Version 1.17.1

Patch release that:

• Bumped to numpy>=1.26
• Lifts restriction from python<3.13 to python<3.14

Version 1.17.0

Installation Changes

• Significant expansion of PypeIt's use of the cache system; see
  :ref:data_installation. Important changes include that most cached
  files are now version dependent. When upgrading to new versions of
  PypeIt, users should delete their cache and start fresh.

Dependency Changes

• Support added for numpy>=2.0.0; numpy<=2.0.0 should still be supported
• Deprecated support for python 3.10
• General update to dependencies to be roughly consistent with release
  of python 3.11

Functionality/Performance Improvements and Additions

• Added the max_overlap parameter, which limits the set of new order
  traces added, to compensate for orders missed during automated
  edge-tracing, to those that have less than a given fractional overlap
  with adjacent orders.
• Added the order_fitrej and order_outlier parameters used to
  set the sigma-clipping threshold used when fitting Legendre functions
  to the order widths and gaps.
• Added the possibility to decide if the extracted standard star
  spectrum should be used as a crutch for tracing the object in the
  science frame (before it was done as default). This is done by
  setting the parameter use_std_trace in FindObjPar.
• Now PypeIt can handle the case where "Standard star trace does not
  match the number of orders in the echelle data" both in run_pypeit
  and in pypeit_coadd_1dspec.
• Added the functionality to use slitless flats to create pixelflats.
  Note: new frametype slitless_pixflat is added to the PypeIt
  frametype list.
• The created pixelflats are stored in the reduction directory and in
  the PypeIt cache directory data/pixelflats.
• Added a functionality that allows, when multiple frames are combined,
  to scale each frame to have the same mean value before combining. To
  use this functionality, the new parameter scale_mean should be set
  to True.
• Added the possibility to use the parameter fwhm_fromlines also for
  the tilts calibration.

Instrument-specific Updates

• Improved LRIS frame typing, including the typing of slitless flats and
  sky flats.

• Improved HIRES frame typing and configuration setup.

• Added support for Keck/KCWI BH3 grating configuration.

• Updated the requirements of a spectral flip for KCWI (blue) data. If
  all amplifiers are used, the data will not be flipped in the spectral
  direction. Otherwise, the data will be flipped.

• Added support for the (decommissioned) AAT/UHRF instrument

• Updated X-Shooter detector gain and read noise to come from header,
  and updated plate scales to the most recent values from the manual.
  Detailed changes are:

  • NIR arm:

    • Platescale updated from 0.197 to 0.245 arcsec/pixel
    • Dark current updated from 0. to 72. e-/pixel/hr
    • Gain updated from 2.12 to 2.29 e-/DN

  • VIS arm:

    • Platescale updated from an order-dependent value, to being
      0.154 arcsec/pixel for all orders

  • UVB arm:

    • Platescale updated from an order-dependent value, to being
      0.164 arcsec/pixel for all orders

• Add new P200/DBSP reid_arxiv template for 1200/7100 with D55 dichroic

• Add B480 as a supported option for Gemini-S/GMOS

Script Changes

• Modifications to the cache-related :ref:install_scripts to
  accommodate expansion of and changes to the cache system.
• Added pypeit_clean_cache script to facilitate both viewing and
  removing files in the cache.
• Changed the name of the multi-dimensional specdata to
  specdata_multi in pypeit_identify and improved the robustness
  of the saving dialog when calibrating single trace spectra.
• Fixed a read-in error for the high resolution A0V PHOENIX model.
• A new script, called pypeit_extract_datacube, allows 1D spectra of
  point sources to be extracted from datacubes.
• The sensitivity function is now generated outside of datacube
  generation.
• The grating_corr column is now used to select the correct grating
  correction file for each spec2d file when generating the datacube.
• Added the --extr parameter in the pypeit_sensfunc script (also
  as a SensFuncPar) to allow the user to specify the extraction
  method to use when computing the sensitivity function (before only
  optimal extraction was used).
• Added pypeit_show_pixflat script to inspect the (slitless) pixel
  flat generated during the reduction and stored in data/pixelflats.
• Added pypeit_chk_flexure script to check both spatial and spectral
  flexure applied to the reduced data.
• Treatment of file names is now more formal. Compression signatures
  are now considered, and filename matching is now more strict.
• Removed --spec_samp_fact and --spat_samp_fact command line
  options from pypeit_coadd_2d. These options are now parameters in
  Coadd2dPar.
• pypeit_show_2dspec now shows the first available detector in the
  2D spectrum by default. The user can specify the detector to show with
  the --det option.
• Added --removetrace command line option to pypeit_ql to not
  show the object trace when displaying the 2D spectrum.
• Change the default value for --skip_display in pypeit_ql to
  True.

Datamodel Changes

• Adjusted spec1d datamodel to enable use with UVES_popler GUI tool

Under-the-hood Improvements

• Introduced :class:~pypeit.pypeitdata.PypeItDataPaths to handle all
  interactions with the pypeit/data directory, which provides a
  unified interface for accessing on-disk and cached files.
• When adding missing orders, the full syncing procedure is no longer
  performed. The code now only checks that the edges are still synced
  after the missed orders are added.
• When detecting overlapping orders/slits, the code now forces each edge
  used to have been directly detected; i.e., if an edge is inserted, the
  fact that the resulting slit is abnormally short should not trigger
  the overlap detection.
• Improved the QA plot resulting from fitting order widths and gaps as a
  function of spatial position.
• Updated general raw image reader so that it correctly accounts for
  spectrographs that read the data and overscan sections directly from
  the file headers.

Bug Fixes

• Fix "The system cannot find the file specified" errors when installing
  on Windows.
• Fixed a fault caused when all frames in a pypeit file are identified
  as being part of all calibration groups.
• Allow for empty 2D wavecal solution in HDU extension of WaveCalib file
• Fixed a bug in the ginga display function, when the user doesn't
  provide the trc_name argument.
• Fix a MAJOR BUT SUBTLE bug in the use of numpy.argsort. When
  using numpy.argsort the parameter kind='stable' should be used
  to ensure that a sorting algorithm more robust than "quicksort" is
  used.
• Fix error "ValueError: setting an array element with a sequence. The
  requested array has an inhomogeneous shape after 1 dimensions..."
  occurring when unpacking the SpecObj spectrum but having an
  attribute of the SpecObj object that is None.
• Fixed a hidden bug that was causing the spatial flexure to fail. The
  bug was in the SlitTraceBitMask class, where the function
  exclude_for_flexure() was not returning the 'BOXSLIT' flag.
• Fix a bug in pypeit_coadd_2d related to how the binning was taken
  into account in the mask definition, and in the calculation of the
  offset between frames.
• Fix bug when trying to open mosaic data from previous versions;
  version checking flag was not being propagated.

Version 1.16.0

Dependency Changes

• PypeIt now only supports python versions >=3.10, numpy>=1.23, and ginga>=5.1.0

• sphinx-rtd-theme updated to 2.0, along with relevant dependencies

Functionality/Performance Improvements and Additions

• Allow the selection of a secondary filter option for all spectrographs that
  need it; see new filter2 parameter.

• When dealing with bkg_redux reduction (i.e., A-B), a sky model (called
  bkg_redux_skymodel) is generated using the A frame, while the existing
  skymodel is generated using the A-B frame. This allows to have an actual 1D
  extracted sky spectrum and to perform the flexure correction for bkg_redux
  reduction.

• Various improvements in the flexure correction and added the possibility to
  use a modeled archive sky spectrum generated with
  pypeit.wavemodel.nearIR_modelsky() to perform the flexure correction.

• Updated the list of available CALSPEC standard star with the latest version
  from the CALSPEC website.

Instrument-specific Updates

• Improvements for SOAR/Goodman

  • Added WAVMODE header keyword to configuration keys and
    raw header cards.

• Added example of improved wavelength solution for GEMINI/GMOS

• Introduces reduction pipeline for high-resolution modes of Keck/NIRSPEC

• Expanded the template for shane_kast_red and the 1200/5000 grating

• Fixed and improved the wavelength template magellan_fire_long

• Updated Gemini/GMOS-S with the new detector parameters for the Hamamatsu CCDs
  replaced on 2023-12-14

Script Changes

• When interactively fitting a single peak with the pypeit_identify script
  (i.e. using the i command), line centroids can now be both updated and added
  interactively.

Datamodel Changes

• Spec2DObj now has an additional image, called bkg_redux_skymodel, which is
  the "actual" sky model in the case of bkg_redux reduction (i.e., dithered
  observations). This image is not generated if bkg_redux is False. In any
  case, the skymodel is always generated.

Bug Fixes

• The subpixel algorithm used to resample datacubes that are generated by
  pypeit_coadd_datacube produced error cubes that were not properly
  propagating the noise. The error cubes of the NGP algorithm were unaffected.
  The error cubes are now regularly inspected with vet tests to ensure the error
  cubes are reliable.

• Fix a bug (introduced in a recent PR) that was generating an error if less
  than 2 spec1d files were used with pypeit_coadd_1dspec. Now the script can
  be run with only one file (as it was before).

• Allow spec_flex_shift() to take as input either the name of an archive sky
  spectrum or directly a sky spectrum. This fixes a bug in the flexure
  correction for SlicerIFU.

• The --show option of the pypeit_coadd_1dspec script was not properly
  displaying the x-axis of the plot. Both the top and bottom panels now scale
  together.

• Fix a bug in pypeit_sensfunc that was causing the script to crash because
  par['fluxcalib'] was not being passed to sensfunc.SensFunc.get_instance().

Version 1.15.0

Installation Changes

• PypeIt will no longer be available through conda-forge and must be installed via pip from PyPI. Users may still use conda for management of PypeIt's virtual environment.

Dependency Changes

• Removes use of deprecated pkg_resources.
• Require version >=1.12 for specutils.
• Add psutil as a dependency for [dev] installs.
• Add pytest-qt as a dependency for [dev] installs.
• Require version >=0.3.1 for linetools

Functionality/Performance Improvements and Additions

• Started the development of instrument-specific scattered light removal. In this release, we only model KCWI/KCRM scattered light.
• Turned on usage of the use_2dmodel_mask parameter for echelle spectrographs
• Added support for Keck/KCRM RL data reduction.
• Allow one to turn off reinit of reduce_bpm in global_skysub and made this the default for the final pass
• Allow pypeit Spectrum1D loaders to circumvent the requirement that reduced spectrum have monotonically increasing wavelength data. Non-monotonic wavelength data usually indicate a problem with the data reduction, but this at least lets users ingest the spectrum.
• Add a sensible error message to the pypeit Spectrum1D loaders in the event a user inadvertently tries to use Spectrum1D instead of SpectrumList for a spec1d file.
• Enabled interpolation and extrapolation of missing echelle orders. This is currently only used for Keck/HIRES, but the code is general.
• Allow the specification of wavelength limits on the flexure cross-correlation against a sky template to limit the effect of unconstrained wavelength solutions at the ends of the spectrum.
• Change overscan_method = 'polynomial' to overscan_method = 'chebyshev' to reflect the type of polynomial being fit. Both names point to the same code, but the name 'polynomial' is deprecated and will be removed in the future.
• Introduced PCA method for telluric corrections
• Added slicer subpixel sampling for DataCube generation
• Added trace_rms_tol parameter for edge tracing, which helps guard against poorly constrained traces for spectrally truncated slits/orders.

Instrument-specific Updates

• Add support for the R4K detector for MDM OSMOS
• Updated archival sensitivity functions for DEIMOS 1200G, 800G, and 600ZD gratings.
• Keck/KCWI and Keck/KCRM: Turned on polynomial correction for sky subtraction.
• We now support the reduction of VLT/FORS2 data taken in MOS mode.
• Fixed fluxing file format in the Keck-DEIMOS HOWTO documentation.
• LDT/DeVeny: default parameter & wavelength template updates, add instrument- specific line lists, use SCITARG for target name if none entered in the LOUI.
• Added support for NTT/EFOSC2 Gr#4
• Keck/KCWI: FeAr are used for wavelength calibration, while the ThAr lamp is used to determine the wavelength tilt.
• Improvement to the wavelength calibration for Keck/HIRES. New arxiv templates added. Templates available for orders 35-117.
• Various updates to default parameters for Keck/HIRES.
• Added Keck-LRIS HOWTO documentation.

Script Changes

• When making datacubes, the user can select a separate frame to use for the sky subtraction. In this case, it is the processed data that will be used for sky subtraction (akin to nodding).
• Allow a list of files to be passed to pypeit_chk_wavecalib.
• A new script has been written (chk_scattlight) to check the generation of the scattered light calibration frame model.
• Added the pypeit_edge_inspector script, which allows users to edit the edge traces by-hand.
• pypeit_parse_slits now prints also the echelle order number, if applicable.
• Column SpatID in the output of pypeit_chk_wavecalib changed to SpatOrderID and now show the echelle order number, if applicable, otherwise the slit number.
• pypeit_chk_edges now load SlitTraceSet (if available) to be able to overlay the echelle order numbers.
• Added a new GUI for creating and editing PypeIt input files: pypeit_setup_gui
• Added a -G option to pypeit_setup and pypeit_obslog that will start the new Setup GUI.
• Improvements and bug fixes for how the mask is displayed by pypeit_show_2dspec, and added pypeit_print_bpm to allow for a quick report on the flags associated with a given bit value.

Datamodel Changes

• A wavelength array is now stored for DataCube()
• WaveCalib and WaveFit datacontainers now store information about echelle order number, if applicable.
• Change to how SlitTraceSet datamodel stores and checks bit flag values.

Under-the-hood Improvements

• The CoAdd3D code has been refactored into a series of core modules and PypeIt-specific routines.
• Polynomial overscan fitting now uses the numpy.polynomial.Chebyshev class instead of the deprecated numpy.polyfit() function.
• Improvements to echelle wavelength calibration. Code changes in: pypeit/core/wavecal/wvutils.py, pypeit/core/wavecal/echelle.py, pypeit/core/wavecal/autoid.py, pypeit/wavecalib.py.
• Fixed some failure modes when matching measured order positions to expected positions for fixed-format echelle spectrographs.
• More extensive propagation of turning off datamodel version checking (using try_old and chk_version) throughout the code.

Bug Fixes

• Fixed bug associated with finding more than one file with the same name (but presumably different extensions).
• Fixed differential atmospheric refraction (DAR) correction bug. This bug affected datacubes combined using CoAdd3D(). Previously, the DAR was being computed, applied, and then later overwritten. The new routine is faster and more accurate.
• Fixed a bug associated with an incorrect date for the transition to the Mark4 detector for Keck/LRIS RED.
• Fixed a bug with the pypeit_identify script when using echelle data. Previously, the sigdetect parameter was a list of all orders, instead of a single value.
• Fixed a bug with the GUI pypeit_skysub_regions. Previously, the calib header information was not included, and this led to a calibration error.
• Corrected the binning scaling for BOXCAR_RADIUS in the object-finding algorithm. Previously, the platescale was multiplied by the spectral binning and not the spatial binning.
• Aligned the documentation and parameters with the code for polynomial overscan subtraction. Docs/params specified 3 values to be passed in overscan_par for overscan_method = 'polynomial', but the code only uses one (poly order).
• Fixed duplicate object bug reported in Issue #1690.

Version 1.14.0

Dependency Changes

• Main dependency bumps: numpy>=1.22, matplotlib>=3.7, ginga>=4.1.1,
  qtpy>=2.0.1

Functionality/Performance Improvements and Additions

• Improvements to wavelength grids and masking in coadd routines.

• Refactored coadding routines to work with lists to support coadding
  data from different setups.

• Sensitivity function models can now be computed relative to the
  flat-field spectrum.

• 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 and Dec for 2D coadded serendips

• Allow wavelength calibrations for specific slits/orders to be redone
  (instead of adopting the value from a processed calibration frame);
  see new redo_slits parameter.

Instrument-specific Updates

• Adds/Improves support for Gemini/GNIRS (IFU), Keck/KCRM, Keck/ESI,
  MDM/Modspec, Keck/HIRES, JWST

• HIRES wavelength solution improvements galore

• 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.

Script Changes

• Added a script to convert a wavelength solution into something that
  can be placed in the reid archive.
• Store user-generated wavelength solution in pypeit cache

Datamodel Changes

• 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'
• Instrumental FWHM map is calculated and output in Calibrations and
  spec1d files.

Under-the-hood Improvements

• Change how masking is dealt with in extraction to fix a bug in how
  masks were being treated for echelle data
• Refactored function that loads wavelength calibration line lists

Bug Fixes

• 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
  • 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.

• Fixed a bug in echelle coadding where the wrong coadded spectra were
  being used in final stacks.

• Fix a bug in spectrograph.select_detectors, where a list of
  slitspatnum could not be used.

Version 1.13.0

Functionality/Performance Improvements and Additions

• Allow user control of the local sky subtraction window
• Implemented a resample algorithm when generating datacubes
• Sensitivity function masking and output updates
• 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.
• Fixed a bug in the variance_model calculation for combined images.

Datamodel Changes

• Removed use of the term "master", renamed to calibration frames/files.
  Default output directory for calibration frames is now Calibrations.
  Calibration frames renamed from, e.g., MasterArc* to Arc*.
• Names of associated calibration frames now written to spec2d file headers.

Dependency Changes

• Deprecate support for python 3.8 with PypeIt, allow python 3.11
• Make pypeit_show_2dspec (somewhat) backwards compatible.
• Added the option to disable strict version checking for 1d coadds.
• Start to deprecate use of os.path in favor of pathlib

Script Changes

• In PypeIt files, 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.
• In PypeIt files, the calibration group numbers can now be anything, as long as
  there are no more than 63 unique integers.
• 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.
• Added coadd2d setup script
• 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).
• Major quicklook updates; see documentation. ql_multislit.py deprecated.

Instrument-specific Updates

• Updates to reduction parameters for LDT/DeVeny

Hotfixes

• Hotfix to docs to ensure pypeit_loaders api doc is generated
• Hotfix for KCWI when using alignment (aka ContBars) frames for the astrometric correction.

Version 1.12.2

Instrument-specific Updates

• Include Gemini/GMOS mask design slurping and usage documentation
• New Gemini/GMOS wavelength solution
• Added NIRES tutorial doc
• reid_arxiv templates for all MMTO Blue Channel gratings and for MMTO Binospec G600 and G1000

Usage Updates

• Added new specutils interface

Datamodel Updates

• Include the S/N of extracted spectra in the SpecObj datamodel

Hotfixes

• Various bug fixes and enhancements to mmt_bluechannel and mmt_binospec support
• Fixed bugs when only performing calibrations and (1) calib groups are all set
  to 'all' or (2) anything other than '0'.

Version 1.12.1

Instrument-specific Updates

• Implemented the upgraded GTC/OSIRIS+
• Added support for more NOT/ALFOSC grisms as well as NOT recommended standards
• Implemented the SOAR/Goodman (blue) M1 only

Minor Updates

• Modify install notes to allow python 3.10; python3.8 not longer explicitly supported
• Allow for bad orders during extraction without crashing

Hotfixes

• Specify sphinx versions to correctly work with sphinx_rtd_theme
• Fixed bug that caused crash of sensfunc routines using telluric grids in offline processing
• Fixed error when showing flats in Ginga when the fine correction is not performed
• Fixed keymap error when displaying GUIs
• New docs on OneSpec

Version 1.11.0

Significant Updates

• Add ability for users to specify custom arc line lists for wavelength
  calibration, saved in the user's PypeIt cache
• Allow for the specification of a specific UVIS extinction file for
  sensitivity function computation and flux calibration.
• 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.
• Refactor and general update of documentation

Instrument-specific Updates

• 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.

Minor

• Added Keck/NIRES frame-typing development doc.
• Allow verbosity specification for various post-processing command-line
  scripts.

Version 1.10.0

Major Changes

• Refactor PypeIt input files. Main pypeit file remains the same, except that inclusion of leading and trailing | characters in the data table (required in previous versions) will now result in DeprecationWarnings. All post-processing scripts (coadding, fluxing, etc) must use the new format. See the main documentation pages.

Minor Changes/Improvements

• Apply find_min_max when clipping the image for object finding
• Mask bad detector regions for global sky flexure calculation
• Added wavelength diagnostics to the spec2d output

Instrument-specific Changes/Improvements

• Modify tweak_standard for Keck-MOSFIRE/J2
• Detector structure correction included in flatfield calibration (Keck-KCWI only)