Merge branch 'lenstronomy:main' into main

sibirrer · Nov 30, 2023 · 6e0842e · 6e0842e
2 parents 279514d + 5c83edc
commit 6e0842e
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Showing 43 changed files with 2,176 additions and 566 deletions.
diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
@@ -26,7 +26,8 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install --upgrade pytest
-          python -m pip install flake8 pytest pytest-cov coveralls
+          python -m pip install flake8 pytest pytest-cov
+          python -m pip install codecov
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
           if [ -f test_requirements.txt ]; then pip install -r test_requirements.txt; fi
           python -m pip install .
@@ -38,13 +39,21 @@ jobs:
       #    flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       - name: Test with pytest
         run: |
-          pytest --cov=lenstronomy
+          pytest --cov=./ --cov-report=xml
+          codecov
 
-      - name: Coveralls
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          coveralls --service=github
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        with:
+          files: ./coverage.xml
+
+#      - name: Coveralls
+#        env:
+#          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#        run: |
+#          coveralls --service=github
 
       # from this source for coveralls: https://github.com/marketplace/actions/coveralls-github-action
       #- uses: actions/checkout@v1

diff --git a/README.rst b/README.rst
@@ -9,8 +9,8 @@
         :target: http://lenstronomy.readthedocs.io/en/latest/?badge=latest
         :alt: Documentation Status
 
-.. image:: https://coveralls.io/repos/github/lenstronomy/lenstronomy/badge.svg?branch=main
-        :target: https://coveralls.io/github/lenstronomy/lenstronomy?branch=main
+.. image:: https://codecov.io/gh/lenstronomy/lenstronomy/graph/badge.svg?token=Pk1FmwQ4Ek 
+        :target: https://codecov.io/gh/lenstronomy/lenstronomy
 
 .. image:: https://img.shields.io/badge/License-BSD_3--Clause-blue.svg
     :target: https://github.com/lenstronomy/lenstronomy/blob/main/LICENSE

diff --git a/codecov.yml b/codecov.yml
@@ -0,0 +1,6 @@
+comment:                  # this is a top-level key
+  layout: " diff, flags, files"
+  behavior: default
+  require_changes: false  # if true: only post the comment if coverage changes
+  require_base: false        # [true :: must have a base report to post]
+  require_head: true       # [true :: must have a head report to post]
diff --git a/lenstronomy/ImSim/image2source_mapping.py b/lenstronomy/ImSim/image2source_mapping.py
diff --git a/lenstronomy/ImSim/image_linear_solve.py b/lenstronomy/ImSim/image_linear_solve.py
@@ -531,8 +531,9 @@ def _linear_response_matrix(
         :return: response matrix (m x n)
         """
         x_grid, y_grid = self.ImageNumerics.coordinates_evaluate
+
         source_light_response, n_source = self.source_mapping.image_flux_split(
-            x_grid, y_grid, kwargs_lens, kwargs_source
+            x_grid, y_grid, kwargs_lens, kwargs_source, kwargs_special
         )
         extinction = self._extinction.extinction(
             x_grid,

diff --git a/lenstronomy/ImSim/image_model.py b/lenstronomy/ImSim/image_model.py
@@ -61,7 +61,7 @@ def __init__(
         if point_source_class is None:
             point_source_class = PointSource(point_source_type_list=[])
         self.PointSource = point_source_class
-        if self.PointSource._lensModel is None:
+        if self.PointSource._lens_model is None:
             self.PointSource.update_lens_model(lens_model_class=lens_model_class)
         x_center, y_center = self.Data.center
         self.PointSource.update_search_window(
@@ -111,7 +111,7 @@ def __init__(
             self.source_mapping = None  # handled with pixelated operator
         else:
             self.source_mapping = Image2SourceMapping(
-                lensModel=lens_model_class, sourceModel=source_model_class
+                lens_model=lens_model_class, source_model=source_model_class
             )
 
         self._pb = data_class.primary_beam
@@ -294,7 +294,12 @@ def _source_surface_brightness_analytical_numerics(
             )
         else:
             source_light = self.source_mapping.image_flux_joint(
-                ra_grid, dec_grid, kwargs_lens, kwargs_source, k=k
+                ra_grid,
+                dec_grid,
+                kwargs_lens,
+                kwargs_source,
+                kwargs_special=kwargs_special,
+                k=k,
             )
             source_light *= self._extinction.extinction(
                 ra_grid,