Stcal

===================

Changes to API
--------------

- Added ``resample`` submodule. (`320
<https://github.com/spacetelescope/stcal/issues/320>`_)
- Refactoring the jump module to improve memory consumption, readability, and
maintenance. (`330 <https://github.com/spacetelescope/stcal/issues/330>`_)
- Removed all references to the unused ramp error array in dark, jump, and ramp
fitting steps. (`334 <https://github.com/spacetelescope/stcal/issues/334>`_)
- Make sregion_to_footprint part of public API (`345
<https://github.com/spacetelescope/stcal/issues/345>`_)


Bug Fixes
---------

- Fix a bug in ``alignment.util.wcs_from_sregions()`` and
``alignment.util.wcs_from_footprints()`` functions that was causing incorrect
WCS bounding boxes
when the ``crpix`` argument was provided. (`326
<https://github.com/spacetelescope/stcal/issues/326>`_)
- Allow tweakreg to parse absolute reference catalogs with skycoord objects in
them (`333 <https://github.com/spacetelescope/stcal/issues/333>`_)
- Fix a bug in the jump step with counting the number of usable groups. (`338
<https://github.com/spacetelescope/stcal/issues/338>`_)
- Do not reset existing JUMP flags at the start of the likelihood ramp fitting
algorithm. (`339 <https://github.com/spacetelescope/stcal/issues/339>`_)
- Fix a bug in ``jump.twopointdifference.calc_med_first_diffs()`` where
``argmax`` was being used instead of ``nanargmax``. (`344
<https://github.com/spacetelescope/stcal/issues/344>`_)
- Changed multiprocessing from forkserver to spawn. (`350
<https://github.com/spacetelescope/stcal/issues/350>`_)


General
-------

- Move common parts of skymatch shared by both jwst and romancal into stcal.
(`310 <https://github.com/spacetelescope/stcal/issues/310>`_)
- Drop support for Python 3.10 and add support for Python 3.13. (`327
<https://github.com/spacetelescope/stcal/issues/327>`_)
- Performance improvements for saturation step (`331
<https://github.com/spacetelescope/stcal/issues/331>`_)
- Performance improvements for jump step targeting both runtime and memory
consumption. Results are mostly identical, but there are some differences in
the MIRI shower flagging (it now flags somewhat fewer showers). (`337
<https://github.com/spacetelescope/stcal/issues/337>`_)
- Refactoring twopoint_difference.py for the jump step. (`340
<https://github.com/spacetelescope/stcal/issues/340>`_)

===================

Changes to API
--------------

- Add maximum_shower_amplitude parameter to MIRI cosmic rays showers routine
to fix accidental flagging of bright science pixels. (`306
<https://github.com/spacetelescope/stcal/issues/306>`_)


Bug Fixes
---------

- Do not evaluate the inverse WCS transform within the bounding box in cases
where a resampled WCS is computed. Do not pass table columns to the WCS
Shared API. (`314 <https://github.com/spacetelescope/stcal/issues/314>`_)
- For `ramp_fitting`, the `CRMAG` element was not originally implemented in
the C-extension for ramp fitting. It is now implemented. A bug in the read
noise recalculation for CHARGELOSS when using the multiprocessing option has
been fixed. Further, in `JWST` regression tests have been added to test for
multiprocessing to ensure testing for anything that could affect
multiprocessing. (`318
<https://github.com/spacetelescope/stcal/issues/318>`_)
- Update weight threshold calculation in outlier detection to work around numpy
bug that introduces small numerical differences for a mean of a masked array.
(`319 <https://github.com/spacetelescope/stcal/issues/319>`_)
- Change flagging of 'pre-saturation' grouped data to use DO_NOT_USE instead of
SATURATION flag to avoid confusing the snowball routine downstream. (`321
<https://github.com/spacetelescope/stcal/issues/321>`_)

===================

Changes to API
--------------

- Add `outlier_detection` median calculators from jwst. (`292
<https://github.com/spacetelescope/stcal/issues/292>`_)
- Deprecate wcs_from_footprints. Use wcs_from_sregions instead. (`307
<https://github.com/spacetelescope/stcal/issues/307>`_)
- Add wcs_from_sregions function to compute a combined WCS from a list of
s_regions. (`307 <https://github.com/spacetelescope/stcal/issues/307>`_)


Bug Fixes
---------

- Fix `IntEnum` saturation flag issue with numpy 2+ for romancal. (`305
<https://github.com/spacetelescope/stcal/issues/305>`_)
- Fix abs_deriv handling of off-edge and nan values. (`311
<https://github.com/spacetelescope/stcal/issues/311>`_)


General
-------

- Added fillval option to ``gwcs_blot`` utility. (`291
<https://github.com/spacetelescope/stcal/issues/291>`_)
- Update downstream tests for jwst and romancal to fix pytest configurations.
(`297 <https://github.com/spacetelescope/stcal/issues/297>`_)
- Changed the default `ramp fitting` CI test algorithm to ``OLS_C``. This also
revealed
a bug in control flow that allowed for the CHARGELOSS recalculation in error,
which
resulted in a crash while attempting to dereference a ``NULL`` pointer.
Further, when
creating the optional results product, the object creation was changed to
`PyArray_ZEROS`
to ensure invalid data was set to zero. The use of `PyArray_EMPTY` does not
initialize
memory, so junk data could be in used array elements. (`298
<https://github.com/spacetelescope/stcal/issues/298>`_)
- Add infrastructure for testing memory usage (`299
<https://github.com/spacetelescope/stcal/issues/299>`_)
- Preparing ramp fitting for the upgrade to python 3.13. In python 3.13, the
C-API
function ``PyLong_AsLong`` raises an exception if the object passed to it is
``NoneType``. There are two integer attributes for the ``RampData`` class
that
can be ``NoneType``, so a check for ``NoneType`` for these attributes was
added. (`303 <https://github.com/spacetelescope/stcal/issues/303>`_)

==================

Changes to API
--------------

- [ramp_fitting] Add the likelihood algorithm to ramp fitting. (`278
<https://github.com/spacetelescope/stcal/issues/278>`_)


Bug Fixes
---------

- [saturation] Add option for using the readout pattern information to improve
saturation flagging in grouped data. (`283
<https://github.com/spacetelescope/stcal/issues/283>`_)


General
-------

- Add clip_accum parameter to alignment methods. (`286
<https://github.com/spacetelescope/stcal/issues/286>`_)
- Improve handling of catalog web service connectivity issues. (`286
<https://github.com/spacetelescope/stcal/issues/286>`_)

==================

Bug Fixes
---------

- Implement byteorder swap method that is forward-compatible with numpy 2.0 in
jwst ramp_fitting. (`282
<https://github.com/spacetelescope/stcal/issues/282>`_)
- [jump] Fix a logical bug in the jump step for usage of > vs >= per JP-3689.
(`285 <https://github.com/spacetelescope/stcal/issues/285>`_)


General
-------

- [ramp_fitting] Moving the read noise recalculation due to CHARGELOSS flagging
from
the JWST ramp fit step code into the STCAL ramp fit C-extension. (`275
<https://github.com/spacetelescope/stcal/issues/275>`_)

==================

Bug Fixes
---------

- Fixed memory leak in C-extension. (`281
<https://github.com/spacetelescope/stcal/issues/281>`_)


General
-------

- use ``towncrier`` to handle changelog entries (`284
<https://github.com/spacetelescope/stcal/issues/284>`_)