Merge pull request #128 from jiajic/jgc_patch #27
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| name: Dev Branch Checks | |
| on: | |
| push: | |
| branches: [ "dev" ] | |
| permissions: | |
| contents: write | |
| packages: read | |
| jobs: | |
| codecov: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/drieslab/ci-giottosuite/ci-env | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.CI_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch all history and tags | |
| - name: catch R deps not in container | |
| run: devtools::install_deps() | |
| shell: Rscript {0} | |
| - name: Generate coverage report and upload | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| branch = "dev", | |
| type = c("tests", "examples", "vignettes"), | |
| combine_types = TRUE, | |
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
| ) | |
| shell: Rscript {0} | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| # **This already seems to be done by covr::codecov()** | |
| # - name: Upload coverage reports to Codecov | |
| # uses: codecov/codecov-action@v4 | |
| # with: | |
| # token: ${{ secrets.CODECOV_TOKEN }} | |
| # fail_ci_if_error: false | |
| # flags: unittests | |
| # verbose: true | |
| rcmdcheck: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/drieslab/ci-giottosuite/ci-env | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.CI_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch all history and tags | |
| - name: catch R deps not in container | |
| run: devtools::install_deps() | |
| shell: Rscript {0} | |
| - name: Check package | |
| run: | | |
| rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error") | |
| shell: Rscript {0} | |
| bioccheck: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/drieslab/ci-giottosuite/ci-env | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.CI_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch all history and tags | |
| - name: catch R deps not in container | |
| run: devtools::install_deps() | |
| shell: Rscript {0} | |
| - name: Build and install | |
| run: | | |
| R CMD build . | |
| R CMD INSTALL *.tar.gz | |
| - name: Run BiocCheck | |
| run: | | |
| BiocCheck::BiocCheck() | |
| shell: Rscript {0} |