inputs.toml and support libRR intracellulars #1128
Workflow file for this run
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| 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: "pwsh" | |
| # compiler: "g++" | |
| # arch: "x64" | |
| defaults: | |
| run: | |
| shell: ${{ matrix.shell }} | |
| 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.name == '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: ${{ matrix.arch }} | |
| - name: Set environment variable PHYSICELL_CPP | |
| run: echo "PHYSICELL_CPP=${{ matrix.compiler }}" >> $GITHUB_ENV | |
| - 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"))' | |
| - uses: julia-actions/julia-buildpkg@v1 | |
| - 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) |