ci: push and PR should be checked #18
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| name: Dev Branch Checks | |
| on: | |
| push: | |
| branches: [ "dev" ] | |
| permissions: | |
| contents: write | |
| packages: read | |
| jobs: | |
| setup: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| container_name: ${{ steps.set-name.outputs.name }} | |
| steps: | |
| - name: Set container name | |
| id: set-name | |
| run: | | |
| LOWER_NAME=$(echo "${{ github.repository }}" | awk '{print tolower($0)}') | |
| echo "name=ghcr.io/${LOWER_NAME}/r-env:latest" >> $GITHUB_OUTPUT | |
| codecov: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ${{ needs.setup.outputs.container_name }} | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch all history and tags | |
| - name: Debug Python environment | |
| shell: Rscript {0} | |
| run: | | |
| print("Checking miniconda location:") | |
| print(list.files("~/.local/share", recursive = FALSE)) | |
| print(Sys.getenv("HOME")) | |
| print("R lib path:") | |
| print(.libPaths()) | |
| print("Available conda environments:") | |
| print(reticulate::conda_list()) | |
| print("\nPython configuration:") | |
| print(reticulate::py_config()) | |
| print("\nChecking r-reticulate specifically:") | |
| print(file.exists("/root/.local/share/r-miniconda/envs/r-reticulate")) | |
| if(file.exists("/root/.local/share/r-miniconda/envs/r-reticulate")) { | |
| print(list.files("/root/.local/share/r-miniconda/envs/r-reticulate", recursive = TRUE)) | |
| } | |
| - name: catch R deps not in container | |
| run: devtools::install_deps() | |
| shell: Rscript {0} | |
| - name: Generate coverage report | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| type = c("tests", "examples", "vignettes"), | |
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
| ) | |
| shell: Rscript {0} | |
| - 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: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ${{ needs.setup.outputs.container_name }} | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_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: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ${{ needs.setup.outputs.container_name }} | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_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} |