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test_python_cplusplus.yml
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name: C++/Python Tests
on:
push:
merge_group:
workflow_dispatch:
pull_request:
branches:
- master
- develop
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)" >> $GITHUB_ENV
- name: Set up AMICI C++ libraries
uses: ./.github/actions/setup-amici-cpp
- name: C++ tests
run: scripts/run-cpp-tests.sh
- name: Install python package
run: scripts/installAmiciSource.sh
- name: Check OpenMP support
run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
- name: Python tests (part 1)
run: |
source build/venv/bin/activate \
&& pytest \
--ignore-glob=*petab* \
--ignore-glob=*test_splines.py \
--ignore-glob=*test_splines_short.py \
--ignore-glob=*test_pysb.py \
--cov=amici \
--cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
--cov-append \
--durations=10 \
${AMICI_DIR}/python/tests
- name: Python tests splines
if: ${{ github.base_ref == 'master' || github.event.merge_group.base_ref == 'master'}}
run: |
source build/venv/bin/activate \
&& pytest \
--cov=amici \
--cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
--cov-append \
--durations=10 \
${AMICI_DIR}/python/tests/test_splines.py
- name: Codecov Python
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
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
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
uses: codecov/[email protected]
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: coverage.info
flags: cpp
fail_ci_if_error: true
- name: Run sonar-scanner
if: ${{ env.SONAR_TOKEN != '' }}
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
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
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
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
uses: codecov/[email protected]
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: coverage.info
flags: cpp_python
fail_ci_if_error: true
- name: Run sonar-scanner
if: ${{ env.SONAR_TOKEN != '' }}
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)" >> $GITHUB_ENV
- name: Set up AMICI C++ libraries
uses: ./.github/actions/setup-amici-cpp
- name: Install python package
run: scripts/installAmiciSource.sh
- name: Install notebook dependencies
run: |
source build/venv/bin/activate \
&& pip install jax[cpu]
- name: example notebooks
run: scripts/runNotebook.sh python/examples/example_*/
- name: doc notebooks
run: scripts/runNotebook.sh documentation/GettingStarted.ipynb
# TODO: Include notebooks in coverage report
macos_cpp_py:
name: Tests MacOS C++/Python
runs-on: macos-latest
env:
AMICI_PARALLEL_COMPILE: ""
steps:
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: 3.9
- uses: actions/checkout@v3
- run: git fetch --prune --unshallow
- run: echo "AMICI_DIR=$(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" >> $GITHUB_ENV
- run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
- run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
# install amici dependencies
- name: homebrew
run: brew install hdf5 swig gcc cppcheck libomp boost
- name: Build AMICI
run: scripts/buildAll.sh
- name: Install python package
run: scripts/installAmiciSource.sh
- name: Check OpenMP support
run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
- name: cppcheck
run: scripts/run-cppcheck.sh
- name: C++ tests
run: scripts/run-cpp-tests.sh
- name: Python tests
run: scripts/run-python-tests.sh test_pregenerated_models.py test_splines_short.py
macos_python:
name: Tests MacOS Python
runs-on: macos-latest
env:
AMICI_PARALLEL_COMPILE: ""
steps:
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: 3.9
- uses: actions/checkout@v3
- run: git fetch --prune --unshallow
- run: echo "AMICI_DIR=$(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" >> $GITHUB_ENV
- run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
- run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
# install amici dependencies
- name: homebrew
run: brew install hdf5 swig gcc cppcheck libomp boost
- name: Install python package
run: |
pip show numpy > /dev/null || python3 -m pip install numpy
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: Get BioNetGen
run: scripts/buildBNGL.sh
- name: Python tests
run: |
scripts/run-python-tests.sh \
--ignore=test_pregenerated_models.py \
--ignore=test_splines_short.py