Add support for DelayedArray reading
#266
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| # Based on workflows from https://github.com/Huber-group-EMBL/rhdf5 | |
| # Uses steps from https://github.com/grimbough/bioc-actions | |
| on: | |
| push: | |
| branches: | |
| - devel | |
| pull_request: | |
| name: R-CMD-check-bioc | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| jobs: | |
| R-CMD-check-bioc: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.bioc-version }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: windows-latest, bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', cache: 1 } | |
| - { os: macOS-latest, bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', cache: 1 } | |
| - { os: macOS-15-intel, bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', cache: 2 } | |
| - { os: ubuntu-latest, bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', cache: 1 } | |
| - { os: ubuntu-latest, bioc-version: 'release', bioc-mirror: 'https://bioconductor.posit.co/', cache: 1 } | |
| steps: | |
| ## R CMD check complains about Windows line endings without this | |
| - name: Configure git | |
| run: | | |
| git config --global core.autocrlf false | |
| - name: Checkout repository | |
| uses: actions/checkout@v6 | |
| - name: Install Linux dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get -y install hdf5-tools libsz2 libaec-dev | |
| ## Install missing libraries for macOS ARM (macOS-latest) | |
| - name: Install macOS dependencies | |
| if: matrix.config.os == 'macOS-latest' | |
| run: | | |
| brew install gettext openssl | |
| mkdir -p ~/.R | |
| echo "CPPFLAGS += -I$(brew --prefix gettext)/include -I$(brew --prefix openssl)/include" >> ~/.R/Makevars | |
| echo "LDFLAGS += -L$(brew --prefix gettext)/lib -L$(brew --prefix openssl)/lib" >> ~/.R/Makevars | |
| - name: Setup R and Bioconductor | |
| uses: rcannood/bioc-actions/setup-bioc@remove-version-map | |
| with: | |
| bioc-version: ${{ matrix.config.bioc-version }} | |
| bioc-mirror: ${{ matrix.config.bioc-mirror }} | |
| - name: Install pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: ${{ matrix.config.cache }} | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| ## Workaround: llvmlite has no pre-built pip wheel on macOS x86_64, | |
| ## but conda-forge does have a build. Use reticulate + conda to install. | |
| ## See https://github.com/numba/numba/issues/10187#issuecomment-3800638403 | |
| - name: Cache conda packages (macOS Intel) | |
| if: matrix.config.os == 'macOS-15-intel' | |
| uses: actions/cache@v5 | |
| with: | |
| path: ~/.local/share/r-miniconda | |
| key: ${{ runner.os }}-conda-${{ hashFiles('DESCRIPTION') }} | |
| restore-keys: | | |
| ${{ runner.os }}-conda- | |
| - name: Install Python packages via conda (macOS Intel) | |
| id: install-conda | |
| if: matrix.config.os == 'macOS-15-intel' | |
| shell: Rscript {0} | |
| run: | | |
| reticulate::install_miniconda() | |
| reticulate::py_install( | |
| c("scanpy", "mudata"), | |
| method = "conda", | |
| channel = "conda-forge" | |
| ) | |
| # need to store this in Renviron because there's no easy way of | |
| # passing env vars to bioc-actions/build-install-check | |
| writeLines( | |
| paste0("RETICULATE_PYTHON=", reticulate::conda_python("r-reticulate")), | |
| "~/.Renviron" | |
| ) | |
| - name: Verify conda installation (macOS Intel) | |
| if: matrix.config.os == 'macOS-15-intel' | |
| shell: Rscript {0} | |
| run: | | |
| stopifnot(reticulate::py_module_available("scanpy")) | |
| stopifnot(reticulate::py_module_available("mudata")) | |
| cat("Python packages verified successfully\n") | |
| - name: Bioc - Build, Install, Check | |
| id: bioc-check | |
| uses: grimbough/bioc-actions/build-install-check@v1 | |
| - name: Show testthat output | |
| if: always() | |
| run: find .. -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() && steps.bioc-check.outputs.check-dir != '' | |
| uses: actions/upload-artifact@v7 | |
| with: | |
| name: ${{ format('{0}-{1}-bioc-{2}-results', runner.os, runner.arch, env.R_BIOC_VERSION) }} | |
| path: ${{ steps.bioc-check.outputs.check-dir }} | |
| - name: Run BiocCheck | |
| if: matrix.config.os == 'ubuntu-latest' && matrix.config.bioc-version == 'devel' | |
| uses: grimbough/bioc-actions/run-BiocCheck@v1 | |
| with: | |
| error-on: 'never' | |
| arguments: '--no-check-bioc-help' |