AMICI/.github/workflows/test_petab_sciml.yml at c0c8ed118e753b980d1bc0f524e93b2af01ff003 · AMICI-dev/AMICI · GitHub

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

jobs:
  build:
    name: PEtab SciML 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@v6
        with:
          python-version: ${{ matrix.python-version }}

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

      # todo, update after https://github.com/sebapersson/petab_sciml_testsuite/issues/14 is merged
      - name: Download PEtab SciML test suite
        run: |
          git clone --depth 1 --branch main \
            https://github.com/FFroehlich/petab_sciml_testsuite \
            tests/sciml/testsuite

      - 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

      - run: |
          echo "${HOME}/.local/bin/" >> $GITHUB_PATH

      # 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

      # retrieve test models
      - name: Download and install PEtab SciML
        run: |
          source ./venv/bin/activate \
            && python -m pip install git+https://github.com/petab-dev/petab_sciml.git@main#subdirectory=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@sciml \

      - name: Run PEtab SciML testsuite
        run: |
          source ./venv/bin/activate \
            && pytest --cov-report=xml:coverage_petab_sciml.xml \
              --cov=amici tests/sciml/test_sciml.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 }}
          file: coverage_petab_sciml.xml
          flags: petab_sciml
          fail_ci_if_error: true