Merge branch 'main' into ci/separate_devdeps

.github/workflows/ci.yml

@@ -32,53 +32,16 @@ jobs:
         - linux: py39-oldestdeps-cov-xdist
         - linux: py39-xdist
         - linux: py310-xdist
-        - linux: py311-xdist
-        - macos: py311-xdist
-        - linux: py3-xdist-cov
+        - linux: py311-cov-xdist
           coverage: codecov
-  data:
-    name: retrieve WebbPSF data
-    runs-on: ubuntu-latest
-    outputs:
-      data_path: ${{ steps.data.outputs.path }}
-      webbpsf_path: ${{ steps.webbpsf_path.outputs.path }}
-      data_hash: ${{ steps.data_hash.outputs.hash }}
-    steps:
-      # webbpsf:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-      - id: data
-        run: |
-          echo "path=/tmp/data" >> $GITHUB_OUTPUT
-          echo "webbpsf_url=https://stsci.box.com/shared/static/n1fealx9q0m6sdnass6wnyfikvxtc0zz.gz" >> $GITHUB_OUTPUT
-      - run: |
-          mkdir -p tmp/data/
-          mkdir -p ${{ steps.data.outputs.path }}
-      - run: wget ${{ steps.data.outputs.webbpsf_url }} -O tmp/minimal-webbpsf-data.tar.gz
-      - run: tar -xzvf tmp/minimal-webbpsf-data.tar.gz -C tmp/data/
-      - id: data_hash
-        run: echo "hash=${{ hashFiles( 'tmp/data' ) }}" >> $GITHUB_OUTPUT
-      - run: mv tmp/data/* ${{ steps.data.outputs.path }}
-      - uses: actions/cache@v3
-        with:
-          path: ${{ steps.data.outputs.path }}
-          key: data-${{ steps.data_hash.outputs.hash }}
-      - id: webbpsf_path
-        run: echo "path=${{ steps.data.outputs.path }}/webbpsf-data" >> $GITHUB_OUTPUT
+        - macos: py311-xdist
   test_downstream:
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
-    needs: [ data ]
     with:
       setenv: |
-        WEBBPSF_PATH: ${{ needs.data.outputs.webbpsf_path }}
-        CRDS_PATH: /tmp/crds_cache
+        CRDS_PATH: /tmp/data/crds_cache
         CRDS_CLIENT_RETRY_COUNT: 3
         CRDS_CLIENT_RETRY_DELAY_SECONDS: 20 
-        WEBBPSF_PATH: ${{ needs.data.outputs.data_path }}/webbpsf-data
-      cache-path: ${{ needs.data.outputs.data_path }}
-      cache-key: data-${{ needs.data.outputs.data_hash }}
       envs: |
-        - linux: py3-jwst-cov-xdist
-        - linux: py3-romancal-cov-xdist
-
+        - linux: py311-jwst-cov-xdist
+        - linux: py311-romancal-cov-xdist

.github/workflows/ci_cron.yml

@@ -22,4 +22,3 @@ jobs:
         - windows: py310-xdist
         - windows: py311-xdist
         - windows: py3-xdist
-

.gitignore

@@ -139,6 +139,9 @@ dmypy.json
 
 # Cython debug symbols
 cython_debug/
+src/stcal/ramp_fitting/ols_cas22/*.c
+src/stcal/ramp_fitting/ols_cas22/*.cpp
+src/stcal/ramp_fitting/ols_cas22/*.html
 
 # setuptools-scm generated module
 src/stcal/_version.py

CHANGES.rst

@@ -3,6 +3,12 @@
 
 - Added ``alignment`` sub-package. [#179]
 
+ramp_fitting
+------------
+
+- Refactor Casertano, et.al, 2022 uneven ramp fitting and incorporate the matching
+  jump detection algorithm into it. [#215]
+
 Changes to API
 --------------
 

setup.py

@@ -6,9 +6,31 @@
 Options.docstrings = True
 Options.annotate = False
 
-extensions = [Extension('stcal.ramp_fitting.ols_cas22',
-                        ['src/stcal/ramp_fitting/ols_cas22.pyx'],
-                        include_dirs=[np.get_include()],
-                        extra_compile_args=['-std=c99'])]
+extensions = [
+    Extension(
+        'stcal.ramp_fitting.ols_cas22._core',
+        ['src/stcal/ramp_fitting/ols_cas22/_core.pyx'],
+        include_dirs=[np.get_include()],
+        language='c++'
+    ),
+    Extension(
+        'stcal.ramp_fitting.ols_cas22._fixed',
+        ['src/stcal/ramp_fitting/ols_cas22/_fixed.pyx'],
+        include_dirs=[np.get_include()],
+        language='c++'
+    ),
+    Extension(
+        'stcal.ramp_fitting.ols_cas22._pixel',
+        ['src/stcal/ramp_fitting/ols_cas22/_pixel.pyx'],
+        include_dirs=[np.get_include()],
+        language='c++'
+    ),
+    Extension(
+        'stcal.ramp_fitting.ols_cas22._fit_ramps',
+        ['src/stcal/ramp_fitting/ols_cas22/_fit_ramps.pyx'],
+        include_dirs=[np.get_include()],
+        language='c++'
+    ),
+]
 
 setup(ext_modules=cythonize(extensions))

src/stcal/ramp_fitting/ols_cas22/__init__.py

@@ -0,0 +1,4 @@
+from ._fit_ramps import fit_ramps, RampFitOutputs
+from ._core import Parameter, Variance, Diff, RampJumpDQ
+
+__all__ = ['fit_ramps', 'RampFitOutputs', 'Parameter', 'Variance', 'Diff', 'RampJumpDQ']