Add new input to allow users to force install dependencies, bypassing cache #170
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| name: rworkflows_static | |
| 'on': | |
| push: | |
| branches: | |
| - master | |
| - main | |
| - devel | |
| - RELEASE_** | |
| pull_request: | |
| branches: | |
| - master | |
| - main | |
| - devel | |
| - RELEASE_** | |
| env: | |
| run_bioccheck: ${{ false }} | |
| run_rcmdcheck: ${{ true }} | |
| as_cran: ${{ true }} | |
| run_vignettes: ${{ true }} | |
| has_testthat: ${{ true }} | |
| run_covr: ${{ true }} | |
| run_pkgdown: ${{ true }} | |
| has_runit: ${{ false }} | |
| has_latex: ${{ false }} | |
| tinytex_installer: TinyTeX-1 | |
| pandoc_version: '2.19' | |
| run_docker: ${{ false }} | |
| docker_registry: ghcr.io | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} | |
| cache_version: cache-v1 | |
| miniforge_variant: ${{ false }} | |
| activate_environment: test | |
| jobs: | |
| rworkflows_static: | |
| permissions: write-all | |
| 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: auto | |
| bioc: release | |
| cont: ghcr.io/bioconductor/bioconductor_docker:RELEASE_3_18 | |
| rspm: ~ | |
| - os: macOS-latest | |
| bioc: release | |
| r: auto | |
| cont: ~ | |
| rspm: ~ | |
| - os: windows-latest | |
| bioc: release | |
| r: auto | |
| cont: ~ | |
| rspm: ~ | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: ${{ true }} | |
| RSPM: ${{ matrix.config.rspm }} | |
| TZ: UTC | |
| GITHUB_REPO: ${{ github.repository }} | |
| RGL_USE_NULL: ${{ true }} | |
| steps: | |
| - name: "\U0001F52D Collect Workflow Telemetry" | |
| uses: runforesight/workflow-telemetry-action@v1 | |
| continue-on-error: ${{ true }} | |
| with: | |
| github_token: ${{ env.GITHUB_TOKEN }} | |
| - name: "\U0001F4BE Free Disk Space" | |
| if: env.free_diskspace == 'true' && runner.os == 'Linux' | |
| uses: jlumbroso/free-disk-space@main | |
| - name: "\U0001F30E Set environment variables" | |
| run: | | |
| echo "RGL_USE_NULL=TRUE" >> $GITHUB_ENV | |
| echo "R_REMOTES_NO_ERRORS_FROM_WARNINGS=${{ true }}" >> $GITHUB_ENV | |
| echo "RSPM=${{ matrix.config.rspm }}" >> $GITHUB_ENV | |
| echo "TZ=UTC" >> $GITHUB_ENV | |
| echo "NOT_CRAN=${{ !env.as_cran }}" >> $GITHUB_ENV | |
| shell: bash {0} | |
| - name: "\U0001F40D Setup Miniconda" | |
| if: env.miniforge_variant != 'false' | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: ${{ false }} | |
| python-version: ${{ matrix.python-version }} | |
| miniforge-variant: ${{ env.miniforge_variant }} | |
| miniforge-version: ${{ env.miniforge_version }} | |
| activate-environment: ${{ env.activate_environment }} | |
| environment-file: ${{ env.environment_file }} | |
| channels: ${{ env.channels }} | |
| - name: "\U0001F4DA Set R library home on Linux" | |
| if: runner.os == 'Linux' | |
| run: | | |
| mkdir -p /__w/_temp/Library | |
| echo ".libPaths('/__w/_temp/Library')" >> ~/.Rprofile | |
| git config --global --add safe.directory '*' | |
| shell: bash {0} | |
| - name: ⏬ Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: "\U0001F6E0 Setup R and Bioconductor" | |
| if: runner.os != 'Linux' | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| with: | |
| bioc-version: ${{ matrix.config.bioc }} | |
| - name: "\U0001F6E0 Install Pandoc" | |
| if: env.pandoc_version != 'false' && runner.os != 'Linux' | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| with: | |
| pandoc-version: ${{ env.pandoc_version }} | |
| - name: ❔ Query dependencies | |
| env: | |
| GITHUB_TOKEN: ${{ env.GITHUB_TOKEN }} | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| install.packages('remotes') | |
| remotes::install_github("r-lib/remotes") | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: "\U0001F3E6 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 }}-biocversion-${{ matrix.config.bioc | |
| }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache_version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc | |
| }}-r-${{ matrix.config.r }}- | |
| - name: "\U0001F3E6 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 }}-biocversion-${{ matrix.config.bioc | |
| }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache_version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc | |
| }}-r-${{ matrix.config.r }}- | |
| - name: "\U0001F6E0 Install Linux system dependencies" | |
| if: runner.os == 'Linux' | |
| run: | | |
| sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))') | |
| echo $sysreqs | |
| sudo -s eval "$sysreqs" | |
| sudo apt-get install -y qpdf rsync | |
| shell: bash {0} | |
| - name: "\U0001F6E0 Install macOS system dependencies" | |
| if: runner.os == 'macOS' | |
| run: | | |
| #### --- Justifications for each package --- #### | |
| ### libxml2 ### | |
| # Enable installing XML from source if needed | |
| ### imagemagick@6 ### | |
| # Required to install magick as noted at | |
| # https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 | |
| ### harfbuzz fribidi ### | |
| # For textshaping, required by ragg, and required by pkgdown | |
| ### libgit2 ### | |
| # For installing usethis's dependency gert | |
| ### xquartz --cask ### | |
| # Required for tcltk | |
| ### libxfont ### | |
| # Required for some ggplot2 functions | |
| ### texlive ### | |
| # Required for rendering Sweave files (even with r-lib/actions/setup-tinytex) | |
| #### --- Install packages --- #### | |
| ### Install normally ### | |
| brew install libxml2 imagemagick@6 harfbuzz fribidi libgit2 texlive | |
| ### Install via cask ### | |
| brew install xquartz --cask | |
| ### Set up xml2 ### | |
| echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV | |
| shell: bash {0} | |
| - name: "\U0001F6E0 Install Windows system dependencies" | |
| if: env.has_latex == 'true' && runner.os == 'Windows' | |
| run: | | |
| #### npm #### | |
| npm install curl | |
| shell: pwsh {0} | |
| - name: "\U0001F6E0 Install latex" | |
| if: env.has_latex == 'true' | |
| uses: r-lib/actions/setup-tinytex@v2 | |
| env: | |
| TINYTEX_INSTALLER: ${{ env.tinytex_installer }} | |
| TINYTEX_VERSION: ${{ env.tinytex_version }} | |
| - name: "\U0001F6E0 Install latex packages" | |
| if: env.has_latex == 'true' | |
| env: | |
| tinytex_installer: ${{ env.tinytex_installer }} | |
| tinytex_version: ${{ env.tinytex_version }} | |
| run: | | |
| install.packages("tinytex") | |
| extra_packages <- c("bera","nowidow","parnotes","marginfix","etoolbox", | |
| "titlesec","sectsty","framed","enumitem","parskip","soul","placeins", | |
| "footmisc","changepage","xstring","caption","mathtools","fancyhdr", | |
| "preprint","ragged2e","pdfcrop","titling","silence","everysel") | |
| tinytex::tlmgr_install(pkgs = extra_packages) | |
| shell: Rscript {0} | |
| - name: "\U0001F6E0 Install dependencies pass 1" | |
| env: | |
| timeout: ${{ env.timeout }} | |
| GITHUB_TOKEN: ${{ env.GITHUB_TOKEN }} | |
| run: | | |
| options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout")) | |
| ## For running the checks | |
| message(paste('****', Sys.time(), 'installing rcmdcheck ****')) | |
| install.packages(c("rmarkdown","BiocManager"), dependencies = TRUE) | |
| message(paste('****', Sys.time(), 'pass number 1 at installing dependencies****')) | |
| repos <- BiocManager::repositories() | |
| remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=TRUE) | |
| continue-on-error: ${{ true }} | |
| shell: Rscript {0} | |
| - name: "\U0001F6E0 Install dependencies pass 2" | |
| env: | |
| timeout: ${{ env.timeout }} | |
| GITHUB_TOKEN: ${{ env.GITHUB_TOKEN }} | |
| run: | | |
| options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout")) | |
| message(paste('****', Sys.time(), 'pass number 2 at installing dependencies****')) | |
| repos <- BiocManager::repositories() | |
| remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=TRUE) | |
| shell: Rscript {0} | |
| - name: "\U0001F6E0 Install RUnit (via BiocGenerics)" | |
| if: env.has_runit == 'true' | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| BiocManager::install("BiocGenerics") | |
| shell: Rscript {0} | |
| - name: "\U0001F6E0 Install covr" | |
| if: env.run_covr == 'true' && runner.os == 'Linux' | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| install.packages("covr") | |
| shell: Rscript {0} | |
| - name: "\U0001F6E0 Install pkgdown" | |
| if: env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| install.packages("pkgdown") | |
| shell: Rscript {0} | |
| - name: ℹ️ Session info ️ | |
| run: | | |
| options(width = 100, crayon.enabled = TRUE) | |
| pkgs <- installed.packages()[,"Package"] | |
| if(!require("sessioninfo", quietly=TRUE)) install.packages("sessioninfo") | |
| tryCatch({ | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| }, error = function(x){utils::sessionInfo()}) | |
| shell: Rscript {0} | |
| - name: ✅ Run CMD check | |
| if: env.run_rcmdcheck == 'true' | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: ${{ false }} | |
| RGL_USE_NULL: ${{ env.RGL_USE_NULL }} | |
| DISPLAY: 99.0 | |
| AS_CRAN: ${{ env.as_cran }} | |
| run_vignettes: ${{ env.run_vignettes }} | |
| timeout: ${{ env.timeout }} | |
| run: | | |
| options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout")) | |
| if(!require("rcmdcheck", quietly=TRUE)) install.packages("rcmdcheck") | |
| as_cran <- if(Sys.getenv("AS_CRAN")=='true') "--as-cran" else NULL | |
| run_build_vignettes <- if(Sys.getenv("run_vignettes")=='true') NULL else "--no-build-vignettes" | |
| run_vignettes <- if(Sys.getenv("run_vignettes")=='true') NULL else "--ignore-vignettes" | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-manual", "--timings", as_cran, run_vignettes), | |
| build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data", run_build_vignettes), | |
| error_on = "warning", | |
| check_dir = "check") | |
| shell: Rscript {0} | |
| - name: "\U0001F4CB Reveal testthat details" | |
| if: env.has_testthat == 'true' | |
| run: | | |
| find . -name testthat.Rout -exec cat '{}' ';' | |
| shell: bash {0} | |
| - name: "\U0001F4CB Run RUnit tests (via BiocGenerics)" | |
| if: env.has_runit == 'true' | |
| env: | |
| timeout: ${{ env.timeout }} | |
| run: | | |
| options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout")) | |
| BiocGenerics:::testPackage() | |
| shell: Rscript {0} | |
| - name: ✅ Run BiocCheck | |
| if: env.run_bioccheck == 'true' | |
| env: | |
| DISPLAY: 99.0 | |
| RGL_USE_NULL: ${{ env.RGL_USE_NULL }} | |
| run_vignettes: ${{ env.run_vignettes }} | |
| as_cran: ${{ env.as_cran }} | |
| timeout: ${{ env.timeout }} | |
| run: | | |
| options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout")) | |
| #### Install deps #### | |
| if(!require("BiocManager", quietly=TRUE)) install.packages("BiocManager") | |
| if(!require("BiocCheck", quietly=TRUE)) BiocManager::install("BiocCheck") | |
| #### Allow for packages on CRAN #### | |
| no_check_vignettes <- Sys.getenv("run_vignettes")=='true' | |
| as_cran <- Sys.getenv("as_cran")=='true' | |
| #### Run checks #### | |
| BiocCheck::BiocCheck( | |
| dir('check', 'tar.gz$', full.names = TRUE), | |
| `quit-with-status` = TRUE, | |
| `no-check-R-ver` = TRUE, | |
| `no-check-vignettes` = no_check_vignettes, | |
| `no-check-CRAN` = as_cran, | |
| `no-check-bioc-help` = as_cran) | |
| shell: Rscript {0} | |
| - name: "\U0001F4CB Test coverage" | |
| if: env.run_covr == 'true' && runner.os == 'Linux' | |
| run: | | |
| covr::codecov() | |
| shell: Rscript {0} | |
| - name: "\U0001F6E0 Install package ️" | |
| if: env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| run: R CMD INSTALL . | |
| shell: bash {0} | |
| - name: ℹ️ Get R package info | |
| if: runner.os == 'Linux' | |
| run: | | |
| #### DockerHub repos must be lowercase (,,) #### | |
| name=$(grep '^Package:' DESCRIPTION | cut -d\ -f2) | |
| echo "packageName=${name,,}" >> $GITHUB_ENV | |
| echo "packageNameOrig=${name}" >> $GITHUB_ENV | |
| echo $name | |
| version=$(grep Version DESCRIPTION | grep -o "[0-9.]\+") | |
| echo "packageVersion=${version}" >> $GITHUB_ENV | |
| echo $version | |
| echo "BASE_IMAGE=${{ matrix.config.cont }}" >> $GITHUB_ENV | |
| shell: bash {0} | |
| - name: "\U0001F4E6 Render README" | |
| if: env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| env: | |
| DISPLAY: 99.0 | |
| run: | | |
| if(file.exists("README.Rmd")){ | |
| options(crayon.enabled = TRUE) | |
| if(!require("rmarkdown", quietly=TRUE)) install.packages("rmarkdown"); | |
| rmarkdown::render("README.Rmd", output_format = rmarkdown::github_document(html_preview = FALSE)); | |
| } | |
| shell: Rscript {0} | |
| - name: "\U0001F4E6 Build pkgdown site" | |
| if: env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | |
| shell: Rscript {0} | |
| - name: "\U0001F4E6\U0001F680 Deploy pkgdown site to GitHub pages" | |
| if: env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| uses: JamesIves/github-pages-deploy-action@releases/v4 | |
| with: | |
| clean: ${{ false }} | |
| branch: gh-pages | |
| folder: docs | |
| token: ${{ env.GITHUB_TOKEN }} | |
| - name: ⏫ Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r | |
| }}-results | |
| path: check | |
| - name: "\U0001F433✏️ Create Docker file" | |
| if: | | |
| (!contains(github.event.head_commit.message, '/nodocker')) && env.run_docker == 'true' && runner.os == 'Linux' | |
| env: | |
| BASE_IMAGE: ${{ matrix.config.cont }} | |
| GITHUB_TOKEN: ${{ env.GITHUB_TOKEN }} | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| if(!require("rworkflows", quietly=TRUE)) remotes::install_github("neurogenomics/rworkflows") | |
| path <- rworkflows::use_dockerfile(base_image=Sys.getenv("BASE_IMAGE")) | |
| shell: Rscript {0} | |
| - name: "\U0001F433\U0001F680 Build and push to GHCR" | |
| if: | | |
| (!contains(github.event.head_commit.message, '/nodocker')) && env.run_docker == 'true' && runner.os == 'Linux' && env.docker_registry == 'ghcr.io' | |
| uses: docker/build-push-action@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ env.GITHUB_TOKEN }} | |
| with: | |
| username: ${{ github.repository_owner }} | |
| password: ${{ env.GITHUB_TOKEN }} | |
| registry: ${{ env.docker_registry }} | |
| repository: ${{ github.repository }} | |
| tag_with_ref: ${{ true }} | |
| tag_with_sha: ${{ false }} | |
| tags: | | |
| ${{ env.packageVersion }}, | |
| latest | |
| build_args: | | |
| PKG=${{ env.packageNameOrig }}, | |
| BASE_IMAGE=${{ matrix.config.cont }} | |
| - name: "\U0001F433\U0001F680 Build and push to DockerHub" | |
| if: | | |
| (!contains(github.event.head_commit.message, '/nodocker')) && env.run_docker == 'true' && runner.os == 'Linux' && env.docker_registry == 'docker.io' | |
| uses: docker/build-push-action@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ env.GITHUB_TOKEN }} | |
| with: | |
| username: ${{ env.docker_user }} | |
| password: ${{ env.DOCKER_TOKEN }} | |
| repository: ${{ env.docker_org }}/${{ env.packageName }} | |
| tag_with_ref: ${{ true }} | |
| tag_with_sha: ${{ false }} | |
| tags: | | |
| ${{ env.packageVersion }}, | |
| latest | |
| build_args: |- | |
| PKG=${{ env.packageNameOrig }}, | |
| BASE_IMAGE=${{ env.BASE_IMAGE }} |