Workflow Changes #463
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| # Workflow derived from https://github.com/r-lib/actions/tree/master/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| # R cmd check for singleCellTK | |
| on: | |
| push: | |
| branches: [master, devel] | |
| pull_request: | |
| branches: [master, devel] | |
| name: R-CMD-check | |
| 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: 'release'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Setup Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.8' | |
| - name: Pip Installer | |
| uses: BSFishy/pip-action@v1 | |
| with: | |
| packages: | | |
| bbknn | |
| pandas | |
| scanorama | |
| scipy | |
| numpy | |
| astroid | |
| six | |
| scrublet | |
| scanpy | |
| - name: isPythonInstalled | |
| if: always() | |
| run: | | |
| python3 --version | |
| which python | |
| shell: bash | |
| - 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 | |
| - name: Install fftw3 on Linux | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get install libfftw3-dev | |
| - name: Install fftw3 on macOS | |
| if: runner.os == 'macOS' | |
| run: brew install fftw | |
| - name: Manual Install | |
| run: | | |
| install.packages("BiocManager") | |
| BiocManager::install("ggtree") | |
| install.packages("remotes") | |
| install.packages("magick") | |
| remotes::install_version("assertive.properties", version = "0.0.5", repos = "http://cran.us.r-project.org", upgrade = "never") | |
| remotes::install_version("assertive.types", version = "0.0.3", repos = "http://cran.us.r-project.org", upgrade = "never") | |
| remotes::install_version("multipanelfigure", version = "2.1.2", repos = "http://cran.us.r-project.org", upgrade = "never") | |
| remotes::install_version("Matrix", version = "1.6.4", repos = "http://cran.us.r-project.org", upgrade = "never") | |
| BiocManager::install("celda") | |
| shell: Rscript {0} | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache: false | |
| extra-packages: | | |
| any::rcmdcheck | |
| needs: check | |
| - name: Install XQuartz on macOS | |
| if: runner.os == 'macOS' | |
| run: brew install xquartz --cask | |
| - name: Install Old Seurat | |
| run: | | |
| remotes::install_version("Matrix", version = "1.6.4", repos = "http://cran.us.r-project.org", upgrade = "never") | |
| remotes::install_version("SeuratObject", version = "4.1.4", repos = "http://cran.us.r-project.org", upgrade = "never") | |
| remotes::install_version("Seurat", version = "4.4.0", repos = "http://cran.us.r-project.org", upgrade = "never") | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| if (Sys.info()[1] == "Windows") { | |
| reticulate::use_python(system('where python', intern=TRUE)[1]) | |
| } else { | |
| reticulate::use_python(system('which python', intern=TRUE)) | |
| } | |
| reticulate::py_config() | |
| rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check | |
| - name: Run codecov | |
| run: | | |
| install.packages("covr") | |
| library(covr) | |
| codecov() | |
| shell: Rscript {0} | |
| - name: Upload codecov | |
| uses: codecov/codecov-action@v2.1.0 |