dont commit on protected branch and remove testthat duplication #974
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| on: | |
| push: | |
| branches-ignore: | |
| - updateREADME | |
| pull_request: | |
| branches: | |
| - master | |
| workflow_dispatch: # Allow manual triggers | |
| schedule: | |
| - cron: '0 8 * * 4' | |
| name: R-CMD-check | |
| jobs: | |
| ## pre-job to determine if a job has been run for the same SHA (e.g. on a different branch) | |
| gatekeeper: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| should_skip: ${{ steps.skip_check.outputs.should_skip }} | |
| steps: | |
| - id: skip_check | |
| uses: fkirc/skip-duplicate-actions@master | |
| with: | |
| github_token: ${{ github.token }} | |
| versions: | |
| needs: gatekeeper | |
| if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name != 'schedule' && (needs.gatekeeper.outputs.should_skip == 'false') && !contains(github.event.head_commit.message, 'worksave') && !contains(github.event.head_commit.message, 'skip-ci')) | |
| runs-on: ubuntu-latest | |
| outputs: | |
| r: ${{ steps.setup.outputs.r }} | |
| bioc: ${{ steps.setup.outputs.bioc }} | |
| dockerise: ${{ steps.setup.outputs.dockerise }} | |
| docker_tag: ${{ steps.setup.outputs.docker_tag }} | |
| steps: | |
| - uses: rlespinasse/github-slug-action@v3.x | |
| - uses: r-lib/actions/setup-r@v2 | |
| - name: Get R/Bioc versions | |
| id: setup | |
| run: | | |
| BRANCH_NAME="${{ env.GITHUB_REF_SLUG }}" | |
| ## R and Bioc versions | |
| Rscript -e "install.packages('BiocManager', Ncpus=2)" | |
| r_devel=$(Rscript -e "vm=BiocManager:::.version_map(); cat(as.character(vm[vm\$BiocStatus == 'devel',]\$R))") | |
| r_release=$(Rscript -e "vm=BiocManager:::.version_map(); cat(as.character(vm[vm\$BiocStatus == 'release',]\$R))") | |
| if [[ $BRANCH_NAME =~ "release_" ]] | |
| then | |
| bioc="latest" | |
| r="$r_release" | |
| else | |
| bioc="devel" | |
| r="$r_devel" | |
| fi | |
| echo "r=$r" >> $GITHUB_OUTPUT | |
| echo "bioc=$bioc" >> $GITHUB_OUTPUT | |
| ## Docker | |
| # Only Dockerise for 'master' or 'RELEASE_*' branches | |
| dockerise='false' | |
| [[ github.event_name != 'schedule' && ($BRANCH_NAME == "master" || $BRANCH_NAME =~ "release_") ]] && dockerise='true' | |
| echo "dockerise=$dockerise" >> $GITHUB_OUTPUT | |
| # Docker tag is 'github' for master and the branch name for release branches | |
| docker_tag="github" | |
| [[ $BRANCH_NAME =~ "release_" ]] && docker_tag=$BRANCH_NAME | |
| echo "docker_tag=$docker_tag" >> $GITHUB_OUTPUT | |
| R-CMD-check: | |
| needs: [gatekeeper, versions] | |
| ## run scheduled jobs only on main repo - do not run a duplicate job for merges etc. Do not run if commit messages include any of 'worksave' or 'skip-ci' | |
| if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name != 'schedule' && (needs.gatekeeper.outputs.should_skip == 'false') && !contains(github.event.head_commit.message, 'worksave') && !contains(github.event.head_commit.message, 'skip-ci')) | |
| runs-on: ${{ matrix.config.os }} | |
| container: ${{ matrix.config.image }} | |
| name: ${{ matrix.config.os }} (r_${{ matrix.config.r }} - bioc_${{ matrix.config.bioc }} - image_${{ matrix.config.image }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: windows-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}'} | |
| - { os: macOS-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}'} | |
| - { os: ubuntu-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}', image: 'bioconductor/bioconductor_docker:${{ needs.versions.outputs.bioc }}'} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| CRAN: ${{ matrix.config.cran }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Check out repo ⬇️ | |
| uses: actions/checkout@v2 | |
| - name: Set up R ▶️ | |
| uses: r-lib/actions/setup-r@v2 | |
| if: matrix.config.image == null | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - name: Create slug/short variables | |
| uses: rlespinasse/github-slug-action@v3.x | |
| - name: Install remotes 🔭 | |
| run: | | |
| install.packages('remotes', Ncpus=2) | |
| shell: Rscript {0} | |
| - name: Set BiocManager version 📆 | |
| if: matrix.config.image == null | |
| run: | | |
| install.packages('BiocManager', Ncpus=2) | |
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, Ncpus=2) | |
| shell: Rscript {0} | |
| - name: Query dependencies ❓ | |
| run: | | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE, repos = c(getOption('repos'), BiocManager::repositories())), 'depends.Rds', version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages 💾 | |
| if: runner.os != 'Windows' && matrix.config.image == null | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}- | |
| - name: Install system and package dependencies using github action 🔧 | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-repositories: 'https://cloud.r-project.org' | |
| - name: Install extra dependencies for macOS | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install --cask xquartz | |
| brew install gcc | |
| - name: Install extra dependencies for linux | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y pandoc-citeproc | |
| sudo apt-get install -y qpdf | |
| - name: Install R dependencies 🔨 | |
| run: | | |
| options(repos = c(CRAN = "https://cran.r-project.org")) | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories(), Ncpus=2) | |
| remotes::install_cran("rcmdcheck", Ncpus=2) | |
| remotes::install_cran("covr", Ncpus=2) | |
| shell: Rscript {0} | |
| - name: Session info 🖥️ | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| # # runs rmdcheck, first runs 'devtools::install to make sure there is a copy of mixOmics the parallel workers can access' | |
| # - name: Check ✅ | |
| # if: (!contains(github.event.head_commit.message, 'skip-check')) | |
| # run: | | |
| # remotes::install_cran("devtools", Ncpus=2) | |
| # devtools::install() | |
| # devtools::check(args = c("--no-manual"), error_on = "warning", check_dir = "check") | |
| # shell: Rscript {0} | |
| # - name: BiocCheck 🧬 ✅ | |
| # if: (!contains(github.event.head_commit.message, 'skip-check')) | |
| # run: | | |
| # BiocManager::install("BiocCheck", Ncpus=2) | |
| # BiocCheck::BiocCheck(".") | |
| # shell: Rscript {0} | |
| # - name: Check --as-cran ✅ ✅ | |
| # if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics') | |
| # env: | |
| # _R_CHECK_CRAN_INCOMING_: false | |
| # run: | | |
| # options(devtools.check.dir = "check/asCRAN", devtools.check.warning = "never") | |
| # devtools::check(args = c("--no-manual", "--as-cran", "--ignore-vignettes", "--run-dontrun"), build_args = c("--no-build-vignettes")) | |
| # shell: Rscript {0} | |
| # - name: Upload check results ⬆️ | |
| # if: failure() | |
| # uses: actions/upload-artifact@master | |
| # with: | |
| # name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| # path: check | |
| # - name: Show testthat output 📖 | |
| # if: always() | |
| # run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| # shell: bash | |
| # - name: Push to DockerHub 📦 | |
| # if: runner.os == 'Linux' && needs.versions.outputs.dockerise == 'true' && !contains(github.event.head_commit.message, 'skip-docker') | |
| # uses: docker/build-push-action@v1 | |
| # with: | |
| # username: ${{ secrets.DOCKER_USERNAME }} | |
| # password: ${{ secrets.DOCKER_PASSWORD }} | |
| # repository: mixomicsteam/mixomics | |
| # tags: ${{ needs.versions.outputs.docker_tag }} | |
| # build_args: BIOC_VERSION=${{ needs.versions.outputs.bioc }} | |
| - name: Check and Install covr | |
| run: | | |
| Rscript -e " | |
| if (!requireNamespace('covr', quietly = TRUE)) { | |
| install.packages('covr') | |
| message('covr package was not installed and has been installed.') | |
| } else { | |
| message('covr package is already installed.') | |
| } | |
| " | |
| - name: Create coverage report 🔍 | |
| if: (runner.os == 'Linux' && github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (runner.os == 'Linux' && github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics') | |
| run: | | |
| Rscript -e " | |
| install_path <- file.path(normalizePath(Sys.getenv('RUNNER_TEMP'), winslash = '/'), 'package') | |
| print(paste('Installation path:', install_path)) | |
| # Enable verbose output and print details during coverage collection | |
| options(covr.verbose = TRUE) | |
| # Wrap in try-catch to handle and print errors | |
| tryCatch({ | |
| cov <- covr::package_coverage( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = install_path, | |
| type = "tests" | |
| ) | |
| print('Coverage successfully generated:') | |
| print(cov) | |
| saveRDS(cov, file.path(Sys.getenv('RUNNER_TEMP'), 'coverage.rds')) | |
| }, error = function(e) { | |
| print('Error during package_coverage:') | |
| print(e) | |
| traceback() | |
| stop(e) # Re-raise the error to halt the process | |
| }) | |
| " | |
| echo "Files in RUNNER_TEMP directory:" | |
| ls $RUNNER_TEMP | |
| set -e | |
| - name: Upload coverage report to Codecov | |
| if: (runner.os == 'Linux' && github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (runner.os == 'Linux' && github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics') | |
| run: | | |
| set +e | |
| echo "Checking for coverage.rds file before uploading..." | |
| if [ -f "coverage.rds" ]; then | |
| echo "coverage.rds found, proceeding with upload..." | |
| Rscript -e "cov <- readRDS('coverage.rds'); covr::codecov(coverage = cov)" | |
| else | |
| echo "Error: coverage.rds not found!" | |
| exit 1 | |
| fi | |
| set -e | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| # - name: Test coverage | |
| # if: (runner.os == 'Linux' && github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (runner.os == 'Linux' && github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics') | |
| # run: | | |
| # cov <- covr::package_coverage( | |
| # quiet = FALSE, | |
| # clean = FALSE, | |
| # install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
| # ) | |
| # print("Coverage calculated!") | |
| # print(cov) | |
| # covr::to_cobertura(cov) | |
| # shell: Rscript {0} | |
| # - uses: codecov/codecov-action@v4 | |
| # if: (runner.os == 'Linux' && github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (runner.os == 'Linux' && github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics') | |
| # with: | |
| # file: ./cobertura.xml | |
| # plugin: noop | |
| # disable_search: true | |
| # token: ${{ secrets.CODECOV_TOKEN }} | |
| # - name: Create coverage report 🔍 | |
| # if: (runner.os == 'Linux' && github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (runner.os == 'Linux' && github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics') | |
| # # the commands between 'set +e' and 'set -e' are run without throwing any error | |
| # run: | | |
| # set +e | |
| # echo "Checking if covr is installed..." | |
| # Rscript -e "if (!requireNamespace('covr', quietly = TRUE)) install.packages('covr')" | |
| # echo "Generating coverage report..." | |
| # Rscript -e "cov <- covr::package_coverage(type = c('tests', 'examples')); print(cov)" | |
| # echo "Uploading coverage report..." | |
| # Rscript -e "covr::codecov(coverage = cov)" | |
| # set -e | |
| # env: | |
| # CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| # - name: Notify Slack 📣 | |
| # uses: 8398a7/action-slack@v3 | |
| # with: | |
| # status: ${{ job.status }} | |
| # fields: repo,message,commit,author,action,eventName,ref,workflow,job,took # selectable (default: repo,message) | |
| # env: | |
| # SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} # set in rep's setting >> secrets |