ci.yml

name: CI

# trigger
on:
  push:
    branches:
    - main
  pull_request:
  schedule:
    # run Monday at 03:18 UTC
    - cron: '18 15 * * MON'

jobs:

  base:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.12', '3.11', '3.10']

    steps:
    - name: Check out repository
      uses: actions/checkout@v2

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v1
      with:
        path: ~/.cache
        key: ci-${{ runner.os }}-${{ matrix.python-version }}-base

    - name: Install dependencies
      run: .github/workflows/install_deps.sh base R

    - name: Run tests
      timeout-minutes: 15
      run: tox -e base

    - name: Run visualization tests
      timeout-minutes: 3
      run: tox -e visualization

    - name: Coverage
      uses: codecov/codecov-action@v2
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml

  external:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.12']

    steps:
    - name: Check out repository
      uses: actions/checkout@v2

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install julia
      uses: julia-actions/setup-julia@v1
      with:
        version: 1.7

    - name: Cache
      uses: actions/cache@v1
      with:
        path: ~/.cache
        key: ci-${{ runner.os }}-${{ matrix.python-version }}-external

    - name: Install dependencies
      run: .github/workflows/install_deps.sh base R

    - name: Run tests
      timeout-minutes: 15
      run: tox -e external

    - name: Coverage
      uses: codecov/codecov-action@v2
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml

  petab:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.11']

    steps:
    - name: Check out repository
      uses: actions/checkout@v2

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v1
      with:
        path: ~/.cache
        key: ci-${{ runner.os }}-${{ matrix.python-version }}-petab

    - name: Install dependencies
      run: .github/workflows/install_deps.sh amici

    - name: Run tests
      timeout-minutes: 20
      run: tox -e petab

    - name: Coverage
      uses: codecov/codecov-action@v2
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml

  mac:
    runs-on: macos-latest
    strategy:
      matrix:
        python-version: ['3.12']

    steps:
      - name: Check out repository
        uses: actions/checkout@v2

      - name: Prepare python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}

      - name: Cache
        uses: actions/cache@v1
        with:
          path: ~/Library/Caches/pip
          key: ci-${{ runner.os }}-${{ matrix.python-version }}-mac

      - name: Install dependencies
        run: .github/workflows/install_deps.sh

      - name: Run tests
        timeout-minutes: 10
        run: tox -e mac

      - name: Coverage
        uses: codecov/codecov-action@v2
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          file: ./coverage.xml

  notebooks1:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.12']

    steps:
    - name: Check out repository
      uses: actions/checkout@v2

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v1
      with:
        path: ~/.cache
        key: ci-${{ runner.os }}-${{ matrix.python-version }}-notebooks1

    - name: Install dependencies
      run: .github/workflows/install_deps.sh

    - name: Run notebooks
      timeout-minutes: 15
      run: tox -e notebooks1

  notebooks2:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.12']

    steps:
    - name: Check out repository
      uses: actions/checkout@v2

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v1
      with:
        path: ~/.cache
        key: ci-${{ runner.os }}-${{ matrix.python-version }}-notebooks2

    - name: Install dependencies
      run: .github/workflows/install_deps.sh R amici

    - name: Run notebooks
      timeout-minutes: 15
      run: tox -e notebooks2

  quality:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.11']

    steps:
    - name: Check out repository
      uses: actions/checkout@v2

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v1
      with:
        path: ~/.cache
        key: ci-${{ runner.os }}-${{ matrix.python-version }}-quality

    - name: Install dependencies
      run: |
        .github/workflows/install_deps.sh doc
        pip install tox

    - name: Run quality checks
      timeout-minutes: 5
      run: tox -e project,flake8

    - name: Build docs
      timeout-minutes: 5
      run: tox -e doc

    - name: Test migration
      timeout-minutes: 5
      run: tox -e migrate

    - name: Coverage
      uses: codecov/codecov-action@v2
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml