From a4323a05bde4dab2819fbcc32c3a69bfd5afca69 Mon Sep 17 00:00:00 2001 From: Tyler Pauly Date: Fri, 20 Dec 2024 16:42:10 -0500 Subject: [PATCH] preparation for 1.17.0 release (#9024) --- CHANGES.rst | 270 +++++++++++++++++++++++++++ CITATION.cff | 7 +- README.md | 19 +- changes/8210.general.rst | 1 - changes/8554.assign_wcs.rst | 2 - changes/8554.resample.rst | 1 - changes/8554.skymatch.rst | 1 - changes/8671.docs.rst | 1 - changes/8726.refpix.rst | 1 - changes/8761.stpipe.rst | 1 - changes/8782.outlier_detection.0.rst | 1 - changes/8782.outlier_detection.1.rst | 1 - changes/8782.resample.rst | 1 - changes/8787.background.rst | 1 - changes/8828.outlier_detection.rst | 1 - changes/8831.datamodels.rst | 1 - changes/8840.outlier_detection.rst | 1 - changes/8843.associations.rst | 1 - changes/8846.ami.rst | 1 - changes/8847.master_background.rst | 1 - changes/8849.emicorr.rst | 1 - changes/8851.outlier_detection.rst | 1 - changes/8852.general.rst | 1 - changes/8853.outlier_detection.rst | 1 - changes/8866.resample.rst | 1 - changes/8870.outlier_detection.rst | 1 - changes/8874.assign_wcs.rst | 1 - changes/8880.outlier_detection.rst | 1 - changes/8885.general.rst | 1 - changes/8890.jump.rst | 2 - changes/8892.skymatch.rst | 1 - changes/8893.resample.rst | 1 - changes/8897.assign_wcs.rst | 1 - changes/8907.pipeline.rst | 1 - changes/8908.resample_spec.rst | 1 - changes/8909.scripts.rst | 1 - changes/8911.cube_build.rst | 1 - changes/8913.cube_build.rst | 1 - changes/8916.background.rst | 1 - changes/8918.datamodels.rst | 1 - changes/8926.docs.rst | 1 - changes/8927.combine_1d.rst | 1 - changes/8927.master_background.rst | 1 - changes/8927.pipeline.rst | 1 - changes/8932.master_background.rst | 1 - changes/8935.general.rst | 1 - changes/8945.stpipe.rst | 1 - changes/8946.rscd.rst | 1 - changes/8947.pipeline.rst | 1 - changes/8950.general.rst | 1 - changes/8952.firstframe.rst | 1 - changes/8957.general.rst | 1 - changes/8958.general.rst | 1 - changes/8961.extract_1d.rst | 1 - changes/8963.assign_wcs.rst | 3 - changes/8966.general.rst | 1 - changes/8974.ami.rst | 1 - changes/8975.resample.rst | 1 - changes/8978.assign_wcs.rst | 1 - changes/8983.extract_1d.rst | 1 - changes/8990.background.rst | 1 - pyproject.toml | 6 +- requirements-sdp.txt | 78 ++++++++ 63 files changed, 366 insertions(+), 76 deletions(-) delete mode 100644 changes/8210.general.rst delete mode 100644 changes/8554.assign_wcs.rst delete mode 100644 changes/8554.resample.rst delete mode 100644 changes/8554.skymatch.rst delete mode 100644 changes/8671.docs.rst delete mode 100644 changes/8726.refpix.rst delete mode 100644 changes/8761.stpipe.rst delete mode 100644 changes/8782.outlier_detection.0.rst delete mode 100644 changes/8782.outlier_detection.1.rst delete mode 100644 changes/8782.resample.rst delete mode 100644 changes/8787.background.rst delete mode 100644 changes/8828.outlier_detection.rst delete mode 100644 changes/8831.datamodels.rst delete mode 100644 changes/8840.outlier_detection.rst delete mode 100644 changes/8843.associations.rst delete mode 100644 changes/8846.ami.rst delete mode 100644 changes/8847.master_background.rst delete mode 100644 changes/8849.emicorr.rst delete mode 100644 changes/8851.outlier_detection.rst delete mode 100644 changes/8852.general.rst delete mode 100644 changes/8853.outlier_detection.rst delete mode 100644 changes/8866.resample.rst delete mode 100644 changes/8870.outlier_detection.rst delete mode 100644 changes/8874.assign_wcs.rst delete mode 100644 changes/8880.outlier_detection.rst delete mode 100644 changes/8885.general.rst delete mode 100644 changes/8890.jump.rst delete mode 100644 changes/8892.skymatch.rst delete mode 100644 changes/8893.resample.rst delete mode 100644 changes/8897.assign_wcs.rst delete mode 100644 changes/8907.pipeline.rst delete mode 100644 changes/8908.resample_spec.rst delete mode 100644 changes/8909.scripts.rst delete mode 100644 changes/8911.cube_build.rst delete mode 100644 changes/8913.cube_build.rst delete mode 100644 changes/8916.background.rst delete mode 100644 changes/8918.datamodels.rst delete mode 100644 changes/8926.docs.rst delete mode 100644 changes/8927.combine_1d.rst delete mode 100644 changes/8927.master_background.rst delete mode 100644 changes/8927.pipeline.rst delete mode 100644 changes/8932.master_background.rst delete mode 100644 changes/8935.general.rst delete mode 100644 changes/8945.stpipe.rst delete mode 100644 changes/8946.rscd.rst delete mode 100644 changes/8947.pipeline.rst delete mode 100644 changes/8950.general.rst delete mode 100644 changes/8952.firstframe.rst delete mode 100644 changes/8957.general.rst delete mode 100644 changes/8958.general.rst delete mode 100644 changes/8961.extract_1d.rst delete mode 100644 changes/8963.assign_wcs.rst delete mode 100644 changes/8966.general.rst delete mode 100644 changes/8974.ami.rst delete mode 100644 changes/8975.resample.rst delete mode 100644 changes/8978.assign_wcs.rst delete mode 100644 changes/8983.extract_1d.rst delete mode 100644 changes/8990.background.rst diff --git a/CHANGES.rst b/CHANGES.rst index 1041652782..55f5f2c371 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,3 +1,273 @@ +1.17.0 (2024-12-20) +=================== + +General +------- + +- Rename default branch to main. (`#8210 + `_) +- Added mypy type checking to CI checks (`#8852 + `_) +- Give regtest okify results unique subdirectories. (`#8885 + `_) +- Include xml and db test data as package data for lib tests. (`#8935 + `_) +- Update minimum required version of crds to allow for "data release style" + contexts. (`#8950 `_) +- remove ``okify_regtests`` script (move to ``ci_watson``) (`#8957 + `_) +- When blending metadata don't store columns containing all missing value + (nans). (`#8958 `_) +- Increase asdf upper pin to 5 (`#8966 + `_) + + +Documentation +------------- + +- use ``towncrier`` to handle change log entries (`#8671 + `_) +- Mention possible need to provide package name to strun when using aliases. + (`#8926 `_) + + +``stpipe`` +---------- + +- Add warning that ``Step.__call__`` is deprecated. (`#8761 + `_) +- Remove all uses of Step.__call__ to allow it's deprecation. (`#8945 + `_) + + +Data Models +----------- + +- Remove memory-saving options from ModelContainer (`#8831 + `_) +- Update ModelLibrary to use meta.asn.exptype instead of meta.exptype. (`#8918 + `_) + + +Associations +------------ + +- Add mosaic association candidates to list of level three candidate types + requiring members from more than one observation (`#8843 + `_) + + +Scripts +------- + +- Remove the outdated schema_editor script. (`#8909 + `_) + + +Pipeline +-------- + +- Fixed a bug leading to incorrect area extensions, and sometimes crashes, in + the coron3 pipeline (`#8907 + `_) +- Add 'mbsub' to the list of known suffixes, for ``master_background`` + correction in ``calwebb_spec3``. (`#8927 + `_) +- Transfer wcsinfo metadata to new MultiSlitModel created during + ``calwebb_spec2`` processing of NIRSpec MSA data. (`#8947 + `_) + + +ami_analyze / ami_normalize / ami_average (ami3) +------------------------------------------------ + +- Change how AMI observables are averaged: average fringe quantities before + calculating additional observables. Update their error calculation: use + covariance of amplitudes/phases (and derived quantities) and standard error + of the mean. Code now expects an ASDF filename string for user-supplied + affine2d and bandpass input arguments. Example file creation in + documentation. (`#8846 + `_) +- Use mask and pupil geometry constants from NRM reference file, and apply + affine distortion from commissioning to LG model as default. (`#8974 + `_) + + +assign_wcs (image2, spec2) +-------------------------- + +- Use the range of points in the TabularModel to adjust the bounding_box in a + MIRI LRS FIXEDSLIT observation. + Ignore the bounding_box in running the inverse WCS transform when computing + crpix. (`#8554 `_) +- Catch NaN values in msa tables for source positions in slit and replace with + slit center. (`#8874 `_) +- Use pixel vertices to define s_region instead of pixel centers." (`#8897 + `_) +- Fix all bounding box assignments to wcs objects so that they are correctly + and + specifically assigned as order ``F`` boxes. This ensures consistency with the + assumptions made by GWCS for bounding boxes. (`#8963 + `_) +- Fix negative SHUTTRID values under numpy 2 (`#8978 + `_) + + +background (image2, spec2) +-------------------------- + +- Fixed crash when combining full and subarray observations for background + subtraction. (`#8787 `_) +- Apply bitwise operations in correct order when counting good pixels in the + background mask during WFSS background subtraction. (`#8916 + `_) +- Compute scaling for WFSS background subtraction using error-weighted mean + (`#8990 `_) + + +combine_1d (spec3) +------------------ + +- Fix wavelength sort order for single input spectrum. (`#8927 + `_) + + +cube_build (spec2 IFU, spec3) +----------------------------- + +- For moving-target IFU data, set RA, Dec header information of s3d products + according to the mean of input models instead of the first input model. + (`#8911 `_) +- Tweak the cube_build spaxel debugging option to provide filename info and + match outputs to the stated ordering. (`#8913 + `_) + + +emicorr (detector1 MIR) +----------------------- + +- Removed the interleaved noise array and do interleaving of noise and + subtraction in-place to avoid creating 2 arrays of equal dimensions to data. + (`#8849 `_) + + +extract_1d (spec2, spec3) +------------------------- + +- Refactor the core extraction algorithm and aperture definition modules for + slit and slitless extractions, for greater efficiency and maintainability. + Extraction reference files in FITS format are no longer supported. Current + behavior for extractions proceeding from extract1d reference files in JSON + format is preserved, with minor improvements: DQ arrays are populated and + error propagation is improved for some aperture types. (`#8961 + `_) +- Set order 2 weights to 1.0 for NIRISS SOSS SUBSTRIP96 data to avoid a + spurious flux drop in spectra around 1.5um. (`#8983 + `_) + + +firstframe (detector1 MIR) +-------------------------- + +- Update the firstframe step to optionally not flag when a ramp saturates in + group 3 (`#8952 `_) + + +jump (detector1) +---------------- + +- Add maximum_shower_amplitude parameter to MIRI cosmic rays showers routine + to fix accidental flagging of bright science pixels. (`#8890 + `_) + + +master_background (spec2 MOS, spec3) +------------------------------------ + +- Include resample, pixel_replace and extract_1d into MOS background pipeline + (`#8847 `_) +- Fix ModelContainer handling for user background input. (`#8927 + `_) +- Added pixel-to-pixel sigma clipping on input backgrounds in the NIRSpec MOS + master_background_mos step. Added option to median filter master background + spectrum in both the master_background and master_background_mos steps. + (`#8932 `_) + + +outlier_detection (image3, tso3, spec3, coron3) +----------------------------------------------- + +- Fix a bug that caused intermediate files to conflict for different slits when + a MultiSlitModel was processed. (`#8782 + `_) +- Decrease the amount of file I/O required to compute the median when in_memory + is set to False. (`#8782 + `_) +- For slit spectra, threshold outliers with a median error across exposures + instead of input error from the exposure itself. (`#8828 + `_) +- Moved median computers out of the jwst repository and into stcal. (`#8840 + `_) +- Update documentation to clarify the interaction between pipeline-level and + step-level `--in_memory` flags. (`#8851 + `_) +- Avoid modifying input and saving duplicate files when resample_data=False. + (`#8853 `_) +- Remove deprecated nlow and nhigh parameters from outlier detection step. + (`#8870 `_) +- reorganize outlier detection documentation (`#8880 + `_) + + +refpix (detector1) +------------------ + +- Implemented SIRS algorithm instead of running median for side pixels of NIR + full-frame data. Running median is still default. (`#8726 + `_) + + +resample (image2, image3, coron3) +--------------------------------- + +- Ignore the bounding_box in the inverse WCS transform in reproject. (`#8554 + `_) +- Permit creating drizzled models one at a time in many-to-many mode. (`#8782 + `_) +- Updated resample code to support the new ``drizzle`` API, see + https://github.com/spacetelescope/drizzle/pull/134 for more details. (`#8866 + `_) +- Use s_region list to calculate output footprint instead of re-computing via + WCS transforms (`#8893 + `_) +- Removed allowed_memory parameter and DMODEL_ALLOWED_MEMORY environment + variable (`#8975 `_) + + +resample_spec (spec2 MOS, spec3) +-------------------------------- + +- Update NIRSpec spectral resampling to add a missing correction factor in + resampled WCS tangent plane transformation. (`#8908 + `_) + + +rscd (detector1 MIR) +-------------------- + +- Updated RSCD step to work on segmented data (`#8946 + `_) + + +skymatch (image3) +----------------- + +- Ignore the bounding_box of an observation when computing sky statistics. + (`#8554 `_) +- Resolve warnings emitted by NumPy 2 when running skymatch. (`#8892 + `_) + + 1.16.1 (2024-10-30) =================== diff --git a/CITATION.cff b/CITATION.cff index 6d933fee0e..c660ccdba4 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -92,8 +92,11 @@ authors: - family-names: "Clarke" given-names: "Melanie" orcid: "https://orcid.org/0009-0002-3561-4347" +- family-names: "Filippazzo" + given-names: "Joseph" + orcid: "https://orcid.org/0000-0002-0201-8306" title: "JWST Calibration Pipeline" -version: 1.16.0 +version: 1.17.0 doi: 10.5281/zenodo.7038885 -date-released: 2024-09-20 +date-released: 2024-12-20 url: "https://github.com/spacetelescope/jwst" diff --git a/README.md b/README.md index 84d50d76c8..91be40ef59 100644 --- a/README.md +++ b/README.md @@ -59,7 +59,7 @@ You can also install a specific version: conda create -n python=3.11 conda activate - pip install jwst==1.9.4 + pip install jwst==1.16.1 ### Installing the development version from Github @@ -89,15 +89,15 @@ used for Linux and Mac OS systems. Linux: - conda create -n jwstdp-1.12.5 --file https://ssb.stsci.edu/releases/jwstdp/1.12.5/conda_python_stable-deps.txt - conda activate jwstdp-1.12.5 - pip install -r https://ssb.stsci.edu/releases/jwstdp/1.12.5/reqs_stable-deps.txt + conda create -n jwstdp-1.16.1 --file https://ssb.stsci.edu/releases/jwstdp/1.16.1/conda_python_stable-deps.txt + conda activate jwstdp-1.16.1 + pip install -r https://ssb.stsci.edu/releases/jwstdp/1.16.1/reqs_stable-deps.txt MacOS: - conda create -n jwstdp-1.12.5 --file https://ssb.stsci.edu/releases/jwstdp/1.12.5/conda_python_macos-stable-deps.txt - conda activate jwstdp-1.12.5 - pip install -r https://ssb.stsci.edu/releases/jwstdp/1.12.5/reqs_macos-stable-deps.txt + conda create -n jwstdp-1.16.1 --file https://ssb.stsci.edu/releases/jwstdp/1.16.1/conda_python_macos-stable-deps.txt + conda activate jwstdp-1.16.1 + pip install -r https://ssb.stsci.edu/releases/jwstdp/1.16.1/reqs_macos-stable-deps.txt Each DMS delivery has its own installation instructions, which may be found in the corresponding release documentation linked from this page: @@ -216,8 +216,9 @@ the specified context and less than the context for the next release. | jwst tag | DMS build | SDP_VER | CRDS_CONTEXT | Released | Ops Install | Notes | |---------------------|-----------|----------|--------------|------------|-------------|-----------------------------------------------| -| 1.16.1 | B11.1.1 | 2024.3.1 | 1298 | 2024-11-13 | TBD | Final release candidate for B11.1 | -| 1.16.0 | B11.1 | 2024.3.0 | 1298 | 2024-09-20 | TBD | First release candidate for B11.1 | +| 1.17.0rc1 | B11.2 | TBD | 1321 | 2024-12-20 | TBD | First release candidate for B11.2 | +| 1.16.1 | B11.1.1 | 2024.3.1 | 1303 | 2024-11-13 | 2024-12-06 | Final release candidate for B11.1 | +| 1.16.0 | B11.1 | 2024.3.0 | 1298 | 2024-09-20 | | First release candidate for B11.1 | | 1.15.1 | B11.0 | 2024.2.2 | 1293 | 2024-07-08 | 2024-09-12 | Final release candidate for B11.0 | | 1.15.0 | B11.0rc1 | | 1274 | 2024-06-26 | | First release candidate for B11.0 | | 1.14.1 | | | 1240 | 2024-06-27 | | PyPI-only release for external users | diff --git a/changes/8210.general.rst b/changes/8210.general.rst deleted file mode 100644 index b923267b54..0000000000 --- a/changes/8210.general.rst +++ /dev/null @@ -1 +0,0 @@ -Rename default branch to main. diff --git a/changes/8554.assign_wcs.rst b/changes/8554.assign_wcs.rst deleted file mode 100644 index c36dd9d167..0000000000 --- a/changes/8554.assign_wcs.rst +++ /dev/null @@ -1,2 +0,0 @@ -Use the range of points in the TabularModel to adjust the bounding_box in a MIRI LRS FIXEDSLIT observation. -Ignore the bounding_box in running the inverse WCS transform when computing crpix. diff --git a/changes/8554.resample.rst b/changes/8554.resample.rst deleted file mode 100644 index bda0397ae8..0000000000 --- a/changes/8554.resample.rst +++ /dev/null @@ -1 +0,0 @@ -Ignore the bounding_box in the inverse WCS transform in reproject. diff --git a/changes/8554.skymatch.rst b/changes/8554.skymatch.rst deleted file mode 100644 index 1561af36b6..0000000000 --- a/changes/8554.skymatch.rst +++ /dev/null @@ -1 +0,0 @@ -Ignore the bounding_box of an observation when computing sky statistics. diff --git a/changes/8671.docs.rst b/changes/8671.docs.rst deleted file mode 100644 index 724817599d..0000000000 --- a/changes/8671.docs.rst +++ /dev/null @@ -1 +0,0 @@ -use ``towncrier`` to handle change log entries diff --git a/changes/8726.refpix.rst b/changes/8726.refpix.rst deleted file mode 100644 index 0639bf5208..0000000000 --- a/changes/8726.refpix.rst +++ /dev/null @@ -1 +0,0 @@ -Implemented SIRS algorithm instead of running median for side pixels of NIR full-frame data. Running median is still default. diff --git a/changes/8761.stpipe.rst b/changes/8761.stpipe.rst deleted file mode 100644 index 3d2985c04f..0000000000 --- a/changes/8761.stpipe.rst +++ /dev/null @@ -1 +0,0 @@ -Add warning that ``Step.__call__`` is deprecated. diff --git a/changes/8782.outlier_detection.0.rst b/changes/8782.outlier_detection.0.rst deleted file mode 100644 index 469e927e44..0000000000 --- a/changes/8782.outlier_detection.0.rst +++ /dev/null @@ -1 +0,0 @@ -Decrease the amount of file I/O required to compute the median when in_memory is set to False. \ No newline at end of file diff --git a/changes/8782.outlier_detection.1.rst b/changes/8782.outlier_detection.1.rst deleted file mode 100644 index a1f9bd8e55..0000000000 --- a/changes/8782.outlier_detection.1.rst +++ /dev/null @@ -1 +0,0 @@ -Fix a bug that caused intermediate files to conflict for different slits when a MultiSlitModel was processed. \ No newline at end of file diff --git a/changes/8782.resample.rst b/changes/8782.resample.rst deleted file mode 100644 index 05b3e87052..0000000000 --- a/changes/8782.resample.rst +++ /dev/null @@ -1 +0,0 @@ -Permit creating drizzled models one at a time in many-to-many mode. diff --git a/changes/8787.background.rst b/changes/8787.background.rst deleted file mode 100644 index 9f04f7e0bd..0000000000 --- a/changes/8787.background.rst +++ /dev/null @@ -1 +0,0 @@ -Fixed crash when combining full and subarray observations for background subtraction. diff --git a/changes/8828.outlier_detection.rst b/changes/8828.outlier_detection.rst deleted file mode 100644 index e0edcecb80..0000000000 --- a/changes/8828.outlier_detection.rst +++ /dev/null @@ -1 +0,0 @@ -For slit spectra, threshold outliers with a median error across exposures instead of input error from the exposure itself. diff --git a/changes/8831.datamodels.rst b/changes/8831.datamodels.rst deleted file mode 100644 index 22289006df..0000000000 --- a/changes/8831.datamodels.rst +++ /dev/null @@ -1 +0,0 @@ -Remove memory-saving options from ModelContainer \ No newline at end of file diff --git a/changes/8840.outlier_detection.rst b/changes/8840.outlier_detection.rst deleted file mode 100644 index 0d1fe91bb7..0000000000 --- a/changes/8840.outlier_detection.rst +++ /dev/null @@ -1 +0,0 @@ -Moved median computers out of the jwst repository and into stcal. \ No newline at end of file diff --git a/changes/8843.associations.rst b/changes/8843.associations.rst deleted file mode 100644 index e6d2334960..0000000000 --- a/changes/8843.associations.rst +++ /dev/null @@ -1 +0,0 @@ -Add mosaic association candidates to list of level three candidate types requiring members from more than one observation \ No newline at end of file diff --git a/changes/8846.ami.rst b/changes/8846.ami.rst deleted file mode 100644 index a965c823ff..0000000000 --- a/changes/8846.ami.rst +++ /dev/null @@ -1 +0,0 @@ -Change how AMI observables are averaged: average fringe quantities before calculating additional observables. Update their error calculation: use covariance of amplitudes/phases (and derived quantities) and standard error of the mean. Code now expects an ASDF filename string for user-supplied affine2d and bandpass input arguments. Example file creation in documentation. \ No newline at end of file diff --git a/changes/8847.master_background.rst b/changes/8847.master_background.rst deleted file mode 100644 index f1b516a1f2..0000000000 --- a/changes/8847.master_background.rst +++ /dev/null @@ -1 +0,0 @@ -Include resample, pixel_replace and extract_1d into MOS background pipeline diff --git a/changes/8849.emicorr.rst b/changes/8849.emicorr.rst deleted file mode 100644 index aee1210d87..0000000000 --- a/changes/8849.emicorr.rst +++ /dev/null @@ -1 +0,0 @@ -Removed the interleaved noise array and do interleaving of noise and subtraction in-place to avoid creating 2 arrays of equal dimensions to data. diff --git a/changes/8851.outlier_detection.rst b/changes/8851.outlier_detection.rst deleted file mode 100644 index da2e49986d..0000000000 --- a/changes/8851.outlier_detection.rst +++ /dev/null @@ -1 +0,0 @@ -Update documentation to clarify the interaction between pipeline-level and step-level `--in_memory` flags. \ No newline at end of file diff --git a/changes/8852.general.rst b/changes/8852.general.rst deleted file mode 100644 index 0a584e8d63..0000000000 --- a/changes/8852.general.rst +++ /dev/null @@ -1 +0,0 @@ -Added mypy type checking to CI checks diff --git a/changes/8853.outlier_detection.rst b/changes/8853.outlier_detection.rst deleted file mode 100644 index abb775f6c8..0000000000 --- a/changes/8853.outlier_detection.rst +++ /dev/null @@ -1 +0,0 @@ -Avoid modifying input and saving duplicate files when resample_data=False. diff --git a/changes/8866.resample.rst b/changes/8866.resample.rst deleted file mode 100644 index f31024d0ee..0000000000 --- a/changes/8866.resample.rst +++ /dev/null @@ -1 +0,0 @@ -Updated resample code to support the new ``drizzle`` API, see https://github.com/spacetelescope/drizzle/pull/134 for more details. diff --git a/changes/8870.outlier_detection.rst b/changes/8870.outlier_detection.rst deleted file mode 100644 index 53ce01221d..0000000000 --- a/changes/8870.outlier_detection.rst +++ /dev/null @@ -1 +0,0 @@ -Remove deprecated nlow and nhigh parameters from outlier detection step. diff --git a/changes/8874.assign_wcs.rst b/changes/8874.assign_wcs.rst deleted file mode 100644 index d27218f8d4..0000000000 --- a/changes/8874.assign_wcs.rst +++ /dev/null @@ -1 +0,0 @@ -Catch NaN values in msa tables for source positions in slit and replace with slit center. \ No newline at end of file diff --git a/changes/8880.outlier_detection.rst b/changes/8880.outlier_detection.rst deleted file mode 100644 index f5642b4e30..0000000000 --- a/changes/8880.outlier_detection.rst +++ /dev/null @@ -1 +0,0 @@ -reorganize outlier detection documentation diff --git a/changes/8885.general.rst b/changes/8885.general.rst deleted file mode 100644 index 435de02426..0000000000 --- a/changes/8885.general.rst +++ /dev/null @@ -1 +0,0 @@ -Give regtest okify results unique subdirectories. diff --git a/changes/8890.jump.rst b/changes/8890.jump.rst deleted file mode 100644 index d04413a547..0000000000 --- a/changes/8890.jump.rst +++ /dev/null @@ -1,2 +0,0 @@ -Add maximum_shower_amplitude parameter to MIRI cosmic rays showers routine -to fix accidental flagging of bright science pixels. diff --git a/changes/8892.skymatch.rst b/changes/8892.skymatch.rst deleted file mode 100644 index 7662782814..0000000000 --- a/changes/8892.skymatch.rst +++ /dev/null @@ -1 +0,0 @@ -Resolve warnings emitted by NumPy 2 when running skymatch. diff --git a/changes/8893.resample.rst b/changes/8893.resample.rst deleted file mode 100644 index 9e48ecea89..0000000000 --- a/changes/8893.resample.rst +++ /dev/null @@ -1 +0,0 @@ -Use s_region list to calculate output footprint instead of re-computing via WCS transforms diff --git a/changes/8897.assign_wcs.rst b/changes/8897.assign_wcs.rst deleted file mode 100644 index fb209a0fdc..0000000000 --- a/changes/8897.assign_wcs.rst +++ /dev/null @@ -1 +0,0 @@ -Use pixel vertices to define s_region instead of pixel centers." diff --git a/changes/8907.pipeline.rst b/changes/8907.pipeline.rst deleted file mode 100644 index c6d1759f93..0000000000 --- a/changes/8907.pipeline.rst +++ /dev/null @@ -1 +0,0 @@ -Fixed a bug leading to incorrect area extensions, and sometimes crashes, in the coron3 pipeline diff --git a/changes/8908.resample_spec.rst b/changes/8908.resample_spec.rst deleted file mode 100644 index 2d69d9feee..0000000000 --- a/changes/8908.resample_spec.rst +++ /dev/null @@ -1 +0,0 @@ -Update NIRSpec spectral resampling to add a missing correction factor in resampled WCS tangent plane transformation. \ No newline at end of file diff --git a/changes/8909.scripts.rst b/changes/8909.scripts.rst deleted file mode 100644 index 0addc426d1..0000000000 --- a/changes/8909.scripts.rst +++ /dev/null @@ -1 +0,0 @@ -Remove the outdated schema_editor script. diff --git a/changes/8911.cube_build.rst b/changes/8911.cube_build.rst deleted file mode 100644 index e6de4d2827..0000000000 --- a/changes/8911.cube_build.rst +++ /dev/null @@ -1 +0,0 @@ -For moving-target IFU data, set RA, Dec header information of s3d products according to the mean of input models instead of the first input model. diff --git a/changes/8913.cube_build.rst b/changes/8913.cube_build.rst deleted file mode 100644 index 2fd2ff006f..0000000000 --- a/changes/8913.cube_build.rst +++ /dev/null @@ -1 +0,0 @@ -Tweak the cube_build spaxel debugging option to provide filename info and match outputs to the stated ordering. diff --git a/changes/8916.background.rst b/changes/8916.background.rst deleted file mode 100644 index e2e4414b14..0000000000 --- a/changes/8916.background.rst +++ /dev/null @@ -1 +0,0 @@ -Apply bitwise operations in correct order when counting good pixels in the background mask during WFSS background subtraction. \ No newline at end of file diff --git a/changes/8918.datamodels.rst b/changes/8918.datamodels.rst deleted file mode 100644 index 2d442399f7..0000000000 --- a/changes/8918.datamodels.rst +++ /dev/null @@ -1 +0,0 @@ -Update ModelLibrary to use meta.asn.exptype instead of meta.exptype. diff --git a/changes/8926.docs.rst b/changes/8926.docs.rst deleted file mode 100644 index 621c1a9254..0000000000 --- a/changes/8926.docs.rst +++ /dev/null @@ -1 +0,0 @@ -Mention possible need to provide package name to strun when using aliases. diff --git a/changes/8927.combine_1d.rst b/changes/8927.combine_1d.rst deleted file mode 100644 index b05b3e95bc..0000000000 --- a/changes/8927.combine_1d.rst +++ /dev/null @@ -1 +0,0 @@ -Fix wavelength sort order for single input spectrum. diff --git a/changes/8927.master_background.rst b/changes/8927.master_background.rst deleted file mode 100644 index cf71da1e52..0000000000 --- a/changes/8927.master_background.rst +++ /dev/null @@ -1 +0,0 @@ -Fix ModelContainer handling for user background input. diff --git a/changes/8927.pipeline.rst b/changes/8927.pipeline.rst deleted file mode 100644 index e03ac78254..0000000000 --- a/changes/8927.pipeline.rst +++ /dev/null @@ -1 +0,0 @@ -Add 'mbsub' to the list of known suffixes, for ``master_background`` correction in ``calwebb_spec3``. diff --git a/changes/8932.master_background.rst b/changes/8932.master_background.rst deleted file mode 100644 index 4ad13be5d5..0000000000 --- a/changes/8932.master_background.rst +++ /dev/null @@ -1 +0,0 @@ -Added pixel-to-pixel sigma clipping on input backgrounds in the NIRSpec MOS master_background_mos step. Added option to median filter master background spectrum in both the master_background and master_background_mos steps. diff --git a/changes/8935.general.rst b/changes/8935.general.rst deleted file mode 100644 index fe0b6a58e2..0000000000 --- a/changes/8935.general.rst +++ /dev/null @@ -1 +0,0 @@ -Include xml and db test data as package data for lib tests. diff --git a/changes/8945.stpipe.rst b/changes/8945.stpipe.rst deleted file mode 100644 index 73937c9f0f..0000000000 --- a/changes/8945.stpipe.rst +++ /dev/null @@ -1 +0,0 @@ -Remove all uses of Step.__call__ to allow it's deprecation. diff --git a/changes/8946.rscd.rst b/changes/8946.rscd.rst deleted file mode 100644 index 5ef30ed606..0000000000 --- a/changes/8946.rscd.rst +++ /dev/null @@ -1 +0,0 @@ -Updated RSCD step to work on segmented data diff --git a/changes/8947.pipeline.rst b/changes/8947.pipeline.rst deleted file mode 100644 index 2c24cc6f0b..0000000000 --- a/changes/8947.pipeline.rst +++ /dev/null @@ -1 +0,0 @@ -Transfer wcsinfo metadata to new MultiSlitModel created during ``calwebb_spec2`` processing of NIRSpec MSA data. \ No newline at end of file diff --git a/changes/8950.general.rst b/changes/8950.general.rst deleted file mode 100644 index 466db73740..0000000000 --- a/changes/8950.general.rst +++ /dev/null @@ -1 +0,0 @@ -Update minimum required version of crds to allow for "data release style" contexts. diff --git a/changes/8952.firstframe.rst b/changes/8952.firstframe.rst deleted file mode 100644 index ff41581d2f..0000000000 --- a/changes/8952.firstframe.rst +++ /dev/null @@ -1 +0,0 @@ -Update the firstframe step to optionally not flag when a ramp saturates in group 3 \ No newline at end of file diff --git a/changes/8957.general.rst b/changes/8957.general.rst deleted file mode 100644 index 91a475dc0f..0000000000 --- a/changes/8957.general.rst +++ /dev/null @@ -1 +0,0 @@ -remove ``okify_regtests`` script (move to ``ci_watson``) diff --git a/changes/8958.general.rst b/changes/8958.general.rst deleted file mode 100644 index a84befe1ff..0000000000 --- a/changes/8958.general.rst +++ /dev/null @@ -1 +0,0 @@ -When blending metadata don't store columns containing all missing value (nans). diff --git a/changes/8961.extract_1d.rst b/changes/8961.extract_1d.rst deleted file mode 100644 index ce89d4c2b9..0000000000 --- a/changes/8961.extract_1d.rst +++ /dev/null @@ -1 +0,0 @@ -Refactor the core extraction algorithm and aperture definition modules for slit and slitless extractions, for greater efficiency and maintainability. Extraction reference files in FITS format are no longer supported. Current behavior for extractions proceeding from extract1d reference files in JSON format is preserved, with minor improvements: DQ arrays are populated and error propagation is improved for some aperture types. diff --git a/changes/8963.assign_wcs.rst b/changes/8963.assign_wcs.rst deleted file mode 100644 index b9f007448a..0000000000 --- a/changes/8963.assign_wcs.rst +++ /dev/null @@ -1,3 +0,0 @@ -Fix all bounding box assignments to wcs objects so that they are correctly and -specifically assigned as order ``F`` boxes. This ensures consistency with the -assumptions made by GWCS for bounding boxes. diff --git a/changes/8966.general.rst b/changes/8966.general.rst deleted file mode 100644 index 5b21ca6897..0000000000 --- a/changes/8966.general.rst +++ /dev/null @@ -1 +0,0 @@ -Increase asdf upper pin to 5 diff --git a/changes/8974.ami.rst b/changes/8974.ami.rst deleted file mode 100644 index ea39be8806..0000000000 --- a/changes/8974.ami.rst +++ /dev/null @@ -1 +0,0 @@ -Use mask and pupil geometry constants from NRM reference file, and apply affine distortion from commissioning to LG model as default. \ No newline at end of file diff --git a/changes/8975.resample.rst b/changes/8975.resample.rst deleted file mode 100644 index 95d48e855e..0000000000 --- a/changes/8975.resample.rst +++ /dev/null @@ -1 +0,0 @@ -Removed allowed_memory parameter and DMODEL_ALLOWED_MEMORY environment variable diff --git a/changes/8978.assign_wcs.rst b/changes/8978.assign_wcs.rst deleted file mode 100644 index 2771c1d3c6..0000000000 --- a/changes/8978.assign_wcs.rst +++ /dev/null @@ -1 +0,0 @@ -Fix negative SHUTTRID values under numpy 2 diff --git a/changes/8983.extract_1d.rst b/changes/8983.extract_1d.rst deleted file mode 100644 index 5bf93662f2..0000000000 --- a/changes/8983.extract_1d.rst +++ /dev/null @@ -1 +0,0 @@ -Set order 2 weights to 1.0 for NIRISS SOSS SUBSTRIP96 data to avoid a spurious flux drop in spectra around 1.5um. diff --git a/changes/8990.background.rst b/changes/8990.background.rst deleted file mode 100644 index ed656009a4..0000000000 --- a/changes/8990.background.rst +++ /dev/null @@ -1 +0,0 @@ -Compute scaling for WFSS background subtraction using error-weighted mean diff --git a/pyproject.toml b/pyproject.toml index 12c5996d16..3342f6b90e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,9 +33,9 @@ dependencies = [ "scikit-image>=0.20.0", "scipy>=1.14.1", "spherical-geometry>=1.2.22", - "stcal @ git+https://github.com/spacetelescope/stcal.git@main", - "stdatamodels @ git+https://github.com/spacetelescope/stdatamodels.git@main", - "stpipe @ git+https://github.com/spacetelescope/stpipe.git@main", + "stcal>=1.11.0,<1.12.0", + "stdatamodels>=2.2.0,<2.3.0", + "stpipe>=0.8.0,<0.9.0", "stsci.imagestats>=1.6.3", "synphot>=1.2", "tweakwcs>=0.8.8", diff --git a/requirements-sdp.txt b/requirements-sdp.txt index a110a4b011..f6f1a9c478 100644 --- a/requirements-sdp.txt +++ b/requirements-sdp.txt @@ -14,3 +14,81 @@ # conda activate sdp # pip install -e .[test,sdp] # pip freeze | grep -v jwst >> requirements-sdp.txt +asdf==4.0.0 +asdf-astropy==0.7.0 +asdf_coordinates_schemas==0.3.0 +asdf_standard==1.1.1 +asdf_transform_schemas==0.5.0 +asdf_wcs_schemas==0.4.0 +astropy==7.0.0 +astropy-iers-data==0.2024.12.16.0.35.48 +attrs==24.3.0 +BayesicFitting==3.2.3 +certifi==2024.12.14 +charset-normalizer==3.4.0 +ci_watson==0.8.0 +colorama==0.4.6 +contourpy==1.3.1 +coverage==7.6.9 +crds==12.0.8 +cycler==0.12.1 +drizzle==2.0.0 +et_xmlfile==2.0.0 +filelock==3.16.1 +fonttools==4.55.3 +future==1.0.0 +gwcs==0.22.1 +idna==3.10 +imageio==2.36.1 +importlib_metadata==8.5.0 +iniconfig==2.0.0 +jmespath==1.0.1 +jplephem==2.22 +jsonschema==4.23.0 +jsonschema-specifications==2024.10.1 +kiwisolver==1.4.7 +lazy_loader==0.4 +lxml==5.3.0 +matplotlib==3.10.0 +networkx==3.4.2 +numpy==1.26.4 +opencv-python-headless==4.10.0.84 +openpyxl==3.1.5 +packaging==24.2 +Parsley==1.3 +photutils==2.0.2 +pillow==11.0.0 +pluggy==1.5.0 +poppy==1.1.1 +pyerfa==2.0.1.5 +pyparsing==3.2.0 +pysiaf==0.24.1 +pytest==8.3.4 +pytest-cov==6.0.0 +pytest-doctestplus==1.3.0 +python-dateutil==2.9.0.post0 +PyYAML==6.0.2 +readchar==4.2.1 +referencing==0.35.1 +requests==2.32.3 +requests-mock==1.12.1 +rpds-py==0.22.3 +ruff==0.8.4 +scikit-image==0.25.0 +scipy==1.14.1 +semantic-version==2.10.0 +setuptools==75.1.0 +six==1.17.0 +spherical_geometry==1.3.2 +stcal==1.11.0 +stdatamodels==2.2.0 +stpipe==0.8.0 +stsci.imagestats==1.8.3 +stsci.stimage==0.2.9 +synphot==1.5.0 +tifffile==2024.12.12 +tweakwcs==0.8.9 +urllib3==2.2.3 +wheel==0.44.0 +wiimatch==0.3.2 +zipp==3.21.0