Compatibility fixes for cmdstan 2.33+ #1573
Workflow file for this run
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| # Github Actions workflow to analyze CmdStanR code, test coverage | |
| # yamllint disable rule:line-length | |
| name: Test coverage | |
| 'on': | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| test-coverage-ubuntu: | |
| name: "Linux" | |
| if: "! contains(github.event.head_commit.message, '[ci skip]')" | |
| runs-on: ubuntu-20.04 | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| NOT_CRAN: true | |
| steps: | |
| - name: cmdstan env vars | |
| run: | | |
| echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV | |
| shell: bash | |
| - uses: n1hility/cancel-previous-runs@v3 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| workflow: Test-coverage.yml | |
| if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'" | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/[email protected] | |
| - uses: r-lib/actions/[email protected] | |
| - name: Install Ubuntu dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| sudo apt-get install -y openmpi-bin openmpi-common openmpi-doc libopenmpi-dev | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ubuntu-r-4.0-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ubuntu-r-4.0-1- | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c("remotes", "curl"), dependencies = TRUE) | |
| remotes::install_local(path = ".", INSTALL_opts = "--no-test-load") | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("covr") | |
| remotes::install_cran("gridExtra") | |
| shell: Rscript {0} | |
| - name: Install cmdstan | |
| run: | | |
| cmdstanr::check_cmdstan_toolchain(fix = TRUE) | |
| cmdstanr::install_cmdstan(cores = 2) | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| run: covr::codecov(type = "tests") | |
| shell: Rscript {0} | |
| test-coverage-windows: | |
| name: "Windows" | |
| if: "! contains(github.event.head_commit.message, '[ci skip]')" | |
| runs-on: windows-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| NOT_CRAN: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/[email protected] | |
| with: | |
| r-version: 'release' | |
| rtools-version: '42' | |
| - uses: r-lib/actions/[email protected] | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c("remotes", "curl"), dependencies = TRUE) | |
| remotes::install_local(path = ".") | |
| cmdstanr::check_cmdstan_toolchain(fix = TRUE) | |
| cmdstanr::install_cmdstan(cores = 2, overwrite = TRUE) | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("covr") | |
| remotes::install_cran("gridExtra") | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| run: | | |
| options(covr.gcov = 'C:/rtools40/mingw64/bin/gcov.exe'); | |
| covr::codecov(type = "tests", function_exclusions = "sample_mpi") | |
| shell: Rscript {0} |