Pjpipe

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

- Removed raised warning in ``multi_tile_destripe_step`` when input images have a variety of
rotations
- Added ``combine_nircam_short`` option in ``level_match_step``, which will match levels
between the four NIRCam short imaging chips before doing matching between mosaic tiles
- ``lv2_step`` will now propagate through individual exposure offset times from backgrounds,
which is necessary for selecting a reference image in ``level_match_step``
- Added ``fit_type`` option to ``level_match_step`` for every option, which allows for
plane fitting in the level matching in a modular way
- ``level_match_step`` fitting method has been changed to resemble the iterative Montage method,
which is necessary for plane fitting
- ``reproject_image`` in ``utils`` can now also reproject error arrays
- ``make_stacked_image`` in ``utils`` can now also reproject the error and readnoise maps
- Exposed ``auto_rotate`` in ``make_stacked_image`` in ``utils``
- Added prefilter option to ``get_wcs_adjust``, which uses constrained diffusion to remove large-scale structure
- Added ``recombine_lyot`` option to ``level_match_step``, which allows for recombining
the lyot coronagraph into the main MIRI science chip before matching between mosaic tiles
- Tidied up ``level_match_step`` to make more modular and functional
- Fix bug in ``astrometric_align_step`` if first pass of alignment succeeds but second
fails
- Add cross-correlation option to ``get_wcs_adjust_step``, which uses ``spacepylot``
- Add control over reproject functions, can be ``reproject_interp`` (default), ``reproject_exact``,
or ``reproject_adaptive``. For MIRI, ``reproject_exact`` may work better. This applies to ``anchoring_step``,
``astrometric_align_step``, ``level_match_step``, ``multi_tile_destripe_step``, ``psf_matching_step``, and
``release_step``
- Fix bug for lv1 hanging on newer Macbooks
- Fix bug for parameters with 'pix' in getting picked up like numbers of pixels
- Updated PHANGS Cy3 config
- Include links to Francesco Belfiore's kernel generation repository in the docs
- Updated various package requirements
- Updated indexing to align with new ``reproject`` updates

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

- If science lv1 data already exists, just copy it over for background data to save processing time
- Include BMAJ in ``psf_matching_step``
- Auto rotate the WCS in ``level_match_step``
- Fix SIP approximation issues in ``apply_wcs_adjust_step``
- ``astrometric_catalog_step`` can now use either DAOStarFinder or IRAFStarFinder. Observatory recommendations seem
to be IRAFStarFinder in general
- Removed factor of 2 for FWHM in lv3 tweakreg-related steps to more closely match observatory recommendations
- Add lower version pins to project requirements to avoid incompatibilities
- Fixed bug in ``astrometric_align_step`` where file might already be closed before saving
- Updated PHANGS Cycle 1 config to v1p1 (last couple of observations, and a few small changes to the config)
- Fix bug with ``process_bgr_like_science`` in ``lv3_step``
- Added 'filename' option for background association
- Fix in ``parse_fits_to_table`` when there is not a defined observation label
- Point Zenodo DOI to "concept" DOI, rather than latest
- Cleaner labels in ``anchoring_step``
- Add acknowledgment for PCA (thanks Liz!)
- Added CITATION.cff

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

- Fix del in ``get_wcs_adjust`` if we skip alignment
- Made plots more consistent and "publication ready" across the board
- Fix bug in ``anchoring step``
- Rename ``anchor_to_external_step.py`` to ``anchor_step.py`` for consistency
- Fix "too many plots open" warning in ``anchoring_step``
- Include useful pjpipe version info in files
- Save anchoring background in metadata properly in ``anchoring_step``
- Add Zenodo badge

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

- Fix packaging to minimise file size
- Error in ``pyproject.toml``

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

- Added documentation
- Ensure ``multi_tile_destripe_step`` is properly imported in the pipeline
- Remove an error in ``multi_tile_destripe_step`` stripes in stacked image don't align with any particular
axis of the array
- Fix crash where quadrants are turned off in median filtering in ``single_tile_destripe_step``
- Fix potential memory leaks in ``get_wcs_adjust_step`` and ``apply_wcs_adjust_step``
- Diagnostic plots are compressed by default in ``release_step``

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

- Can specify CRDS context at the pipeline level
- median_filter is now the default in ``single_tile_destripe_step``
- Added fallback for median_filter in ``single_tile_destripe_step`` when too much data is masked
- Remove mask option in median_filter in ``single_tile_destripe_step``, since it's always used
anyway
- Changed up how ``do_large_scale`` works in ``multi_tile_destripe_step``,
which seems significantly improved and simplified
- Added fallback for in ``multi_tile_destripe_step`` when too much data is masked in quadrants
- Changed how tweakreg grouping is done in ``get_wcs_adjust_step`` and ``lv3_step`` to account
for code changes in the pipeline
- Added option to decouple the short NIRCam chips for tweakreg in ``lv3_step``
- Added option to move the various diagnostic plots in ``release_step``
- ``remove_bloat`` is now False by default in ``release step``, to maintain datamodels compatibility
- ``remove_bloat`` also applies to PSF matched files in ``release_step``