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Fix codecov coverage for Cython modules #837

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Merged
alongd merged 1 commit into from
Mar 22, 2026
Merged

Fix codecov coverage for Cython modules #837

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2 changes: 2 additions & 0 deletions .coveragerc
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
# .coveragerc to control coverage.py
[run]
plugins = Cython.Coverage
branch = True
source = arc
omit =
Expand All @@ -10,6 +11,7 @@ omit =
*/examples/*
*/ipython/*
*/logo/*
arc/**/*_test.py

[report]
show_missing = True
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14 changes: 11 additions & 3 deletions .github/workflows/ci.yml
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Expand Up @@ -88,12 +88,17 @@ jobs:
- name: Compile ARC molecule
shell: micromamba-shell {0}
working-directory: ARC
env:
ARC_COVERAGE: 1
run: |
make compile

- name: Run Unit Tests
shell: micromamba-shell {0}
working-directory: ARC
env:
ARC_COVERAGE: 1
CYTHON_TRACE: 1
run: |
echo "Running Unit Tests..."
export PYTHONPATH="${{ github.workspace }}/AutoTST:${{ github.workspace }}/KinBot:$PYTHONPATH"
Expand All @@ -102,16 +107,19 @@ jobs:
- name: Run Functional Tests
shell: micromamba-shell {0}
working-directory: ${{ github.workspace }}/ARC
env:
ARC_COVERAGE: 1
CYTHON_TRACE: 1
run: |
echo "Running Functional Tests from $(pwd)..."
export PYTHONPATH="${{ github.workspace }}/AutoTST:${{ github.workspace }}/KinBot:$PYTHONPATH"
pytest functional/ -ra -vv -n auto
pytest functional/ --cov --cov-append --cov-report=xml -ra -vv -n auto

- name: Upload coverage data
uses: codecov/codecov-action@v3
uses: codecov/codecov-action@v5
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: ARC/coverage.xml
files: ARC/coverage.xml
flags: unittests,functionaltests
name: codecov-umbrella
verbose: true
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36 changes: 21 additions & 15 deletions setup.py
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Expand Up @@ -27,26 +27,32 @@

Options.annotate = False # HTML annotation

# Check if we are building for a coverage report
BUILD_FOR_COVERAGE = os.environ.get("ARC_COVERAGE") == "1"

directives = {
'language_level': 3,
'linetrace': BUILD_FOR_COVERAGE,
}

macros = [('CYTHON_TRACE', '1'), ('CYTHON_TRACE_NOGIL', '1')] if BUILD_FOR_COVERAGE else []

ext_modules = [
Extension('arc.molecule.atomtype', ['arc/molecule/atomtype.py'], include_dirs=['.']),
Extension('arc.constants', ['arc/constants.py'], include_dirs=['.']),
Extension('arc.molecule.element', ['arc/molecule/element.py'], include_dirs=['.']),
Extension('arc.molecule.graph', ['arc/molecule/graph.pyx'], include_dirs=['.']),
Extension('arc.molecule.group', ['arc/molecule/group.py'], include_dirs=['.']),
Extension('arc.molecule.molecule', ['arc/molecule/molecule.py'], include_dirs=['.']),
Extension('arc.molecule.symmetry', ['arc/molecule/symmetry.py'], include_dirs=['.']),
Extension('arc.molecule.vf2', ['arc/molecule/vf2.pyx'], include_dirs=['.']),
Extension('arc.molecule.converter', ['arc/molecule/converter.py'], include_dirs=['.']),
Extension('arc.molecule.translator', ['arc/molecule/translator.py'], include_dirs=['.']),
Extension('arc.molecule.util', ['arc/molecule/util.py'], include_dirs=['.']),
Extension('arc.molecule.inchi', ['arc/molecule/inchi.py'], include_dirs=['.']),
Extension('arc.molecule.resonance', ['arc/molecule/resonance.py'], include_dirs=['.']),
Extension('arc.molecule.pathfinder', ['arc/molecule/pathfinder.py'], include_dirs=['.']),
Extension('arc.molecule.kekulize', ['arc/molecule/kekulize.pyx'], include_dirs=['.']),
Extension('arc.molecule.atomtype', ['arc/molecule/atomtype.py'], include_dirs=['.'], define_macros=macros),
Extension('arc.constants', ['arc/constants.py'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.element', ['arc/molecule/element.py'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.graph', ['arc/molecule/graph.pyx'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.group', ['arc/molecule/group.py'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.molecule', ['arc/molecule/molecule.py'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.symmetry', ['arc/molecule/symmetry.py'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.vf2', ['arc/molecule/vf2.pyx'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.converter', ['arc/molecule/converter.py'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.translator', ['arc/molecule/translator.py'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.util', ['arc/molecule/util.py'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.inchi', ['arc/molecule/inchi.py'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.resonance', ['arc/molecule/resonance.py'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.pathfinder', ['arc/molecule/pathfinder.py'], include_dirs=['.'], define_macros=macros),
Extension('arc.molecule.kekulize', ['arc/molecule/kekulize.pyx'], include_dirs=['.'], define_macros=macros),
]

if 'main' in sys.argv:
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