test_python_cplusplus.yml

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/codecov-action@v3.1.0
      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/codecov-action@v3.1.0
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: coverage_cpp.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/codecov-action@v3.1.0
      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/codecov-action@v3.1.0
      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