PypeIt

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.