Merge branch 'dev' into staging #33
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [ staging ] | |
| schedule: | |
| - cron: '0 0 * * 0' # Run at midnight every Sunday | |
| workflow_dispatch: # Allow manual trigger | |
| name: STAGING final checks | |
| permissions: | |
| contents: read | |
| packages: read | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macos-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: false # use standard CRAN | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - name: Install reticulate and create miniconda | |
| run: | | |
| Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); install.packages(c('reticulate', 'pdflatex'))" | |
| Rscript -e "reticulate::install_miniconda()" | |
| Rscript -e "reticulate::conda_create('r-reticulate')" | |
| Rscript -e "reticulate::conda_install(packages = 'scipy', envname = 'r-reticulate')" | |
| # Get the Python path and set environment variable | |
| PYTHON_PATH=$(Rscript -e "cat(reticulate::conda_python('r-reticulate'))") | |
| echo "RETICULATE_PYTHON=$PYTHON_PATH" >> $GITHUB_ENV | |
| # Print debug info | |
| echo "Python path: $PYTHON_PATH" | |
| Rscript -e "cat('Conda environments:\n'); print(reticulate::conda_list())" | |
| shell: bash | |
| - name: Run rcmdcheck | |
| run: | | |
| Rscript -e "print(Sys.getenv('RETICULATE_PYTHON'))" | |
| Rscript -e "tryCatch({print(reticulate::py_config())}, error = function(e) {print(paste('Error:', e))})" | |
| Rscript -e "rcmdcheck::rcmdcheck()" | |
| codecov: | |
| needs: R-CMD-check | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/drieslab/ci-giottosuite/ci-env | |
| 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: Set RETICULATE_PYTHON environment variable | |
| run: | | |
| echo "RETICULATE_PYTHON=/opt/miniconda/envs/r-reticulate/bin/python" >> $GITHUB_ENV | |
| shell: bash | |
| - name: Generate coverage report and upload | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| branch = "staging", | |
| 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 }} | |
| bioccheck: | |
| needs: R-CMD-check | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/drieslab/ci-giottosuite/ci-env | |
| 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} | |