. [njcuk9999]
Test fitting versus interpolation. [njcuk9999]
Updated test to only show “good” orders. [njcuk9999]
Fixed a comment and updated the berv variable. [njcuk9999]
Fixed logging all analysed files and printing to screen. [njcuk9999]
Fixed off_listing printing only a few rows (now prints all) [njcuk9999]
Moved berv calculation to extraction. [njcuk9999]
Moved berv calculation to extraction. [njcuk9999]

0.2.060 (2018-07-05)¶

Fix and test of find_lines. [Neil Cook]

0.5.033 (2018-07-04)¶

Merge pull request #372 from njcuk9999/neil. [Neil Cook]

Neil
Update changelog/date/version. [Neil Cook]

0.2.059 (2018-07-04)¶

Update change log. [Neil Cook]
Update change log. [Neil Cook]
The output changelog. [Neil Cook]
Added functionality to update VERSION.txt and the version in the spirouConst.py file. [Neil Cook]
DRS version added to VERSION.txt. [Neil Cook]
Recipe to get/update change log (moved to spirouTools - final location) [Neil Cook]
Recipe to get/update change log. [Neil Cook]
Output: the change log (backup) [Neil Cook]
Recipe to update change log. [Neil Cook]
Merge pull request #371 from njcuk9999/neil. [Neil Cook]

Neil

0.2.074 (2018-07-04)¶

Removed duplicated function calculate_stokes_I in spirouPOLAR.py. [Eder]

0.2.058 (2018-07-03)¶

Add generic change log (not used but for history) [Neil Cook]
Make sure object name is “good” with function: get_good_object_name. [Neil Cook]
Correct typo. [Neil Cook]
Rebuild pdfs. [Neil Cook]
Remove change log. [Neil Cook]
Add user_dir and cal_reset constants. [Neil Cook]
Add pp mode variable. [Neil Cook]
Update using the DRS with H4RG example. [Neil Cook]
Update todo list (remove done + add new) [Neil Cook]
Update quick installation. [Neil Cook]
Update output keywords (not finished) [Neil Cook]
Update installation. [Neil Cook]
Update input keywords. [Neil Cook]
Update date architecture. [Neil Cook]
Removed old change log. [Neil Cook]
Add pp_mode (the way to switch on/off) file type suffix adding. [Neil Cook]
Add output files to p (and thus sent back to main() function call) [Neil Cook]
Update commentation. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Merge pull request #370 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #369 from njcuk9999/dev. [Neil Cook]

Dev
Merge remote-tracking branch ‘origin/dev’ into dev. [Neil Cook]
Updated doc strings to be consistent with rest of DRS. [Neil Cook]
Merge pull request #368 from njcuk9999/dev. [Neil Cook]

Dev - confirmed runs + some very minor fixes to pep8
Update pol_spirou.py. [Neil Cook]

fix to pep8
Update spirouPOLAR.py. [Neil Cook]

fix to pep8
Merge pull request #367 from njcuk9999/eder. [Neil Cook]

Eder
Update spirouPlot.py. [Neil Cook]

pep 8 fixes
Improved polar continuum routine. [Eder]
Improved polar continuum routine. [Eder]
Swap exposure 3 and 4 to agree with actual SPIRou sequence, and added doc string to spirouPolar functions. [Eder]
Swap exposure 3 and 4 to agree with actual SPIRou sequence, and added doc string to spirouPolar functions. [Eder]
Fixed bugs in plot and added new keywords to polar products. [Eder]
Fixed bugs in plot and added new keywords. [Eder]
Updated module definitions in spirouPOLAR. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated date and version. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Added variable definitions to wave solution section and qulaity control section. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated date and version. [Neil Cook]
Updated date and version. [Neil Cook]

0.5.031 (2018-06-29)¶

Merge pull request #366 from njcuk9999/neil. [Neil Cook]

Neil - just document changes and some code clean up.
Rebuild pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Added variabels to cal_hc/cal_wave variable definitions. [Neil Cook]
Added more cal_hc/cal_wave variable definitions. [Neil Cook]
Removed old cal_hc constants. [Neil Cook]
Removed old cal_hc code. [Neil Cook]
Rebuild pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Update version, date and module root definitions. [Neil Cook]
Update variable definitions. [Neil Cook]

0.5.030 (2018-06-28)¶

Merge pull request #364 from njcuk9999/neil. [Neil Cook]

Neil

0.2.057 (2018-06-28)¶

Updated date and version and added new recipes. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Added more variable definitions. [Neil Cook]
Update to variables - adding new ones. [Neil Cook]
Update to comment. [Neil Cook]
Tried to speed up plotting + fixed a bug with call to spirouTHORCA.GetLampParams (now requires header) [Neil Cook]
Fix python 2/python 3 incompatibility with numpy change. [Neil Cook]
Fix call to fiber_params change (from circular import bug) [Neil Cook]
Doc string update - requires spirouPOLAR command. [Neil Cook]
Fix circulate import bug –> move fiber_params from spirouLOCOR to spirouFile and update calls accordingly. [Neil Cook]

0.2.075 (2018-06-28)¶

Visu_WAVE_spirou.py: correct call to GetLampParams. [melissa-hobson]

0.2.056 (2018-06-27)¶

First commit of spirouPOLOAR module tex file. [Neil Cook]
Update main init. [Neil Cook]
Add spirouPOLAR to aliases. [Neil Cook]
Doc string update. [Neil Cook]
Doc string update. [Neil Cook]
Doc string update. [Neil Cook]
Move functions around and add todo/fixme. [Neil Cook]
Doc string update. [Neil Cook]
Update date and version. [Neil Cook]
Rebuild pdf after doc string update. [Neil Cook]
Update date and versions. [Neil Cook]
Doc string update. [Neil Cook]
Doc string update. [Neil Cook]
Doc string update. [Neil Cook]
Doc string update. [Neil Cook]
Doc string update. [Neil Cook]
Doc string update. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Merge pull request #361 from njcuk9999/neil. [Neil Cook]

Neil
Added new tool to calculate barycentric velocity and add it to the header of the input file. [Neil Cook]
Added a skip check to check_file. [Neil Cook]

0.2.055 (2018-06-26)¶

Added cal_hc and cal_wave to unit test definitions. [Neil Cook]
Fix to cal_HC and cal_WAVE added to unit test runs. [Neil Cook]
Added printout of max time for calibDB. [Neil Cook]
Added cal_HC, cal_WAVE (and setup for cal_WAVE_NEW) to all run. [Neil Cook]
We have FIBER therefore use FIBER not FIB_TYP, modified error reporting give we use header keys. [Neil Cook]
Fixed bug that allows reduced files to be None (should be found by file name or generate error) [Neil Cook]
Added e2dsff files to recipe control for cal_HC and cal_WAVE, added cal_WAVE_NEW files (same as cal_WAVE) [Neil Cook]
Fixed typo (bug?) [Neil Cook]
Updated to work with odometer identification (like rest of DRS) [Neil Cook]
Merge pull request #360 from njcuk9999/melissa. [Neil Cook]

Melissa
Update spirouTHORCA.GetLampParams to identify lamp type from fiber position header key Update all functions using GetLampParams (cal_HC, cal_WAVE, cal_WAVE_NEW) visu_WAVE) to pass the header. [melissa- hobson]
Visu_WAVE_spirou: higher base level for lines. [melissa-hobson]
Update for visu_WAVE_spirou.py - now working. [melissa-hobson]
Cal_HC_E2DS_spirou.py: added fiber position identification from fiber type spirouTHORCA.decide_on_lamp_type: - changed to identify lamp from fiber position (for use w/odometer names) - previous version moved to decide_on_lamp_type_old. [melissa-hobson]
Cal_HC_E2DS_spirou.py: added fiber position identification from fiber type spirouTHORCA.decide_on_lamp_type: - changed to identify lamp from fiber position (for use w/odometer names) - previous version moved to decide_on_lamp_type_old. [melissa-hobson]
Update for use with e2dsff files as well as e2ds files. [Neil Cook]
Merge pull request #357 from njcuk9999/neil. [Neil Cook]

Neil
Fixed bug in header key berv_max. [Neil Cook]
Add calibDB setup to cal_validiate. [Neil Cook]
Add BERV corrections to header. [Neil Cook]
Update pol_spirou.py. [Neil Cook]

code duplicated in bad merge @edermartioli
Merge pull request #356 from njcuk9999/eder. [Neil Cook]

Eder
Reset config.py. [Eder]
Merging changes. [Eder]
Merge branch ‘master’ into eder. [Eder]
Updates from master. [Eder]
Update output name without _A, save errors to output using WriteImageMulti. [Eder]
Update output name without _A, save errors to output using WriteImageMulti. [Eder]
Update output name without _A, save errors to output using WriteImageMulti. [Eder]
Merged master and resolved conflict in pol_spirou. [Eder]
Implemented total flux (Stokes I) calculation. [Eder]
Merge branch ‘master’ into eder. [Eder]
Merge pull request #354 from njcuk9999/neil. [Neil Cook]

Neil - confirmed test of H4RG
Added cal_preprocess, off_listing, visu_raw, visa_e2ds and pol_spirou to the unit testing. [Neil Cook]
Modified a warning message to be slightly more descriptive. [Neil Cook]
Merge pull request #353 from njcuk9999/neil. [Neil Cook]

Neil
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Merge pull request #351 from njcuk9999/dev. [Neil Cook]

Dev
Revert changes to get wave solution from calibDB (errors were due to badly set up calibDB) [Neil Cook]
Merged changes from @edermartioli: added alias to calculate_stokes_I and added aliases to __all__ [Neil Cook]
Merged changes from @edermartioli: Update output name with _A, save errors to output using WriteImageMulti, Implemented total flux (Stokes I) calculation, implemented polarimetric error calculation. [Neil Cook]
Merged changes from @edermartioli: aqdded stokesI plot, spelling correction + polarisation is now percentage (bug was missing in conversion) [Neil Cook]
Merged changes from @edermartioli: Update output name with _A, save errors to output using WriteImageMulti, Implemented total flux (Stokes I) calculation, implemented polarimetric error calculation. [Neil Cook]
Added warning in config.py to not change PATHs here (todo in docs) [Neil Cook]
Merged changes from @edermartioli: Update output name with _A, save errors to output using WriteImageMulti, Implemented total flux (Stokes I) calculation, implemented polarimetric error calculation. [Neil Cook]
Merge pull request #350 from njcuk9999/neil. [Neil Cook]

Neil
Issue #348 - fixed definition of WLOG in spirouPlot (“sometimes” causes a crash sometimes doesn’t) [Neil Cook]
Update date and version. [Neil Cook]
Undo bad merge by @melissa-hobson. [Neil Cook]
Cal_HC_E2DS_spirou.py: added fiber position identification from fiber type spirouTHORCA.decide_on_lamp_type: - changed to identify lamp from fiber position (for use w/odometer names) - previous version moved to decide_on_lamp_type_old. [melissa-hobson]
Update date and version. [Neil Cook]
Fix for loggers being out of range. [Neil Cook]

0.2.073 (2018-06-26)¶

Cal_HC_E2DS_spirou.py: added fiber position identification from fiber type spirouTHORCA.decide_on_lamp_type: - changed to identify lamp from fiber position (for use w/odometer names) - previous version moved to decide_on_lamp_type_old. [Melissa Hobson]
Cal_HC_E2DS_spirou.py: added fiber position identification from fiber type spirouTHORCA.decide_on_lamp_type: - changed to identify lamp from fiber position (for use w/odometer names) - previous version moved to decide_on_lamp_type_old. [Melissa Hobson]
Log calibDB match method. [melissa-hobson]
Cal_WAVE_NEW_E2DS_spirou.py: first version (untested) [melissa-hobson]
Merge pull request #347 from njcuk9999/master. [melissa-hobson]

Melissa
Merge pull request #345 from njcuk9999/neil. [Neil Cook]

Neil - confirmed tested on H4RG files
Fixed to run with new setup. [Neil Cook]
Fix for warninglogger. [Neil Cook]
Log handled exits! [Neil Cook]
Fixed setup for badpix. [Neil Cook]
Fix set up changes. [Neil Cook]
Update set up begin function. [Neil Cook]
Updated setup (use of spirouStartup.Begin) [Neil Cook]
Dealt with recipe name handling better. [Neil Cook]
Fix program with recipe name instead of sys.argv (unless not present) [Neil Cook]
Fix recipe setup. [Neil Cook]
Updated master time. [Neil Cook]
Fixed system exit quitting automated run. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Now cleaning WLOG in run_begin (via WLOG.clean_log()), and added main_end_script (to push logging to p and run clean_log) [Neil Cook]
Added function write_image_multi (aliased to WriteImageMulti) to save multiple extensions to filename - for @edermartioli and the pol_spirou code specifically. [Neil Cook]
Defined logger function into class (allows storage or any errors/warnings/info and piping back into p at the end of recipe. Must clear WLOG at start and end of recipes! [Neil Cook]
Fix for issue #337 - add e2dsff as well as e2ds (defaults to e2dsff if present) and added log_storage_keys pseudo variable. [Neil Cook]
Updated trigger to add error and logger values to HISTORY.txt. [Neil Cook]
Updated recipes main end script (to allow piping of logging into p - thus accessible outside via ll[‘p’][‘LOGGING_ERROR’] for example. [Neil Cook]
Cal_WAVE_NEW_E2DS_spirou.py: first version (untested) [melissa-hobson]
Merge pull request #344 from njcuk9999/master. [melissa-hobson]

Update
Merge pull request #343 from njcuk9999/neil. [Neil Cook]

Neil
Fix to print out. [Neil Cook]
Updated files for reset. [Neil Cook]
Added new wavesolution to cal reset. [Neil Cook]
Merge pull request #342 from njcuk9999/neil. [Neil Cook]

Work on Issue #338
Work on Issue #338 - added possibility to enter debug mode and added the table printed to screen. [Neil Cook]
Update date and version. [Neil Cook]
Merge pull request #341 from njcuk9999/neil. [Neil Cook]

fix - spirouUnitRecipes.wrapper requires true python strings
Fix - spirouUnitRecipes.wrapper requires true python strings. [Neil Cook]
Merge pull request #340 from njcuk9999/dev. [Neil Cook]

Dev
Added catch of warnings with polyfit. [Neil Cook]
Added catch warning for polyfit, fixed bug with lamp_type in decide_on_lamp_type. [Neil Cook]
Added missing plot function (wave_fp_wavelength_residuals), added iteration number to plots for wave_littrow_check_plot and wave_plot_final_fp_order. [Neil Cook]
Added doc string to cal_HC main function. [Neil Cook]
Merge pull request #339 from njcuk9999/francois. [Neil Cook]

Merge Francois to Dev
Work on issue #337: modified decide_on_lamp_type function to accept ic_lamps values as lists (and iterate through) - still must only have one of the two. [Neil Cook]
Updated constants in H2RG to match H4RG. [Neil Cook]
Work on issue #337: changed ic_lamps values to be lists + cleaned up constants (pep8) [Neil Cook]
Work on Issue #337: slight clean up of @FrancoisBouchy changes. Renamed part1b to part2 and commented out old part 2. [Neil Cook]
Merge remote-tracking branch ‘origin/francois’ into francois. [FrancoisBouchy]
Merge pull request #336 from njcuk9999/neil. [Neil Cook]

Neil
Part 1b created as a copy of Part 2 and Modified Part 1b repeats the Littrow extrapolation for the second pass The second Littrow extrapolation is used for to join orders Part 2 is no more useful and we do not need CCF. [FrancoisBouchy]
Adaptation of all the parameters for cal_HC ic_lamps still need to be adapted for hc1 and hcone exposures. [FrancoisBouchy]
Change e2ds with e2dsff to define the wave filename but it will be useful to keep both possibility (e2ds and e2dsff) Correction on the format of the wave filename. [FrancoisBouchy]
Define ord_start and ord_final for the first guess solution Compute correctly E2DS orders from echelle orders for the display LOG Display the right number of good lines Count the total number of good lines Add possibility to change Littrow fit degree for the two iterations For second iteration the initial catalog is used again Let the possibility to join extrapolated orders in the blue ll_free-span set as a list of two parameters in COnstante File Require at least 4 points to fit a Gaussian Order limits are define with min and max of ll_lines. [FrancoisBouchy]
Merge remote-tracking branch ‘origin/francois’ into francois. [FrancoisBouchy]

Conflicts:
INTROOT/SpirouDRS/spirouEXTOR/spirouEXTOR.py INTROOT/bin/off_listing_RAW_spirou.py
Merge pull request #334 from njcuk9999/master. [melissa-hobson]

update branch
Cal_WAVE_NEW_E2DS_spirou.py: first version (untested) [melissa-hobson]
Merge pull request #328 from njcuk9999/master. [melissa-hobson]

Update Melissa branch
Fitgaus - python version. [melissa-hobson]

Python version of the fitgaus.f functions. - contains two versions of Gauss-Jordan algorithm, an exact copy of the fortran code with all loops (gaussj_fortran) and an attempt to make it more efficient via numpy (gaussj, but is currently slower). - function covstr was omitted as it does nothing in our use case.
Merge pull request #321 from njcuk9999/master. [melissa-hobson]

Update branche
Merge pull request #286 from njcuk9999/master. [melissa-hobson]

update
Merge pull request #273 from njcuk9999/master. [melissa-hobson]

update melissa
Merge pull request #269 from njcuk9999/master. [melissa-hobson]

update melissa

0.2.052 (2018-06-21)¶

Implemented polarimetric errors calculation. [Eder]
Implemented polarimetric errors calculation. [Eder]
Changed polarimetry stuff to adapt changes made by Neil. [Eder]
Config.py. [Eder]
Merge branch ‘eder’ of https://github.com/njcuk9999/spirou_py3 into eder. [Eder]

No big changes, just testing a few things

0.2.051 (2018-06-20)¶

No main file. [Neil Cook]
Must use unit test to run recipes. [Neil Cook]
Undo print test. [Neil Cook]
Updated chmod. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Merge pull request #335 from njcuk9999/neil. [Neil Cook]

Neil
Fixes to main raw trigger. [Neil Cook]
Corrected bug where OFF_LISTING_FILE was missing. [Neil Cook]
Corrected bug where no night name does give good error. [Neil Cook]
Fixed bug that arg_night_name and files not checked any more. [Neil Cook]
Fixed bug with no DRPTYPE assigned. [Neil Cook]
Modified recipe control (added order and detector validity) [Neil Cook]
Fisrt commit - raw file trigger (cal_dark to cal_extract) [Neil Cook]
Merge pull request #333 from njcuk9999/neil. [Neil Cook]

Neil

0.2.049 (2018-06-19)¶

Corrected bug in night_name error reporting. [Neil Cook]
Updated documentation (function definitions) [Neil Cook]
Improved functionality in reset (allow reset of calibDB or reduced or log or all via user input) [Neil Cook]
Improved reporting of bad night name. [Neil Cook]
Removed old misc files. [Neil Cook]
Add obj name to raw files if no other suffix added (for objects) [Neil Cook]
Added preprocessed trigger (for automating pre-processing on DRS_RAW_DATA directory) [Neil Cook]
Fixed bug with processed suffix. [Neil Cook]

0.2.050 (2018-06-19)¶

Changed config to my local paths. [Eder]
Put config back. [Eder]
Non. [Eder]
Merge pull request #332 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #331 from njcuk9999/neil. [Neil Cook]

Neil
Update config.py. [Neil Cook]

removed master need for user config file

0.2.048 (2018-06-18)¶

Rebuilt pdfs. [Neil Cook]
Updated doc strings. [Neil Cook]
Updated author list. [Neil Cook]
Udpated date and version and added spirouFile command. [Neil Cook]
Updated some function descriptions. [Neil Cook]
Issue #330 - fixed comment description. [Neil Cook]
Issue #330 - fix WLOG message. [Neil Cook]
Issue #330 - add pol_spirou to recipe control. [Neil Cook]
Issue #330 - fix entry value, set sources keys, and float(nexp) –> int(nexp) [Neil Cook]
Issue #330 - change scatter –> plot. [Neil Cook]
Issue #330 - add keyword kw_CMMTSEQ. [Neil Cook]
Issue #330 - fix constant value (run tested correction) [Neil Cook]
Issue #330 - fix setup and a few other minor (run tested correction) [Neil Cook]
Fix bug and cleanup the imports. [Neil Cook]
Renamed and chmod files. [Neil Cook]
Renaming file. [Neil Cook]
Rename file. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]

Conflicts:
INTROOT/SpirouDRS/spirouConfig/spirouConst.py
Merge pull request #329 from njcuk9999/dev. [Neil Cook]

Dev
Issue #330 - Adding plots for polarimetry. [Neil Cook]
Issue #330 - alaises for spirouPOLAR. [Neil Cook]
Issue #330 - re-write of SPIROU polarimetry module (for DRS compatibility class –> functions) [Neil Cook]
Issue #330 - Adding keywords for polarimetry. [Neil Cook]
Updated date and version. [Neil Cook]
Issue #330 - Adding file name definitions for polarimetry. [Neil Cook]
Issue #330 - Adding constants for polarimetry. [Neil Cook]
Issue #330: integrating pol_spirou from @edermartioli into DRS format. [Neil Cook]

0.2.046 (2018-06-15)¶

Fixed hidden bug (formats should be allowed to be None - chosen by astropy. [Neil Cook]
Fixed hidden bug. [Neil Cook]
Added extra check for bad key in WLOG (dev issue only) [Neil Cook]
Added some keys (OBJNAME, SBCDEN_P) [Neil Cook]
Updated date and version and added OFF_LISTING_FILE function. [Neil Cook]
@FrancoisBouchy - Added commit: Creation of off_listing_RAW_spirou - modified to conform with DRS standards + functions + keywords + parameters. [Neil Cook]
@FrancoisBouchy - Added commit: Flux ratio display with 3 digit. [Neil Cook]
@FrancoisBouchy - Added commit: Background correction of the ref file. [Neil Cook]
@FrancoisBouchy - Added commit: Correction to avoid division by zero. [Neil Cook]
Merge pull request #327 from njcuk9999/neil. [Neil Cook]

verified - tested all recipes on H2RG and H4RG (except cal_HC, cal_WAVE - which just run through to end - untested + unverified)

0.2.047 (2018-06-15)¶

Flux ratio display with 3 digit. [FrancoisBouchy]
Background correction of the ref file. [FrancoisBouchy]
#300 Bug on the fit_ccf on individual orders to investigate. [FrancoisBouchy]
Correction to avoid division by zero. [FrancoisBouchy]

0.2.045 (2018-06-14)¶

Work on Issue #155 - fix for new single file return. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Merge pull request #326 from njcuk9999/neil. [Neil Cook]

Neil
Work on issues #167, #176 and #231 - first commmit spirouWAVE file with cal_WAVE (only) functions. [Neil Cook]
Work on issues #167, #176 and #231 - renamed ‘DATA’ to ‘HCDATA’, moved get_ll, get_dll to spirouMath. [Neil Cook]
Work on Issue #155 - modified multi_file_setup function and return of single_file_setup work on issues #167, #176 and #231 - modified custom getting of args/load_arguments to help with cal_wave. [Neil Cook]
Moved get_dll to spirouMath. [Neil Cook]
Work on issues #167, #176 and #231 - added read_hcref, fixed bug with NBFRAMES append_source –> set_source. [Neil Cook]
Work on Issue #155 - fixing bugs for multi file setup (custom) [Neil Cook]
Added aliases. [Neil Cook]
Added aliases. [Neil Cook]
Renamed correct_flat to get_flat. [Neil Cook]
Added aliases. [Neil Cook]
Work on issue #167, #176, #231 - added wave_plot_instrument_drift, wave_plot_final_fp_order, wave_local_width_offset_plot, and wave_fp_wavelength_residuals. [Neil Cook]
Moved get_ll_from_coefficients and get_dll_from_coefficients here. [Neil Cook]
Added aliases. [Neil Cook]
Updated date and version. [Neil Cook]
Modified comment. [Neil Cook]
Work on Issue #176, #167, #231 - added constants. [Neil Cook]
Work on Issue #176, #167, #231. [Neil Cook]
Work on Issue #155 - modified return of recipe. [Neil Cook]
Work on Issue #155 - modified return of recipe. [Neil Cook]
Work on Issue #155 - modified return of recipe. [Neil Cook]
Work on Issue #155 - modified return of recipe. [Neil Cook]

0.2.044 (2018-06-13)¶

Modified run order. [Neil Cook]
Work on issue #176 - changes from variable names (in line with other recipes) [Neil Cook]
Work on issue #155 - modified initial_file_setup, added single_file_setup and multi_file_setup, set todo’s to remove now obsolete functions, added new get_file function. [Neil Cook]
Added aliases. [Neil Cook]
Added rotate function, fix non pre-processed files function. [Neil Cook]
Work on issue #155 - finished id checking functions. [Neil Cook]
Added aliases. [Neil Cook]
Updated date and version, shortened log_opt (no suffix just program name) [Neil Cook]
Shorterned calibration –> cal. in log messages (for copying/not copying cal files) [Neil Cook]
Work on issue #155 - added more files to control. [Neil Cook]
Updated constant name. [Neil Cook]
Added constants (preprocessing, exposuremeter, cal_hc, cal_wave) [Neil Cook]
Fix for non pre-processed files. [Neil Cook]
Fixed bug in gfkwargs. [Neil Cook]
Work on issue #155 - modified set up to accommodate checks via filename and header (via InitialFileSetup), fix for non pre-processed files. [Neil Cook]
Made rotation a function based on a given rotation from constant. [Neil Cook]
Work on issue #155 - modified set up to accommodate checks via filename and header (via InitialFileSetup), fix for non pre-processed files. [Neil Cook]
Work on issue #155 - modified set up to accommodate checks via filename and header (via InitialFileSetup), fix for non pre-processed files, added H2RG compatibility fix. [Neil Cook]
Work on issue #155 - modified set up to accommodate checks via filename and header (via InitialFileSetup), fix for non pre-processed files. [Neil Cook]
Work on issue #155 - modified set up to accommodate checks via filename and header (via InitialFileSetup), fix for non pre-processed files. [Neil Cook]
Work on issue #155 - modified set up to accommodate checks via filename and header (via InitialFileSetup), fix for H2RG compatibility, added H4RG kw objects needed for berv calculation. [Neil Cook]
Work on issue #155 - modified set up to accommodate checks via filename and header (via SingleFileSetup + MultiFileSetup) [Neil Cook]
Work on issue #155 - modified set up to accommodate checks via filename and header (via SingleFileSetup) [Neil Cook]
Work on issue #155 - modified set up to accommodate checks via filename and header (via SingleFileSetup) [Neil Cook]
Work on issue #155 - modified set up to accommodate checks via filename and header (via InitialFileSetup), fix for H2RG compatibility. [Neil Cook]
Work on issue #155 - modified set up to accommodate checks via filename and header (via SingleFileSetup) [Neil Cook]
Work on issue #155 - modified set up to accommodate checks via filename and header (via SingleFileSetup) [Neil Cook]

0.2.043 (2018-06-12)¶

Work on issue #155 - added recipe control file. [Neil Cook]
Work on issue #155 - (un-finished) added new initial_file_setup and get file (now use single_file_setup) [Neil Cook]
Work on issue #155 - modified read_header to optionally return comments. [Neil Cook]
Work on issue #155 - added ID functions. [Neil Cook]
Work on issue #155 - reworked aliases and __ALL__ [Neil Cook]
Work on issue #155 - updated DPRTYPE comment. [Neil Cook]
Work on issue #155 - added some required keywords. [Neil Cook]
Work on issue #155 - rearranged some constants, added data constant directory. [Neil Cook]
Work on issue #155 - changed import to deal with change in location of spirouFile. [Neil Cook]
Work on issue #155 - test of ID-ing files. [Neil Cook]
Work on issue #155 - added section to ID files and modify the header accordingly (based on filename OR header keys) [Neil Cook]
Merge pull request #325 from njcuk9999/neil. [Neil Cook]

updated date and version
Merge pull request #324 from njcuk9999/neil. [Neil Cook]

Neil

0.2.041 (2018-06-11)¶

Updated date and version. [Neil Cook]
Continued work on cal_HC (Issue #176) - added two masks for cal_HC. [Neil Cook]
Continued work on cal_HC (Issue #176) - updated keywords, renamed some loc variables (for clarity) [Neil Cook]
Continued work on cal_HC (Issue #176) - added some fixes to coravelation (to accommodate cal_hc) [Neil Cook]
Continued work on cal_HC (Issue #176) - added merge table and added some fixes to small bugs. [Neil Cook]
Continued work on cal_HC (Issue #176) - added alias to spirouTable.merge_table (MergeTable) [Neil Cook]
Continued work on cal_HC (Issue #176) - added FWHM calculation (from sigma) [Neil Cook]
Continued work on cal_HC (Issue #176) - added keywords for cal_hc. [Neil Cook]
Continued work on cal_HC (Issue #176) - added wave file output filename definitions. [Neil Cook]
Continued work on cal_HC (Issue #176) - added constants. [Neil Cook]
Continued work on cal_HC (Issue #176) - output to file + ccf calculation (from cal_CCF mainly) [Neil Cook]
Continued work on cal_HC (Issue #176) - fixed value of FWHM from sigma. [Neil Cook]

0.2.039 (2018-06-08)¶

Continued work on cal_HC (Issue #176) - test of fit gauss functions. [Neil Cook]
Continued work on cal_HC (Issue #176) - modified first_guess_at_wave_solution, detect_bad_lines, fit_1d_solution, calculate_littrow_sol, extrapolate_littrow_sol, second_guess_at_wave_solution. Added join_orders. [Neil Cook]
Continued work on cal_HC (Issue #176) - added alias to spirouTHORCA.join_orders (JoinOrders) [Neil Cook]
Continued work on cal_HC (Issue #176) - added wave_littrow_check_plot and corrected wave_littrow_extrap_plot. [Neil Cook]
Continued work on cal_HC (Issue #176) - corrected imports and a bug in fitgaussian functions. [Neil Cook]
Continued work on cal_HC (Issue #176) - added how to compile fortran. [Neil Cook]
Continued work on cal_HC (Issue #176) - python version of fitgaus by @melissa-hobson. [Neil Cook]
Continued work on cal_HC (Issue #176) - added new constants. [Neil Cook]
Continued work on cal_HC (Issue #176) - added new constants. [Neil Cook]
Continued work on cal_HC (Issue #176) [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [njcuk9999]
Merge pull request #323 from njcuk9999/dev. [Neil Cook]

Dev

0.2.036 (2018-06-07)¶

Find lines test (cal_HC test) [njcuk9999]
Continued work on cal_HC - aliases for new THORCA functions. [njcuk9999]
Continued work on cal_HC - wave littrow plot. [njcuk9999]
Continued work on cal_HC - experimentation with fitting. [njcuk9999]
Continued work on cal_HC. [njcuk9999]
Continued work on cal_HC - constants for cal_HC. [njcuk9999]
Continued work on cal_HC. [njcuk9999]

0.2.037 (2018-06-07)¶

Added default user config path. [Neil Cook]
Added my path. [Neil Cook]
Merge pull request #322 from njcuk9999/dev. [Neil Cook]

Dev
@FrancoisBouchy changes - merge confirmed, added some pe8 and comments and simplifications. [Neil Cook]
@FrancoisBouchy changes - merge confirmed. [Neil Cook]
@FrancoisBouchy changes - merge confirmed + added ff_rms_plot function. [Neil Cook]
@FrancoisBouchy changes - merge confirmed. [Neil Cook]
@FrancoisBouchy changes - merge confirmed + added ff_rms_plot_skip_orders. [Neil Cook]
Added ff_rms_plot_skip_orders (blank for H2RG) [Neil Cook]
@FrancoisBouchy changes - merge confirmed. [Neil Cook]
@FrancoisBouchy changes - merge confirmed. [Neil Cook]
@FrancoisBouchy changes - merge confirmed. [Neil Cook]
@FrancoisBouchy changes - merge confirmed. [Neil Cook]
@FrancoisBouchy changes - merge confirmed, moved plotting to spirouPlot. [Neil Cook]
@FrancoisBouchy changes - merge confirmed, some pep8 and commenting. [Neil Cook]
@FrancoisBouchy changes - merge confirmed. [Neil Cook]

0.2.035 (2018-05-29)¶

Fix matplotlib bug. [njcuk9999]
Fix small bug. [njcuk9999]
Update date and version. [njcuk9999]
Merge pull request #319 from njcuk9999/neil. [Neil Cook]

Neil
Update config.py. [njcuk9999]
Re-added BERV correction just for H4RG. [njcuk9999]
Added masks to correct folder. [njcuk9999]
Merge remote-tracking branch ‘origin/neil’ into neil. [njcuk9999]
Merge pull request #318 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #317 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #316 from njcuk9999/cfht. [Neil Cook]

new masks added on data
New masks added on data. [Spirou DRS]
Added new SpirouDRS data directories. [njcuk9999]
Added new SpirouDRS data directories. [njcuk9999]
Added new SpirouDRS data directories. [njcuk9999]
Added new SpirouDRS data directories. [njcuk9999]
Sorted SpirouDRS data folder. [njcuk9999]
Barycorrpy leap sec files (moved to drs) [njcuk9999]
Added constant for berv (ccf) [njcuk9999]
Updated ccf function. [njcuk9999]
Edited ccf. [njcuk9999]

0.2.034 (2018-05-28)¶

Updated for cal_hc. [njcuk9999]
Removed redundant comment. [njcuk9999]
Added test from old drs. [njcuk9999]
Merge remote-tracking branch ‘origin/neil’ into neil. [njcuk9999]
Merge pull request #314 from njcuk9999/neil. [Neil Cook]

updated date and version number
Merge pull request #313 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #312 from njcuk9999/neil. [Neil Cook]

Update cal_CCF_E2DS_spirou.py
Update value for speed of light, added invert_1ds_ll_solution. [njcuk9999]
Added new trial method to newbervmain (using barycorrpy) [njcuk9999]

0.2.033 (2018-05-26)¶

Updated date and version number. [njcuk9999]
Update tests with CCF test. [njcuk9999]
Update h2rg constant file (to be same as h4rg) [njcuk9999]
Fix typos. [njcuk9999]
Fix runtime errors on ccf test (set order to empty) [njcuk9999]
Added ee. [njcuk9999]
Removed fortran code. [njcuk9999]
Update unit tests. [njcuk9999]
Update fortran codes. [njcuk9999]
Updated script doc string. [njcuk9999]
Update unit tests (cal_FF_raw needs flat_flat) [njcuk9999]
Synced h2rg and h4rg. [njcuk9999]
Correct the comments and indentation of the background. [njcuk9999]
Merge branch ‘francois’ into neil. [njcuk9999]

Conflicts:
INTROOT/SpirouDRS/spirouConfig/spirouKeywords.py INTROOT/SpirouDRS/spirouRV/spirouRV.py INTROOT/bin/cal_CCF_E2DS_spirou.py INTROOT/bin/cal_FF_RAW_spirou.py INTROOT/config/constants_SPIROU_H4RG.py
First wavelength solution added to SpirouDRS/data. [FrancoisBouchy]
Telluric mask added on SpirouDRS/data. [FrancoisBouchy]
Fortran module for BERV computation : Require f2py -c -m newbervmain –noopt –quiet newbervmain.f. [FrancoisBouchy]
Update of cal_CCF_E2DS with target parameters and BERV computation from the fortran module newbervmain. [FrancoisBouchy]
Update of cal_DRIFT_E2DS_spirou. Results now comparable to cal_DRIFTPEAK_E2DS_spirou. [FrancoisBouchy]
Background correctionis now an option. [FrancoisBouchy]
Cal_FF_RAW_spirou must run on flat_flat and provide flat and blaze for A, B, AB and C fibers. [FrancoisBouchy]
New recipes to display the full spectral range of an E2DS file. [FrancoisBouchy]
Typo on the name corrected. [FrancoisBouchy]
Added CFHT parameters and option for background correction on cal_DRIFT. [FrancoisBouchy]
Add targets keywords + Date of observations for cal_CCF_E2DS_spirou. [FrancoisBouchy]
All wavelength are in nm. [FrancoisBouchy]
#300 Bug on the fit_ccf on individual orders to investigate. [FrancoisBouchy]
Merge remote-tracking branch ‘origin/francois’ into francois. [FrancoisBouchy]

Conflicts:
INTROOT/SpirouDRS/spirouCore/spirouPlot.py INTROOT/bin/cal_DARK_spirou.py INTROOT/bin/cal_DRIFTPEAK_E2DS_spirou.py INTROOT/bin/cal_extract_RAW_spirou.py INTROOT/bin/visu_RAW_spirou.py INTROOT/config/constants_SPIROU_H4RG.py
@FrancoisBouchy change (merged by @njcuk9999) - why comment out this line? [njcuk9999]
@FrancoisBouchy change (merged by @njcuk9999) - plot labels should be in nm not angstrom. [njcuk9999]
@FrancoisBouchy change (merged by @njcuk9999) - added new required input HEADER keywords. [njcuk9999]
@FrancoisBouchy change (merged by @njcuk9999) [njcuk9999]
@FrancoisBouchy change (merged by @njcuk9999) [njcuk9999]
@FrancoisBouchy change (merged by @njcuk9999) [njcuk9999]
Update H2RG dependency flag. [njcuk9999]
@ Francois Bouchy - fixed changes dark_flat/flat_dark –> flat_flat. [njcuk9999]

0.2.029 (2018-05-25)¶

Update of cal_DRIFT_E2DS_spirou. Results now comparable to cal_DRIFTPEAK_E2DS_spirou. [FrancoisBouchy]

(cherry picked from commit 86ee03b)
@FrancoisBouchy added earth_velocity_correction, newbervmain functions and modified coravelation. [njcuk9999]
@FrancoisBouchy - added alias to earth_velocity_correction. [njcuk9999]
@FrancoisBouchy added read star parameters and earth velocity calculation. [njcuk9999]
Merge remote-tracking branch ‘origin/neil’ into neil. [njcuk9999]

0.2.030 (2018-05-25)¶

Worked on fit_1d_solution (complete?), added to doc strings (gparams) [njcuk9999]
Added alias to fit_1d_solution (Fit1DSolution) [njcuk9999]
Added new cal_hc variables. [njcuk9999]
Change FirstGuessSolution mode to new (to avoid needing fortran fitgaus code) [njcuk9999]

0.2.031 (2018-05-25)¶

Update cal_CCF_E2DS_spirou.py. [melissa-hobson]

Changed filetype to accept all E2DS files.
Merge pull request #311 from njcuk9999/neil. [Neil Cook]

Neil

0.2.026 (2018-05-18)¶

Update readme. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Fixed bug when config files only have one or zero lines. [Neil Cook]
Reset constant back to default. [Neil Cook]
Fix to Issue #232 - added cal_exposure_meter to unit tests. [Neil Cook]
Fix to Issue #232 - added cal_exposure_meter to unit tests. [Neil Cook]
Fix to Issue #232 - add file names for cal_exposure_meter. [Neil Cook]
Fix to Issue #232 - add different outputs. [Neil Cook]
Fix to Issue #232 - add different outputs. [Neil Cook]
Fix to Issue #232 - bug in applying badpixmask. [Neil Cook]
Commented out work-in-progress function. [Neil Cook]
Fix to Issue #232 - added get_badpixel_map and modified correct_for_badpix functions. [Neil Cook]
Fix to Issue #232 - added exposure-meter functions to new sub-module in spirouImage. [Neil Cook]
Fix to Issue #232 - added alias to get_badpixel_map function (GetBadPixMap) [Neil Cook]
Fix to Issue #232 - added output keywords to spirouKeywords. [Neil Cook]
Fix to Issue #232 - added telluric exposure meter maps to calibDB. [Neil Cook]
Fix to Issue #232 - added expsoure-meter constants. [Neil Cook]
Fix to Issue #232 - produce expsoure-meter recipe (compatible with H2RG and H4RG) [Neil Cook]
Work on cal_HC (restore from bad merge) [Neil Cook]
Merge pull request #310 from njcuk9999/neil. [Neil Cook]

Neil
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Added wavelength solution file for H4RG. [Neil Cook]
Added H4RG wavelength solution files to the calib DB default files (for reseting) [Neil Cook]
@FrancoisBoucy - 4 digit to diplay the dark statistics. [Neil Cook]
@FrancoisBouchy - new lower limit in dark level plot (with H2RG compatibility) [Neil Cook]
Fix error message in get_database (calibDB) [Neil Cook]
Update default master_calib_spirou file (with H2RG and H4RG default wave solutions) [Neil Cook]
Update date and version. [Neil Cook]
@FrancoisBouchy - update to dark constants. [Neil Cook]
@FrancoisBouchy - visu_RAW_spirou adapted for preprocessed files. [Neil Cook]
@FrancoisBouchy - Use the wavelength solution from the calibDB, set all negative pixels to zero and update ext_sorder_fit upper limit. [Neil Cook]
@FrancoisBouchy - Use the wavelength solution from the calibDB. [Neil Cook]
@FrancoisBouchy - Quality control of the dark level on the blue part of the detector. [Neil Cook]
Added recipe to reset (while in development only) [Neil Cook]

0.2.027 (2018-05-18)¶

4 digit to diplay the dark statistics. [FrancoisBouchy]
Range adjusted to display Dark frame Blue window displayed in White Cut parameter added in extract plotting function Wavelength solution used in extract plotting function. [FrancoisBouchy]
Dark constant and Dark quality control adjusted. [FrancoisBouchy]
Visu_RAW_spirou adapted for preprocessed files. [FrancoisBouchy]
Negative pixels are set to zero Read wavelength solution on calibDB Set the cut to max_signal/10 to display the order location. [FrancoisBouchy]
Use the first wavelength solution from the calibDB spirou_wave_H4RG_v0.fits. [FrancoisBouchy]
Quality control of the dark level on the blue part of the detector. [FrancoisBouchy]
Merge remote-tracking branch ‘origin/francois’ into francois. [FrancoisBouchy]
Merge pull request #307 from njcuk9999/neil. [Neil Cook]

Neil
Merge remote-tracking branch ‘origin/francois’ into francois. [FrancoisBouchy]
Merge pull request #305 from njcuk9999/master. [FrancoisBouchy]

Update README.md
Merge remote-tracking branch ‘origin/francois’ into francois. [FrancoisBouchy]

Conflicts:
INTROOT/SpirouDRS/spirouEXTOR/spirouEXTOR.py INTROOT/SpirouDRS/spirouImage/spirouImage.py INTROOT/bin/cal_BADPIX_spirou.py INTROOT/bin/cal_DRIFTPEAK_E2DS_spirou.py INTROOT/bin/cal_extract_RAW_spirou.py INTROOT/config/constants_SPIROU_H4RG.py

0.2.025 (2018-05-17)¶

Fix to Issue #227 - added cal_drift and drift peak to tests. [Neil Cook]
Fix to Issue #227 - added cal_drift and drift peak to tests. [Neil Cook]
Fix to Issue #227 - added cal_drift and drift peak to tests. [Neil Cook]
Work on issue #176 - Attempt to get First Guess solution working and detection of badlines. [Neil Cook]
Work on issue #176 - Attempt to get First Guess solution working and detection of badlines (aliases) [Neil Cook]
Work on issue #176 - added three cal_HC constants. [Neil Cook]
Work on issue #176 - Attempt to get First Guess solution working and detection of badlines. [Neil Cook]

0.2.024 (2018-05-16)¶

Removed dependency on cal_drift_raw. [Neil Cook]
Updated test.run. [Neil Cook]
Fix to Issue #227 - dealt with warnings for cal_driftpeak. [Neil Cook]
Updated date and version. [Neil Cook]
Fake file comments added. [Neil Cook]
Added fake fp_fp files for drift (copies of fp_fp_001) [Neil Cook]
Fix to Issue #227 - removed support for cal_drift_raw_spirou. [Neil Cook]
Fix to Issue #227 - removed cal_DRIFT_RAW_spirou. [Neil Cook]
Fix to Issue #227 - refactored warnlog. [Neil Cook]
Fix to Issue #227 - added cal_drift and drift peak to tests. [Neil Cook]
Fix to Issue #227 - deal with warnings. [Neil Cook]
Fix to Issue #227 - refactor warnlog (+ fix bug) [Neil Cook]
Update date and version. [Neil Cook]
Fix to Issue #227 - refactor warnlog. [Neil Cook]
Fix to Issue #227 - apply H4RG fixes to drift codes. [Neil Cook]
Enchancement - compare function gets ARG_NIGHT_NAME from ll, prints old and new file locations (for extra confirmation) [Neil Cook]
Update oldpath (don’t include path) [Neil Cook]
Updated test run. [Neil Cook]
Fix for bug when HEADER time not string (should always be string but can be interpreted as number and thus break function) [Neil Cook]
Fix - removed unneeded comment. [Neil Cook]
Merge pull request #306 from njcuk9999/neil. [Neil Cook]

Neil
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]

0.2.023 (2018-05-15)¶

Updated run. [Neil Cook]
Fixed typo. [Neil Cook]
Added runname to comparison table. [Neil Cook]
Added run name to comparison table (to name table) [Neil Cook]
Corrected bug with unit test (files were duplicated in list i.e. file1 file1 file2 file3. [Neil Cook]
Tool file - clear out cached .pyc files (useful when rebuilding) [Neil Cook]
H2RG compatibility - fitsfilename = arg_file_names[-1] and only adding SNR keys and EXTM/FUNC for H4RG, p returned to call. [Neil Cook]
Fixed pep8 in smoothed_box_mean_image1 function. [Neil Cook]
Updated date and version + rebuild pdfs. [Neil Cook]
Updated date and version. [Neil Cook]
H2RG compatibility - fitsfilename = arg_file_names[-1] and only adding SNR keys and EXTM/FUNC for H4RG. [Neil Cook]
H2RG compatibility - fitsfilename = arg_file_names[-1] [Neil Cook]
True on comparison in H2RG run. [Neil Cook]
Fix to calling from python (bug introduced in last update) [Neil Cook]
Fix to unit_test comparison table. [Neil Cook]
Fix to unit_test comparison table. [Neil Cook]
Fix to unit_test comparison table. [Neil Cook]

0.2.022 (2018-05-14)¶

Update README.md. [Neil Cook]
Merge pull request #304 from njcuk9999/neil. [Neil Cook]

Neil
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Merge pull request #303 from njcuk9999/neil. [Neil Cook]

Neil
Updated date and versions. [Neil Cook]
Fix for issue #296 - was mistake in argument to test_suffix = suffix.format - called dictionary incorrectly. [Neil Cook]
Fix for issue #302 - IC_COSMIC_THRES –> IC_COSMIC_THRESH. [Neil Cook]
Updated test run. [Neil Cook]
Fix for issue #302 - added IC_COSMIC_SIGCUT and IC_COSMIC_THRES. [Neil Cook]
Fix for issue #302 - added IC_COSMIC_SIGCUT and IC_COSMIC_THRES. [Neil Cook]
Fix to Issue #296 - added alias (CheckPreProcess) for spirouStartup.check_preprocess. [Neil Cook]
Fix to Issue #296 - added IC_FORCE_PREPROCESS and added all other preprcess constants to constants file. [Neil Cook]
Fix to #296 - added .fits to suffix. [Neil Cook]
Fix to Issue #296 - added call to CheckPreProcess - check for preprocessed files. [Neil Cook]
Fix to #296 - added check_preprocess function. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Merge pull request #301 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #293 from njcuk9999/neil. [Neil Cook]

Neil
Fix to unit_test - bug in logic when file does not exist –> True to False. [Neil Cook]
Fix to issue #292 - get_fiber_type modified to accept and require suffix to get fiber type. [Neil Cook]

0.2.021 (2018-05-12)¶

Fix to issue #300 - added correct_for_badpix function. [Neil Cook]
Fix to issue #300 - alias to correct_for_badpix function. [Neil Cook]
Fix to issue #298 - exit script should deal with new DRS_INTERACTIVE parameter. [Neil Cook]
Fix to issue #298 - DRS_INTERACTIVE should be set to 1 by default. [Neil Cook]
Fix to bug identified - no exit script in AB or C. [Neil Cook]
Fix to issue #298 - set DRS_PLOT to zero if DRS_INTERACTIVE == 0 and if DRS_INTERACTIVE == 0 do not prompt user at the end of recipes about exiting and plotting. [Neil Cook]
Fix to issue #298 - set DRS_PLOT to zero if DRS_INTERACTIVE == 0 and if DRS_INTERACTIVE == 0 do not prompt user at the end of recipes about exiting and plotting. [Neil Cook]
Fix to issue #298 - added DRS_INTERACTIVE to config.py. [Neil Cook]
Fix to issue #297 - Unit test to display current files if no argument. [Neil Cook]
Fixes to unit_tests for internal bugs and to correct for issue #295. [Neil Cook]
Fix to issue #294 - H2RG needs to return “bstats2” too (set to zero) [Neil Cook]
Fix to Issue #295 - complete reworking of wrapper function (which is now called from recipes) [Neil Cook]
Fix to Issue #295 - updated alias functions. [Neil Cook]
Fix to Issue #295 - added E2DS_EXTM and E2DS_FUNC HEADER keys to report extract type and extract function. [Neil Cook]
Fix for Issue #295 - removed EXTRACT_E2DS_ALL_FILES - not needed any more. [Neil Cook]
Fix to Issue #295 - change the way extraction is managed - modified IC_EXTRACT_TYPE and added IC_FF_EXTRACT_TYPE. [Neil Cook]
Fix to Issue #295 - change the way extraction is managed - now type IC_FF_EXTRACT_TYPE. [Neil Cook]
Fix to Issue #295 - change the way extraction is managed - now type 2. [Neil Cook]
Fix to Issue #295 - change the way extraction is managed - now type 2. [Neil Cook]
Fix to Issue #295 - change the way extraction is managed. [Neil Cook]
Fix to Issue #294 - stats for bad_pixel_map_2 in cal_BADPIX_spirou. [Neil Cook]
Fix to Issue #294 - stats for bad_pixel_map_2 in cal_BADPIX_spirou. [Neil Cook]
Start of fix to issue #295 - Switch between extraction routines in constants_SPIROU file - unfinished. [Neil Cook]
Fix to issue #294 - stats for bad_pixel_map_2 in cal_BADPIX_spirou. [Neil Cook]
Fix imports for python 2 and make runs sorted (again for python 2) [Neil Cook]
Fix imports for python 2. [Neil Cook]
Update units tests with new run names (sortable) - python 2 safe. [Neil Cook]
Fix unit test import (should be inner call to function) [Neil Cook]
Fix typo. [Neil Cook]
Fix for typo. [Neil Cook]
Fix to import statements (for python 2 compatibility) [Neil Cook]
New extraction_tilt_weight2cosm with cosmic correction. Mode=2 is by default this new extraction. [Neil Cook]
Display of bad pixels with 4 digits. [Neil Cook]
Ic_blake_fitn set to 7 ic_ext_sigdet set to -1. [Neil Cook]
ConvertToADU convert from ADU/s to ADU (not e-) Faction of dead pixels display with 4 digits Display the number of cosmic rays (bad pixels) detected by the extraction. [Neil Cook]
Fake wavelength solution to run without WAVE fiel in the calibDB. [Neil Cook]
Correction of the display of the image size. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Merge pull request #290 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #288 from njcuk9999/neil. [Neil Cook]

Neil

0.2.019 (2018-05-09)¶

Fitgaus fortan code (for testing only) [Neil Cook]
Example in ipynb and tex format. [Neil Cook]
Modified test run unit test. [Neil Cook]
Added new unit test runs (all and minimum required) [Neil Cook]
Removed old unit test runs. [Neil Cook]
Added cal_extract_RAW_spirou AB and C to unit tests. [Neil Cook]
Fix problem with reset = False. [Neil Cook]
Fix so wrapper extractions work with unit_tests (and can be called from python) [Neil Cook]
Ic_ext_sigdet should be -1. [Neil Cook]
Fix to Issue #289 - was a problem with WLOG message (argument missing from format) [Neil Cook]

0.2.020 (2018-05-09)¶

Faction of dead pixels display with 4 digits Display the number of cosmic rays (bad pixels) detected by the extraction. [FrancoisBouchy]
Fake wavelength solution due to missing WAVE in calibDB. [FrancoisBouchy]
Display of the format of the resized image. [FrancoisBouchy]
Merge remote-tracking branch ‘origin/francois’ into francois. [FrancoisBouchy]

Conflicts:
INTROOT/bin/cal_BADPIX_spirou.py INTROOT/bin/cal_DRIFTPEAK_E2DS_spirou.py INTROOT/bin/cal_extract_RAW_spirou.py
New extraction_tilt_weight2cosm with cosmic correction. Mode=2 is by default this new extraction. [FrancoisBouchy]
Display of bad pixels with 4 digits. [FrancoisBouchy]
Ic_blake_fitn set to 7 ic_ext_sigdet set to -1. [FrancoisBouchy]
ConvertToADU convert from ADU/s to ADU (not e-) Faction of dead pixels display with 4 digits Display the number of cosmic rays (bad pixels) detected by the extraction. [FrancoisBouchy]
Fake wavelength solution to run without WAVE fiel in the calibDB. [FrancoisBouchy]
Correction of the display of the image size. [FrancoisBouchy]
Merge pull request #271 from njcuk9999/master. [Neil Cook]

update to master

0.2.018 (2018-05-07)¶

Fix to latex format. [Neil Cook]
Fix to install (cal validate from cmd line needs .py) [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Added retrun possibility to list_modules, and added find_all_missing_modules wrapper function. [Neil Cook]
Completed doc string. [Neil Cook]
Corrected __all__ [Neil Cook]
Added missing doc strings. [Neil Cook]
Added missing doc strings. [Neil Cook]
Added missing functions from tex files. [Neil Cook]
Added tex and pdf versions of the examples (auto-generated from notebooks) [Neil Cook]
Added unit tests and tools to SpirouDRS __all__ list (and imported) [Neil Cook]
Example 10 in html format. [Neil Cook]
Example 10 - how to use spirou tools. [Neil Cook]
Fixed bug in display_calibdb (use LoadMinimum not LoadArguments) [Neil Cook]
Updated date and version. [Neil Cook]
Updated date and version. [Neil Cook]
Updated variables (added CCF variables and missed cal_BADPIX variabels) [Neil Cook]
Update to ic_ext_tilt_bord description. [Neil Cook]
H4RG by default. [Neil Cook]
Update to unit_test file (post unit_test changes) [Neil Cook]
Fix to issue #287 - extra issue log statements with errors inside - print warnings first then internal errors after - set key after too (avoids printing errors inbetween warnings) [Neil Cook]
Fix to issue #287 - extra issue of crash before config loads (IC_IMAGE_TYPE) missing from needed spirouKeyword USE_PARAMS. [Neil Cook]
Fix to issue #287 - deal with DRS_UCONFIG warning printing. [Neil Cook]
Update README.md. [Neil Cook]
Merge pull request #285 from njcuk9999/neil. [Neil Cook]

updated date and versions
Merge pull request #284 from njcuk9999/neil. [Neil Cook]

Neil

0.2.017 (2018-05-04)¶

Updated date and versions. [Neil Cook]
Merge remote-tracking branch ‘origin/neil’ into neil. [Neil Cook]
Merge pull request #283 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #282 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #275 from njcuk9999/neil. [Neil Cook]

pep8 update all ParamDict constants to capitals
Merge pull request #274 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #270 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #268 from njcuk9999/neil. [Neil Cook]

Neil
Unit_test fix - add total time to log_timings print out. [Neil Cook]
Fix to Issue #278 - make cal_extract_RAW_spirouAB and cal_extract_RAW_spirouC work again. [Neil Cook]
Fix to Issue #278 - make cal_extract_RAW_spirouAB and cal_extract_RAW_spirouC work again. [Neil Cook]
Fix to issue #281 - small function to deal with some extensions being corrupted (will still crash if all extensions bad) and will assume first valid extension (i.e. with shape) is the image to be used. [Neil Cook]
Fix to issue #277 - check “files” and if it is a string force it into a length=1 list, if not string or list throw error. [Neil Cook]
Fix to issue #277 - added doc string to main functions to make it clear what inputs are expected. [Neil Cook]
Fix to issue #277 - added doc string to main functions to make it clear what inputs are expected. [Neil Cook]
Fix to issue #277 - added doc string to main functions to make it clear what inputs are expected. [Neil Cook]
Fix to issue #277 - added doc string to main functions to make it clear what inputs are expected. [Neil Cook]
Fix to issue #277 - added doc string to main functions to make it clear what inputs are expected. [Neil Cook]
Fix to issue #277 - added doc string to main functions to make it clear what inputs are expected. [Neil Cook]
Fix to issue #277 - added doc string to main functions to make it clear what inputs are expected. [Neil Cook]
Fix to issue #277 - added doc string to main functions to make it clear what inputs are expected. [Neil Cook]
Fix to issue #277 - added doc string to main functions to make it clear what inputs are expected. [Neil Cook]
Fix to issue #277 - added doc string to main functions to make it clear what inputs are expected. [Neil Cook]
Fix to issue #277 - added doc string to main functions to make it clear what inputs are expected. [Neil Cook]
Fix to issue #277 - added doc string to main functions to make it clear what inputs are expected. [Neil Cook]

0.2.016 (2018-05-03)¶

Pep8 update all ParamDict constants to capitals. [Neil Cook]
Unit_test - added additional run files. [Neil Cook]
Unit_test fix - DRS_Reset modification, loading arguments modification and set_type –> check_Type change. [Neil Cook]
Unit_test fix - set_type doesn’t work - just check type instead (and throw error) [Neil Cook]
Unit_test fix - rename set_type to check_type. [Neil Cook]
Unit_test fix - alias to load_minimum. [Neil Cook]
Unit_test fix - reset_confirmation modification and log successful completion. [Neil Cook]
Unit_test fix - do not require night_name. [Neil Cook]

0.2.015 (2018-05-02)¶

Notebook additions - conversion to html. [Neil Cook]
Notebook additions - added a quiet mode for notebooks (no user input needed) [Neil Cook]
Notebook additions - added unit_test alias to init file (for loading up from python) [Neil Cook]
Notebook additions - test unit test for notebooks. [Neil Cook]
Notebook additions - example 9 - unit tests. [Neil Cook]
Notebook additions - example 8 - wlog. [Neil Cook]
Notebook additions - code to convert. [Neil Cook]

0.2.014 (2018-05-01)¶

Rebuild pdfs. [Neil Cook]
Updated date and versions. [Neil Cook]
Redefining unit tests - example run files (for unit test) [Neil Cook]
Redefining unit tests - first commit - slight changes (logging) [Neil Cook]
Redefining unit tests - first commit - new recipe for unit test. [Neil Cook]
Redefining unit tests - first commit - new functions for unit test. [Neil Cook]
Redefining unit tests - first commit - new recipe definitions for unit tests. [Neil Cook]
Redefining unit tests - added new function aliases. [Neil Cook]
Redefining unit tests - moved old. [Neil Cook]
Redefining unit tests - moved old. [Neil Cook]
Redefining unit tests - moved old. [Neil Cook]
Redefining unit tests - moved old. [Neil Cook]
Redefining unit tests - moved old. [Neil Cook]
Redefining unit tests - moved old. [Neil Cook]
Redefining unit tests - allowing silent reset (not advised) [Neil Cook]
Updating versions. [Neil Cook]
Redefining unit tests - add function alias. [Neil Cook]

0.2.012 (2018-04-30)¶

Regarding issue #264 - change no longer needed - revert to earlier version. [Neil Cook]
Fix to issue #267 - SNR saved in the headers - added keys to E2DS header. [Neil Cook]
Fix to issue #267 - SNR saved in the headers - added new keyword to list. [Neil Cook]
Fix to code dependency. [Neil Cook]
Merge pull request #266 from njcuk9999/francois. [Neil Cook]

Francois
Update cal_FF_RAW_spirou.py. [Neil Cook]

keep compatibility with H2RG version
Update spirouLOCOR.py. [Neil Cook]

keep compatibility with H2RG

0.2.013 (2018-04-30)¶

Update constant parameters for localization, flat-field and blaze. [FrancoisBouchy]
Plot the central column threshold for DRS_DEBUG=0. [FrancoisBouchy]
Add the plot of the central column with miny and maxy for DRS_DEBUG=0. [FrancoisBouchy]
Plot values of e2ds>0 and values of blaze>1. [FrancoisBouchy]
Force the curvature of orders in case of no detection. [FrancoisBouchy]
Merge pull request #265 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #260 from njcuk9999/neil. [Neil Cook]

manually adding francois changes

0.2.009 (2018-04-27)¶

Fix to issue #264 - spirouFLAT.MEasurEBlazeForOrder now requires p (for H2RG dependency) [Neil Cook]
Fix to issue #264 - stop blaze setting zero or negative values to 1. [Neil Cook]
Update? [Neil Cook]
Issue #263 and Issue #262 - tilt borders added and mask for negative pixel added to all functions. [Neil Cook]
Added function to extract valid order numbers from constants_SPIROU (via ParamDict) [Neil Cook]
Added function to extract valid order numbers from constants_SPIROU (via ParamDict) [Neil Cook]
Added function to extract valid order numbers from constants_SPIROU (via ParamDict) [Neil Cook]
Addressing issues #225 and #226 - compatability with both H2RG and H4RG by adding “method” (switch between average and median), pep8 fixes. [Neil Cook]
Pep8 fixes and Issue #226 - compatibility with both H2RG and H4RG. [Neil Cook]
Issue #263 - allowed tilt border to be changed in constants and first and last order to be selected. [Neil Cook]
Issue #250 - average –> median and dependency with H2RG. [Neil Cook]
Allowed valid orders to be changed in constants. [Neil Cook]
Dealt with dependency of H2RG (Issue #266) and allowed valid orders to be changed in constants. [Neil Cook]
Merge pull request #261 from njcuk9999/francois. [Neil Cook]

Francois

0.2.010 (2018-04-27)¶

Update constant parameters for flat-field and blaze. [FrancoisBouchy]
Modification of spirouPLot to Display all orders with correct NBFIB parameter. [FrancoisBouchy]
Start extraction from order 4th in cal_extract_RAW_spirou. [FrancoisBouchy]
Start extraction from order 4th in cal_FF_RAW_spirou. [FrancoisBouchy]
Merge pull request #259 from njcuk9999/neil. [Neil Cook]

Neil

0.2.011 (2018-04-27)¶

Manually adding francois changes. [njcuk9999]
Manually adding francois changes. [njcuk9999]
Merge pull request #258 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #256 from njcuk9999/revert-254-francois. [Neil Cook]

Revert “Francois”
Revert “Francois” [Neil Cook]
Merge pull request #255 from njcuk9999/revert-254-francois. [Neil Cook]

Revert “Francois”
Revert “Francois” [Neil Cook]
Merge pull request #254 from njcuk9999/francois. [Neil Cook]

update accepted.
Update config.py. [Neil Cook]
Update visu_RAW_spirou.py. [Neil Cook]

call to plt should come via sPlt i.e.: instead of: python import matplotlib.pyplot as plt

use

python from SpirouDRS.spirouCore import sPlt plt = sPlt.plt

This avoids all errors with matplotlib backends.
Change. [njcuk9999]
Change. [njcuk9999]
Update vcs.xml. [Neil Cook]
Cleaning up files. [njcuk9999]
Removed cached files. [njcuk9999]
Reset to master. [njcuk9999]

0.2.008 (2018-04-26)¶

Reset paths to defaults (shouldn’t have overwritten) [Neil Cook]
Merge pull request #249 from njcuk9999/francois. [Neil Cook]

Francois
Merge branch ‘dev’ into francois. [Neil Cook]
Merge pull request #248 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #247 from njcuk9999/neil. [Neil Cook]

Neil
Add files via upload. [Neil Cook]

Added francois files manually (via direct upload)
Add files via upload. [Neil Cook]

Added francois files via direct upload

0.2.007 (2018-04-25)¶

Fix to cal_badpix to allow use with H2RG (required bool mask for bad_pixel_mask2) [Neil Cook]
Merge pull request #246 from njcuk9999/melissa. [Neil Cook]

Melissa

0.2.0097 (2018-04-25)¶

Cal_DARK: increased decimals shown constants_SPIROU_H4RG: adjusted dark cut limit spirou_PLOT: added labels and titles to figures; changed histograms to normalised frequency spirou_IMAGE.measure_dark: changed histograms to density histograms, increased decimals. [melissa-hobson]
Merge pull request #245 from njcuk9999/master. [melissa-hobson]

update
Merge pull request #244 from njcuk9999/neil. [Neil Cook]

Neil
Updated order of cal_BADPIX_spirou in the unit test functions. [Neil Cook]
Fix for Issue #229 - added alias to spirouImage.locate_bad_pixels_full (LocateFullBadPixels) [Neil Cook]
Code to un-resize and un-flip the image (for back processing files created by the DRS) [Neil Cook]
Fix for Issue #229 - full flat detector image from engineering data (required for badpix fit) [Neil Cook]
Fix for Issue #229 - wrote locate_bad_pixel_full to workout threshold from full flat engineering data. [Neil Cook]
Fix for Issue #229 - added parameters to constants_spirou file. [Neil Cook]
Fix for Issue #229 - added parameters to constants_spirou file. [Neil Cook]
Fix to Issue #193 - try statement to import matplotlib and error output via WLOG (does not fix but catches exceptions) [Neil Cook]
Fix for Issue #229 - added call to spirouImage.LocateFullBadPixels, plotted graph, added resizing and flipping the image to match other recipes. [Neil Cook]
Merge pull request #243 from njcuk9999/master. [melissa-hobson]

update branch
Merge pull request #242 from njcuk9999/neil. [Neil Cook]

Neil
Re-built pdfs. [Neil Cook]
Updated date and versions. [Neil Cook]
Updated version in readme. [Neil Cook]
Added alias to load_other_config_file (LoadOtherConfig) - used in tools. [Neil Cook]
Fixed bug in __all__ statement. [Neil Cook]
Update to style. [Neil Cook]
New tool - drs documentation - doc functions useful for keeping the docs up-to-date. [Neil Cook]
Added % comments to doc (in variables) - needed to know which are missing. [Neil Cook]
Fix to suggestion in Issue #229 - changed argument order around to avoid confusion. [Neil Cook]
Merge pull request #241 from njcuk9999/neil. [Neil Cook]

Neil
Changed plot colour to “gist_gray” and linetype to “red” to help ID fits better (pink on rainbow was bad) [Neil Cook]
Updated preporecess for use with H2RG. [Neil Cook]
Fix for issue #220 - added alias to InterpolateBadRegions (call to spirouImage.interp_bad_regions) [Neil Cook]
Fix for issue #220 - added interp_bad_regions function and added doc strings for other new functions. [Neil Cook]
Fix for issue #220 - added bad_region constants. [Neil Cook]
Fix for issue #220 - added call to spirouImage.InterpolateBadRegions. [Neil Cook]
Merge pull request #238 from njcuk9999/master. [Neil Cook]

update to master

0.2.006 (2018-04-23)¶

Corrected order of inputs in cal_BADPIX main definition. [melissa- hobson]
Merge pull request #240 from njcuk9999/master. [melissa-hobson]

Update branch
Merge pull request #239 from njcuk9999/dev. [Neil Cook]

Merge pull request #237 from njcuk9999/master
Merge pull request #237 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #236 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #234 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #233 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #217 from njcuk9999/master. [melissa-hobson]

Update branch melissa from master
Merge pull request #216 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #213 from njcuk9999/master. [melissa-hobson]

Update branch from master
Merge pull request #211 from njcuk9999/dev. [Neil Cook]

Merge pull request #207 from njcuk9999/master
Merge pull request #207 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #210 from njcuk9999/melissa. [Neil Cook]

Merge pull request #206 from njcuk9999/master
Merge pull request #206 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #209 from njcuk9999/neil. [Neil Cook]

Neil

0.2.005 (2018-04-20)¶

Fix¶

Exit script should only ask to close graphs if we have plots (see “has_plots” keyword) [Neil Cook]

Other¶

Fix for issue #235 - added TODO to remove from cal_DARK eventually. [Neil Cook]
Fix for issue #235 changed BADPIX to BADPIX_OLD for calibDB key. [Neil Cook]
Added the has_plots=False to exit script. [Neil Cook]
Fix to issue #176 (unfinished) - avoids the importing of cal_HC in unit tests running the code (currently doesn’t have .main() for ease of debugging) [Neil Cook]
Fix to issue #212 - night_name now is allowed a backslash at the end and now gives error if incorrectly defined (before wasn’t checked specifically) fix to issue regarding type of custom argument (was incorrect - big bug fixed - customarg recipes will now be able to run again) [Neil Cook]
Updated date and versions. [Neil Cook]
Fix for issue #218 - threshold in find_order_centers should be in constnats file - also updated documentation with new constant. [Neil Cook]
Issue #219 - Added PP function aliases to spirouImage (called in cal_preprocess_spirou) [Neil Cook]
Issue #219 - pre-processing add Etienne’s code to recipe- added functions “ref_top_bottom”, “median_filter_dark_amp”, “median_one_over_f_noise” [Neil Cook]
Issue #219 - pre-processing add Etienne’s code to recipe. [Neil Cook]
Issue #219 - Add Etiennes pre-processing code to recipe. [Neil Cook]

0.2.004 (2018-04-19)¶

Fix to handling of custom arguments to accept only a list of filenames. [Neil Cook]
New way to handle files (with wildcards built in) [Neil Cook]
Dealing with Issue #219 - pre-processing - unfinished. [Neil Cook]

0.2.003 (2018-04-18)¶

Fix to Issue #215 - spirouImage.WriteImage do not use dtype=’float64’ [Neil Cook]
Fix to Issue #215 - spirouImage.WriteImage do not use dtype=’float64’ [Neil Cook]

0.2.001 (2018-04-17)¶

Continuation of Issue #176 - writing cal_HC - very stuck on replacing fitgaus.fitgaus. [Neil Cook]
Fix for Issue #183 - now checks module and version. [Neil Cook]
Merge pull request #208 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #205 from njcuk9999/neil. [Neil Cook]

Neil
Change to doc logo size. [Neil Cook]
Change to doc logo size. [Neil Cook]
Edit - test version needed main. [Neil Cook]
Merge pull request #204 from njcuk9999/dev. [Neil Cook]

Merge pull request #201 from njcuk9999/master
Merge pull request #201 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #203 from njcuk9999/melissa. [Neil Cook]

Merge pull request #202 from njcuk9999/master
Merge pull request #202 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #200 from njcuk9999/neil. [Neil Cook]

Neil
Updated documentation and added example custom configs to config folder. [Neil Cook]
Issue # 193 - matplotlib dependency. [Neil Cook]
Merge pull request #199 from njcuk9999/master. [Neil Cook]

merge
Merge pull request #197 from njcuk9999/neil. [Neil Cook]

Neil
Issue # 194 - Fix to python version string parsing failing if format isn’t as expected. [Neil Cook]
Merge pull request #196 from njcuk9999/import-fixes. [Neil Cook]

Import fixes
Update spirouPlot.py. [Neil Cook]

added __test_smoothed_boxmean_image temporarily to spirouPlot.py
Update spirouLOCOR.py. [Neil Cook]

remove __test_smoothed_boxmean_image from here (isn’t needed)
Update spirouPlot.py. [Neil Cook]

0.2.002 (2018-04-17)¶

Copied the matplotlib backend fix into spirouLOCOR.py. [Chris Usher]
Only import IPython when it will be used. [Chris Usher]
Prevent failed import for missing matplotlib backends. [Chris Usher]
Merge pull request #192 from njcuk9999/revert-191-melissa. [Neil Cook]

Revert “Melissa”
Revert “Melissa” [Neil Cook]
Merge pull request #191 from njcuk9999/melissa. [Neil Cook]

Melissa - updated to master
Merge branch ‘master’ into melissa. [Neil Cook]
Merge pull request #190 from njcuk9999/isabelle. [Neil Cook]

Merge pull request #188 from njcuk9999/master
Merge pull request #188 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #189 from njcuk9999/francois. [Neil Cook]

Merge pull request #187 from njcuk9999/master
Merge pull request #187 from njcuk9999/master. [Neil Cook]

update to master
Merge pull request #182 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #181 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #180 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #179 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #178 from njcuk9999/neil. [Neil Cook]

Merge pull request #177 from njcuk9999/master
Preprocessing script (currently does rotation only) [melissa-hobson]

0.1.037 (2018-04-16)¶

Spirou tools addition - compare two files (plot images and diff in a user-friendly manner) [Neil Cook]
Issue #176 - continued development of find_lines. [Neil Cook]
Issue #176 - Added FirstGuessSolution alias to init. [Neil Cook]
Issue #176 - continued to build cal_HC_E2DS. [Neil Cook]
Fix for bug introduced in last build - night_name now set in arg_file_names. [Neil Cook]
Merge from Melissa - H4RG constants_SPIROU file (values set from Melissa) [Neil Cook]
Merge from Melissa - update constants_SPIROU_H2RG with pep8 styling. [Neil Cook]
Merge from Melissa - switch between constants in H2RG and H4RG now constants_SPIROU.py is different for both. [Neil Cook]
Merge from Melissa - pre-processing script for H4RG images (currently only rotation) [Neil Cook]

0.1.036 (2018-04-13)¶

Issue #176 - Added catalogue line lists to SpirouDRS data folder. [Neil Cook]
Issue 176 - continued update of first_guess_solution (unfinished), added find_lines function (unfinished), added fit_emi_line (unfinished) [Neil Cook]
Fit gaussian moved to spirouCore.spirouMath. [Neil Cook]
Read table modified to display numbe rof columns on error. [Neil Cook]
Issue #176 - read line list function modified. [Neil Cook]
Added overwrite to hdu.writeto function in spirouFits.writeimage function. [Neil Cook]
Issue #176 - alias for ReadLineList. [Neil Cook]
Moved fit gaussian to spirouMath. [Neil Cook]
Issue #185 and #186 - kw_ACQTIME_KEY and kw_ACQTIME_KEY_UNIX are different between H2RG and H4RG. [Neil Cook]
Issue #185 and #186 - DATE_FMT_HEADER now requires p to function. [Neil Cook]
Issue #185 and #186 - DATE_FMT_HEADER now requires p to function. [Neil Cook]
Issue #186 - added “ic_image_type”, Issue #176 - modified ic_lamp types. [Neil Cook]
Issue #186 - modified DRS_UCONFIG for H2RG/H4RG configs. [Neil Cook]
Issue #176 - modified to allow running without function (temporarily) [Neil Cook]

0.1.035 (2018-04-12)¶

Issue #176 - added get_lamp_parameters, fiirst_guess_at_wave_soltuion (unfinished), and decide_on_lamp_type functions. [Neil Cook]
Issue #176 - added GetLampParams alias. [Neil Cook]
Issue #176 - renamed cdata_folder. [Neil Cook]
Issue #176 - created a read_line_list function (unfinished) [Neil Cook]
Issue #176 - modified GetFile call (with required key) [Neil Cook]
Issue #176 - added correct_flat function. [Neil Cook]
Issue #176 - added CorrectFlat. [Neil Cook]
Issue #176 - renamed cdata folder - make it more clear it is a relative path. [Neil Cook]
Issue #176 - modifications to get_file_name. [Neil Cook]
Issue #176 - added some cal_HC params. [Neil Cook]
Issue #176 - added fiber getting, application of flat and start of first guess at solution. [Neil Cook]
Update to version ready for new alpha release 0.1.035. [Neil Cook]
Update to version ready for new alpha release 0.1.035. [Neil Cook]
Update to version ready for new alpha release 0.1.035. [Neil Cook]
Update to version ready for new alpha release 0.1.035. [Neil Cook]
Update to version ready for new alpha release 0.1.035. [Neil Cook]

0.1.0349 (2018-04-11)¶

Added unit test for cal_HC_E2DS_spirou. [Neil Cook]
Added hcone extraction to unit test. [Neil Cook]
Replacement of rawfile with p[‘ARG_FILE_DIR’] [Neil Cook]
Replacement of rawfile with p[‘ARG_FILE_DIR’] [Neil Cook]
Place holder function for flat correction. [Neil Cook]
Replacement of rawfile with p[‘ARG_FILE_DIR’] [Neil Cook]
Replacement of rawfile with p[‘ARG_FILE_DIR’] [Neil Cook]
Fix to issue #176 - in progress - updating cal_HC_E2DS. [Neil Cook]

0.1.0348 (2018-04-09)¶

Fix to issue #152 - User/Custom config.py file - rebuilt pdfs. [Neil Cook]
Fix to issue #152 - User/Custom config.py file - updated documentation. [Neil Cook]
Fix to issue #152 - User/Custom config.py file - updated documentation. [Neil Cook]
Fix to issue #152 - User/Custom config.py file - rebuilt pdfs. [Neil Cook]
Fix to issue #152 - User/Custom config.py file - updated documentation. [Neil Cook]
Fix to issue #152 - User/Custom config.py file - updated documentation. [Neil Cook]
Fix to issue #152 - User/Custom config.py file - updated documentation. [Neil Cook]
Fix to issue #152 - User/Custom config.py file - updated documentation. [Neil Cook]
Fix to issue #152 - User/Custom config.py file. [Neil Cook]
Fix to issue #152 - User/Custom config.py file. [Neil Cook]
Fix to issue #152 - User/Custom config.py file. [Neil Cook]
Fix to issue #152 - User/Custom config.py file. [Neil Cook]
Fix to issue #152 - User/Custom config.py file. [Neil Cook]
Fix to issue #152 - User/Custom config.py file. [Neil Cook]
Fix to issue #152 - User/Custom config.py file. [Neil Cook]
Fix to issue #152 - User/Custom config.py file. [Neil Cook]
Merge pull request #177 from njcuk9999/master. [Neil Cook]

merge with master
Merge pull request #175 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #172 from njcuk9999/neil. [Neil Cook]

Neil
Merge pull request #153 from njcuk9999/francois. [Neil Cook]

Merge pull request #151 from njcuk9999/dev
Merge pull request #151 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #150 from njcuk9999/dev. [Neil Cook]

same?
Merge pull request #149 from njcuk9999/dev. [Neil Cook]

removed new constant (test)

0.1.0346 (2018-04-06)¶

Fix to issue #173 - Need a versioned text file. [Neil Cook]
Fix to issue #174 - License required. [Neil Cook]
Fixed call to python (was python3 now python) [Neil Cook]
Fix issue #170 - PYTHONPATH in installation - what happens if not defined? [Neil Cook]
Fix issue #170 - PYTHONPATH in installation - what happens if not defined? [Neil Cook]
Fix issue #170 - PYTHONPATH in installation - what happens if not defined? [Neil Cook]
Fix issue #170 - PYTHONPATH in installation - what happens if not defined? [Neil Cook]
Fix issue #170 - PYTHONPATH in installation - what happens if not defined? [Neil Cook]
Fix issue #170 - PYTHONPATH in installation - what happens if not defined? [Neil Cook]
Fix issue #165 - cal_extract plotting issue with bounding edges. [Neil Cook]
Fix issue #163 - cal_ff plot fit edges error. [Neil Cook]
Fix issue #161 - cal_SLIT plot wrong offse - offset is now corrected. [Neil Cook]
Fixed plots closing automatically in an interactive session –> now user is asked. [Neil Cook]
Fix to issue #159 - updated fix giving several allowed backends. [Neil Cook]
Fix to issue #159 - matplotlib plots freeze on macOSX. [Neil Cook]

0.1.0344 (2018-04-05)¶

Fixed typo in call to deal_with+prefixes (requires filename if p not defined) and fixed __NAME__ [Neil Cook]
Removed call to calibDB (note needed) [Neil Cook]
Added quick mention of startswith, contains and endswith method to documentation. [Neil Cook]
Added contains and endswith methods to ParamDict. [Neil Cook]
Moved blank recipe to spirouTools. [Neil Cook]
Wrote some generic tools: list raw/reduced/calib files (with filter), display calibDB (with date filter) [Neil Cook]
DRS reset moved to spirouTools. [Neil Cook]
Dependencies corrected and moved to SpirouTools. [Neil Cook]
Moved tools to separate package. [Neil Cook]
Updated change log with changes to calibdb. [Neil Cook]
Added quiet modes for run_begin and load_arguments. [Neil Cook]
CalibDB now also contains humantime and unixtime accessible from dictionary call. [Neil Cook]
Updated module descriptions (based on changes) [Neil Cook]
Fix of issue #156 - Parameter dictionary source dictionary not case insensitive. [Neil Cook]
Fix of issue #162 - cal_SLIT save TILT to file using Add1Dlist - slight change. [Neil Cook]
Fix of issue #162 - cal_SLIT save TILT to file using Add1Dlist. [Neil Cook]
Fix of issue #171 - fixed cal_validate_spirou –> cal_validate_spirou.py. [Neil Cook]
Fix of issue #168 - Documentation: chapter installation weird <PATH> variable #168. [Neil Cook]
Fix of issue #166 - cal_DRIFTPEAK should accept hc or fp. [Neil Cook]
Fix of issue #164 - cal_extract kind is incorrect. [Neil Cook]
Fix of issue #160 - too many decimal places in quality control - fixed. [Neil Cook]
Fix of issue #157 (Unix time doesn’t match human time for UT) bug was only in “fake” wave solution files. [Neil Cook]
Fixed Issue #154 (Installation type update to config.txt and constants_SPIROU.txt (now .py files) [Neil Cook]
Same? [Neil Cook]

0.1.0342 (2018-03-28)¶

Removed new constant (test) [Neil Cook]
Merge pull request #147 from njcuk9999/dev. [Neil Cook]

added new constant
Added new constant. [Neil Cook]
Merge pull request #146 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #145 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #144 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #143 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #142 from njcuk9999/dev. [Neil Cook]

Dev

0.1.034 (2018-03-25)¶

New unit test (not comp full run) [Neil Cook]
Updated date and version. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Added new test full run no compare. [Neil Cook]

0.1.033 (2018-03-22)¶

New example 7. [Neil Cook]
New example 6. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Updated versions and dates. [Neil Cook]
Moved examples to subfolder. [Neil Cook]
Moved examples to subfolder. [Neil Cook]
Moved examples to subfolder. [Neil Cook]
Moved examples to subfolder. [Neil Cook]
Moved examples to subfolder. [Neil Cook]
Moved examples to subfolder. [Neil Cook]
Spelling check. [Neil Cook]
Spelling check. [Neil Cook]
Spelling check. [Neil Cook]
Spelling check. [Neil Cook]
Updates to comments. [Neil Cook]
Spelling check. [Neil Cook]
Fixed error in call. [Neil Cook]
Updates to comments. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Update date and versions. [Neil Cook]
Spell check. [Neil Cook]
Spell check. [Neil Cook]
Spell check. [Neil Cook]
Spell check. [Neil Cook]
Spell check. [Neil Cook]
Page split. [Neil Cook]
Added parameters to record file. [Neil Cook]
Added return_filename for added functionality. [Neil Cook]
Improvements to telluric file - added header keys. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Updated edit date and versions. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]

0.1.032 (2018-03-19)¶

Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Corrected spelling. [Neil Cook]
Merge pull request #141 from njcuk9999/dev. [Neil Cook]

Dev
Examples 5 convert to html. [Neil Cook]
First commit - common python 3 functions different from old python 2. [Neil Cook]
Merge pull request #140 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #139 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #138 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #137 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #136 from njcuk9999/dev. [Neil Cook]

Dev

0.1.031 (2018-03-14)¶

Updated image size. [Neil Cook]
Update readme. [Neil Cook]

0.1.030 (2018-03-13)¶

Conversion to html. [Neil Cook]
First commit - using custom arguments. [Neil Cook]
Update date and version. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Updated date and version. [Neil Cook]
Updated docs for GetCustomFromRuntime function. [Neil Cook]
Added spacer. [Neil Cook]
Reformatted customargs (to be like cal_CCF) for consistency. [Neil Cook]
Example3 in html format. [Neil Cook]
First commit - the debugger. [Neil Cook]
Rerun code. [Neil Cook]

0.1.029 (2018-03-07)¶

Ipython notebooks converted to html. [Neil Cook]
First commit: ipython notebook example: “What is a parameter dictionary?” [Neil Cook]
First commit ipython notebook example1: “Calling recipes from python” [Neil Cook]
Added blank template file. [Neil Cook]
Updated date and version. [Neil Cook]
Modified read_config_file to be able to return just filename. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Set config_file name so sources are correct. [Neil Cook]
Updated date and version. [Neil Cook]
Set debug to 0. [Neil Cook]
Updated exit message. [Neil Cook]
Updated exit message. [Neil Cook]
Updated exit message. [Neil Cook]
Updated exit message. [Neil Cook]
Updated exit message. [Neil Cook]
Updated exit message. [Neil Cook]
Updated exit message. [Neil Cook]
Updated exit message. [Neil Cook]
Updated exit message. [Neil Cook]
Updated exit message. [Neil Cook]
Updated exit message. [Neil Cook]
Updated exit message. [Neil Cook]

0.1.028 (2018-03-06)¶

Added note about using texteidter and smart speechmarks. [Neil Cook]
Fixed importing issues. [Neil Cook]
Fixed importing issues. [Neil Cook]
Fixed importing issues. [Neil Cook]
Fixed importing issues. [Neil Cook]
Updated date and version. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated date and version. [Neil Cook]
Updated dependencies. [Neil Cook]
Added a test of text file having bad (illegal) characters (non letters, punctuation, whitespace, digits) as defined by python string module. [Neil Cook]
Added .bash_profile for mac install. [Neil Cook]
Added .bash_profile for mac install. [Neil Cook]
Test of bad characters. [Neil Cook]
Added a run time debug option and reformatted logging. [Neil Cook]
Merge remote-tracking branch ‘origin/master’ [Neil Cook]
Merge pull request #135 from njcuk9999/dev. [Neil Cook]

Merge pull request #134 from njcuk9999/master
Merge pull request #134 from njcuk9999/master. [Neil Cook]

sync
Merge pull request #133 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #132 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #131 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #130 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #129 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #128 from njcuk9999/dev. [Neil Cook]

pep8 fixes + suppress known-required exceptions
Merge pull request #127 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #126 from njcuk9999/dev. [Neil Cook]

Dev - confirm docs built and code runs
Merge pull request #125 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #124 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #123 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #122 from njcuk9999/dev. [Neil Cook]

major changes to code
Merge pull request #121 from njcuk9999/dev. [Neil Cook]

Dev
Updated unit test - py2 error is valueerror not importerror. [Neil Cook]
Updated unit test - py2 error is valueerror not importerror. [Neil Cook]
Updated unit test - py2 error is valueerror not importerror. [Neil Cook]
Updated unit test - py2 error is valueerror not importerror. [Neil Cook]

0.1.027 (2018-03-01)¶

Rebuilt pdfs. [Neil Cook]
Updated tabbing in TOC. [Neil Cook]
Updated versions and dates. [Neil Cook]
Modified initial_file_setup to include a “contains” keyword, to make sure all files (arg_file_names) contain this substring if contains is not None. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Added description. [Neil Cook]
Added chagnes to initial_file_steup. [Neil Cook]
Added placeholder sections and added setup and exit sections. [Neil Cook]
Modified recipe description. [Neil Cook]
Modified recipe description. [Neil Cook]
Modified recipe description. [Neil Cook]
Modified recipe description. [Neil Cook]
Modified recipe description. [Neil Cook]
Modified recipe description. [Neil Cook]
Modified recipe description. [Neil Cook]
Modified recipe description. [Neil Cook]
Modified recipe description. [Neil Cook]
Modified recipe description. [Neil Cook]
Modified recipe description. [Neil Cook]
Updated pep8 fixes + added sys info. [Neil Cook]
Updated display_title and display_system_info doc strings. [Neil Cook]
Added DisplayTitle and DisplaySysInfo aliases in __init__ [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated dependencies with python versions. [Neil Cook]
Added DisplayTitle and DisplaySysInfo to spirouStartup public functions. [Neil Cook]
Twaeked import. [Neil Cook]

0.1.026 (2018-02-27)¶

Changed printing in function + added warning that user will reset all processed files. [Neil Cook]
Changed printing in function. [Neil Cook]
Changed display_title function. [Neil Cook]
Modified printlog function and added printcolour function. [Neil Cook]
Added printlog and printcolour aliases. [Neil Cook]
Added dependencies and updated latest versions of py modules. [Neil Cook]
Added printlog and printcolour functions. [Neil Cook]
Tweaked display title. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Fixed bug: set_souce -> set_source. [Neil Cook]
Updated date and version. [Neil Cook]
Minor text change. [Neil Cook]
Corrected cal_loc example and call. [Neil Cook]
Update date and version. [Neil Cook]
Add get_folder_name function and fix file name of comparison results file (name it by input program) [Neil Cook]
Update test comparison dir. [Neil Cook]
Update test comparison dir. [Neil Cook]
Same? [Neil Cook]
First commit - get dependencies for the drs (and current versions) [Neil Cook]
Added source to arg_file_names, nbframes and fitsfilename. [Neil Cook]
Corrected BIG bug (NBframes not redefined when arg_file_names redefined) [Neil Cook]
Corrected error statement (format missing) [Neil Cook]
Support astropy < 2.0.1 bug in astro.io.fits hdu.scale (this fixes it) [Neil Cook]
Updated plot imshow should not take True and False array (convert to ints) [Neil Cook]
Removed use of tqdm (unnecessary dependency) [Neil Cook]
Added new page preak for TOC. [Neil Cook]
Example - slight change to format. [Neil Cook]

0.1.025 (2018-02-26)¶

Small fixes to refix pep8 across module/suppressing known and required pep8 exceptions. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes + doc strings. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Updated date and version. [Neil Cook]
Added summary of properties and graphs section. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]
Pep8 fixes. [Neil Cook]

0.1.024 (2018-02-23)¶

Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Cal ccf figure 3. [Neil Cook]
Cal ccf figure 2. [Neil Cook]
Cal ccf figure 1. [Neil Cook]
First commit of cal ccf recipe doc (unfinished) [Neil Cook]
Updated reffile to e2ds file. [Neil Cook]
Updated date and version. [Neil Cook]
First commit - new faster version of telluric mask generation - using polyderivatives. [Neil Cook]
Updated telluric 2d mask. [Neil Cook]
Updated date and version. [Neil Cook]
Added ccf filenames to variables. [Neil Cook]
Added calccf recipe to inputs. [Neil Cook]
Changed reffile to e2dsfile. [Neil Cook]
Take some things out loop to speed up. [Neil Cook]
Fixes to tilt above and below central fit (untested) [Neil Cook]
Moved setting of fitsfilename and arg_file_names (when files is not None) to a separate function to deal with run time vs call. [Neil Cook]
Moved some constants outside a loop. [Neil Cook]
Added cal driftpeak figure. [Neil Cook]
Added cal driftpeak figure. [Neil Cook]
Added cal driftpeak figure. [Neil Cook]
Added cal driftpeak figure. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated the versions and date. [Neil Cook]
Updated the versions and date. [Neil Cook]
Updated examples and interactive mode figures. [Neil Cook]

0.1.023 (2018-02-21)¶

Cal drift raw plot files for docs. [Neil Cook]
Cal drift raw plot files for docs. [Neil Cook]
Cal drift e2ds plot files for docs. [Neil Cook]
Cal drift e2ds plot files for docs. [Neil Cook]
First commit - cal drift recipe (unfinished) [Neil Cook]
Updated quick todo list. [Neil Cook]
Moved the arg_file_name/fitsfilename setting when we have custom args to after we read from runtime. [Neil Cook]
Updated date and versions. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated date and versions. [Neil Cook]
Added drift filenames. [Neil Cook]
Updated todo list. [Neil Cook]
Input the caldrift section. [Neil Cook]
Fix for loadcalibdb. [Neil Cook]
Fix for loadcalibdb. [Neil Cook]

0.1.022 (2018-02-20)¶

Major changes to code. [Neil Cook]

0.1.021 (2018-02-19)¶

Rebuilt pdfs. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Added extract figure. [Neil Cook]
Added extract figure. [Neil Cook]
Added extract figure. [Neil Cook]
First commit of verify recipe section. [Neil Cook]
First commit of extract recipe section. [Neil Cook]
Added ReadBlazeFile. [Neil Cook]
Updated doc strings and minor code fixes (for no header in writeimage) [Neil Cook]
Updated date and versions. [Neil Cook]
Added function to convert waveimage to interpretted spectrum. [Neil Cook]
Updated date and version. [Neil Cook]
Added extract file variables. [Neil Cook]
Changed order + added input for extract and validate. [Neil Cook]
Changes to example code run. [Neil Cook]
Changes to example code run. [Neil Cook]
Fixed cmdbox typo. [Neil Cook]
Changed some doc strings. [Neil Cook]
Changed comment. [Neil Cook]

0.1.020 (2018-02-16)¶

Update README.md. [Neil Cook]
Merge pull request #120 from njcuk9999/dev. [Neil Cook]

Dev - confirmed tested and all run
Rebuilt pdfs. [Neil Cook]
Added current default files (for reset) [Neil Cook]
First commit - a reset switch - setting DRS back to default. [Neil Cook]
Added mainfitsdir for when we are using custom arguments, resorted functions, added get_custom_arg_files_fitsfilename to deal with setting arg_file_names and fitsfilename with custom arguments. [Neil Cook]
Fixed problem with plot (wave_ll only for CCF - so use x instead) normally want “wave” [Neil Cook]
Moved log_file_name getting to constants file. [Neil Cook]
Added log_file_name to constants. [Neil Cook]
Fixed bug for arg_file_names from custom args. [Neil Cook]
Updated doc string. [Neil Cook]
Added mainfitsdir for custom loadarguments. [Neil Cook]
Merge pull request #119 from njcuk9999/dev. [Neil Cook]

Dev
Rebuilt pdf. [Neil Cook]
Readded cal_slit plots for interactive sessions (accidentally overwritten) [Neil Cook]
Readded cal_FF_raw plots for interactive sessions. [Neil Cook]
Added cal_FF_raw plots for interactive sessions. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Added cal_FF_raw file definitions. [Neil Cook]
Updated cal_FF_raw change log. [Neil Cook]
Fixed errors in default recipe. [Neil Cook]
Added paths for example files, fixed example run. [Neil Cook]
Added paths for example files. [Neil Cook]
Added all sections (previously empty) [Neil Cook]
Added paths for example files. [Neil Cook]
Added path for example file. [Neil Cook]
Updated date and version. [Neil Cook]
Updated date and version. [Neil Cook]
Replace use of log_opt (not valid in load_arguments) with DPROG (Defaults to sys.argv[0]) [Neil Cook]
Renamed GetKwValues to GetKeywordValues. [Neil Cook]
Renamed GetKwValues to GetKeywordValues. [Neil Cook]
Renamed GetKwValues to GetKeywordValues. [Neil Cook]
Added blaze to calibDB. [Neil Cook]
Merge pull request #118 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #117 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #116 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #115 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #114 from njcuk9999/dev. [Neil Cook]

Dev - confirmed untested
Merge pull request #113 from njcuk9999/dev. [Neil Cook]

Dev - confirmed docs only and docs build
Merge pull request #112 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #111 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #110 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #109 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #108 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #107 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #106 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #105 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #104 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #103 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #102 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #101 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #100 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #99 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #98 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #97 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #96 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #95 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #94 from njcuk9999/dev. [Neil Cook]

added test data link
Merge pull request #93 from njcuk9999/dev. [Neil Cook]

link to logo change

0.1.019 (2018-02-15)¶

Corrected need for mainfitsfile to define arg_file_names and fitsfilename. [Neil Cook]
Corrected doc string typo. [Neil Cook]
Added return_header/return_shape options to readdata function, corrected readrawdata function. [Neil Cook]
First commit of telluric mask file (currently a pseudo-recipe) [Neil Cook]
Updated doc strings. [Neil Cook]
Changed typo and updated some doc strings. [Neil Cook]
Fixed needing mainfitsfile for custom files. [Neil Cook]
Fixed needing mainfitsfile for custom files. [Neil Cook]
Updated edit date and version. [Neil Cook]
Updated edit date and version. [Neil Cook]
Added calff. [Neil Cook]
First commit - blank cal_ff recipe. [Neil Cook]
Added package descriptions (from CTAN) [Neil Cook]
Updated keys (missed order_profile) [Neil Cook]

0.1.018 (2018-02-14)¶

Cal_slit graphs. [Neil Cook]
Cal_slit graphs. [Neil Cook]
Cal_slit graphs. [Neil Cook]
First commit - recipe for cal_slit_spirou. [Neil Cook]
Added labels to slit plot (were missed before) [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated date and version info. [Neil Cook]
Updated date and version info. [Neil Cook]
Commented TOC separator (may use later to clean up) [Neil Cook]
Removed TOC separator. [Neil Cook]
Removed use of caption in favour of capt-of (screwdriver vs hammer) [Neil Cook]
Added some named labels, fixed typo namdlabels –> namedlabels. [Neil Cook]
Added calslit include. [Neil Cook]
Added labels to sections. [Neil Cook]
Corrected errors in windows sections (ref links) [Neil Cook]
Addede Interactive mode section. [Neil Cook]
Fixed program call typo and ref to calDARK. [Neil Cook]
Fixed subsection title and some paths. [Neil Cook]

0.1.017 (2018-02-13)¶

Cal loc figures. [Neil Cook]
Windows environment figures. [Neil Cook]
Display system info, moved header bar to a constant. [Neil Cook]
Modified logger to accept printonly and logonly inputs. [Neil Cook]
Updated version and date. [Neil Cook]
Changed the windows installation section. [Neil Cook]
Rebuild pdf. [Neil Cook]
Modified end of code section to reflect changes. [Neil Cook]
Modified doc string for logger. [Neil Cook]
Updated shebang, added exit_script dealing with interactive sessions in __main__ call. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]
Updated shebang. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]
Updated shebang and __main__ exiting. [Neil Cook]

0.1.016 (2018-02-12)¶

Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated date and versions. [Neil Cook]
Updated date and versions. [Neil Cook]
Fix for only one file name in readimage_and_combine. [Neil Cook]
Changed rawfits to orderpfile (name change) [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Change back to doc class comment. [Neil Cook]
Change to doc class? [Neil Cook]
Made cmdboxprintspecial breakable. [Neil Cook]
Added some named labels and some new file names. [Neil Cook]
Input calloc. [Neil Cook]
Edited receipe. [Neil Cook]
Edited receipe. [Neil Cook]
Edited receipe. [Neil Cook]
Edited receipe. [Neil Cook]

0.1.015 (2018-02-09)¶

Rebuilt pdfs. [Neil Cook]
Moved calibration database loading to separate function (for custom arg recipes), tweaked functions accordingly, added getting of multi arguments (as last param) + wrapper around get_file (get_files) [Neil Cook]
Added new aliases. [Neil Cook]
Tweaked readimage_and_combine and math_controller to be more generic. [Neil Cook]
Removed Config Error from messages (shouldn’t be an error unless error=error) [Neil Cook]
Added to custom arg section + added setup summary. [Neil Cook]
Added/edited section. [Neil Cook]
Rewrote section. [Neil Cook]
Edited/updated doc strings. [Neil Cook]
Edited/updated doc strings. [Neil Cook]
Designed basic layout (setup + sections) [Neil Cook]
Updated ghost template. [Neil Cook]
Added loading of calibDB. [Neil Cook]
Update date and version numbers. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Updated TILT and WAVE fixes (with todo) [Neil Cook]
Updated todolist. [Neil Cook]
Added indents to minipages, added alias/internal function definition. [Neil Cook]
Added titles to some code boxes. [Neil Cook]
Added titles to some code boxes. [Neil Cook]
Added titels to some code boxes, changes paths for print outputs. [Neil Cook]
Added some new packages to dependencies, added that custom args can be added to code boxes. [Neil Cook]
Added recipe and module reference sections and some titles for calibDB text file examples. [Neil Cook]
Changed a bashbox to a cmdbox. [Neil Cook]
Added example of addition to calibration database. [Neil Cook]
Updated indentation of minipages. [Neil Cook]
Updated indentation of minipages. [Neil Cook]
Updated indentation of minipages. [Neil Cook]
Updated indentation of minipages. [Neil Cook]
Updated indentation of minipages. [Neil Cook]
Updated indentation of minipages. [Neil Cook]
Updated indentation of minipages. [Neil Cook]
Updated indentation of minipages. [Neil Cook]
Updated indentation of minipages. [Neil Cook]
Updated indentation of minipages. [Neil Cook]
Updated indentation of minipages. [Neil Cook]
Updated indentation of minipages. [Neil Cook]

0.1.014 (2018-02-07)¶

First commit - move recipe to individual file. [Neil Cook]
First commit - move recipe to individual file. [Neil Cook]
First commit - move recipe to individual file. [Neil Cook]
First commit - move recipe to individual file. [Neil Cook]
First commit - move recipe to individual file. [Neil Cook]
Updated date and version. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated date and version. [Neil Cook]
Updated the highlight parameters for doc string. [Neil Cook]
Moved individual recipes to indivudal files. [Neil Cook]

0.1.013 (2018-02-06)¶

First commit module description for thorca. [Neil Cook]
First commit module description for startup. [Neil Cook]
Updated doc strings with p and loc descriptions. [Neil Cook]
Updated doc strings with p and loc descriptions. [Neil Cook]
Updated doc strings with p and loc descriptions. [Neil Cook]
Updated wave to wave_ll. [Neil Cook]
Rebuild pdf. [Neil Cook]
Added startup and THORCA. [Neil Cook]
Added doc strings to RV tex file. [Neil Cook]
Changed wave to wave_ll in loc. [Neil Cook]

0.1.012 (2018-02-05)¶

Added spirouRV and spirouTHORCA imports to init. [Neil Cook]
Started updating doc strings (p and loc) [unfinished] [Neil Cook]
Started updating doc strings (p and loc) [unfinished] [Neil Cook]
Updated date and version. [Neil Cook]
Started module writing (incomplete) [Neil Cook]
Rebuilt pdf. [Neil Cook]
Added inputs. [Neil Cook]
Updated imports. [Neil Cook]
Removed unneeded comment for alias. [Neil Cook]
Modified some doc strings. [Neil Cook]
Refactored “imageLocSuperimp” –> “ImageLocSuperimp” [Neil Cook]
Modified comments for several functions (more concise) [Neil Cook]
Modified doc_string for writeimage. [Neil Cook]
Modified doc_string for warninglogger. [Neil Cook]
Added to __all__ [Neil Cook]
Modified get_keywords doc_string. [Neil Cook]
Added doc strings for ConfigError methods. [Neil Cook]
First commit - added doc strings + sub-module func descriptions (based on spirouBLANK.tex) [Neil Cook]
First commit - added doc strings + sub-module func descriptions (based on spirouBLANK.tex) [Neil Cook]
First commit - added doc strings + sub-module func descriptions (based on spirouBLANK.tex) [Neil Cook]
First commit - added doc strings + sub-module func descriptions (based on spirouBLANK.tex) [Neil Cook]
First commit - added doc strings + sub-module func descriptions (based on spirouBLANK.tex) [Neil Cook]
First commit - added doc strings + sub-module func descriptions (based on spirouBLANK.tex) [Neil Cook]
Rebuilt pdf. [Neil Cook]
Changed subsection and section size in nav bar menu. [Neil Cook]
Added spirouCore and spirouFLAT to constants , modified paths for WLOG, ParamDict and ConfigError (to module file) [Neil Cook]
Added blue to the special cmd colours. [Neil Cook]
Added introduction. [Neil Cook]
Added doc strings. [Neil Cook]
Changed default module tex file template. [Neil Cook]
Refactor imageLocSuperimp –> ImageLocSuperimp. [Neil Cook]

0.1.011 (2018-02-02)¶

First commit - module tex file. [Neil Cook]
First commit - module tex file. [Neil Cook]
First commit - module tex file. [Neil Cook]
First commit - module tex file. [Neil Cook]
Edited doc string. [Neil Cook]
Rebuild pdf. [Neil Cook]
Changed size of subsubsection. [Neil Cook]
Added new package. [Neil Cook]
Added docstring tcbox. [Neil Cook]
Changing format input module tex files. [Neil Cook]
Updated doc strings with parameter dictionary descriptions. [Neil Cook]
Updated doc strings with parameter dictionary descriptions. [Neil Cook]
Updated date and version. [Neil Cook]
Rebuild pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Updated latest edit and version. [Neil Cook]
Updated some constants descriptions. [Neil Cook]

0.1.010 (2018-02-01)¶

Updated doc strings with parameter dictionary descriptions. [Neil Cook]
Updated doc strings with parameter dictionary descriptions. [Neil Cook]
Rebuild pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Updated date and version. [Neil Cook]
Updated date and version. [Neil Cook]
Add res to loc (for debug_locplot_fit_residual) [Neil Cook]
Update doc string (p and loc) [Neil Cook]
Update doc string (p and loc) [Neil Cook]
Update doc string (p and loc) [Neil Cook]
Updated doc strings. [Neil Cook]
Update doc string (p and loc) [Neil Cook]

0.1.009 (2018-01-31)¶

Updated doc strings. [Neil Cook]
Updated doc strings. [Neil Cook]
Updated doc strings. [Neil Cook]
Removed doc strings + added __all__ functions. [Neil Cook]
Removed doc strings. [Neil Cook]
Removed doc strings. [Neil Cook]
Removed doc strings. [Neil Cook]
Removed doc strings. [Neil Cook]
Removed doc strings. [Neil Cook]
Removed doc strings. [Neil Cook]
Removed doc strings. [Neil Cook]
Removed doc strings. [Neil Cook]
Removed doc strings. [Neil Cook]
Removed doc strings. [Neil Cook]
Removed doc strings. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Updated date and version. [Neil Cook]
Updated todo list. [Neil Cook]
Cosmetic change to comment. [Neil Cook]

0.1.008 (2018-01-30)¶

Added spacing. [Neil Cook]
Edit of doc string (unfinished) [Neil Cook]
Create DEFAULT_LOG_OPT() from sys.argv[0] [Neil Cook]
Replace sys.argv[0] in logs with spirouConfig.Constant.DEFAULT_LOG_OPT() [Neil Cook]
Added doc strings, moved gaussian function and added some error handling. [Neil Cook]
Moved gaussian function here. [Neil Cook]
Added doc strings. [Neil Cook]
Added doc strings. [Neil Cook]
Corrected error “mean_background” –> “mean_backgrd” [Neil Cook]
Updated back to my data folder. [Neil Cook]
Rebuild pdfs. [Neil Cook]
Updated version. [Neil Cook]
Updated doc_strings and error handling. [Neil Cook]
Updated doc_strings and error handling. [Neil Cook]
Updated doc_strings. [Neil Cook]
Updated version and date. [Neil Cook]
Updated version and date. [Neil Cook]
Added badpix_norm_percentile constant constant. [Neil Cook]
Added badpix_norm_percentile constant constant. [Neil Cook]

0.1.007 (2018-01-29)¶

Rebuild pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Updated versions + dates. [Neil Cook]
Updated versions + dates. [Neil Cook]
Updated versions + dates. [Neil Cook]
Doc strings and error handling (unfinished) [Neil Cook]
Doc strings and error handling (unfinished) [Neil Cook]
Doc strings and error handling. [Neil Cook]
Updated doc strings [unfinished] [Neil Cook]

0.1.006 (2018-01-26)¶

Added test help file - for cal_DARK_spirou. [Neil Cook]
Updated todo list with help files that are needed. [Neil Cook]
Update doc strings. [Neil Cook]
Update doc string. [Neil Cook]
Update doc strings + help file management. [Neil Cook]
Update doc strings. [Neil Cook]
Update doc strings. [Neil Cook]
Update doc strings. [Neil Cook]
Update doc strings, remove __main__ [Neil Cook]
Update doc strings. [Neil Cook]
Update doc strings. [Neil Cook]
Update doc strings. [Neil Cook]
Update doc. [Neil Cook]
Rebuild pdfs. [Neil Cook]
Update todo list with man files need writing. [Neil Cook]
Modified MANUAL FILE (corrected) [Neil Cook]
Updated date and version. [Neil Cook]
Rebuild pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Updated the date and version numbers. [Neil Cook]
Added/corrected some cal drift variables. [Neil Cook]
Added descriptions. [Neil Cook]
Added doc string for sPlt. [Neil Cook]
Added constant for drift peak. [Neil Cook]
Fixed plotting function calls. [Neil Cook]
Updated descriptions (UNFINISHED) [Neil Cook]
Updated descriptions and unix/string time getting. [Neil Cook]
Updated descriptions and unix/string time getting. [Neil Cook]
Added doc strings + math time functions. [Neil Cook]
Added more formats (defaults + log), removed main code. [Neil Cook]
Updated config error. [Neil Cook]
Updated descriptions and unix/string time getting. [Neil Cook]

0.1.005 (2018-01-24)¶

Update versions + date. [Neil Cook]
Rebuild pdfs. [Neil Cook]
Version + date update. [Neil Cook]
Updated __all__ [Neil Cook]
Added to warninglogger (funcname), changed end card colour. [Neil Cook]
Added warnlog alias. [Neil Cook]
Better error handling + reporting. [Neil Cook]
Better error handling + reporting. [Neil Cook]
Better error handling + reporting. [Neil Cook]
Better error handling + reporting. [Neil Cook]
Better error handling. [Neil Cook]
Doc strings added. [Neil Cook]
Doc strings added. [Neil Cook]
Warnings added, better error handling. [Neil Cook]
Update of code. [Neil Cook]
Config param change (debug mode active) [Neil Cook]
Submodule clean up and doc string writing. [Neil Cook]
First commit of quick install guide. [Neil Cook]
Added DARK_CUTLIMIT to keyword used variables, added a hack to avoid not having config file ICDP_NAME (will complain elsewhere) [Neil Cook]
Added DARK_CUTLIMIT to keyword used variables, added a hack to avoid not having config file ICDP_NAME. [Neil Cook]
Added logic for quick install guide (false) [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Fixed installDIR. [Neil Cook]
Sorted out environment paths. [Neil Cook]
Sorted out environment paths. [Neil Cook]
Fixed debug mode. [Neil Cook]
Fixed comment. [Neil Cook]
Fixed init __all__ call. [Neil Cook]
Editted log to print message even if we cannot log to file. [Neil Cook]
Updated version and latest edit date. [Neil Cook]
Added additional way to read config file (slow using python open) or give good error message if cannot open. [Neil Cook]
Allowed ConfigError “message” to take list as input. [Neil Cook]
Streamlined config strings. [Neil Cook]
Streamlined config strings. [Neil Cook]
Fixed error with DRS_NAME, DRS_VERSION. [Neil Cook]

0.1.004 (2018-01-22)¶

Added test data link. [Neil Cook]
Link to logo change. [Neil Cook]
Merge pull request #92 from njcuk9999/dev. [Neil Cook]

Merge pull request #91 from njcuk9999/master
Merge pull request #91 from njcuk9999/master. [Neil Cook]

merge
Merge remote-tracking branch ‘origin/master’ [Neil Cook]
Merge pull request #90 from njcuk9999/dev. [Neil Cook]

Merge pull request #89 from njcuk9999/master
Merge pull request #89 from njcuk9999/master. [Neil Cook]

master to dev
Rebuilt pdfs. [Neil Cook]
Updated version. [Neil Cook]
Added spacing to constants. [Neil Cook]
Changed the cmd code boxes. [Neil Cook]
Added a general section. [Neil Cook]
Removed definevariablecmd variables. [Neil Cook]
Added some namedlabels. [Neil Cook]
Fixed typo in log message. [Neil Cook]
Updated readme. [Neil Cook]
Updated date and rebuilt. [Neil Cook]
Added quick install chapter. [Neil Cook]
Updated date + version. [Neil Cook]
Rebuild pdfs. [Neil Cook]
Updated version. [Neil Cook]
Unchanged. [Neil Cook]
Updated dirs. [Neil Cook]
Fixed errors. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated log colourring. [Neil Cook]
Updated paths. [Neil Cook]
Added readme files. [Neil Cook]
Added example data readme files. [Neil Cook]
Added calibDB minimum files. [Neil Cook]
Restructure of drs file. [Neil Cook]
Merge pull request #88 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #87 from njcuk9999/dev. [Neil Cook]

Merge pull request #86 from njcuk9999/master
Rebuilt pdfs. [Neil Cook]
Updated version. [Neil Cook]
Added spacing to constants. [Neil Cook]
Changed the cmd code boxes. [Neil Cook]
Added a general section. [Neil Cook]
Removed definevariablecmd variables. [Neil Cook]
Added some namedlabels. [Neil Cook]
Fixed typo in log message. [Neil Cook]
Updated readme. [Neil Cook]
Updated date and rebuilt. [Neil Cook]
Added quick install chapter. [Neil Cook]
Updated date + version. [Neil Cook]
Rebuild pdfs. [Neil Cook]
Updated version. [Neil Cook]
Unchanged. [Neil Cook]
Updated dirs. [Neil Cook]
Fixed errors. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated log colourring. [Neil Cook]
Updated paths. [Neil Cook]
Added readme files. [Neil Cook]
Added example data readme files. [Neil Cook]
Added calibDB minimum files. [Neil Cook]
Restructure of drs file. [Neil Cook]
Updated version and date. [Neil Cook]
Updated version and date. [Neil Cook]
Merge pull request #86 from njcuk9999/master. [Neil Cook]

merge

0.1.003 (2018-01-16)¶

Update README.md. [Neil Cook]
Merge pull request #85 from njcuk9999/dev. [Neil Cook]

Dev - confirmed update
Updated to alpha 0.1. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated to alpha 0.1. [Neil Cook]
Merge pull request #84 from njcuk9999/dev. [Neil Cook]

rotated speed table + rebuild pdf
Rotated speed table + rebuild pdf. [Neil Cook]
Merge pull request #83 from njcuk9999/dev. [Neil Cook]

Dev - confirmed doc + version updates
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated python module versions. [Neil Cook]
Updated readme (quick manual out of date and useless - use pdfs) [Neil Cook]
Updated dates and version. [Neil Cook]
Updates architecture. [Neil Cook]
Merge pull request #82 from njcuk9999/dev. [Neil Cook]

Dev - confirmed testing and doc
Cal_ccf fitting difference graph. [Neil Cook]
Cal_dark graph 3. [Neil Cook]
Cal_dark graph 2. [Neil Cook]
Cal_dark graph 1. [Neil Cook]
Changed reporting of errors to “differences” [Neil Cook]
First commit unit test including all current recipes (with comparison) + cal_drift_raw and cal_driftpeak_e2ds. [Neil Cook]
Updated name of unit test 3. [Neil Cook]
Updated name of unit test 2. [Neil Cook]
Added new and old methods for calulating badpix normalisation constant (for testing purposes) [Neil Cook]
Changed location of TOC page break. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Commented conflicting text (do not use memoir captions) [Neil Cook]
Added new packages. [Neil Cook]
Added new constants. [Neil Cook]
Added named labels to some constants. [Neil Cook]
Added calibdb section (unfinished) [Neil Cook]
Updated todo list. [Neil Cook]
Added caldark to recipes. [Neil Cook]
Updated versions. [Neil Cook]
Updated change log and moved around sections. [Neil Cook]
Updated imports in placeholder file. [Neil Cook]
Updated imports in placeholder file. [Neil Cook]
Added reffilename to paramdict. [Neil Cook]
Added to log printing in qc. [Neil Cook]
Allowed norm median flat to be old or new method. [Neil Cook]
Merge pull request #81 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #80 from njcuk9999/dev. [Neil Cook]

Dev - confirmed run and tested
Merge pull request #79 from njcuk9999/dev. [Neil Cook]

Dev - confirmed doc changes
Merge pull request #78 from njcuk9999/dev. [Neil Cook]

Dev - confirmed - cal_ccf now runs
Merge pull request #77 from njcuk9999/dev. [Neil Cook]

Dev - confirmed changes
Merge pull request #76 from njcuk9999/dev. [Neil Cook]

Dev - confirmed tested
Merge pull request #75 from njcuk9999/dev. [Neil Cook]

Dev - confirmed run
Merge pull request #74 from njcuk9999/dev. [Neil Cook]

Dev - confirmed untested
Merge pull request #73 from njcuk9999/dev. [Neil Cook]

Dev - confirmed cal_ccf completed but not tested
Merge pull request #72 from njcuk9999/dev. [Neil Cook]

Dev - confirmed cal_CCF stuff
Merge pull request #71 from njcuk9999/dev. [Neil Cook]

Dev - confirmed unfinished and untested
Merge pull request #70 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #69 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #68 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #67 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #66 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #65 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #64 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #63 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #62 from njcuk9999/dev. [Neil Cook]

Dev - confirmed checked for consistency and that codes run
Merge pull request #61 from njcuk9999/dev. [Neil Cook]

Dev - confirmed cal_drift_e2ds not working
Merge pull request #60 from njcuk9999/dev. [Neil Cook]

Dev - confirmed untested cal_badpix
Merge pull request #59 from njcuk9999/dev. [Neil Cook]

Dev - confirmed pdf build
Merge pull request #58 from njcuk9999/dev. [Neil Cook]

Dev - documentation edits: confirm pdf builds
Merge pull request #57 from njcuk9999/dev. [Neil Cook]

readme link update
Merge pull request #56 from njcuk9999/dev. [Neil Cook]

doc change - pdfs build correctly
Merge pull request #55 from njcuk9999/dev. [Neil Cook]

image change
Merge pull request #54 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #53 from njcuk9999/dev. [Neil Cook]

added pdf manuals to readme
Merge pull request #52 from njcuk9999/dev. [Neil Cook]

added pdf manuals to readme
Merge pull request #51 from njcuk9999/dev. [Neil Cook]

Dev - confirmed documentation and cosmetic changes only
Merge pull request #50 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #49 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #48 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #47 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #46 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #45 from njcuk9999/dev. [Neil Cook]

Added latex gitignore
Merge pull request #44 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #43 from njcuk9999/dev. [Neil Cook]

updated links in table of contents
Merge pull request #42 from njcuk9999/dev. [Neil Cook]

Dev
Delete fits2ramp.py. [eartigau]
Add files via upload. [eartigau]

latest version of fits2ramp
Merge pull request #41 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #40 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #39 from njcuk9999/dev. [Neil Cook]

Dev - confirm run
Merge pull request #38 from njcuk9999/dev. [Neil Cook]

Dev - confirmed cosmetic only
Merge pull request #37 from njcuk9999/dev. [Neil Cook]

Dev - confirm runs
Merge pull request #36 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #35 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #34 from njcuk9999/dev. [Neil Cook]

Dev - confirmed checked runs and consistency
Merge pull request #33 from njcuk9999/dev. [Neil Cook]

Dev - confirmed codes run + bug fixes are correct
Merge pull request #32 from njcuk9999/dev. [Neil Cook]

Dev - confirmed cosmetic nature - extract still not working (unfinished)
Merge pull request #31 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #30 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #29 from njcuk9999/dev. [Neil Cook]

readme update - confirmed
Merge pull request #28 from njcuk9999/dev. [Neil Cook]

confirmed consitency
Merge pull request #27 from njcuk9999/dev. [Neil Cook]

Confirm check of consistency
Merge pull request #26 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #25 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #24 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #23 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #22 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #21 from njcuk9999/dev. [Neil Cook]

added to general section, cal_dark section and cal_loc section
Merge pull request #20 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #19 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #18 from njcuk9999/dev. [Neil Cook]

confirmed runs and consistent
Merge pull request #17 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #16 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #15 from njcuk9999/dev. [Neil Cook]

cosmetic changes only - confirmed running
Merge pull request #14 from njcuk9999/dev. [Neil Cook]

Check runs and consistent (visually)
Merge pull request #13 from njcuk9999/dev. [Neil Cook]

checked they still run
Merge pull request #12 from njcuk9999/dev. [Neil Cook]

Tested consistency
Merge pull request #11 from njcuk9999/dev. [Neil Cook]

Confirmed still runs and same output
Merge pull request #10 from njcuk9999/dev. [Neil Cook]

Confirmed agrees with original code
Merge pull request #9 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #8 from njcuk9999/dev. [Neil Cook]

Tested and verified as consistent
Merge pull request #7 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #6 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #5 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #4 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #3 from njcuk9999/dev. [Neil Cook]

Dev
Merge pull request #2 from njcuk9999/dev. [Neil Cook]

push to master
Merge pull request #1 from njcuk9999/dev. [Neil Cook]

Commit to Master

0.1.002 (2018-01-12)¶

Updated progress. [Neil Cook]
Rebuilt pdf file. [Neil Cook]
Updated todo list. [Neil Cook]
Added fortran python conversion (for test purposes only) [Neil Cook]
Unignore fitgaus.so. [Neil Cook]
Added fitgaus.f (for test purposes only) [Neil Cook]
Added comparison + tests + nanstats in order to pass or fail found errors. [Neil Cook]
Set a threshold for order of magnitude difference (in comparison) [Neil Cook]
Added a test_fit_ccf to compare “fortran fit” with “python fit” [Neil Cook]
Cosmetic comment fix. [Neil Cook]
Added writeimage dtype fix. [Neil Cook]
Added kw_drs_QC keyword. [Neil Cook]
Cosmetic fixes. [Neil Cook]
Moved qc and fixed header bugs. [Neil Cook]
Fixed badpixelfits error. [Neil Cook]
Added logs. [Neil Cook]
Fixed header error. [Neil Cook]

0.1.001 (2018-01-11)¶

Updated progress. [Neil Cook]
Fixed list not appending. [Neil Cook]
First commit - comparison functions for old vs new test. [Neil Cook]
Added ability to test outputs. [Neil Cook]
Added aliases to utc. [Neil Cook]
Added fiber definition to fiber loop. [Neil Cook]
First commit unit_Test3 - testing the outputs. [Neil Cook]
Added output assignment to all unit tests. [Neil Cook]
Added output filename functions, reordered functions for better clarity. [Neil Cook]
Removed output filenaming to spirouConfig.spirouConst. [Neil Cook]
Removed output filenaming to spirouConfig.spirouConst. [Neil Cook]
Removed output filenaming to spirouConfig.spirouConst. [Neil Cook]
Removed output filenaming to spirouConfig.spirouConst. [Neil Cook]
Removed output filenaming to spirouConfig.spirouConst. [Neil Cook]
Removed output filenaming to spirouConfig.spirouConst. [Neil Cook]
Added a question re fiber type for wave file. [Neil Cook]
Updated version. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Modified date and version. [Neil Cook]
Added cdata_folder constant. [Neil Cook]
Added spirouTHORCA placeholder section. [Neil Cook]
Added cal_CCF section. [Neil Cook]

0.1.000 (2018-01-10)¶

Readded cal_CCF to unit test 2. [Neil Cook]
Moved UrNe.mas to data folder. [Neil Cook]
Added a locate_mask function - to local file if filename is not a valid path and found by os.path.exists, make ic_debug drs_debug==2. [Neil Cook]
Make ic_debug drs_debug==2. [Neil Cook]
Corrected typo in debug plot. [Neil Cook]
Added CDATA_FOLDER constant. [Neil Cook]
Added get_relative_folder function. [Neil Cook]
Added aliases to init. [Neil Cook]
Added removal of lockfile in generated error. [Neil Cook]
Make ic_debug drs_debug==2. [Neil Cook]
Rebuild pdf. [Neil Cook]
Added spaces to some commands. [Neil Cook]
Added listing style and tcolorbox to print out cmd prompt in colours red/yellow/green. [Neil Cook]
Added to variables. [Neil Cook]
Added to todo. [Neil Cook]
Added coloured log section. [Neil Cook]
Change log updated (ccf update needs doing) [Neil Cook]
Debug mode explained in comments. [Neil Cook]
Moved file. [Neil Cook]
Make ic_debug drs_debug==2. [Neil Cook]
Remove template logging (moved into spirouRv.GetCCFMask function. [Neil Cook]
Removed ic_debug and replaced with drs_debug. [Neil Cook]
Removed ic_debug (replaced with drs_debug) [Neil Cook]
Added an option in debug_start to allow no coloured text. [Neil Cook]
Changed order to allow reading of config file (to access certain parameters without running recipe) [Neil Cook]
First commit - config file reading (base level no drs imports allowed) [Neil Cook]
Moved config file reading to new code. [Neil Cook]
Removed ic_debug (now drs_debug) [Neil Cook]
Added input keyword chapter for user. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Removed devguide if statements. [Neil Cook]
Created named label command (to allow linking to individual text via phantom sections) [Neil Cook]
Changed label to namedlabel. [Neil Cook]
Changed label to namedlabel. [Neil Cook]
Removed typo. [Neil Cook]
Changed label to namedlabel. [Neil Cook]
Changed label to named label. [Neil Cook]
Made links to modules only for dev guide. [Neil Cook]
Modified variables. [Neil Cook]
Made most of input keywords section devguide only. [Neil Cook]
Removed ic_debug constant. [Neil Cook]
Added drs_debug and coloured_log constants. [Neil Cook]
Removed ic_debug and replaced with drs_debug. [Neil Cook]
Removed ic_debug and replaced with drs_debug. [Neil Cook]

0.0.048 (2018-01-09)¶

Fixed import and removed cal_CCF (problem with code) from unit tests. [Neil Cook]
Fixed import. [Neil Cook]
Reformatted multi-line error message. [Neil Cook]
Fixed comments. [Neil Cook]
Better dealing with calibDB file. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Overlhaul of define variable function. [Neil Cook]
Readded qc_max_signal, added calib_db_match constant. [Neil Cook]
Placeholder for cal_WAVE. [Neil Cook]
Placeholder for cal_HC. [Neil Cook]
Moved wave into fiber loop (now needs fiber) [Neil Cook]
Added calibdb prefix (from update to V48) [Neil Cook]

0.0.046 (2018-01-08)¶

Updated text for conversion from .txt to .py config files. [Neil Cook]
Added return_locals for debugging purposes. [Neil Cook]
Added aliases for unit_test_functions. [Neil Cook]
Added/modified renamed functions for setup, changed errors that span multiple lines to list argument for logger. [Neil Cook]
Added/modified renamed functions for setup. [Neil Cook]
Removed call to unused constant (update to V48) [Neil Cook]
Corrected change for update to V48. [Neil Cook]
Updated text for config files from .txt to .py conversion. [Neil Cook]
Allow list log messages, coloured log messages, and launch debugger in DEBUG mode on error. [Neil Cook]
Updated text for change of .txt config to .py. [Neil Cook]
Added colour levels and debug pseudo constants. [Neil Cook]
Fixed error with getting dictionaries from config files. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Added qc constants. [Neil Cook]
Converts to py file (but still read as text file) + added some qc constants. [Neil Cook]
Converts to py file (but still read as text file) [Neil Cook]
Moved exit function to top, changed startup alias. [Neil Cook]
Updated for V48 of old code. [Neil Cook]
Updated for V48 of old code. [Neil Cook]
Updated for V48 of old code. [Neil Cook]
Modified startup functions. [Neil Cook]
Modified startup functions. [Neil Cook]
Modified startup functions. [Neil Cook]
Modified startup functions. [Neil Cook]
Added date and release type to codes for modules. [Neil Cook]
Added date and release type to codes for recipes. [Neil Cook]
Rebuilt pdfs after variables changes. [Neil Cook]
Unit test 2 now uses unit_test_functions. [Neil Cook]
Unit test 1 now uses unit_test_functions. [Neil Cook]
Moved argument definitions of unit tests to functions file (can call from multiple files without having to update all) [Neil Cook]
Modified create_drift_file (V48 update) [Neil Cook]
Added fiber to ‘WAVE’ calib key (V48 update) [Neil Cook]
Added drift_peak_plot_llpeak_amps function (V48 update) [Neil Cook]
Added calib_prefix const function. [Neil Cook]
Updated descriptions of drift_peak variables. [Neil Cook]
Added and updated drift_peak constants. [Neil Cook]
Added ‘ALL’ fiber type option and error if fiber_type is not understood. [Neil Cook]
Updated to version 48 (untested) [Neil Cook]
Updated to version 48 (untested) [Neil Cook]

0.0.045 (2017-12-21)¶

Added coravelation and sub functions, added ccf fit functions and misc functions. [Neil Cook]
Added aliases for coravelation and fitccf. [Neil Cook]
Added ccf plots. [Neil Cook]
Added ccf keywords. [Neil Cook]
Added ccf table and fits pseudo constants. [Neil Cook]
Added ccf constants. [Neil Cook]
Unchanged. [Neil Cook]
Unchanged. [Neil Cook]
Unchanged. [Neil Cook]
Added correlation sections - code finished but untested. [Neil Cook]
What. [Neil Cook]

0.0.044 (2017-12-20)¶

Temporarily put mask in bin folder (where does it go?) [Neil Cook]
Corrected mistakes in get_e2ds_ll. [Neil Cook]
Added aliases for getll and getdll. [Neil Cook]
Added to coravelation function (not finished), added calculate_ccf function (not finished), added raw_correlbin function, added correlbin function (not finished) [Neil Cook]
Added to coravelation function (not finished), added calculate_ccf function (not finished), added raw_correlbin function, added correlbin function (not finished) [Neil Cook]
Fixed error in read_table (with colnames != None) [Neil Cook]
Added keyword. [Neil Cook]
Updated configerror error message. [Neil Cook]
Added constants. [Neil Cook]
Added data to loc. [Neil Cook]

0.0.043 (2017-12-19)¶

Need to finish code. [Neil Cook]
Redefined wave getting (GetE2DSll) and added a micron mask checking section. Code unfinished. [Neil Cook]
First commit added get_e2ds_ll, get_ll_from_coeffiecients, and get_dll_from_coefficients functions. [Neil Cook]
First commit added GetE2DSll alias. [Neil Cook]
Need to finish coravelation function. [Neil Cook]
Added get_ccf_mask function, added coravelation function (not finished) [Neil Cook]
Added to write_table, added read_table function, added update_docs function and call to function at end. [Neil Cook]
Modified read_wave_file. [Neil Cook]
Added ReadTable alias. [Neil Cook]
Added keywords to use list. [Neil Cook]
Added cal_CCF keywords (input from WAVE_AB) [Neil Cook]
Added GetKwValues alias to get_keyword_values_from_header. [Neil Cook]
Cosmetic changes to comments. [Neil Cook]

0.0.042 (2017-12-18)¶

First commit (similar to cal_drift_e2ds) – currently unfinished. [Neil Cook]
Modified get_custom_from_run_time_Args function (Added for function arguments) to allow more functionality, commented old function. [Neil Cook]
Added start of get_ccf_mask function (not finished) [Neil Cook]
Added alias to get_ccf_mask (GetCCFMask) [Neil Cook]
Added ability to define x and y in drift_plot_Selected_wave_ref. [Neil Cook]
Added two cal_CCF constants. [Neil Cook]
Added dividers between sections 2.7 - 2.10. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Updated progress. [Neil Cook]

0.0.041 (2017-12-14)¶

Rebuilt pdf. [Neil Cook]
Updated drift_peak_exp_width function calls. [Neil Cook]
Changed hardcoded width to width from constant in get_drift() [Neil Cook]
Rebuilt pdf. [Neil Cook]
Added TOC page divider. [Neil Cook]
Added caldriftpeak command. [Neil Cook]
Added drift peak section and constants. [Neil Cook]
Updated constants. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Deep copy on speref in create_drift_file function, other modifications to correct errors. [Neil Cook]
Corrected errors in drift_peak_plot_dtime_against_drift. [Neil Cook]
Added to change log. [Neil Cook]
Added drift-peak constants. [Neil Cook]
Fixes to cal_drift-peak - now works in gaussfit and non-gaussfit mode. [Neil Cook]

0.0.040 (2017-12-13)¶

Rebuild pdf. [Neil Cook]
Updated todo list. [Neil Cook]
Updated progress in readme. [Neil Cook]
Added drift-peak plot to documentation figures. [Neil Cook]
Added RV aliases. [Neil Cook]
Corrected some code, added warning catch, added sigma_clip function, added drift_per_order and drift_all_orders functions. [Neil Cook]
Added drift_peak plot, drift_plot_correlation_comp and working function. [Neil Cook]
Added drift_peak constants. [Neil Cook]
Cosmetic change to logging. [Neil Cook]
Cosmetic change to logging. [Neil Cook]
Added many sections (code finished - untested) [Neil Cook]

0.0.039 (2017-12-12)¶

Corrected cal_drift_e2ds test (file was wrong) [Neil Cook]
First commit - copy of cal_drift_e2ds - in process of modifying - not tested. [Neil Cook]
Added global c constant, added create_drift_file, gauss_function, remove_wide_peaks, remove_zero_peaks, get_drift, pearson_rtest functions (not tested) [Neil Cook]
Rearranged function aliases, added drift_peak function aliases. [Neil Cook]
Change MeasureMinMax function name. [Neil Cook]
Added append_source, append_sources, append_all methods to ParamDict. [Neil Cook]
Changed doc string of measure_box_min_max. [Neil Cook]
Added drift constants. [Neil Cook]
Change MeasureMinMax function name. [Neil Cook]
Change MeasureMinMax function name. [Neil Cook]
Cosmetic changes. [Neil Cook]
Cosmetic changes. [Neil Cook]

0.0.038 (2017-12-11)¶

Updated readme progress. [Neil Cook]
First commit unit test 2. [Neil Cook]
Updated latest edit date. [Neil Cook]
Updated todo list. [Neil Cook]
Removed unneeded comment. [Neil Cook]
Checked against old versions and updated edit date. [Neil Cook]
Checked against old versions and updated edit date. [Neil Cook]
Checked against old versions and updated edit date. [Neil Cook]
Checked against old versions and updated edit date. [Neil Cook]
Checked against old versions and updated edit date. [Neil Cook]
Checked against old versions and updated edit date. [Neil Cook]
Checked against old versions and updated edit date. [Neil Cook]
Checked against old versions and updated edit date. [Neil Cook]
Checked against old versions and updated edit date, added badpix key. [Neil Cook]
Checked against old versions and updated edit date. [Neil Cook]

0.0.037 (2017-12-08)¶

Rebuild pdfs. [Neil Cook]
Updated readme. [Neil Cook]
Updated readme. [Neil Cook]
Added description of some variables. [Neil Cook]
Added to changelog. [Neil Cook]
Fixed fibertype function (now got from constants) [Neil Cook]
Fixed bug with LOC_FILE not being used. [Neil Cook]
Added root to copy root keys - now works as supposed to (only copies keys with root not all keys) [Neil Cook]
Moved ww calc to function and calculating for all unique combinations (up to 4) of ww0 and ww1 (caused by rounding) [Neil Cook]
Added closeall funciton, modified ext and drift functions. [Neil Cook]
Changed root_drs keywords (now used in code) [Neil Cook]
Rebuild pdfs. [Neil Cook]
Updated date. [Neil Cook]
Rebuild pdf. [Neil Cook]
Added DRIFT-E2DS and changed rootdrs keywords. [Neil Cook]
Updated todo list. [Neil Cook]
Removed duplicate sections (i.e. drifts should all be in one section etc), renamed placeholder sections. [Neil Cook]
Added new extract and drift constants, added spacing. [Neil Cook]
Added new extract and drift keywords. [Neil Cook]
Added fiber_types, reworked extract and drift constants. [Neil Cook]
Added return locals. [Neil Cook]
Added return locals. [Neil Cook]
Added return locals. [Neil Cook]
Added return locals. [Neil Cook]
Added return locals, added extra input to make like old extractrawC. [Neil Cook]
Added return locals, added extra input to make like old extractrawAB. [Neil Cook]
Added return locals, fixed changes from old to new. [Neil Cook]
Added return locals, fixed minor differences. [Neil Cook]
Added return locals, fixed minor differences between old and new code. [Neil Cook]
Added return locals. [Neil Cook]
Returned locals. [Neil Cook]

0.0.036 (2017-12-07)¶

Added get_fiber_type function. [Neil Cook]
Added Get Fiber type function. [Neil Cook]
Modified get_all_similar_files. [Neil Cook]
Added readdata function and modified readimage, added read_flat_file function. [Neil Cook]
Added MakeTable and WriteTable to init. [Neil Cook]
Made sure we dont get filename unless we need it in get_acquision_time. [Neil Cook]
Added extra drift constants. [Neil Cook]
Updated. [Neil Cook]
First commit (no working) [Neil Cook]
Changed __main__ to main() in sources. [Neil Cook]
Updated readme with badpix section. [Neil Cook]
Corrected typo in wmed - in normalise_median_flat function (flat_median_width to badpix_flat_med_wid) [Neil Cook]
Corrected type (comma) in USE_KEYS. [Neil Cook]
Rebuild pdfs. [Neil Cook]
Added numbered pdf bookmarks + contents to bookmarks. [Neil Cook]
Added TOC commands to change spacing in TOC. [Neil Cook]
Added tocloft package. [Neil Cook]
Added calbadpix constant. [Neil Cook]
Added badpix section. [Neil Cook]
Updated todo section. [Neil Cook]
Added badpix section. [Neil Cook]
Added badpix section. [Neil Cook]
Added badpix constants. [Neil Cook]
Fixed badpixelfits construction. [Neil Cook]

0.0.035 (2017-12-06)¶

Moved unit_Test1 to unit test module. [Neil Cook]
First commit if unit test init file. [Neil Cook]
Modified run_time_custom_args (now works and tested), added get_custom_from_run_time_args and get_file functions, modified display_custom_args function. [Neil Cook]
Added GetCustomFromRuntime and GetFile aliases. [Neil Cook]
Added normalise_median_flux and locate_bad_pixel functions. [Neil Cook]
Added functionality to readimage. [Neil Cook]
Added LocateBadPixels and NormMedianFlat aliases. [Neil Cook]
Added badpix keywords. [Neil Cook]
Added startswith function to ParamDict. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Cosmetic changes to commenting. [Neil Cook]
Commented packages. [Neil Cook]
Updated to-do list. [Neil Cook]
Added placeholder module sections. [Neil Cook]
Added badpix constants. [Neil Cook]
Fixed Addkey not assigning to hdict. [Neil Cook]
First commit cal_BADPIX. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Added to question. [Neil Cook]
First commit to do list chapter. [Neil Cook]
First commit documentation chapter. [Neil Cook]
Added todolist and documentation chapters to main tex. [Neil Cook]
Added package ulem (For strikethrough) removed duplicate packages. [Neil Cook]
Removed visibility level from pseudoparamentry. [Neil Cook]
Added latexbox (and latexbox1) [Neil Cook]
Removed visibility level for pseudo code (should be all private) [Neil Cook]
Added new code sections. [Neil Cook]
Added latex code example. [Neil Cook]

0.0.034 (2017-12-05)¶

First commit of output_keywords chapter (filled and completed) [Neil Cook]
Added output_keywords chapter. [Neil Cook]
Rebuild pdf. [Neil Cook]
Added keyword aliases. [Neil Cook]
Added keywordentry command (similar to parmeterentry) [Neil Cook]
Added escaping to inline python text. [Neil Cook]
Added text. [Neil Cook]
Readme link update. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuild pdf. [Neil Cook]
Cosmetic change. [Neil Cook]
Added EXIT_LEVELS definition. [Neil Cook]
Changed exit vairable to log_exit_type. [Neil Cook]
Added main init paramdict commands and move mac command. [Neil Cook]
Changed title size to tiny. [Neil Cook]
Changed title size to tiny. [Neil Cook]
Modified sections. [Neil Cook]
Added section. [Neil Cook]
Removed sections added intro paragraph. [Neil Cook]

0.0.033 (2017-12-04)¶

Image change. [Neil Cook]
Image change. [Neil Cook]
Added pdf manuals to readme. [Neil Cook]
Added pdf manuals to readme. [Neil Cook]
Added pdf manuals to readme. [Neil Cook]
Added pdf manuals to readme. [Neil Cook]
Cosmetic changes only. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Removed .py from recipe command added more hskips for module commands. [Neil Cook]
Added psuedoparamentry command. [Neil Cook]
Added blank pythonbox tcblisting. [Neil Cook]
Added sections. [Neil Cook]
Changed note to dev note. [Neil Cook]
Wrote section (from readme) [Neil Cook]

0.0.032 (2017-12-01)¶

Rebuilt pdf. [Neil Cook]
Corrected syntax errors and line breaking. [Neil Cook]
Rebuilt pdf files. [Neil Cook]
Changed coi to os_fac and called from ic_tilt_coi. [Neil Cook]
Added getting DRS_NAME and DRS_VERSION from spirouConfig.Constants. [Neil Cook]
Moved the internal hyperlink setup out of preamble. [Neil Cook]
Moved the internal hyperlink setup out of preamble. [Neil Cook]
Added module aliases, added hslip 0pt for long variable names (so they can split on line break) [Neil Cook]
Moved colour definitions to commands, modified ParameterEntry to add called from form (for devguide only) [Neil Cook]
Moved colour definitions to commands. [Neil Cook]
Reformated ParameterEntry (added call from for devguide), added many new variables (still not complete) [Neil Cook]
Added error if calibDB file does not exist (and proper exception + log/print message) [Neil Cook]
Corrected typo. [Neil Cook]
Added sources for some constants, renamed coi to ic_tilt_coi. [Neil Cook]
Added source for fib_type. [Neil Cook]

0.0.031 (2017-11-30)¶

Cosmetic change to spacing. [Neil Cook]
Added placeholder sections. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Changed the user manual from yellow to red (and updated the margin label) [Neil Cook]
Changed the level of green on the dev margin. [Neil Cook]
Added new constants. [Neil Cook]
Modified ParameterEntry command. [Neil Cook]
Added a python inline style. [Neil Cook]
Added variable file locations section, image variable section, fiber variable section, dark calibration section. [Neil Cook]
Minor spelling changes to comments. [Neil Cook]
Rebuilt pdfs. [Neil Cook]
Now getting DRS_NAME and DRS_VERSION from spirouConfig.Consants. [Neil Cook]
Added a NAME function constant. [Neil Cook]
Added spirouCONSt and spirouKeywords constants. [Neil Cook]
Added minipage to parameter definition (to force items on one page) [Neil Cook]
Modified drs_name and drs_version - only in dev version. [Neil Cook]
Removed drs_name and drs_version from config.txt (now in spirouConst) [Neil Cook]

0.0.030 (2017-11-29)¶

Rebuilt pdf files. [Neil Cook]
Renamed preample to preamble. [Neil Cook]
First commit of preamble file. [Neil Cook]
First commit of packages file. [Neil Cook]
First commit of merged variables file. [Neil Cook]
First commit of merged recipes file. [Neil Cook]
First commit of merged intro file. [Neil Cook]
Updated folder path for figures in readme. [Neil Cook]
Rebuilt pdf files. [Neil Cook]
Moved bulk of same code to packages file and preample file, added ifdevguide (to distinguish between dev and user) added coloured border, moved chapters around after merges. [Neil Cook]
Added masterclibddbfile, configtxtfile, acqtimekey, folderdateformat constants. [Neil Cook]
Added paraeter command and devnote devsection (all dependent on devguide or userguide) [Neil Cook]
Attempted breakable tcolorbox. [Neil Cook]
First full commit - wrote section. [Neil Cook]
Corrected spelling and added command in place of filename. [Neil Cook]
Added from old manual. [Neil Cook]
Added more sections. [Neil Cook]
Deleted (not used) [Neil Cook]
Deleted and merged dev and user. [Neil Cook]
Deleted and merged dev and user. [Neil Cook]
Deleted. [Neil Cook]
Deleted and merged dev and user. [Neil Cook]
Deleted and merged dev and user. [Neil Cook]
Deleted and merged dev and user. [Neil Cook]
Deleted and merged dev and user. [Neil Cook]
Deleted and merged dev and user. [Neil Cook]

0.0.029 (2017-11-28)¶

First commit of user version of data_architecture (not to be kept - use if statements?) [Neil Cook]
First commit of dev version of data_architecture (not to be kept - use if statements?) [Neil Cook]
Rebuilt pdf. [Neil Cook]
Rebuilt pdf. [Neil Cook]
Added packages, modified abstract (noindent) [Neil Cook]
Added packages, modified abstract (noindent) [Neil Cook]
Ignored .listing files. [Neil Cook]
Added recipe constants. [Neil Cook]
Added a definevariablecmd function (cyan instead of blue for definevariable) [Neil Cook]
Complete redo of code formatting (using newtcblistings) [Neil Cook]
Updated label for chapter. [Neil Cook]
Updated label for chapter. [Neil Cook]
Updated label for chapter. [Neil Cook]
Added code blocks section. [Neil Cook]
Added code block sections. [Neil Cook]
Updated notes to environment, code to code environments. [Neil Cook]
Added folder layout section, installation root dir section, bin dir section, spirou module directory section. [Neil Cook]
Renamed cal_validate_drs to cal_validate_spirou. [Neil Cook]

0.0.028 (2017-11-27)¶

Added latex gitignore. [Neil Cook]
Memoir chapter styles (for pdf building) [Neil Cook]
First commit dev guide. [Neil Cook]
First commit user guide. [Neil Cook]
Added logo to figures. [Neil Cook]
Added constants first commit. [Neil Cook]
Added commands (from old manual) [Neil Cook]
Added coding formats (using new styles) [Neil Cook]
Added installation process (first commit) for linux+mac and windows. [Neil Cook]
What. [Neil Cook]
Added placeholder first commit tex files (empty other than title) [Neil Cook]
Updated progress in readme (with documentation needs) [Neil Cook]
Added a function to check write level, corrected bug in logging (was print_level needed to be log_level) [Neil Cook]
Added logo to documentation files. [Neil Cook]
Edited comments. [Neil Cook]
Added validation code (to test imports and display user setup) [Neil Cook]
Updated links in table of contents. [Neil Cook]

0.0.027 (2017-11-24)¶

Updated section naming in readme. [Neil Cook]
Added installation process to readme. [Neil Cook]
Added ic_ext_all constant. [Neil Cook]
Added timing to debug run. [Neil Cook]
Added posibility to save all extraction types to file (simple, tilt, tiltweight, weight) [Neil Cook]
Added timed unit tests sections. [Neil Cook]
Corrected unit test. [Neil Cook]

0.0.026 (2017-11-23)¶

Made unit test compatible with python 2 (ordered dict) [Neil Cook]
Updated progress in readme. [Neil Cook]
Added to table of contents, added section 2.3 (to be filled out like section 2.2) [Neil Cook]
Imported division from __future (to make sure all division is float division not int), cleaned up code, applied pep8 convensions. [Neil Cook]
Removed debug timing stuff. [Neil Cook]
Update readme with cal_extract and cal_drift sections, added unit test timing section. [Neil Cook]
Renamed run_inital_startup to run_initial_startup. [Neil Cook]
Wrapper around cal_extract_RAW_spirou to allow fiber_type defined as ‘C’ [Neil Cook]
Wrapper around cal_extract_RAW_spirou to define AB as the fiber type. [Neil Cook]
First commit - unit test for all tested files (with timings) [Neil Cook]
Modified run_inital_startup function to allow night_name and files arguments to be passed from main function calls. [Neil Cook]
Moved measure_dark function here from cal_DARK_spirou, added ‘human’/’unix’ time to get_acqtime. [Neil Cook]
Added alias to MeasureDark function. [Neil Cook]
Cosmetic change to __all__ [Neil Cook]
Added drift_plot_dtime_Against_mdrift function. [Neil Cook]
Added kw_ACQTIME_KEY_UNIX. [Neil Cook]
Modified ARG_FILE_NAMES and ARG_NIGHT_NAME to accept value already in p (from function call over command line arguments) [Neil Cook]
Added human/unix acqtime getting. [Neil Cook]
Added ic_drift_n_order_max parameter, cosmetic changes (spaces between sections increased) [Neil Cook]
Moved __main__ code to main function. [Neil Cook]
Moved __main__ code to main function. [Neil Cook]
Moved __main__ code to main function. [Neil Cook]
Moved __main__ code to main function. [Neil Cook]
Moved __main__ code to main function, added rv properties section, added plot section, added save drift values to file section. [Neil Cook]
Moved __main__ code to main function. [Neil Cook]

0.0.025 (2017-11-22)¶

Cosmetic changes to layout. [Neil Cook]
Fixed some bugs, added compute cosmic+renorm section, added calculate RV drift section. [Neil Cook]
Changed mask1 and mask to flag in delta_v_rms_2d, added renormalise_cosmic2d and calculate_RV_drifts_2D functions. [Neil Cook]
Added aliases for ReNormCosmic2D and CalcRVdrift2D. [Neil Cook]
Fixed error in get_all_similar_files (filelist not returned) [Neil Cook]
Fixed error in drift_plot_photon_uncertainty (‘number_orders’ in loc not p) [Neil Cook]
Added ic_drift_cut, renamed ic_dv_maxflux and ic_dv_boxsize. [Neil Cook]

0.0.024 (2017-11-21)¶

Modified readme with change in plot function. [Neil Cook]
Added imports, added startup section, read ref image section, get basic ref props section, resize ref image section, get loc/tilt/wave sections, merge coeffs section, extract ref section, computer dvrms section, plot ref section, get all files section, started all file loop (not finished) [Neil Cook]
First commit, added delta_v_rms_2d function. [Neil Cook]
Added get_all_similar_files function, modified correct_for_dark function (now can return dark for use later), modified get_exptime, get_gain, get_sigdet, get_param, added get_acqtime. [Neil Cook]
Redefined readimage (no combining) and added readimage_and_combine (to do reading and combining), updated readimage functions throughout. [Neil Cook]
Updated __all__ [Neil Cook]
Added GetAllSimilarFiles, GetAcqTime, ReadImage and ReadImageAndCombine functions. [Neil Cook]
Modified extract functions to have and look for keywords in function calls before using defaults (allows customisation) [Neil Cook]
Renamed plots for clarity, added drift_plot_selected_wave_ref, drift_plot_photo_uncertainty. [Neil Cook]
Added filename arg to get_acquisaion_time and code to deal with it. [Neil Cook]
Added ic_ext_d_range_fpall, ic_drift_noise, ic_dv_maxflux, ic_dv_boxsize, drift_nlarge, drift_file_skip, modified ic_ext_range_fpall. [Neil Cook]
Renamed ReadImage to ReadImageAndCombine for clarity and renamed plotting functions (for clarity) [Neil Cook]
Renamed ReadImage to ReadImageAndCombine for clarity and renamed plotting functions (for clarity) [Neil Cook]
Renamed ReadImage to ReadImageAndCombine for clarity, changed fiber to p[‘fiber’], and renamed plotting functions (for clarity) [Neil Cook]
Renamed ReadImage to ReadImageAndCombine for clarity. [Neil Cook]
Renamed ReadImage to ReadImageAndCombine for clarity. [Neil Cook]

0.0.023 (2017-11-20)¶

Updated progress section. [Neil Cook]
Added function copy_root_keys function, modified read_header function. [Neil Cook]
Added alias for CopyRootKeys to init and __all__ [Neil Cook]
Modified extract_AB_order, extract_order, extract_tilt_order, extract_tilt_weight_order, extract_tilt_weight_order2, extract_weight_order, extract_const_range, extract_const_range_fortran, extract_const_range_wrong and extract_wrapper added code for extract_tilt, extract_weight, extract_tilt_weight2, extract_tilt_weight, extract, check_for_none, get_tilt_matrix. [Neil Cook]
Updated __all__ [Neil Cook]
Added alias to ExtractTiltWeightOrder2. [Neil Cook]
Added cal_extract plot functions. [Neil Cook]
Moved EXIT definition to constants. [Neil Cook]
Added kw_LOCO_FILE keyword. [Neil Cook]
Added EXIT function (to return exit statement based on log_exit_type() [Neil Cook]
Added ic_ext_range_fpall, modified ic_ff_plot_all_orders, added ic_extmeanzone constants. [Neil Cook]
Renamed extracttiltweightorder function to extracttiltweightorder2. [Neil Cook]
Added timing to extraction comparison, corrected noise calculation, added plot section, added saving e2ds to file. [Neil Cook]

0.0.021 (2017-11-17)¶

Added p to spiouCDB.GetDatabase (for max_time constants) [Neil Cook]
Added p to spiouCDB.GetDatabase (for max_time constants), added read out of max_time in error (helps to identify why error was caused) [Neil Cook]
Fixed call to spirouEXTOR.ExtractABOrder, added p to spiouCDB.GetDatabase (for max_time constants) [Neil Cook]
Fixed error in add_key_2d_list. [Neil Cook]
Fixed selected_order_fit_and_edges, added function all_order_fit_and_edges. [Neil Cook]
Added stringtime2unixtime and unixtime2stringtime functions (fixed from spirouCDB) [Neil Cook]
Added DATE_FMT_HEADER and DATE_FMT_CALIBDB constants. [Neil Cook]
Added ic_ff_plot_all_orders constant, fixed loc_file_fpall and orderp_file_fpall. [Neil Cook]
Fixed acqtime key error, fixed time getting error (inconsistent times), made check that times are consistent, added max_time_human and max_time_unix to p. [Neil Cook]
Added due test mode. [Neil Cook]
Added due test mode, added plot all orders (instead of just selected) - slower, added flat to calibDB. [Neil Cook]
Modified imports, added version/author from constants. [Neil Cook]
Modified imports, added version/author from constants, and added __all__ function. [Neil Cook]
Modified imports, added version/author from constants, changed lloc to loc, added functions for extract_order, extract_order_0, extract_tilt_order, extract_weight_order (None currently working) - will need to edit extract_wrapper to make work. [Neil Cook]
Modified imports, added version/author from constants and interactive plot constant. [Neil Cook]
Modified imports, added version/author from constants, added TRIG_KEY, WRITE_LEVEL, EXIT and WARN from constants, added CONFIG_KEY_ERROR warning. [Neil Cook]
Added constants PACKAGE(), VERSION(), AUTHORS(), LATEST_EDIT(), CONFIGFOLDER(), CONFIGFILE(), INTERACTIVE_PLOT_ENABLED(), LOG_TRIG_KEYS(), WRITE_LEVEL(), LOG_EXIT_TYPE(), LOG_CAUGHT_WARNINGS(), CONFIG_KEY_ERROR, add set version and author from constants. [Neil Cook]
Modified imports, added version/author from constants, added package config_file, configfolder and trig key from Constants. [Neil Cook]
Modified imports, added version/author from constants. [Neil Cook]
Modified imports, added version/author from constants. [Neil Cook]
Modified imports, added version/author from constants. [Neil Cook]
Modified imports, added version/author from constants, added __all__ aliases, added printing of sub-package names. [Neil Cook]
First commit, modified imports, added version/author from constants, added __all__ aliases, moved RunInitialStartup and RunStartup here (from SpirouCore) [Neil Cook]
Modified imports, added version/author from constants, added __all__ aliases. [Neil Cook]
Modified imports, added version/author from constants, added __all__ aliases, added aliases for different extraction types. [Neil Cook]
Modified imports, added version/author from constants, added __all__ aliases, moved RunInitialStartup and RunStartup to spirouStartup module. [Neil Cook]
Modified imports, added version/author from constants, added __all__ aliases. [Neil Cook]
Modified imports, added version/author from constants, added __all__ aliases. [Neil Cook]
Modified imports, added version/author from constants, added __all__ aliases. [Neil Cook]
Editted comments for ic_extopt. [Neil Cook]
Modified imports, moved spirouStartup to own module, added calls to extract functions. [Neil Cook]
Modified imports, moved spirouStartup to seperate module. [Neil Cook]
Modified get_loc_coefficients to look for keyword ‘LOC_FILE’ [Neil Cook]
Added key to arguments of read_tilt_file function, added read_wave_file function, modified read_order_profile_superposition to look for keyword ‘ORDERP_FILE’ [Neil Cook]
Added ReadWaveFile alias. [Neil Cook]
Added A and B to fiber type parameters, added loc_fil and orderp_file parameters. [Neil Cook]
Moved dprtype from header getting section, added fiber A B and AB replacement for AB (in merging coefficients) [Neil Cook]
Added read image section, added basic image properties section, added correction of dark, added resize image, added the logging of dead pixels, added minmax max_signal section, added background computation section, added tilt reading section, added wave solution reading section, added localaization coefficient getting section, added order profile getting section, added order loop, added noise/flux/SNR calculation, added saturation warning section, added quality control section. [Neil Cook]

0.0.020 (2017-11-16)¶

Add calibDB to p in startup if calibdb required (should be faster than reloading it each time) [Neil Cook]
Corrected cal_ff extractiltweightorder spelling mistake. [Neil Cook]
Added check for calibDB in p. [Neil Cook]
Added check for ‘calibDB’ in p. [Neil Cook]
Moved forbidden_copy_keys to constants, added get_type_from_header function, added read_raw_header function. [Neil Cook]
Added GetTypeFromHeader alias to init. [Neil Cook]
Added dealing with customargs and added run_time_custom_args + display_custom_args functions. [Neil Cook]
Added kw_DPRTYPE. [Neil Cook]
Added FORBIDDEN_COPY_KEYS constant. [Neil Cook]
Added tests for calibDB in p. [Neil Cook]
Reformatted comments on variables. [Neil Cook]
Added dprtype find from header, modified test code. [Neil Cook]
Added dprtype find from header, modified test code. [Neil Cook]
Added dprtype find from header, modified test code. [Neil Cook]
Added dprtype find from header, added test code, added __NAME__, added setup section. [Neil Cook]
Added dprtype find from header, added test code. [Neil Cook]

0.0.019 (2017-11-15)¶

Added cal_FF_RAW summary of changes section, updated progress. [Neil Cook]
Added add_key_1d_list function, updated add_key_2d_list to be more generic (with header comment) [Neil Cook]
Added AddKey1DList alias to init. [Neil Cook]
Added selected_order_fit_and_edges, selected_order_tilt_adjusted_e2ds_blaze and selected_order_flat plot functions. [Neil Cook]
Added kw_EXTRA_SN and kw_FLAT_RMS. [Neil Cook]
Added ic_ff_order_plot constant. [Neil Cook]
Cosmetic change. [Neil Cook]
Added plot section, added saving blaze and flat field section. [Neil Cook]

0.0.018 (2017-11-14)¶

Added convert_to_adu function, fixed get_gain/get_sigdet/get_param functions. [Neil Cook]
Removed reducedfolder call and fixed order_profile key. [Neil Cook]
Added ConvertToADU alias to init. [Neil Cook]
First commit spirouFLAT.py added measure_blaze_for_order function. [Neil Cook]
First commit spirouFLAT init (added MeasureBlazeForOrder alias) [Neil Cook]
Modified extract_tilt_weight_order and extract_wrapper functions, added extract_tilt_weight function and extract_tilt_weight_old function. [Neil Cook]
Fixed error in gain/exptime keyword. [Neil Cook]
Fixed hard coded key in get_file_name function. [Neil Cook]
Cosmetic change. [Neil Cook]
Added ic_ff_sigdet, ic_extfblaz, ic_blaze_fitn constants. [Neil Cook]
Added storage set up for extraction, added extract with tilt+weight loop, added skip for max_signal QC. [Neil Cook]

0.0.017 (2017-11-13)¶

First commit, added some well used constants (constants but need input and functions so not formed from basic string/int/float/list) [Neil Cook]
Reworked fiber_params to get dictionaries of constants with particular suffix, added more logging to get_loc_coefficients, added merge_coefficients function. [Neil Cook]
Added mergecoefficients alias. [Neil Cook]
Added masterfile constant, added get_gain, get_sigdet, get_param functions. [Neil Cook]
Moved bulk of getting file name from calibDB to spirouCDB, added read_order_profile_superposition function. [Neil Cook]
Added GetSigdet, GetExptime, GetGain and ReadOrderProfile aliases to init. [Neil Cook]
Added extract_tilt_weight_order function (not finished), added extract_tilt_weight skeleton code, changed extraction_wrapper to fit changes of other functions. [Neil Cook]
Added ExtractTiltWeightOrder alias to init file. [Neil Cook]
Added reduced folder constant, fixed calibd_dir path on line 150 (now 149) [Neil Cook]
Fixed logging to file (date wasn’t working) [Neil Cook]
Added sigdet, exptime and gain keywords, moved acqtime to “required header keys” section. [Neil Cook]
Added extract_dict_params function. [Neil Cook]
Added ExtractDictParam to init. [Neil Cook]
Added raw and reduced dir constants, added new function get_file_name, added lock_file and master file constants. [Neil Cook]
Added GetFile command to init. [Neil Cook]
Chagned fiber param variables to dictionaries. [Neil Cook]
Changed getting sigdet, exptime and gain to functions, added reduced folder constant, added new fiber params command. [Neil Cook]
Changed getting sigdet, exptime and gain to functions, added reduced folder constant. [Neil Cook]
Changed getting sigdet, exptime and gain to functions, added reduced folder constant, added read tilt slit angle, added start of fiber extract loop (not finished) [Neil Cook]
Changed getting sigdet, exptime and gain to functions, added reduced folder constant. [Neil Cook]
Added pep8 cosmetic corrections. [Neil Cook]
Added pep8 cosmetic corrections. [Neil Cook]
Added filename option to readimage function, added read_tilt_file function. [Neil Cook]
Added ReadTiltFile to init. [Neil Cook]
Added image to doc string for extract_AB_order. [Neil Cook]
Added ic_tilt_nbo constant. [Neil Cook]
Added space between comma. [Neil Cook]
Added read tilt slit angle section. [Neil Cook]

0.0.016 (2017-11-10)¶

Added fib_type to fiber types constants, added cal_ff params, added a qc param. [Neil Cook]
Moved measure_box_min_max and measure_background_and_get_central_pixels to spirouBACK. [Neil Cook]
Added measure_background_and_get_central_pixels, measure_box_min_max to spirouBACK measure_background_flatfield (not finished) to init. [Neil Cook]
Moved measure_background_and_get_central_pixels, measure_box_min_max to spirouBACK, added measure_background_flatfield (not finished) [Neil Cook]
Moved measure_background_and_get_central_pixels, measure_box_min_max to spirouBACK. [Neil Cook]
Moved MeasureBkgrdGetCentPixs to spirouBACK. [Neil Cook]
Added setup section, added read image section, added correction of dark section, added resize image section, , added max_signal section. [Neil Cook]
Chnaged ccdsigdet to sigdet, added test (no need to specific files) [Neil Cook]

0.0.015 (2017-11-09)¶

Added cal_slit section. [Neil Cook]
Stricked done progress. [Neil Cook]
Added hlines. [Neil Cook]
Edit table of contents, added back to top, added future sections. [Neil Cook]
Added table of contents. [Neil Cook]
Section numbering. [Neil Cook]
Added WLOG update. [Neil Cook]
Added WLOG update, and configError update. [Neil Cook]
Added jpg py3 logo. [Neil Cook]
Added picture as jpg. [Neil Cook]
Changed path for plot. [Neil Cook]
Correlation with a box test plot. [Neil Cook]
Change test function for smoothed_boxmean_image. [Neil Cook]
Added to general section, cal_dark section and cal_loc section. [Neil Cook]
Moved kw_TILT to own section. [Neil Cook]
Edited description of slit param. [Neil Cook]

0.0.014 (2017-11-08)¶

Added doc string for extract and added ExtractABorder alias to init. [Neil Cook]
Added FitTilt and GetTilt to init. [Neil Cook]
Moved extract_AB_order here (from cal_SLIT_spirou) [Neil Cook]
Removed get_tilt and fit_filt functions (to spirouImage) [Neil Cook]
Moved get_tilt and fit_filt functions here. [Neil Cook]
Added doc strings for slit plotting functions. [Neil Cook]
Updated USE_KEYS list formatting. [Neil Cook]
Updated readme. [Neil Cook]
Reworked get_tilt function, added extract AB order function and fit filt function, added plotting section, added tilt calculation section, added todo quality control section, added update calibDB section. [Neil Cook]
Added coi ic_tilt_fit and ic_slit_order_plot constants. [Neil Cook]
Added kw_TILT keyword. [Neil Cook]
Added slit plotting functions: selected_order_plot and slit_tilt_angle_and_fit_plot. [Neil Cook]
Added doc string for extract_wrapper, extract_const_range, added test functions extract_const_range_fortran and moved extract_const_range to extract_const_range_wrong (updates former) [Neil Cook]
Changed plt.ion to sPlt controller function. [Neil Cook]

0.0.013 (2017-11-07)¶

Added doc for get_loc_coefficients, initial_order_fit, sigmaclip_oder_fit and image_localization_superposition added calcualte_location_fits function. [Neil Cook]
First commit - added extract wrapper alias. [Neil Cook]
First commit - added extract wrapper and first attempt at extract code. [Neil Cook]
First commit - added fast polyval function. [Neil Cook]
Added doc string comments for all functions. [Neil Cook]
Edited kw_loco_ctr_coeff and kw_loco_fwhm_coeff. [Neil Cook]
Allowed max_time to be None and get max_time from p[‘fitsfilename’] [Neil Cook]
Added some slit parameters. [Neil Cook]
Added extract function. [Neil Cook]
Added test via sys.argv. [Neil Cook]
Added get_loc_coefficients function. [Neil Cook]
Added GetCoeffs to init. [Neil Cook]
Called GetAcqTime in correct_for_dark function. [Neil Cook]
Added read_header, read_key and read_key_2d_list functions. [Neil Cook]
Added ReadHeader, ReadKey, Read2Dkey to init. [Neil Cook]
Added CopyCDBfiles call to run_startup function. [Neil Cook]
Added get_acquision_time and copy_files function. [Neil Cook]
Added CopyCDB and GetAcqTime to init. [Neil Cook]
Updates cal_SLIT with __NAME__ and new functions, updated startup section, added read image section, correction of dark section, resize image section, get coefficients section. [Neil Cook]
Removed unused cocde from cal_loc_RAW. [Neil Cook]

0.0.012 (2017-11-03)¶

Updated comments in constants_SPIROU. [Neil Cook]
Added a label to locplot_order. [Neil Cook]
Changed splt to sPlt. [Neil Cook]

0.0.011 (2017-11-02)¶

Added timer, moved plots to spirouPlots, moved functions to spirouLOCOR, updated AddNewKey –> AddKey, added quality control section and add to calibDB section. [Neil Cook]
Added timer, moved plots to spirouPlots, updated AddNewKey–> Addkey, [Neil Cook]
Added __getitem__, __contains, __delitem__ functions, forced all keys to uppercase (now ParamDict is case-insensitive), added source_keys, __capitalise_keys__, __capitalise__key__ functions, added list to set of evaluate allowed types. [Neil Cook]
Reloaded keywords USE_KEYS, added ParamDict call, added kw_LOC_ keys, added source to overwritten warning. [Neil Cook]
Renamed AddNewKey to AddKey. [Neil Cook]
Added wrapper function for add_new_key (add_new_keys), [Neil Cook]
Renamed image_localazation_superposition to image_localization_superposition. [Neil Cook]
Added functions from cal_loc –> spirouLOCOR, added image_localazation_superposition function. [Neil Cook]
Added functions from cal_loc –> spirouLOCOR to init. [Neil Cook]
Moved fiber variables to own section, added qc for cal_loc. [Neil Cook]
Changed keys as now param dict all uppercase. [Neil Cook]
First commit - all plotting functions moved here. [Neil Cook]

0.0.010 (2017-11-01)¶

Set_source for param dicts. [Neil Cook]
Set_source for param dicts. [Neil Cook]
Renamed set_source function to set_source_for_defaulting_statements (to avoid confusion) [Neil Cook]
Added set_source. [Neil Cook]
Added documentation to ConfigException, added new class ParamDict (custom dictionary), added set_source to param dicts and a set_source function for dealing with default values from check_params() [Neil Cook]
Added ParamDict to init. [Neil Cook]
Added set source + c_Database –> ParamDict. [Neil Cook]
Added set source + fparam –> ParamDict. [Neil Cook]
Added set source + updated keywords to match spirouKeywords. [Neil Cook]

0.0.009 (2017-10-31)¶

Modified measure_background_and_get_central_pixels to accept and return loc made a copy of data2 (data2o) for localisation with 0 on fit data dump added code for “Save and record of image of localization with order center and keywords” section added code for “Save and record of image of sigma” section placeholder code for “Save and Record of image of localization” section. [Neil Cook]
Added empty holder for image_localazation_super function (not finished) [Neil Cook]
Updated call for ACQTIME_KEY to kw_ACQTIME_KEY. [Neil Cook]
Moved functions into sections added function “add_new_key” and “add_key_2d_list” [Neil Cook]
Updated init file. [Neil Cook]
Updated call to spirouConfig moved check_params moved load_other_config_file (kept wrapper function for logging) [Neil Cook]
Removed log constants (to spirouConfig) [Neil Cook]
Updated spirouCore init. [Neil Cook]
First commit moved from config/keywords. [Neil Cook]
Moved some constants to here (TRIG_KEY, WRITE_LEVEL, EXIT) added config exception class added config error class moved load_config_from_file from startup functions to spirouConfig added doc for check_config moved check_params from startup to spirouConfig created get_default_config_file function. [Neil Cook]
First commit for spirouConfig ini - moved config and keyword function calls to here. [Neil Cook]
Added ic_locfitp, ic_loc_delta_width, ic_locopt1 to config file. [Neil Cook]
Added SPECIAL_NAME back to config. [Neil Cook]
Updated function calls. [Neil Cook]
Updated function calls. [Neil Cook]
Added call to AddNewKey. [Neil Cook]

0.0.008 (2017-10-30)¶

File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
Tmp file for keyword args? - sort this out. [Neil Cook]
File migration and new imports plot order num against rms. [Neil Cook]
File migration and new imports. [Neil Cook]
File migration and new imports. [Neil Cook]
Reordered files. [Neil Cook]

0.0.007 (2017-10-27)¶

Reworked fit order into “initial order fit” and “sigmaclip_order_fit” added and tested order fitting sections. [Neil Cook]
Added some more location parameters. [Neil Cook]
Updated locate center order position into two functions. [Neil Cook]
Return header from last “added” fits and set fitsfilename to last file (as in original code) - not sure it this is wanted but it is how it is. [Neil Cook]
Changed locate_center_order_positions to two functions one for center finding one for center + width of individual (subtle differences) [Neil Cook]

0.0.006 (2017-10-26)¶

Revert “added example of BoxSmoothedImage with mode ‘convolve’ vs ‘manual’” This reverts commit f7637bf. [Neil Cook]
Changed the logged to exit via sys.exit. [Neil Cook]
Added a minimum width requirement and return widths in “locate_center_order_position” functions. [Neil Cook]
Closed the hdu and added a header extension argument (default = 0) [Neil Cook]
Changed name of locate_central_position alias. [Neil Cook]
Added constants from cal_loc_RAW_spirou. [Neil Cook]
Added to position and width finding (incomplete + untested) [Neil Cook]
Fixed formatting. [Neil Cook]
Reformatted BoxSmoothedimage and LocateCentralPosition descriptions in change log. [Neil Cook]
Wrapped for locate_order_positions to go between manual and convolve versions. [Neil Cook]
Added more documentation for smoothed_boxmean_image. [Neil Cook]
Added BoxSmoothedImage ‘convolve’ vs ‘manual’ change to change log. [Neil Cook]
Added BoxSmoothedImage with mode ‘convolve’ vs ‘manual’ [Neil Cook]

0.0.005 (2017-10-25)¶

Added locate_central_positions function. [Neil Cook]
Added some code for locating central positions. [Neil Cook]
Removed sys.exit (now in WLOG for key=’error’) add a warning that parameter dictionary key is duplicated and overwrite when loading other config file. [Neil Cook]
Added keys argument to write_file_to_master added log statement to log updated calibDB. [Neil Cook]
Moved smoothed_boxmean_image function to spirouLOCOR added function measure_box_min_max. [Neil Cook]
Moved smoothed_boxmean_image function to spirouLOCOR. [Neil Cook]
Corrected typo ‘Adding’ –> ‘ADD’ [Neil Cook]
Updates init with boxsmoothedminmax moved boxsmoothed image to spirouLOCOR. [Neil Cook]
Added config readme at top added some cal_loc variables added -[code] tag to comments to show where constant is used (currently) [Neil Cook]
Added measure background function and plot_y_miny_maxy and plot_min_ycc_loc_threshold updated data2 to be a copy of order_profile. [Neil Cook]
Changed updatemaster key to variable instead of hardcoded string. [Neil Cook]
Added cal_loc_RAW_spirou section to changelog. [Neil Cook]
First commit of spirouLOCOR (empty) [Neil Cook]
Added flip_image, convert_to_e, and smoothed_boxmean_image functions. [Neil Cook]
Added ‘BoxSmoothedImage, ConvertToE and FlipImage functions. [Neil Cook]
Added loc_box_size constant and localisation parameters section. [Neil Cook]
Added construct image order_profile section and write order_profile to file/calibDB sections. [Neil Cook]
Updated comment with spelling correction. [Neil Cook]

0.0.004 (2017-10-24)¶

Set out plan for code. [Neil Cook]
Move config file. [Neil Cook]
Add warning logger and remove sys.exit from all but logger. [Neil Cook]

0.0.003 (2017-10-16)¶

Added nbframes as a parameter to get in run_startup function. [Neil Cook]
Changed ACQTIME_KEY to getting from config file added checks for ACQTIME_KEY. [Neil Cook]
Allow math_controller arg “framemath” to be None –> pass straight through. [Neil Cook]
Added correct_for_dark function changed raise value errors to WLOG + sys.exit(1) [Neil Cook]
Added CorrectForDark to init. [Neil Cook]
Added ACQTIME_KEY constant. [Neil Cook]
Added read image file section added call to CorrectForDark function added resize image section. [Neil Cook]
Added rotation and conversion to e- (commented out currently) [Neil Cook]
Added fiber_params function added startup.RunInitialStartup call added custom startup.RunStartup call (with parameters to add for each prefix case) [Neil Cook]
Added a requirement that calibdb is defined in run_startup function. [Neil Cook]
Updated the README with summary of changes to cal_DARK_spirou.py. [Neil Cook]

0.0.002 (2017-10-13)¶

Added check for reduced directory (and make if needed) added check from calib directory (and make if needed) [Neil Cook]
First commit added update_datebase and put_file functions added get_check_lock_file, wriite_files_to_master, and time2unixtime functions. [Neil Cook]
Added PutFile and UpdateMaster functions. [Neil Cook]
Added writeimage and copy_original_keys functions. [Neil Cook]
Added readimage and writeimage function to init. [Neil Cook]
Added dark quality control parameters added calibDB parameters. [Neil Cook]
Added short name to measure_dark function added dadead_{0} to parameter dictionary (p) added comments dictionary from ReadImage added quality control section added save dark to fits section added save bad pixel mask added calibDB update. [Neil Cook]
Added more TODO’s regarding user defined config file. [Neil Cook]
Added DRS_PLOT variable. [Neil Cook]
Added image region plot added datacut plot added histogram plot. [Neil Cook]
Added dark histogram variables. [Neil Cook]
Added measure dark function changed pp –> p added dark measurement section added identification of bad pixels section. [Neil Cook]

0.0.001 (2017-10-12)¶

Added evaluate value function to try to interpret the value in a config file (i.e. set to float/int/bool before setting to a string) [Neil Cook]
Added line separator. [Neil Cook]
Added __version__ [Neil Cook]
Added keyslookup function added numpy import. [Neil Cook]
First commit added resize function. [Neil Cook]
Added GetKeys + ResizeImage function to init added __version__ [Neil Cook]
Added ic_cc(x/y)_(blue/red)_(low/high) variables added qc_dark_Time variable. [Neil Cook]
Added read image and resize iamge sections. [Neil Cook]
Modified run_startup to deal with no fitfilename file. [Neil Cook]
Updated DRS_ROOT path. [Neil Cook]
Added readimage+read_raw_Data documentation and keylookup+math_controller function. [Neil Cook]
Added ReadImage and GetKey to init. [Neil Cook]
Added ReadImage functions and got keys from header. [Neil Cook]
Added initial files, added readimage and read_raw_data functions. [Neil Cook]
Added initial files. [Neil Cook]
Updated title of readme. [Neil Cook]