ci.yml

name: CI

# trigger
on:
  push:
    branches:
    - main
    - develop
  pull_request:
  workflow_dispatch:
  merge_group:
  schedule:
    # run Monday and Thursday at 03:42 UTC
    - cron: '42 3 * * MON,THU'

env:
  # use all available cores for compiling amici models
  AMICI_PARALLEL_COMPILE: ""
  # non-interactive backend for matplotlib
  MPLBACKEND: "agg"

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

    steps:
    - name: Check out repository
      uses: actions/checkout@v4

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v4
      with:
        path: |
          ~/.cache/pip
          .tox/
        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

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

    - name: Run tests
      timeout-minutes: 30
      run: tox -e base
      env:
        CC: clang
        CXX: clang++

    - name: Coverage
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./coverage.xml

  mac:
    runs-on: macos-13  # TODO: change to macos-latest after the next release
    strategy:
      matrix:
        python-version: ['3.12']

    steps:
    - name: Check out repository
      uses: actions/checkout@v4

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v4
      with:
        path: |
          ~/.cache/pip
          .tox/
        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

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

    - name: Run tests
      timeout-minutes: 30
      run: ulimit -n 65536 65536 && tox -e base

    - name: Coverage
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./coverage.xml

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

    steps:
    - name: Check out repository
      uses: actions/checkout@v4

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v4
      with:
        path: |
          ~\AppData\Local\pip\Cache
          .tox
        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

    - name: Install dependencies
      run: |
        pip install --upgrade pip
        pip install tox

    - name: Run tests
      shell: bash
      timeout-minutes: 10
      run: tox -e windows

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

    steps:
    - name: Check out repository
      uses: actions/checkout@v4

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v4
      with:
        path: |
          ~/.cache/pip
          .tox/
        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

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

    - name: Run tests
      timeout-minutes: 35
      run: tox -e petab && tox e -e petab -- pip uninstall -y amici
      env:
        CC: clang
        CXX: clang++

    - name: Coverage
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./coverage.xml

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

    # needed to allow julia-actions/cache to delete old caches that it has created
    permissions:
      actions: write
      contents: read

    steps:
    - name: Check out repository
      uses: actions/checkout@v4

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache tox and cache
      uses: actions/cache@v4
      with:
        path: |
          ~/.cache/pip
          .tox/
        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

    - name: Install julia
      uses: julia-actions/setup-julia@v2
      with:
        version: 1.11

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

    - name: Install PEtabJL dependencies
      run: >
        julia -e 'using Pkg; Pkg.add("PEtab");
        Pkg.add("OrdinaryDiffEq"); Pkg.add("Sundials")'

    - name: Run tests
      timeout-minutes: 25
      run: tox -e julia

    - name: Coverage
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./coverage.xml

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

    steps:
    - name: Check out repository
      uses: actions/checkout@v4

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v4
      with:
        path: |
          ~/.cache/pip
          .tox/
        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

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

    - name: Run tests
      timeout-minutes: 25
      run: tox -e optimize

    - name: Coverage
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./coverage.xml

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

    steps:
    - name: Check out repository
      uses: actions/checkout@v4

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v4
      with:
        path: |
          ~/.cache/pip
          .tox/
        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

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

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

    - name: Coverage
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./coverage.xml

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

    steps:
    - name: Check out repository
      uses: actions/checkout@v4

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v4
      with:
        path: |
          ~/.cache/pip
          .tox/
        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

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

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

    - name: Coverage
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./coverage.xml

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

    steps:
    - name: Check out repository
      uses: actions/checkout@v4

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v4
      with:
        path: |
          ~/.cache/pip
          .tox/
        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

    - name: Install dependencies
      run: pip install tox pre-commit

    - name: Check repository size
      run: tox -e size

    - name: Run pre-commit hooks
      run: pre-commit run --all-files

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

    steps:
    - name: Check out repository
      uses: actions/checkout@v4

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v4
      with:
        path: |
          ~/.cache/pip
          .tox/
        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

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

    - name: Validate CITATION.cff
      run: pip install cffconvert && cffconvert --validate

    - name: Build doc
      timeout-minutes: 30
      run: tox -e doc

  notebooks1:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.10']

    steps:
    - name: Check out repository
      uses: actions/checkout@v4

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v4
      with:
        path: |
          ~/.cache/pip
          .tox/
        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

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

    - name: Run notebooks 1
      timeout-minutes: 20
      run: tox -e notebooks1

  notebooks2:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.10']

    steps:
    - name: Check out repository
      uses: actions/checkout@v4

    - name: Prepare python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache
      uses: actions/cache@v4
      with:
        path: |
          ~/.cache/pip
          .tox/
        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

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

    - name: Run notebooks 2
      timeout-minutes: 20
      run: tox -e notebooks2