CI.yml

name: CI
on:
  push:
    branches:
      - main
      - development
      - test*
    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:
          - 'lts' # long-term support
          - '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: 'lts'
            shell: "bash"
            compiler: "g++-14"
            arch: "arm64"
          - os: "macOS-latest"
            julia-version: '1'
            shell: "bash"
            compiler: "g++-14"
            arch: "arm64"
          - os: "windows-latest"
            julia-version: '1'
            shell: "msys2"
            compiler: "g++"
            arch: "x64"

    defaults:
      run:
        shell: ${{ matrix.shell }} {0}
    
    steps:
    - name: Checkout repository
      uses: actions/checkout@v4

    - name: Install ImageMagick on macOS
      if: matrix.os == 'macOS-latest'
      run: |
        brew install imagemagick
        brew install ffmpeg
      
    - name: Install MSYS2 on Windows
      if: matrix.os == 'windows-latest'
      uses: msys2/setup-msys2@v2
      with:
        update: true
        install: mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-headers-git mingw-w64-x86_64-gcc-libs mingw-w64-x86_64-libwinpthread-git mingw-w64-x86_64-lapack mingw-w64-x86_64-openblas mingw-w64-x86_64-libxml2 mingw-w64-x86_64-bzip2 mingw-w64-x86_64-python mingw-w64-x86_64-python-zstandard mingw-w64-x86_64-python-cffi make bison flex mingw-w64-x86_64-ca-certificates mingw-w64-x86_64-diffutils
      
    - uses: julia-actions/setup-julia@v2
      with:
        version: ${{ matrix.julia-version }}
        arch: ${{ matrix.arch }}

    - name: Add Julia to PATH on Windows
      if: matrix.os == 'windows-latest'
      run: echo "C:\\hostedtoolcache\\windows\\julia\\${{ matrix.julia-version }}\\${{ matrix.arch }}\\bin" >> $GITHUB_PATH

    - name: Set environment variable PHYSICELL_CPP
      run: echo "PHYSICELL_CPP=${{ matrix.compiler }}" >> $GITHUB_ENV

    - uses: julia-actions/cache@v2

    - name: Add PCVCTRegistry (Windows)
      if: matrix.os == 'windows-latest'
      shell: pwsh
      run: julia -e 'import Pkg; Pkg.Registry.add("General"); Pkg.Registry.add(Pkg.RegistrySpec(url="https://github.com/drbergman/PCVCTRegistry.git"))'

    - name: Add PCVCTRegistry (non-Windows)
      if: matrix.os != 'windows-latest'
      run: julia -e 'import Pkg; Pkg.Registry.add("General"); Pkg.Registry.add(Pkg.RegistrySpec(url="https://github.com/drbergman/PCVCTRegistry.git"))'

    - uses: julia-actions/julia-buildpkg@v1

    - name: Install libRoadRunner dependencies on Ubuntu
      if: matrix.os == 'ubuntu-latest'
      run: |
        sudo apt-get update
        wget http://security.ubuntu.com/ubuntu/pool/universe/n/ncurses/libtinfo5_6.3-2ubuntu0.1_amd64.deb
        sudo apt-get install -y ./libtinfo5_6.3-2ubuntu0.1_amd64.deb

    - name: Run all tests
      uses: julia-actions/julia-runtest@v1
      env:
        PCVCT_NUM_PARALLEL_SIMS: 8
        PHYSICELL_CPP: ${{ matrix.compiler }} # maybe necessary for windows??
        PCVCT_PUBLIC_REPO_AUTH: ${{ secrets.PUBLIC_REPO_AUTH }}

    - uses: julia-actions/julia-processcoverage@v1
    
    - uses: codecov/codecov-action@v5
      with:
        files: 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: Add PCVCTRegistry
        run: julia -e 'import Pkg; Pkg.Registry.add("General"); Pkg.Registry.add(Pkg.RegistrySpec(url="https://github.com/drbergman/PCVCTRegistry.git"))'

      - 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)