test_petab_test_suite.yml

name: PEtab
on:
  push:
    branches:
      - main
      - 'release*'
  pull_request:
    branches:
      - main
  merge_group:
  workflow_dispatch:

jobs:
  petab_v1:
    name: PEtab Testsuite

    runs-on: ubuntu-latest

    env:
      ENABLE_GCOV_COVERAGE: TRUE

    strategy:
      matrix:
        python-version: ["3.14"]

    steps:
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}

      - uses: actions/checkout@v5
        with:
          fetch-depth: 20

      - name: Install apt dependencies
        uses: ./.github/actions/install-apt-dependencies

      # install dependencies
      - name: apt
        run: |
          sudo apt-get update \
            && sudo apt-get install -y python3-venv

      - name: Build BNGL
        run: scripts/buildBNGL.sh

      - run: |
          echo "${HOME}/.local/bin/" >> $GITHUB_PATH
          echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH
          echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV

      # install AMICI
      - name: Install python package
        run: scripts/installAmiciSource.sh

      - name: Install petab
        run: |
          source ./venv/bin/activate \
            && pip3 install wheel pytest shyaml pytest-cov pysb>=1.16

      # retrieve test models
      - name: Download and install PEtab test suite
        # FIXME: Until we have proper PEtab v2 import
        #  (https://github.com/AMICI-dev/AMICI/issues/2662),
        #  we need `10ffb050380933b60ac192962bf9550a9df65a9c`
        #  with the pseudo-v2 format instead of `main`
#        run: |
#          git clone --depth 1 --branch main \
#            https://github.com/PEtab-dev/petab_test_suite \
#            && source ./venv/bin/activate \
#            && cd petab_test_suite && pip3 install -e .
        run: |
          git clone https://github.com/PEtab-dev/petab_test_suite \
            && source ./venv/bin/activate \
            && cd petab_test_suite \
            && git checkout 10ffb050380933b60ac192962bf9550a9df65a9c \
            && pip3 install -e .

      - name: Install PEtab benchmark collection
        run: |
          git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
            && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
            && source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python

      - name: Install petab
        run: |
          source ./venv/bin/activate \
            && python3 -m pip uninstall -y petab \
            && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@8dc6c1c4b801fba5acc35fcd25308a659d01050e \
            && python3 -m pip install git+https://github.com/pysb/pysb@master \
            && python3 -m pip install sympy>=1.12.1


      - name: Run PEtab-related unit tests
        run: |
          source ./venv/bin/activate \
            && pytest --cov-report=xml:coverage.xml \
              --cov=./ python/tests/test_*petab*.py python/tests/petab_/

      # run test models
      - name: Run PEtab test suite
        run: |
          source ./venv/bin/activate \
          && AMICI_PARALLEL_COMPILE="" pytest -rxXs -v \
            --cov-report=xml:coverage.xml \
            --cov-append \
            --cov=amici \
            tests/petab_test_suite/test_petab_suite.py

      - name: Codecov
        if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
        uses: codecov/codecov-action@v5
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          files: coverage.xml
          flags: petab
          fail_ci_if_error: true


  petab_v2:
    name: PEtab v2 Testsuite

    runs-on: ubuntu-latest

    env:
      ENABLE_GCOV_COVERAGE: TRUE

    strategy:
      matrix:
        python-version: ["3.12"]

    steps:
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - uses: actions/checkout@v4
        with:
          fetch-depth: 20

      - name: Install apt dependencies
        uses: ./.github/actions/install-apt-dependencies

      # install dependencies
      - name: apt
        run: |
          sudo apt-get update \
            && sudo apt-get install -y python3-venv

      - name: Build BNGL
        run: scripts/buildBNGL.sh

      - run: |
          echo "${HOME}/.local/bin/" >> $GITHUB_PATH
          echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH
          echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV

      # install AMICI
      - name: Install python package
        run: scripts/installAmiciSource.sh

      - name: Install petab
        run: |
          source ./venv/bin/activate \
            && pip3 install wheel pytest shyaml pytest-cov pysb>=1.16

      # retrieve test models
      - name: Download and install PEtab test suite
        run: |
          git clone https://github.com/PEtab-dev/petab_test_suite \
            && source ./venv/bin/activate \
            && cd petab_test_suite \
            && git checkout c12b9dc4e4c5585b1b83a1d6e89fd22447c46d03 \
            && pip3 install -e .

# TODO: once there is a PEtab v2 benchmark collection
#      - name: Install PEtab benchmark collection
#        run: |
#          git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
#            && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
#            && source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python

      - name: Install petab
        run: |
          source ./venv/bin/activate \
            && python3 -m pip uninstall -y petab \
            && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@8dc6c1c4b801fba5acc35fcd25308a659d01050e \
            && python3 -m pip install git+https://github.com/pysb/pysb@master \
            && python3 -m pip install sympy>=1.12.1

      # run test models
      - name: Run PEtab test suite
        run: |
          source ./venv/bin/activate \
          && AMICI_PARALLEL_COMPILE="" pytest -rxXs -v \
            --cov-report=xml:coverage.xml \
            --cov-append \
            --cov=amici \
            tests/petab_test_suite/test_petab_v2_suite.py

      - name: Codecov
        if: (github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev') && github.actor != 'dependabot[bot]'
        uses: codecov/codecov-action@v5
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          files: coverage.xml
          flags: petab
          fail_ci_if_error: true