Doc: Update reference list (#2172) #9512
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name: C++/Python Tests | |
on: | |
push: | |
merge_group: | |
workflow_dispatch: | |
pull_request: | |
branches: | |
- master | |
jobs: | |
ubuntu-cpp-python-tests: | |
name: C++/Python 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)" >> $GITHUB_ENV | |
- name: Set up AMICI C++ libraries | |
uses: ./.github/actions/setup-amici-cpp | |
- name: C++ tests | |
run: scripts/run-cpp-tests.sh | |
- name: Install python package | |
run: scripts/installAmiciSource.sh | |
- name: Python tests (part 1) | |
run: | | |
source build/venv/bin/activate \ | |
&& pytest \ | |
--ignore-glob=*petab* \ | |
--ignore-glob=*test_splines.py \ | |
--ignore-glob=*test_splines_short.py \ | |
--ignore-glob=*test_pysb.py \ | |
--cov=amici \ | |
--cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \ | |
--cov-append \ | |
--durations=10 \ | |
${AMICI_DIR}/python/tests | |
- name: Python tests splines | |
if: ${{ github.base_ref == 'master' || github.event.merge_group.base_ref == 'master'}} | |
run: | | |
source build/venv/bin/activate \ | |
&& pytest \ | |
--cov=amici \ | |
--cov-report=xml:"${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 | |
- name: Capture coverage info (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 | |
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-python-tests: | |
name: Python 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)" >> $GITHUB_ENV | |
- name: Set up AMICI C++ libraries | |
uses: ./.github/actions/setup-amici-cpp | |
- name: Install python package | |
run: scripts/installAmiciSource.sh | |
- name: Python tests | |
run: | | |
source build/venv/bin/activate \ | |
&& pytest \ | |
--cov=amici \ | |
--cov-report=xml:"${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] | |
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: | | |
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)" >> $GITHUB_ENV | |
- name: Set up AMICI C++ libraries | |
uses: ./.github/actions/setup-amici-cpp | |
- name: Install python package | |
run: scripts/installAmiciSource.sh | |
- name: Install notebook dependencies | |
run: | | |
source build/venv/bin/activate \ | |
&& pip install jax[cpu] | |
- name: example notebooks | |
run: scripts/runNotebook.sh python/examples/example_*/ | |
- name: doc notebooks | |
run: scripts/runNotebook.sh documentation/GettingStarted.ipynb | |
# TODO: Include notebooks in coverage report | |
osx: | |
name: Tests OSX | |
runs-on: macos-latest | |
steps: | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.9 | |
- uses: actions/checkout@v3 | |
- run: git fetch --prune --unshallow | |
- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV | |
- run: echo "BNGPATH=${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 | |
# 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 | |
- name: Build AMICI | |
run: scripts/buildAll.sh | |
- name: Install python package | |
run: scripts/installAmiciSource.sh | |
- name: cppcheck | |
run: scripts/run-cppcheck.sh | |
- name: Python tests | |
run: scripts/run-python-tests.sh | |
- name: C++ tests | |
run: scripts/run-cpp-tests.sh |