Fix checking of assignments for empty modularexperiment #82
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| # Workflow partially based on | |
| # - The output of: biocthis::use_bioc_github_action() | |
| # - The workflow: https://github.com/r-lib/actions/tree/v2/examples | |
| on: push | |
| name: build-test-deploy | |
| # These environment variables control whether to run GitHub Actions (GHA) code | |
| # later on that is specific to testthat, and pkgdown. | |
| # | |
| # If you need to clear the cache of packages, update the number inside | |
| # cache-version as discussed at https://github.com/r-lib/actions/issues/86. | |
| # Note that you can always run a GHA test without the cache by using the word | |
| # "/nocache" in the commit message. | |
| env: | |
| has_testthat: 'true' | |
| run_bioc: 'true' | |
| run_pkgdown: 'true' | |
| run_docker: 'true' | |
| cache-version: 'cache-v2' | |
| jobs: | |
| build-test: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| container: ${{ matrix.config.cont }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_20", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } | |
| - { os: macOS-latest, r: '4.4', bioc: '3.20'} | |
| - { os: windows-latest, r: '4.4', bioc: '3.20'} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| NOT_CRAN: true | |
| TZ: UTC | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Set R Library home on Linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| mkdir /__w/_temp/Library | |
| echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| # R is already included in the Bioconductor docker images | |
| - name: Setup R from r-lib | |
| if: runner.os != 'Linux' | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| # Install pandoc for non-Linux platforms | |
| - name: Setup Pandoc | |
| if: runner.os != 'Linux' | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Restore R package cache | |
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ env.cache-version }}-${{ runner.os }}-bioc-${{ env.BIOC_VERSION }}-r-${{ env.R_VERSION }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-bioc-${{ env.BIOC_VERSION }}-r-${{ env.R_VERSION }}- | |
| - name: Cache R packages on Linux | |
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " | |
| uses: actions/cache@v3 | |
| with: | |
| path: /home/runner/work/_temp/Library | |
| key: ${{ env.cache-version }}-${{ runner.os }}-bioc-${{ env.BIOC_VERSION }}-r-${{ env.R_VERSION }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-bioc-${{ env.BIOC_VERSION }}-r-${{ env.R_VERSION }}- | |
| - name: Install macOS system dependencies | |
| if: matrix.config.os == 'macOS-latest' | |
| run: | | |
| # Enable installing XML from source if needed | |
| brew install libxml2 | |
| echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV | |
| # Required to install magick as noted at | |
| # https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 | |
| brew install imagemagick@6 | |
| # For textshaping, required by ragg, and required by pkgdown | |
| brew install harfbuzz fribidi | |
| # For installing usethis's dependency gert | |
| brew install libgit2 | |
| # Required for tcltk | |
| brew install xquartz --cask | |
| - name: Install Windows system dependencies | |
| if: runner.os == 'Windows' | |
| run: | | |
| # Edit below if you have any Windows system dependencies | |
| shell: Rscript {0} | |
| - name: Install BiocManager | |
| run: | | |
| message(paste('****', Sys.time(), 'installing BiocManager ****')) | |
| remotes::install_cran("BiocManager") | |
| shell: Rscript {0} | |
| - name: Set BiocVersion | |
| run: | | |
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE) | |
| shell: Rscript {0} | |
| - name: Install dependencies pass 1 | |
| run: | | |
| # Try installing the package dependencies in steps. First the local | |
| # dependencies, then any remaining dependencies to avoid the | |
| # issues described at | |
| # https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html | |
| # https://github.com/r-lib/remotes/issues/296 | |
| # Ideally, all dependencies should get installed in the first pass. | |
| # For running the checks | |
| message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | |
| install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories()) | |
| # Pass #1 at installing dependencies | |
| message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) | |
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) | |
| continue-on-error: true | |
| shell: Rscript {0} | |
| - name: Install dependencies pass 2 | |
| run: | | |
| # Pass #2 at installing dependencies | |
| message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) | |
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE) | |
| shell: Rscript {0} | |
| - name: Install BiocGenerics | |
| if: env.has_RUnit == 'true' | |
| run: | | |
| # Install BiocGenerics | |
| BiocManager::install("BiocGenerics") | |
| shell: Rscript {0} | |
| - name: Install pkgdown | |
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| run: | | |
| remotes::install_cran("pkgdown") | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Run CMD check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| DISPLAY: 99.0 | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-manual", "--no-vignettes", "--timings"), | |
| build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), | |
| error_on = "warning", | |
| check_dir = "check" | |
| ) | |
| shell: Rscript {0} | |
| # Might need an to add this to the if: && runner.os == 'Linux' | |
| - name: Reveal testthat details | |
| if: env.has_testthat == 'true' | |
| run: find . -name testthat.Rout -exec cat '{}' ';' | |
| - name: Run BiocCheck | |
| if: env.run_bioc == 'true' | |
| env: | |
| DISPLAY: 99.0 | |
| run: | | |
| BiocCheck::BiocCheck( | |
| dir('check', 'tar.gz$', full.names = TRUE), | |
| `quit-with-status` = TRUE, | |
| `no-check-R-ver` = TRUE, | |
| `no-check-bioc-help` = TRUE | |
| ) | |
| shell: Rscript {0} | |
| - name: Install package | |
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| run: R CMD INSTALL . | |
| - name: Prepare pkgdown figures | |
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| run: | | |
| mkdir vignettes/figures | |
| cp inst/stability.png vignettes/figures/stability.png | |
| shell: bash | |
| - name: Build pkgdown site | |
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | |
| shell: Rscript {0} | |
| - name: Install deploy dependencies | |
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| run: | | |
| apt-get update && apt-get -y install rsync | |
| - name: Deploy pkgdown site to GitHub pages | |
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| uses: JamesIves/github-pages-deploy-action@releases/v4 | |
| with: | |
| clean: false | |
| branch: gh-pages | |
| folder: docs | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-biocversion-RELEASE_3_20-r-4.5-results | |
| path: check | |
| # 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 | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| needs: build-test | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::covr, any::xml2 | |
| needs: coverage | |
| - name: Test coverage | |
| run: | | |
| cov <- covr::package_coverage( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
| ) | |
| covr::to_cobertura(cov) | |
| shell: Rscript {0} | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} | |
| file: ./cobertura.xml | |
| plugin: noop | |
| disable_search: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| # -------------------------------------------------------------------- | |
| find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload test results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-test-failures | |
| path: ${{ runner.temp }}/package | |
| # Code adapted from | |
| # https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92 | |
| docker-build-and-push: | |
| runs-on: ubuntu-latest | |
| needs: build-test | |
| steps: | |
| - name: Checkout Repository | |
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | |
| uses: actions/checkout@v3 | |
| - name: Register repo name and get package version | |
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | |
| id: reg_repo_name | |
| run: | | |
| echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV | |
| echo PKG_VERSION=$(grep "Version:" DESCRIPTION | cut -d' ' -f2) >> $GITHUB_ENV | |
| - name: Set up QEMU | |
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | |
| uses: docker/setup-qemu-action@v2 | |
| - name: Set up Docker Buildx | |
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Login to Docker Hub | |
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | |
| uses: docker/login-action@v2 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and Push Docker | |
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()" | |
| uses: docker/build-push-action@v4 | |
| with: | |
| context: . | |
| file: ./inst/docker/Dockerfile | |
| push: true | |
| tags: | | |
| ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest, | |
| ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel, | |
| ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:${{ env.PKG_VERSION }} |