Merge branch 'main' of https://github.com/spacetelescope/jwst into AL…

…-837

.github/workflows/build.yml

@@ -16,7 +16,7 @@ jobs:
     name: check that `requirements-sdp.txt` is populated
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871  # v4.2.1
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
       - run: grep -v '^ *#' requirements-sdp.txt
   build:
     needs: [ check ]

.github/workflows/changelog.yml

@@ -18,10 +18,10 @@ jobs:
     if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-changelog-entry-needed') }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3  # v5.2.0
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b  # v5.3.0
         with:
           python-version: 3
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871  # v4.2.1
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
         with:
           fetch-depth: 0
       - run: pip install .
@@ -32,7 +32,7 @@ jobs:
     if: ${{ !contains(github.event.pull_request.labels.*.name, 'allow-manual-changelog-edit') }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871  # v4.2.1
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
         with:
           fetch-depth: 0
       - name: prevent direct changes to `CHANGES.rst`

.github/workflows/ci.yml

@@ -34,8 +34,8 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871  # v4.2.1
-    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3  # v5.2.0
+    - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
+    - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b  # v5.3.0
       with:
         python-version: '3.12'
     - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd  # v3.0.1

changes/8907.pipeline.rst

@@ -0,0 +1 @@
+Fixed a bug leading to incorrect area extensions, and sometimes crashes, in the coron3 pipeline

changes/8926.docs.rst

@@ -0,0 +1 @@
+Mention possible need to provide package name to strun when using aliases.

docs/jwst/user_documentation/running_pipeline_command_line.rst

@@ -48,6 +48,14 @@ has the alias ``calwebb_detector1`` and can be run as
 
 A full list of pipeline aliases can be found in :ref:`Pipeline Stages <pipelines>`.
 
+
+.. note::
+
+   When using an **alias** with strun (for example ``strun resample``) you may
+   need to provide the ``jwst`` package name if you have other packages installed
+   that also use the same **alias**. The package name is provided prior to the
+   **alias** separated by ``::`` (for example ``strun jwst::resample``).
+
 .. _exit_status:
 
 Exit Status

jwst/pipeline/calwebb_coron3.py

@@ -30,7 +30,14 @@ def to_container(model):
                 'var_poisson', 'var_rnoise', 'var_flat'
         ]:
             try:
-                setattr(image, attribute, model.getarray_noinit(attribute)[plane])
+                arr = model.getarray_noinit(attribute)
+                if arr.ndim == 3:
+                    setattr(image, attribute, arr[plane])
+                elif arr.ndim == 2:
+                    setattr(image, attribute, arr)
+                else:
+                    msg = f"Unexpected array shape for extension {attribute}: {arr.shape}"
+                    raise ValueError(msg)
             except AttributeError:
                 pass
         image.update(model)

jwst/pipeline/tests/test_calwebb_coron3.py

@@ -3,6 +3,7 @@
 from stdatamodels.jwst.datamodels import CubeModel
 
 from jwst.pipeline.calwebb_coron3 import to_container
+import numpy as np
 
 
 # Generate data
@@ -22,6 +23,26 @@ def make_container():
 ]
 
 
+def test_to_container():
+    """Cover bug where IndexError would be raised when area extension of CubeModel
+    has shape (x,y) instead of (nints,x,y). In this case area extension should
+    be copied to each ImageModel in the ModelContainer.
+    """
+    shp = (10,5,5)
+    cube = CubeModel(shp)
+    extensions_3d = ['data', 'dq', 'err',]
+    for extension in extensions_3d:
+        setattr(cube, extension, np.random.rand(*shp))
+    cube.area = np.random.rand(5,5)
+
+    container = to_container(cube)
+    for i, model in enumerate(container):
+        for extension in extensions_3d:
+            assert np.all(getattr(model, extension) == getattr(cube, extension)[i])
+        assert hasattr(model, 'area')
+        assert np.all(model.area == cube.area)
+
+
 @pytest.mark.parametrize('cube, container', [(cube, container)])
 def test_container_shape(cube, container):
     """Test container shape"""