main.yml

name: CI
on:
  push:
    branches:
      - main
      - development
      - tests
    tags: ['*']
  pull_request:
  workflow_dispatch:
concurrency:
  # Skip intermediate builds: always.
  # Cancel intermediate builds: only if it is a pull request build.
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}

jobs:
  test:
    name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
    runs-on: ${{ matrix.os }}
    timeout-minutes: 60
    permissions:  # needed for julia-actions/cache to delete old caches
      actions: write
      contents: read
    strategy:
      fail-fast: false
      matrix:
        julia-version:
          - '1.10.4' # the one I have been developing with
          - '1' # to check the latest v1 version
          - 'pre' # check upcoming releases
        os: ["ubuntu-latest"]
        arch: ["x64"]
        shell: ["bash"]
        compiler: ["g++"]
        include:
          - os: "macOS-latest"
            julia-version: '1'
            shell: "bash"
            compiler: "g++-13"
            arch: "arm64"

    defaults:
      run:
        shell: ${{ matrix.shell }}
    
    steps:
    - name: Checkout repository
      uses: actions/checkout@v4
      with:
        submodules: true
        token: ${{ secrets.GH_PCVCT }}
    - name: Set up test project
      run: |
        mkdir -p ./test/test-project/data/inputs/configs/default
        cp ./test/PhysiCell/sample_projects/template/config/PhysiCell_settings.xml ./test/test-project/data/inputs/configs/default/PhysiCell_settings.xml
        mkdir -p ./test/test-project/data/inputs/custom_codes/default
        cp ./test/PhysiCell/sample_projects/template/main.cpp ./test/test-project/data/inputs/custom_codes/default/main.cpp
        cp ./test/PhysiCell/sample_projects/template/Makefile ./test/test-project/data/inputs/custom_codes/default/Makefile
        cp -r ./test/PhysiCell/sample_projects/template/custom_modules ./test/test-project/data/inputs/custom_codes/default/custom_modules
        mkdir -p ./test/test-project/data/inputs/rulesets_collections/default
        touch ./test/test-project/data/inputs/rulesets_collections/default/base_rulesets.csv
        echo "default,pressure,decreases,cycle entry,0,0.5,4,0" >> ./test/test-project/data/inputs/rulesets_collections/default/base_rulesets.csv
        echo "Template project files are in place within ./test/test-project/data/inputs"
    - uses: julia-actions/setup-julia@v2
      with:
        version: ${{ matrix.julia-version }}
        arch: ${{ matrix.arch }}
    - name: Set environment variable PHYSICELL_CPP
      run: echo "PHYSICELL_CPP=${{ matrix.compiler }}" >> $GITHUB_ENV
    - uses: julia-actions/cache@v2
    - uses: julia-actions/julia-buildpkg@v1
    - uses: julia-actions/julia-runtest@v1
    - uses: julia-actions/julia-processcoverage@v1
    - uses: codecov/codecov-action@v4
      with:
        file: lcov.info
        token: ${{ secrets.CODECOV_TOKEN }}
        fail_ci_if_error: false
        
  docs:
    name: Documentation
    runs-on: ubuntu-latest
    permissions:
      actions: write # needed to allow julia-actions/cache to proactively delete old caches that it has created
      contents: write
      statuses: write
    steps:
      - uses: actions/checkout@v4
      - uses: julia-actions/setup-julia@v2
        with:
          version: '1'
      - uses: julia-actions/cache@v2
      - name: Configure doc environment
        shell: julia --project=docs --color=yes {0}
        run: |
          using Pkg
          Pkg.develop(PackageSpec(path=pwd()))
          Pkg.instantiate()
      - uses: julia-actions/julia-buildpkg@v1
      - uses: julia-actions/julia-docdeploy@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
      - name: Run doctests
        shell: julia --project=docs --color=yes {0}
        run: |
          using Documenter: DocMeta, doctest
          using pcvct
          DocMeta.setdocmeta!(pcvct, :DocTestSetup, :(using pcvct); recursive=true)
          doctest(pcvct)