Pypeit

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- Add support for Gemini/GNIRS (IFU)
- Add support for Keck/KCRM
- Added a script to convert a wavelength solution into something that can be placed in the reid archive.
- Hotfix for GTC/OSIRIS lamp list
- Hotfix for Arc1D stats annotations on the QA
- Hotfix for metadata (correctly set config_independent frames when multiple configurations are being setup)
- Hotfix for metadata (support lists in ``config_independent_frames()``)
- Hotfix for rebin (speed-up and conserves flux)
- Hotfix for skysub regions GUI that used np.bool
- Hotfix to stop pypeit_setup from crashing on data from lbt_luci1, lbt_luci2, magellan_fire,
magellan_fire_long, p200_tspec, or vlt_sinfoni.
- Hotfix to set BPM for each type of calibration file.
- Adds Keck/ESI to PypeIt
- Instrumental FWHM map is calculated and output in ``Calibrations`` and ``spec1d`` files.
- Adds Keck/ESI to PypeIt
- Add MDM/Modspec spectrograph
- Store user-generated wavelength solution in pypeit cache
- Improvements to wavelength grids and masking in coadd routines.
- Fixed a bug in echelle coadding where the wrong coadded spectra were being
used in final stacks.
- Sensitivity function models can now be computed relative to the blaze
spectrum.
- Refactored coadding routines to work with lists to support coadding data from
different setups.
- Changes to how masking is dealt with in extraction to fix a bug in how masks
were being treated for echelle data
- Various fixes and changes required to add more support for Keck/HIRES and JWST
- Fix a bug in ``spectrograph.select_detectors``, where a list of ``slitspatnum`` could not be used.
- Improvements in 2D coaddition
- Fix a bug in `pypeit_setup_coadd2d` for the output file name of the .coadd2d file
- Added possibility to specify more than one Science folder in `pypeit_setup_coadd2d`
- Now ``only_slits`` parameter in `pypeit_coadd_2dspec` includes the detector number (similar to ``slitspatnum``)
- Added ``exclude_slits`` parameter in `pypeit_coadd_2dspec` to exclude specific slits
- Fix wrong RA & Dec for 2D coadded serendips
- Changed calibration frame naming as an attempt to avoid very long names for
files with many calibration groups. Sequential numbers are reduced to a
range; e.g., ``'0-1-2-3-4'`` becomes ``'0+4'`` and
``'3-5-6-10-11-12-15-18-19'`` becomes ``'3-5+6-10+12-15-18+19'``
- HIRES wavelength solution improvements galor
- Added `redo_slits` option
- Refactored ``load_line_lists()`` yet again!
- Improvements for keck/LRIS
- Generated wavelength templates for all the LRIS grism & grating
- Added FeAr line list
- Improved calibration association and frame typing
- Improved and added documentation
- Changes to ``metadata.py`` including commenting out, in the pypeit file,
files that have frametype None (this prevent ``run_pypeit`` to crash)
- Added a function ``check_spectrograph()`` (currently only defined for LRIS),
that checks (during ``pypeit_setup``) if the selected spectrograph is the
corrected one for the data used.

--------------------

- Implemented a resample algorithm when generating datacubes
- Hotfix to docs to ensure pypeit_loaders api doc is generated
- Allow user control of the local sky subtraction window
- Deprecate use of python 3.8 with PypeIt, allow python 3.11
- Make pypeit_show_2dspec (somewhat) backwards compatible.
- Hotfix for KCWI when using alignment (aka ContBars) frames for the astrometric correction.
- Sensitivity function masking and output updates
- Fixed a bug in the `variance_model` calculation for combined images.
- Added the possibility to use dither offsets saved in the header of the science frames for
coadding 2D spectra (``dithoff`` must be part of the spectrograph metadata).
- Calibration group numbers can now be anything, as long as there are no more
than 63 unique integers.
- Removed use of the term "master", renamed to calibration frames/files.
Default output directory for calibration frames is now ``Calibrations``.
Calibration frames renamed; e.g., ``MasterArc`` is now ``Arc``.
- Calibration frame naming now done via ``calibframe.CalibFrame`` class.
- Start to deprecate use of ``os.path`` in favor of ``pathlib``
- Deprecated ``pypeit_parse_calib_id`` script, but improved the ``.calib`` file
provided by ``pypeit_setup``. The ``.calib`` file is now always written, and
provides a direct association between input raw files and output calibration
files. Discussed in new docs.
- The ``'calib'`` column is now always added to the pypeit file, regardless of
whether or not you also request the ``'comb_id'`` and ``'bkg_id'`` columns.
- Names of associated calibration frames now written to ``spec2d`` file headers.
- Added the option to disable strict version checking for 1d coadds.
- Major quicklook updates. ql_multislit.py temporarily deprecated.
- Improve speed in ginga visualization of traces and added
`pypeit_chk_tilts`. Note that this script uses an update
of the tilts datamodel, so it will not work on older reductions.
- Updates to reduction parameters for LDT/DeVeny

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- Gemini/GMOS mask design slurping and usage
- New GMOS wavelength solution
- Added NIRES tutorial doc
- reid_arxiv templates for all MMTO Blue Channel gratings and for MMTO Binospec G600 and G1000
- Various bug fixes and enhancements to mmt_bluechannel and mmt_binospec support
- Include the S/N of extracted spectra in the SpecObj datamodel
- Added new specutils interface
- Fixed bugs when only performing calibrations and (1) calib groups are all set
to 'all' or (2) anything other than '0'.
- Added `MASKDEF_OBJMAG` and `MASKDEF_OBJMAG_BAND` in spec1d datamodel.
- Improved NIRES dither pattern parsing and automatic assignment of `comb_id` and `bkg_id`.

--------------------

- (Hotfix) Specify sphinx versions to correctly work with
sphinx_rtd_theme
- (Hotfix) Fixed bug that caused crash of sensfunc routines using
telluric grids in offline processing
- (Hotfix) Fixed error when showing flats in Ginga when the fine correction is not performed
- Implemented the upgraded GTC/OSIRIS+
- (Hotfix) keymap error when displaying GUIs
- Added support for more NOT/ALFOSC grisms as well as NOT recommended standards
- Implemented the SOAR/Goodman blue 400 grating (setup M1)
- Added support for SOAR/Goodman red 600 grating (setup RED)
- Implemented the SOAR/Goodman (blue) M1 only
- New docs on OneSpec
- Modify install notes to allow python 3.10; python3.8 no longer explicitly supported
- Allow for bad orders during extraction (without crashing)

--------------------

- (Hotfix) Fixed bug that allowed science frames to be assigned to multiple
instrument configurations
- (Hotfix) Fixed typo related to GitHub download for offline processing
- Started modifications and support for JWST.
- Limit LRISr header crashes
- Added spectral flexure and reference frame corrections for IFU data
- Allow separate sky frame to be used for sky subtraction with IFU data
- Limit the images written to the MasterEdges file to only the trace
image, mask, and detector.
- Refactor quicklook scripts
- OpenMP link fix
- Enable boxcar_radius for manual extraction
- Prevent flexure crash
- Fixed error with deprecated numpy types
- Improved optimization of bspline c code
- Parse Keck/NIRES dither patterns, similar to MOSFIRE
- Introduce BitMaskArray class to ease use of bitmasks
- Fixed memory hogging by matplotlib when using version >= 3.6.1

--------------------

- Add ability for users to specify custom arc line lists for
wavelength calibration, saved in the user's PypeIt cache
- Added Keck/NIRES frame-typing development doc.
- Now more than one setup can be assigned to the same calibration frame,
allowing to associate the same calibration frames to different science/standard
frames, if desired.
- Correctly associate calibrations with science data for MOSFIRE longslit and long2pos masks.
- Automatically assign `comb_id` and `bkg_id` to MOSFIRE science data,
using the information on the dither pattern.
- Allow verbosity specification for various post-processing command-line scripts.
- Allow for the specification of a specific UVIS extinction file for sensitivity
function computation and flux calibration.
- Adding Keck/HIRES functionality.
- Restructred coadd2d in order to work with images that have different
sizes.
- Restructured extraction and find_objects classes to work
better with 2d coadds.
- Refactor and general update of documentation