ci.yml

name: CI

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

# jobs
jobs:
  base:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        # update to 3.11 when numba allows (needed in umap)
        python-version: ['3.9', '3.10']

    steps:
    - name: Check out repository
      uses: actions/checkout@v3

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

    - name: Cache
      uses: actions/cache@v3
      with:
        path: ~/.cache
        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-base

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

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

    - name: Coverage
      uses: codecov/codecov-action@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml

  petab:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.9', '3.11']

    steps:
    - name: Check out repository
      uses: actions/checkout@v3

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

    - name: Cache
      uses: actions/cache@v3
      with:
        path: ~/.cache
        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-petab

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

    - name: Run tests
      timeout-minutes: 35
      run: tox -e petab

    - name: Coverage
      uses: codecov/codecov-action@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml

  julia:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.9', '3.11']

    steps:
    - name: Check out repository
      uses: actions/checkout@v3

    - 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: 1.9

    - name: Cache
      uses: actions/cache@v3
      with:
        path: |
          ~/.cache
          ~/.julia/artifacts
        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-julia

    - 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@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml

  optimize:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        # update to 3.11 when nlopt allows
        python-version: ['3.9', '3.10']

    steps:
    - name: Check out repository
      uses: actions/checkout@v3

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

    - name: Cache
      uses: actions/cache@v3
      with:
        path: ~/.cache
        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-optimize

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

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

    - name: Coverage
      uses: codecov/codecov-action@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml

  hierarchical:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.9', '3.11']

    steps:
    - name: Check out repository
      uses: actions/checkout@v3

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

    - name: Cache
      uses: actions/cache@v3
      with:
        path: ~/.cache
        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-hierarchical

    - 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@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml

  select:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.9', '3.11']

    steps:
    - name: Check out repository
      uses: actions/checkout@v3

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

    - name: Cache
      uses: actions/cache@v3
      with:
        path: ~/.cache
        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-select

    - 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@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml

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

    steps:
    - name: Check out repository
      uses: actions/checkout@v3

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

    - name: Cache
      uses: actions/cache@v3
      with:
        path: ~/.cache
        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-quality

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

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

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

    - 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@v3

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

    - name: Cache
      uses: actions/cache@v3
      with:
        path: ~/.cache
        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-docs

    - 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: 10
      run: tox -e doc

  notebooks1:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.9']

    steps:
    - name: Check out repository
      uses: actions/checkout@v3

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

    - name: Cache
      uses: actions/cache@v3
      with:
        path: ~/.cache
        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-notebooks1

    - 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: ['3.9']

    steps:
    - name: Check out repository
      uses: actions/checkout@v3

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

    - name: Cache
      uses: actions/cache@v3
      with:
        path: ~/.cache
        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-notebooks2

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

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