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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| name: Set up AMICI C++ | ||
| description: | | ||
| Build the AMICI C++ interface and set things for for coverage analysis. | ||
| (Currently ubuntu-only). | ||
| runs: | ||
| using: "composite" | ||
| steps: | ||
| # BioNetGen Path | ||
| - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV | ||
| shell: bash | ||
|
|
||
| # use all available cores | ||
| - run: echo "AMICI_PARALLEL_COMPILE=" >> $GITHUB_ENV | ||
| shell: bash | ||
|
|
||
| # enable coverage | ||
| - run: echo "ENABLE_GCOV_COVERAGE=TRUE" >> $GITHUB_ENV | ||
| shell: bash | ||
|
|
||
| - name: Set up Sonar tools | ||
| uses: ./.github/actions/setup-sonar-tools | ||
|
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| - name: Install apt dependencies | ||
| uses: ./.github/actions/install-apt-dependencies | ||
|
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| - name: Install additional apt dependencies | ||
| run: | | ||
| sudo apt-get update \ | ||
| && sudo apt-get install -y \ | ||
| cmake \ | ||
| python3-venv \ | ||
| lcov | ||
| shell: bash | ||
|
|
||
| - name: Build AMICI dependencies | ||
| run: scripts/buildDependencies.sh | ||
| shell: bash | ||
|
|
||
| - name: Build AMICI | ||
| run: scripts/buildAmici.sh | ||
| shell: bash | ||
| env: | ||
| CI_SONARCLOUD: "TRUE" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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|
@@ -8,20 +8,13 @@ on: | |
| - master | ||
|
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| jobs: | ||
| build: | ||
| name: Tests Ubuntu | ||
|
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| # TODO: prepare image with more deps preinstalled | ||
| ubuntu-cpp-python-tests: | ||
| name: C++/Python tests Ubuntu | ||
| runs-on: ubuntu-22.04 | ||
|
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||
| env: | ||
| AMICI_PARALLEL_COMPILE: "" | ||
| ENABLE_GCOV_COVERAGE: "TRUE" | ||
| CI_SONARCLOUD: "TRUE" | ||
|
|
||
| strategy: | ||
| matrix: | ||
| python-version: [ 3.9 ] | ||
| python-version: [ "3.9" ] | ||
|
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| steps: | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
|
|
@@ -33,48 +26,33 @@ jobs: | |
| - run: git fetch --prune --unshallow | ||
|
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||
| - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV | ||
| - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV | ||
|
|
||
| - name: Set up Sonar tools | ||
| uses: ./.github/actions/setup-sonar-tools | ||
|
|
||
| - name: Install apt dependencies | ||
| uses: ./.github/actions/install-apt-dependencies | ||
|
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||
| # install amici dependencies | ||
| - name: apt | ||
| run: | | ||
| sudo apt-get update \ | ||
| && sudo apt-get install -y \ | ||
| cmake \ | ||
| python3-venv \ | ||
| lcov | ||
| - name: Build AMICI dependencies | ||
| run: scripts/buildDependencies.sh | ||
|
|
||
| - name: Build AMICI | ||
| run: CI_SONARCLOUD=TRUE scripts/buildAmici.sh | ||
| - name: Set up AMICI C++ libraries | ||
| uses: ./.github/actions/setup-amici-cpp | ||
|
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||
| - name: C++ tests | ||
| run: scripts/run-cpp-tests.sh | ||
|
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||
| - name: Install python package | ||
| run: scripts/installAmiciSource.sh | ||
|
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| - name: Python tests | ||
| - name: Check OpenMP support | ||
| run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())" | ||
|
|
||
| - name: Python tests (part 1) | ||
| run: | | ||
| source build/venv/bin/activate \ | ||
| && pytest \ | ||
| --ignore-glob=*petab* \ | ||
| --ignore-glob=*test_splines.py \ | ||
| --ignore-glob=*test_splines_short.py \ | ||
| --ignore-glob=*test_pysb.py \ | ||
| --cov=amici \ | ||
| --cov-report=xml:"${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: | | ||
|
|
@@ -86,16 +64,77 @@ jobs: | |
| --durations=10 \ | ||
| ${AMICI_DIR}/python/tests/test_splines.py | ||
| - name: Install notebook dependencies | ||
| - 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: Capture coverage info (lcov) | ||
| run: | | ||
| source build/venv/bin/activate \ | ||
| && pip install jax[cpu] | ||
| 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: example notebooks | ||
| run: scripts/runNotebook.sh python/examples/example_*/ | ||
| - name: Codecov CPP | ||
| uses: codecov/[email protected] | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: coverage.info | ||
| flags: cpp | ||
| fail_ci_if_error: true | ||
|
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||
| - name: doc notebooks | ||
| run: scripts/runNotebook.sh documentation/GettingStarted.ipynb | ||
| - 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-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)" >> $GITHUB_ENV | ||
|
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| - name: Set up AMICI C++ libraries | ||
| uses: ./.github/actions/setup-amici-cpp | ||
|
|
||
| - name: Install python package | ||
| run: scripts/installAmiciSource.sh | ||
|
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| - name: Python tests | ||
| run: | | ||
| source build/venv/bin/activate \ | ||
| && pytest \ | ||
| --cov=amici \ | ||
| --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \ | ||
| --cov-append \ | ||
| --durations=10 \ | ||
| ${AMICI_DIR}/python/tests/test_pysb.py \ | ||
| ${AMICI_DIR}/python/tests/test_splines_short.py | ||
| - name: Codecov Python | ||
| uses: codecov/[email protected] | ||
|
|
@@ -106,7 +145,7 @@ jobs: | |
| fail_ci_if_error: true | ||
| verbose: true | ||
|
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| - name: lcov | ||
| - name: Capture coverage info (lcov) | ||
| run: | | ||
| lcov --compat-libtool --no-external \ | ||
| -d ${AMICI_DIR}/build/CMakeFiles/amici.dir/src \ | ||
|
|
@@ -121,7 +160,7 @@ jobs: | |
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: coverage.info | ||
| flags: cpp | ||
| flags: cpp_python | ||
| fail_ci_if_error: true | ||
|
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| - name: Run sonar-scanner | ||
|
|
@@ -133,6 +172,45 @@ jobs: | |
| -Dsonar.cfamily.build-wrapper-output=bw-output \ | ||
| -Dsonar.projectVersion="$(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)" >> $GITHUB_ENV | ||
|
|
||
| - name: Set up AMICI C++ libraries | ||
| uses: ./.github/actions/setup-amici-cpp | ||
|
|
||
| - name: Install python package | ||
| run: scripts/installAmiciSource.sh | ||
|
|
||
| - name: Install notebook dependencies | ||
| run: | | ||
| source build/venv/bin/activate \ | ||
| && pip install jax[cpu] | ||
| - name: example notebooks | ||
| run: scripts/runNotebook.sh python/examples/example_*/ | ||
|
|
||
| - name: doc notebooks | ||
| run: scripts/runNotebook.sh documentation/GettingStarted.ipynb | ||
|
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| # TODO: Include notebooks in coverage report | ||
|
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||
| osx: | ||
| name: Tests OSX | ||
| runs-on: macos-latest | ||
|
|
@@ -150,22 +228,22 @@ jobs: | |
| - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV | ||
| # Ensure CMake is using the python version that we will use for the python tests later on | ||
| - run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV | ||
| - run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV | ||
| - run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV | ||
|
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| # install amici dependencies | ||
| - name: homebrew | ||
| run: | | ||
| brew install hdf5 swig gcc cppcheck libomp boost \ | ||
| && brew ls -v boost \ | ||
| && brew ls -v libomp \ | ||
| && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.81.0_1/lib/" >> $GITHUB_ENV \ | ||
| && echo CPPFLAGS="-I /usr/local/Cellar/boost/1.81.0_1/include/" >> $GITHUB_ENV | ||
| run: brew install hdf5 swig gcc cppcheck libomp boost | ||
|
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| - name: Build AMICI | ||
| run: scripts/buildAll.sh | ||
|
|
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| - name: Install python package | ||
| run: scripts/installAmiciSource.sh | ||
|
|
||
| - name: Check OpenMP support | ||
| run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())" | ||
|
|
||
| - name: cppcheck | ||
| run: scripts/run-cppcheck.sh | ||
|
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|
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||
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