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@@ -50,155 +50,6 @@ jobs: | |
| -Dsonar.cfamily.build-wrapper-output=bw-output \ | ||
| -Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')" | ||
| ubuntu-python-tests: | ||
| name: Python tests Ubuntu | ||
| runs-on: ubuntu-22.04 | ||
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| strategy: | ||
| matrix: | ||
| python-version: [ "3.9" ] | ||
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| steps: | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
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| - uses: actions/checkout@v3 | ||
| - run: git fetch --prune --unshallow | ||
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| - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV | ||
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| - name: Set up AMICI C++ libraries | ||
| uses: ./.github/actions/setup-amici-cpp | ||
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| - name: Install python package | ||
| run: scripts/installAmiciSource.sh | ||
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| - name: Python tests | ||
| run: | | ||
| source build/venv/bin/activate \ | ||
| && pytest \ | ||
| --ignore-glob=*petab* \ | ||
| --ignore-glob=*test_splines.py \ | ||
| --cov=amici \ | ||
| --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \ | ||
| --cov-append \ | ||
| --durations=10 \ | ||
| ${AMICI_DIR}/python/tests | ||
| - name: Python tests splines | ||
| if: ${{ github.base_ref == 'master' || github.event.merge_group.base_ref == 'master'}} | ||
| run: | | ||
| source build/venv/bin/activate \ | ||
| && pytest \ | ||
| --cov=amici \ | ||
| --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \ | ||
| --cov-append \ | ||
| --durations=10 \ | ||
| ${AMICI_DIR}/python/tests/test_splines.py | ||
| - name: Codecov Python | ||
| uses: codecov/[email protected] | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: build/coverage_py.xml | ||
| flags: python | ||
| fail_ci_if_error: true | ||
| verbose: true | ||
|
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||
| - name: lcov | ||
| run: | | ||
| lcov --compat-libtool --no-external \ | ||
| -d ${AMICI_DIR}/build/CMakeFiles/amici.dir/src \ | ||
| -b ${AMICI_DIR} -c -o coverage_cpp.info \ | ||
| && lcov --compat-libtool --no-external \ | ||
| -d ${AMICI_DIR}/python/sdist/build/temp_amici/CMakeFiles/amici.dir/src \ | ||
| -b ${AMICI_DIR}/python/sdist -c -o coverage_py.info \ | ||
| && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info | ||
| - name: Codecov CPP | ||
| uses: codecov/[email protected] | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: coverage.info | ||
| flags: cpp_python | ||
| fail_ci_if_error: true | ||
|
|
||
| - name: Run sonar-scanner | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} | ||
| run: | | ||
| sonar-scanner \ | ||
| -Dsonar.cfamily.build-wrapper-output=bw-output \ | ||
| -Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')" | ||
| ubuntu-notebook-tests: | ||
| name: Notebook tests Ubuntu | ||
| runs-on: ubuntu-22.04 | ||
|
|
||
| strategy: | ||
| matrix: | ||
| python-version: [ "3.9" ] | ||
|
|
||
| steps: | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
|
|
||
| - uses: actions/checkout@v3 | ||
| - run: git fetch --prune --unshallow | ||
|
|
||
| - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV | ||
|
|
||
| - name: Set up AMICI C++ libraries | ||
| uses: ./.github/actions/setup-amici-cpp | ||
|
|
||
| - name: Install python package | ||
| run: scripts/installAmiciSource.sh | ||
|
|
||
| - name: Install notebook dependencies | ||
| run: | | ||
| source build/venv/bin/activate \ | ||
| && pip install jax[cpu] | ||
| - name: example notebooks | ||
| run: scripts/runNotebook.sh python/examples/example_*/ | ||
|
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| - name: doc notebooks | ||
| run: scripts/runNotebook.sh documentation/GettingStarted.ipynb | ||
|
|
||
| - name: Codecov Python | ||
| uses: codecov/[email protected] | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: build/coverage_py.xml | ||
| flags: python | ||
| fail_ci_if_error: true | ||
| verbose: true | ||
|
|
||
| - name: lcov | ||
| run: | | ||
| lcov --compat-libtool --no-external \ | ||
| -d ${AMICI_DIR}/build/CMakeFiles/amici.dir/src \ | ||
| -b ${AMICI_DIR} -c -o coverage_cpp.info \ | ||
| && lcov --compat-libtool --no-external \ | ||
| -d ${AMICI_DIR}/python/sdist/build/temp_amici/CMakeFiles/amici.dir/src \ | ||
| -b ${AMICI_DIR}/python/sdist -c -o coverage_py.info \ | ||
| && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info | ||
| - name: Run sonar-scanner | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} | ||
| run: | | ||
| sonar-scanner \ | ||
| -Dsonar.cfamily.build-wrapper-output=bw-output \ | ||
| -Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')" | ||
| osx: | ||
| name: Tests OSX | ||
| runs-on: macos-latest | ||
|
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