JWST Calibration Pipeline

What's Changed Prepare for post-1.17.0 development by @tapastro in https://github.com/spacetelescope/jwst/pull/9025 JP-3784: Fix off-nominal pixel_replace and cube_build output names by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9019 Add suffix for SIRS refpix output so it can be okified by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9027 Bugfix for SIRS reference pixel subtraction by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/9037 JP-3664: Fix pixel replace numpy 2.0 issues by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/9004 Update CRDS cache workflow usage to reduce random failures by @braingram in https://github.com/spacetelescope/jwst/pull/9040 JP-3834: Update default values for the source finding in tweakreg to match the algorithm by @mcara in https://github.com/spacetelescope/jwst/pull/9036 Metadata updates for 1.17.1 by @jhunkeler in https://github.com/spacetelescope/jwst/pull/9043 Fix GWCS failures due to the API spring cleaning PR by @WilliamJamieson in https://github.com/spacetelescope/jwst/pull/8965 try to ignore requirements-sdp.txt for dependabot by @braingram in https://github.com/spacetelescope/jwst/pull/9051 JP-3822: restructure outlier detection unit tests by @emolter in https://github.com/spacetelescope/jwst/pull/9052 JP-3794: Add trace-based extraction option for NIRSpec by @hayescr in https://github.com/spacetelescope/jwst/pull/9022 Update CODEOWNERS and remove unused files by @braingram in https://github.com/spacetelescope/jwst/pull/9055 Update MRS photom documentation by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/9065 JP-3840: Include gwcs install warning and stasis install details by @tapastro in https://github.com/spacetelescope/jwst/pull/9066 Fix extract_1d unit test failure under numpy 2 by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9069 JP-1649: Add option for user-defined sky levels in skymatch by @emolter in https://github.com/spacetelescope/jwst/pull/9053 JP-3838: Update README description of CRDS setup by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/9078 JP-3769: Add code style F, E, W rules by @emolter in https://github.com/spacetelescope/jwst/pull/9076 JP-3755: Remove unused options and add unit tests to SOSS extraction algorithm by @emolter in https://github.com/spacetelescope/jwst/pull/9000 remove no longer needed warning filter by @braingram in https://github.com/spacetelescope/jwst/pull/9084 JP-3829: Add flat handling to clean_flicker_noise by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9064 Convert np.int to int for logging in numpy 2 by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9101 JP-3664: Testing changes for numpy 2.0 compatibility by @tapastro in https://github.com/spacetelescope/jwst/pull/8718 JP-3769: Style rules example case by @emolter in https://github.com/spacetelescope/jwst/pull/9081 Fix msa frame transform for opaque images by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9102 build sdist with python 3.13 (point to workflow fork) by @braingram in https://github.com/spacetelescope/jwst/pull/9106 Move mypy type hint checking into pre-commit by @emolter in https://github.com/spacetelescope/jwst/pull/9108 JP-3862: Apply code style to pixel_replace module by @tapastro in https://github.com/spacetelescope/jwst/pull/9107 JP-3851: Remove fits_generator by @emolter in https://github.com/spacetelescope/jwst/pull/9111 Remove unused .flake8 config file by @emolter in https://github.com/spacetelescope/jwst/pull/9115 Add Codespell to pre-commit by @emolter in https://github.com/spacetelescope/jwst/pull/9097 Fix sonar scan failures on AMI changes by @emolter in https://github.com/spacetelescope/jwst/pull/9112 Emicorr speedup by @t-brandt in https://github.com/spacetelescope/jwst/pull/9077 Style fixes for assign_mtwcs by @emolter in https://github.com/spacetelescope/jwst/pull/9113 JP-251: Optimal extraction support for MIRI LRS by @melanieclarke in https://github.com/spacetelescope/jwst/pull/8967 JP-3859: Apply code style to clean_flicker_noise and nsclean by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9114 drop support for python 3.10 by @braingram in https://github.com/spacetelescope/jwst/pull/9116 Fix code style in outlier detection by @emolter in https://github.com/spacetelescope/jwst/pull/9127 JP-3777: Select first and last groups in ramp fitting by @stscirij in https://github.com/spacetelescope/jwst/pull/9095 JP-3697: Jump Step Refactor by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/9039 Remove tomli, no longer relevant for 3.11 by @emolter in https://github.com/spacetelescope/jwst/pull/9133 set stcal to main, allow python 3.13 by @braingram in https://github.com/spacetelescope/jwst/pull/9105 JP-3859: Apply code style rules to msaflagopen by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9124 Bump actions/setup-python from 5.3.0 to 5.4.0 by @dependabot in https://github.com/spacetelescope/jwst/pull/9134 Bump OpenAstronomy/github-actions-workflows from 1.15.0 to 1.16.0 by @dependabot in https://github.com/spacetelescope/jwst/pull/9135 JP-3116: Do not create observation-only Level 2 associations if part of a background candidate by @tapastro in https://github.com/spacetelescope/jwst/pull/9098 Add line length ignores for spec strings by @emolter in https://github.com/spacetelescope/jwst/pull/9139 Apply code style rules to source_catalog by @emolter in https://github.com/spacetelescope/jwst/pull/9138 Fix formatting error by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9142 replace usage of random.random() with np.random.random() by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/9137 JP-3796: Scale barshadow correction to long slits by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9085 JP-3827: Remove unused error from ramp data by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9109 Apply code style rules to tweakreg by @emolter in https://github.com/spacetelescope/jwst/pull/9130 Apply code style rules to badpix_selfcal by @emolter in https://github.com/spacetelescope/jwst/pull/9140 JP-3830: MRS residual cosmic ray shower straylight correction by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/9126 Apply code style rules to datamodels submodule by @emolter in https://github.com/spacetelescope/jwst/pull/9131 Apply code style rules to stpipe by @emolter in https://github.com/spacetelescope/jwst/pull/9150 Correct error in MSA metadata coordinate description by @hayescr in https://github.com/spacetelescope/jwst/pull/9154 Apply code style rules to wfss_contam by @emolter in https://github.com/spacetelescope/jwst/pull/9151 Apply basic code style changes to lastframe step by @jemorrison in https://github.com/spacetelescope/jwst/pull/9147 Replace hidden wcs pipeline attribute with public one by @emolter in https://github.com/spacetelescope/jwst/pull/9165 Apply code style rules to soss_extract by @emolter in https://github.com/spacetelescope/jwst/pull/9156 Xfail test_fgs_guider until CRDS files are repaired by @tapastro in https://github.com/spacetelescope/jwst/pull/9169 Update codestyle for first frame step by @jemorrison in https://github.com/spacetelescope/jwst/pull/9170 JP-3859: Apply code style rules to combine_1d by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9121 JP-3859: Apply code style rules to master_background by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9123 Apply code style rules to model_blender by @emolter in https://github.com/spacetelescope/jwst/pull/9157 JP-3856: Style Updates for Group Scale by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/9163 JP-3856: Code Style Updates to Jump Step by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/9159 JP-3856: Style Updates for Ramp Fitting by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/9158 JP-3855: Style Updates for DQ init by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/9161 JP-3856: Style Updates for Charge Migration by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/9162 increase minimum version of asdf-astropy by @braingram in https://github.com/spacetelescope/jwst/pull/9177 JP-3765: Update documentation of ramp fitting step arguments by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/9176 JP-3859: Apply code style rules to wavecorr by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9128 Move common resample code to stcal by @mcara in https://github.com/spacetelescope/jwst/pull/8986 JP-3879: Fix resample failure to ingest single datamodels from file by @emolter in https://github.com/spacetelescope/jwst/pull/9183 JP-3856: Style Updates for Gain Scale by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/9164 JP-3786: Remove hard assigning NON_SCIENCE to DO_NOT_USE in flatfield by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/9174 Fix a bug in resampled_wcs_from_models by @mcara in https://github.com/spacetelescope/jwst/pull/9186 Apply code style rules to pipelines by @emolter in https://github.com/spacetelescope/jwst/pull/9144 Use skymatch from stcal by @WilliamJamieson in https://github.com/spacetelescope/jwst/pull/8901 Fix unsafe initialization of CubeModel from ImageModel by @emolter in https://github.com/spacetelescope/jwst/pull/9192 JP-3815: Add support for selecting a list of slit names or source ids… by @stscirij in https://github.com/spacetelescope/jwst/pull/9171 Document crpix convention for resample step by @mcara in https://github.com/spacetelescope/jwst/pull/9195 Apply code style checks to skymatch step by @emolter in https://github.com/spacetelescope/jwst/pull/9202 JP-3852 and JP-3853: Fix imprint associations for NRS IFU by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9190 Document image group usage for sky matching by @mcara in https://github.com/spacetelescope/jwst/pull/9080 Fix test for custom WCS for imaging by @mcara in https://github.com/spacetelescope/jwst/pull/9017 JP-3861: Apply code style changes for pathloss step by @stscirij in https://github.com/spacetelescope/jwst/pull/9203 use astropy for interpret_bit_flags by @braingram in https://github.com/spacetelescope/jwst/pull/9212 JP-3808: Store scaling factor for WFSS data in background step by @emolter in https://github.com/spacetelescope/jwst/pull/9204 JP-3744: set outlier step default to in-memory processing by @emolter in https://github.com/spacetelescope/jwst/pull/9214 JP-3812: Add output_ext documentation by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9224 replace uses of DataModel.write with save by @braingram in https://github.com/spacetelescope/jwst/pull/9219 JP-3859: Apply code style rules to extract_1d by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9194 JP-3862: Clean up guider_cds step for code style and CRDS inconsistencies by @tapastro in https://github.com/spacetelescope/jwst/pull/9141 Fix interpolated flat suffix in MOS/FS case by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9209 JP-3897: Fix bad input type to median computation for cubemodels in outlier detection by @emolter in https://github.com/spacetelescope/jwst/pull/9227 JP-3858-exp_to_source by @penaguerrero in https://github.com/spacetelescope/jwst/pull/9201 JP-3691: Add links to JDox by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9228 JP-3773: Store logs from calibration pipeline in datamodel by @braingram in https://github.com/spacetelescope/jwst/pull/9211 test with latest supported Python version by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/9217 Remove mention of unused SOSS reference files in docs by @emolter in https://github.com/spacetelescope/jwst/pull/9041 JP-3811: Update imprint documentation to mention association input by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9222 Apply basic code style checks to test configuration files by @emolter in https://github.com/spacetelescope/jwst/pull/9146 Fix inaccurate warning message for median_error computation by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9247 JP-3608: Document slit low/high parameters by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9223 JP-3789 Add more FITS comparison support for regression tests by @penaguerrero in https://github.com/spacetelescope/jwst/pull/9082 JP-3790 add residual fringe correction to extract1d table by @jemorrison in https://github.com/spacetelescope/jwst/pull/9073 JP-3858-superbias by @penaguerrero in https://github.com/spacetelescope/jwst/pull/9232 JP-3848 MIRI LRS s_region and resample WCS by @jemorrison in https://github.com/spacetelescope/jwst/pull/9193 mention cal_logs in docs by @braingram in https://github.com/spacetelescope/jwst/pull/9257 JP-3858-srctype by @penaguerrero in https://github.com/spacetelescope/jwst/pull/9239 JP-3858-white_light by @penaguerrero in https://github.com/spacetelescope/jwst/pull/9241 Add flexible log_watcher fixture by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9262 JP-3790: apply aperture correction of residual fringe corrected data by @jemorrison in https://github.com/spacetelescope/jwst/pull/9260 JP-3915: Bugfix to SIRS kernel subtraction by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/9267 Apply code style rules to resample by @emolter in https://github.com/spacetelescope/jwst/pull/9248 JP-3857 update reset step to new code style rules by @jemorrison in https://github.com/spacetelescope/jwst/pull/9264 JP-3896: Deprecate or remove various assign_wcs utility functions by @emolter in https://github.com/spacetelescope/jwst/pull/9221 JP-3597: Add new algorithm for EMI fit; clean up existing code by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9216 JP-3913: Add sirskernel to refpix reference types by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9261 Import stdatamodels warnings from new exceptions namespace by @emolter in https://github.com/spacetelescope/jwst/pull/9280 JP-3917: Apply code style rules to engdblog by @pllim in https://github.com/spacetelescope/jwst/pull/9276 JP-3860: Apply code style rules to assign_wcs by @emolter in https://github.com/spacetelescope/jwst/pull/9255 Jp 3861 refpix style by @stscirij in https://github.com/spacetelescope/jwst/pull/9234 JP-3500: Associate pure parallel WFSS grism images with long wave direct images by @tapastro in https://github.com/spacetelescope/jwst/pull/9277 JP-3914: Catch incomplete extraction gracefully by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9266 actually remove script as followup to #8957 by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/9289 JP-3901: Enable Detector1Pipeline processing of DHS data by @tapastro in https://github.com/spacetelescope/jwst/pull/9243 JP-3900: Tests, clean up, and code style for residual_fringe by @melanieclarke in https://github.com/spacetelescope/jwst/pull/9242 JP-3901: Bugfix and regression coverage by @tapastro in https://github.com/spacetelescope/jwst/pull/9304 metadata for 1.18.0rc1 by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/9306 Backport PR #9326 on branch release/1.18.x (JP-3953: Extrapolate barshadow correction to cover wavelength gaps) by @meeseeksmachine in https://github.com/spacetelescope/jwst/pull/9335 Backport PR #9338 on branch release/1.18.x (Fix inadvertent removal of all) by @meeseeksmachine in https://github.com/spacetelescope/jwst/pull/9339 Backport PR #9337 on branch release/1.18.x (JP-3947 Fix MIRI LRS Flux error) by @meeseeksmachine in https://github.com/spacetelescope/jwst/pull/9344 Backport PR #9301 on branch release/1.18.x (JP-3686: Test using source catalog output as tweakreg abs_refcat) by @meeseeksmachine in https://github.com/spacetelescope/jwst/pull/9346 Metadata for 1.18.0rc2 by @jhunkeler in https://github.com/spacetelescope/jwst/pull/9354 Backport PR #9361 on branch release/1.18.x (JP-3978: Allow unequal number of target and psf exposures in calwebb_ami3) by @meeseeksmachine in https://github.com/spacetelescope/jwst/pull/9363 Revert "Backport PR #9301 on branch release/1.18.x (JP-3686: Test using source catalog output as tweakreg abs_refcat)" by @tapastro in https://github.com/spacetelescope/jwst/pull/9375 Metadata for release 1.18.0 by @jhunkeler in https://github.com/spacetelescope/jwst/pull/9374 New Contributors @meeseeksmachine made their first contribution in https://github.com/spacetelescope/jwst/pull/9335 Full Changelog: https://github.com/spacetelescope/jwst/compare/1.17.0...1.18.0