===================
ami
---
- Replaced use of deprecated ``scipy.integrate.simps``
with ``scipy.integrate.simpson``. [8320]
- Overhaul of AMI processing. See documentation for full details. [7862]
- Additional optional input arguments for greater user processing flexibility.
See documentation for details. [7862]
- Bad pixel correction applied to data using new NRM reference file to calculate
complex visibility support (M. Ireland method implemented by J. Kammerer). [7862]
- Make ``AmiAnalyze`` and ``AmiNormalize`` output conform to the OIFITS standard. [7862]
- Disable ``AmiAverage`` step. [7862]
associations
------------
- Updated the level-2 rules for handling NIRSpec MOS nods that include
sub-pixel dithers, so that only exposures from other nod positions
are used as background members in "spec2" associations. [8184]
- Isolate candidate processing into their own pools [8227]
- Update the level-3 rules for "tso3" associations so that NIRISS SOSS
exposures with NINTS=1 are excluded. [8359]
- Removed blanket warning ignore for duplicate level 2 associations. [8320]
background
----------
- Updated to allow multi-integration (rateints) background exposures to have
a different value of NINTS than the science exposure. [8326]
charge_migration
----------------
- Updated the CHARGELOSS flagging. In an integration ramp, the first group in
the SCI data is found that is above the CHARGELOSS threshold and not flagged
as DO_NOT_USE. This group, and all subsequent groups, are then flagged as
CHARGELOSS and DO_NOT_USE. The four nearest pixel neighbor are then flagged
in the same group. [8336]
- Added warning handler for expected NaN and inf clipping in the
``sigma_clip`` function. [8320]
cube_build
----------
- Add a warning message to log if no valid data is found on the detector. [8220]
dark_current
------------
- Adds new parameter ``average_dark_current``, either from step params or
pulled from dark reference file, and stores in RampModel for use downstream
in ``RampFitStep``. [8302]
datamodels
----------
- Fixed a bug in the ``ModelContainer`` data model, due to which the ``models_grouped``
property would return opened data models instead of file names. [8191]
- Removed ``test_all_datamodels_init`` test, which is a duplicate of a test in
``stdatamodels``. [8320]
documentation
-------------
- Remove ``sphinx-asdf`` fix issue where menu does not scroll. [8196]
- Fixed small typo in ``user_documentation`` docs. [8178]
- Added additional information for the ``scale`` and ``snr`` parameters
in the ``outlier_detection`` step docs. [8177]
- Updated installation instructions to include a warning that Python<=3.11
must be used. [8200]
- Change docs theme to ``sphinx-rtd-theme`` [8224]
- Reorganized ``jump`` and ``ramp_fitting`` step docs content that's split between
the jwst and stcal repos. [8253]
- Correct the names of parameter options ``usigma`` and ``lsigma`` for ``sky_match``. [8356]
- Updated ``outlier_detection`` for IFU data to explain the method more clearly. [8360]
- Adds documentation on the 1-D residual fringe correction for MIRI MRS data that is done in ``extract_1d``. [8371]
emicorr
-------
- Set skip=True by default in the code, to be turned on later by a parameter
reference file. [8171]
- Step is skipped when no reference file is found and to add a parameter to
allow the user to run the step for given frequencies with an on-the-fly
generated reference file. [8270]
- Fixed bug for finding correction data for subarray FULL. [8375]
exp_to_source
-------------
- Fixed a bug for multislit data that bunit values, model_type and wcsinfo was
was being overwritten with the top multispec model values. [8294]
extract_1d
----------
- Fixed a bug in the calling of optional MIRI MRS 1d residual fringe
correction that could cause defringing to fail in some cases. [8180]
- Added a hook to bypass the ``extract_1d`` step for NIRISS SOSS data in
the FULL subarray with warning. [8225]
- Fixed a bug in the ATOCA matrix solve for NIRISS SOSS that would cause failures on
good input data in some cases. [8273]
- Added a trap in the NIRISS SOSS ATOCA algorithm for cases where nearly all
pixels in the 2nd-order spectrum are flagged and would cause the step
to fail. [8265]
- Fixed ifu auto-centroiding to only use wavelengths shortward of 26 microns
to avoid failures for moderate-brightness sources due to extremely low
throughput at the long wavelength end of MRS band 4C. [8199]
- Replaced instances of deprecated interp2d with
RectBivariateSpline in ``apply_apcorr``. [8291]
- Added saving the extraction aperture x/y limits for slit-like modes to
keywords in the output header. [8278]
- Fixed deprecated conversions of single-element numpy arrays to scalar
in ``apply_apcorr``. [8320]
- Increased specificity of warning filters in ``atoca`` and ``soss_centroids``. [8320]
extract_2d
----------
- Fixed crash when user provides an integer value for the `slit_name` argument,
by converting to a string. This change had been done in 8108, but it got undone
by another PR. [8272]
general
-------
- Update minimum required photutils version to 1.5.0 [8211]
- Update minimum required stdatamodels version to include 1.10.0 [8322]
- Update minimum required gwcs version to include 0.21.0 [8337]
- Remove unused asdf-transform-schemas dependency [8337]
- Replaced all instances of pytest ``tmpdir`` and ``tmpdir_factory``
fixtures with ``tmp_path`` and ``tmp_path_factory``. [8327]
- Replaced the ``_jail`` fixture from ``ci_watson`` with custom
``tmp_cwd`` to enforce ``no:legacypath`` in the CI tests. [8327]
- Renamed the ``jail`` fixture with ``tmp_cwd_module``. [8327]
- Replaced deprecated ``tool.ruff.ignore`` and ``tool.ruff.per-file-ignores``
with ``tool.ruff.lint.ignore`` and ``tool.ruff.lint.per-file-ignores``. [8320]
jump
----
- Add parameters that control the flagging of saturated cores of snowballs in
the next integration. [8303]
- Removed a unit test in ``jump`` that was moved to STCAL to decrease
the coupling of the two repos. [8319]
- To improve performance an additional parameter to the jump step was added
that sets the threshold number of differences above which iterative flagging
of one CR at a time is turned off. [8304]
lib
---
- Updated ``set_velocity_aberration`` to use datamodels instead of `astropy.io.fits` for opening
and manipulating input files. [8285]
- Added new function set_nans_to_donotuse in ``lib.basic_utils`` to
check the science data array for NaN values and check if they have
a DQ flag of DO_NOT_USE, or set it if not. [8292]
outlier_detection
-----------------
- Removed ``grow`` from the ``outlier_detection`` step parameters,
because it's no longer used in the algorithms. [8190]
- Fixed bug in removing intermediate files, so that the search for intermediate
files does not rely on the input files having a "cal" suffix, which was causing
original input files to accidentally get deleted instead of just the intermediate
files. [8263]
- Removed any reference to the "tophat" kernel for ``outlier_detection``
step. [8364]
pathloss
--------
- Added a check to find all NaN values in the data with a corresponding
even value flag in the DQ array, and convert them to DO_NOT_USE. [8292]
photom
------
- Set bunit_data and bunit_error to None in the top level meta data for
``MultiSlitModel`` data models, forcing information on units to only come
from individual slit meta data. [8189]
- Updated photom step to include spectral dispersion when applying NIRCam WFSS and TSGRISM
flux calibration, because the dispersion varies with location in the field and wavelength.
The PHOTOM reference files have the dispersion factored out, requiring that
the pipeline put the (variable, calculated per pixel) dispersion back in. Assumes that
the dispersion needs to be in Angstroms/pixel to match the required factor of ~10. [8207]
- Get the values of PIXAR_A2 and PIXAR_SR from AREA reference file
instead of PHOTOM reference file to avoid missmatching values. [8187]
- Added a hook to bypass the ``photom`` step when the ``extract_1d`` step
was bypassed and came before the ``photom`` step, e.g. for NIRISS SOSS
data in the FULL subarray. [8225]
- Removed blanket warning ignore for ``find_row``. [8320]
pipeline
--------
- Updated the ``calwebb_spec2`` pipeline to include NRS_BRIGHTOBJ in
the list of modes for running the ``nsclean`` step. [8256]
pixel_replace
-------------
- Fixed a bug that caused array size mismatches when the ``mingrad`` algorithm
was applied to NIRSpec data. [8312]
ramp_fitting
------------
- Modified one runtime warning filter. [8320]
- Updated tests to properly handle the C extension (forcing arrays to be
of an expected type. Modified the CHARGELESS portion of the ramp fit
step code to update read noise ramps only affected by CHARGELOSS. [8355]
refpix
------
- Modify NIRSpec IRS2 bad reference pixel flagging to consider values from
all groups in each integration and robustly replace bad values from their
nearest neighbors. [8197, 8214]
- Add option for NIRSpec IRS2 to preserve interleaved reference pixels in the
output file, for calibration and diagnostic purposes. [8255]
- Add option to correct for mean reference pixel offsets by amplifier and detector
column in NIRSpec IRS2 mode. [8143]
resample
--------
- Updated exposure time weighting to use the measurement time
(TMEASURE) when available. [8212]
- Removed product exposure time (``TEXPTIME``) from all computations
in the resample step. [8212]
- Use the same ``iscale`` value for resampling science data and variance arrays. [8159]
- Changed to use the high-level APE 14 API (``pixel_to_world_values`` and
``world_to_pixel_values``) for reproject, which also fixed a bug, and
removed support for astropy model [8172]
- Added sleep + check of output files that are median combined to fix intermittent
corruption of these files in operations [8305]
- Replace use of ``check_memory_allocation``. [8324]
- Removed any reference to the "tophat" kernel for resample step. [8364]
- Removing unnecessary warning. Errors are propagated identically for
the 'exptime' and 'ivm' weight options. [8258]
- Increased specificity of several warning filters. [8320]
- Changed deprecated ``stpipe.extern.configobj`` to ``astropy.extern.configobj``. [8320]
residual_fringe
---------------
- Fix a bug with 1d residual fringe zeroing out negative fluxes instead of
ignoring them. [8261]
scripts
-------
- Updated ``set_velocity_aberration`` to have an optional ``--force-level1bmodel``
flag. [8285]
- Remove ``migrate_data`` and ``move_wcs`` scripts. [8321]
stpipe
------
- Changed deprecated ``stpipe.extern.configobj`` to ``astropy.extern.configobj``. [8320]
source_catalog
--------------
- Suppress warnings from ``photutils.background.Background2D`` regarding
NaNs in the input data. [8308]
tweakreg
--------
- Update ``sregion`` after WCS corrections are applied. [8158]
- Add option to choose IRAFStarFinder and segmentation.SourceFinder
instead of DAOStarFinder and exposed star finder parameters. [8203]
- Suppress warnings from ``photutils.background.Background2D`` regarding
NaNs in the input data. [8308]
- Fixed a bug that caused failures instead of warnings when no GAIA sources
were found within the bounding box of the input image. [8334]
- Suppress AstropyUserWarnings regarding NaNs in the input data. [8320]
wfs_combine
-----------
- Fixed deprecated conversions of single-element numpy arrays to scalar. [8320]