Chore: customize github workflows to correctly install system dependencies #172
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| # Source: https://github.com/pharmaverse/admiralci | |
| # Stripped down version of admiralci checks. Good for | |
| # the developement process. When package is ready to | |
| # be published, revisit and add release-related | |
| # workflows. | |
| # Instead of using reusable actions provided by admiralci, | |
| # the actions are inlined in the workflow file. This is | |
| # because some of the R dependencies required system packages | |
| # not available/installable using reusable actions. | |
| # If any updates are available, the workflow should be | |
| # updated manually. | |
| # Last update: 2025-01-07 | |
| name: Modified Admiral CI/CD Wortkflows | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| concurrency: | |
| group: admiral-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| R_VERSION: "release" | |
| jobs: | |
| get_r_version: | |
| name: Get R version | |
| runs-on: ubuntu-latest | |
| outputs: | |
| r-version: ${{ steps.get_r_version.outputs.R_VERSION }} | |
| steps: | |
| - name: Get R Version for Downstream Container Jobs | |
| id: get_r_version | |
| run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT | |
| shell: bash | |
| spellcheck: | |
| name: Spelling | |
| runs-on: ubuntu-latest | |
| needs: get_r_version | |
| container: | |
| image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest" | |
| steps: | |
| - name: Get branch names | |
| id: branch-name | |
| uses: tj-actions/branch-names@v8 | |
| - name: Checkout repo | |
| uses: actions/[email protected] | |
| if: github.event_name == 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Restore cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.staged.dependencies | |
| key: staged-deps | |
| - name: Run Staged dependencies | |
| uses: insightsengineering/staged-dependencies-action@v1 | |
| with: | |
| run-system-dependencies: true | |
| renv-restore: false | |
| enable-check: false | |
| direction: upstream | |
| git-ref: ${{ steps.branch-name.outputs.current_branch }} | |
| - name: Run Spellcheck | |
| uses: insightsengineering/r-spellcheck-action@v3 | |
| lint: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| needs: get_r_version | |
| container: | |
| image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest" | |
| steps: | |
| - name: Get branch names | |
| id: branch-name | |
| uses: tj-actions/branch-names@v8 | |
| - name: Checkout repo | |
| uses: actions/[email protected] | |
| if: github.event_name == 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Restore cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.staged.dependencies | |
| key: staged-deps | |
| - name: Run Staged dependencies | |
| uses: insightsengineering/staged-dependencies-action@v1 | |
| with: | |
| run-system-dependencies: true | |
| renv-restore: false | |
| enable-check: false | |
| direction: upstream | |
| git-ref: ${{ steps.branch-name.outputs.current_branch }} | |
| - name: Install latest release of lintr | |
| shell: Rscript {0} | |
| run: | | |
| install.packages("lintr", repos = "https://packagemanager.posit.co/cran/latest/") | |
| - name: Lint | |
| shell: Rscript {0} | |
| run: | | |
| lints <- lintr::lint_package() | |
| if (length(lints) > 0L) { | |
| print(lints) | |
| stop("Lints detected. Please review and adjust code according to the comments provided.", call. = FALSE) | |
| } | |
| man-pages: | |
| name: Man Pages | |
| runs-on: ubuntu-latest | |
| needs: get_r_version | |
| container: | |
| image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest" | |
| steps: | |
| - name: Get branch names | |
| id: branch-name | |
| uses: tj-actions/branch-names@v8 | |
| - name: Checkout repo | |
| uses: actions/[email protected] | |
| if: github.event_name == 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| - name: Restore cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.staged.dependencies | |
| key: staged-deps | |
| - name: Run Staged dependencies | |
| uses: insightsengineering/staged-dependencies-action@v1 | |
| with: | |
| run-system-dependencies: false | |
| renv-restore: false | |
| enable-check: false | |
| direction: upstream | |
| git-ref: ${{ steps.branch-name.outputs.current_branch }} | |
| - name: Install dependencies | |
| run: | | |
| Rscript -e 'pak::local_install_deps(dependencies = TRUE)' | |
| - name: Generate man pages | |
| run: roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace')) | |
| shell: Rscript {0} | |
| - name: Set-up safe dir | |
| run: git config --global --add safe.directory "${GITHUB_WORKSPACE}" | |
| shell: bash | |
| - name: Roxygen check | |
| run: | | |
| git status -s | |
| if [[ -n `git status -s | grep -E "man|DESCRIPTION"` ]] | |
| then { | |
| ROXYGEN_VERSION="$(Rscript -e 'packageVersion("roxygen2")' | awk '{print $NF}')" | |
| echo "🙈 Manuals are not up-to-date with roxygen comments!" | |
| echo "🔀 The following differences were noted:" | |
| git diff man/* DESCRIPTION | |
| echo -e "\n💻 Please rerun the following command on your workstation and push your changes" | |
| echo "--------------------------------------------------------------------" | |
| echo "roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))" | |
| echo "--------------------------------------------------------------------" | |
| echo "ℹ roxygen2 version that was used in this workflow: $ROXYGEN_VERSION" | |
| echo "🙏 Please ensure that the 'RoxygenNote' field in the DESCRIPTION file matches this version" | |
| exit 1 | |
| } else { | |
| echo "💚 Manuals are up-to-date with roxygen comments" | |
| } | |
| fi | |
| shell: bash | |
| tests: | |
| name: Tests | |
| runs-on: ubuntu-latest | |
| needs: get_r_version | |
| container: | |
| image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest" | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| - name: Install dependencies | |
| run: | | |
| Rscript -e 'pak::local_install_deps(dependencies = TRUE)' | |
| - name: Run tests | |
| shell: Rscript {0} | |
| run: | | |
| devtools::load_all(".") | |
| devtools::test() | |
| check: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - spellcheck | |
| - tests | |
| - lint | |
| - man-pages | |
| container: | |
| image: "ghcr.io/pharmaverse/admiralci-${{ matrix.r_version }}:latest" | |
| name: Check (${{ matrix.r_version }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| r_version: ["release", "devel", "oldrel"] | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: true | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| R_REPOS: "https://cran.r-project.org" | |
| DEPS_IGNORE: >- | |
| pharmaversesdtm, | |
| pharmaverseadam, | |
| admiral, | |
| admiraldev, | |
| admiralophtha, | |
| admiralonco, | |
| admiralvaccine, | |
| staged.dependencies | |
| steps: | |
| - name: Get branch names | |
| id: branch-name | |
| uses: tj-actions/branch-names@v8 | |
| - name: Checkout repo | |
| uses: actions/[email protected] | |
| if: | | |
| github.event_name == 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Restore cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.staged.dependencies | |
| key: staged-deps | |
| - name: Run Staged dependencies | |
| uses: insightsengineering/staged-dependencies-action@v1 | |
| if: | | |
| (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') || | |
| matrix.r_version != 'devel' | |
| with: | |
| git-ref: ${{ steps.branch-name.outputs.current_branch }} | |
| run-system-dependencies: false | |
| renv-restore: false | |
| enable-check: false | |
| cran-repos: "https://cloud.r-project.org" | |
| direction: upstream | |
| - name: Install dependencies from DESCRIPTION | |
| if: | | |
| (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') || | |
| matrix.r_version != 'devel' | |
| run: | | |
| Rscript -e 'pak::local_install_deps(dependencies = TRUE)' | |
| - name: Upload dependencies artifact | |
| if: | | |
| (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') || | |
| matrix.r_version != 'devel' | |
| run: | | |
| dir.create("/workspace/tmp") | |
| library(dplyr) | |
| installed_packages <- as.data.frame(installed.packages()) | |
| packages_to_remove <- Sys.getenv("DEPS_IGNORE", "") | |
| packages_to_remove <- unlist(strsplit(packages_to_remove, ",")) | |
| installed_packages <- installed_packages %>% filter(LibPath != "/usr/local/lib/R/library") %>% # remove pre-built deps | |
| filter(!Package %in% packages_to_remove) | |
| # save deps as csv file | |
| write.csv(installed_packages, "/workspace/tmp/deps-${{ matrix.r_version }}.csv", row.names = FALSE) | |
| # create also renv.lock file | |
| setwd("/workspace/tmp") | |
| renv_lock <- list( | |
| "R" = list( | |
| "Version" = paste(R.version$major, R.version$minor, sep=".") | |
| ), | |
| "Repositories" = list( | |
| list(Name = "CRAN", URL = Sys.getenv("R_REPOS")) | |
| ), | |
| "Packages" = list() | |
| ) | |
| # Populate with information about each package | |
| for (package in installed_packages$Package) { | |
| dep_name <- package | |
| dep_version <- installed_packages[installed_packages$Package == package, "Version"] | |
| version_parts <- strsplit(dep_version, "\\.")[[1]] | |
| if (length(version_parts) == 4) { | |
| print(sprintf("skipping installation of dep %s", dep_name)) | |
| } else { | |
| print(sprintf("append dependency %s - version %s", dep_name, dep_version)) | |
| requirements <- tools::package_dependencies(dep_name, recursive = TRUE) | |
| have_requirements <- length(requirements[[1]]) > 0 | |
| if (have_requirements) { | |
| renv_lock[["Packages"]][[dep_name]] <- list( | |
| "Package" = dep_name, | |
| "Version" = dep_version, | |
| "Source" = "Repository", | |
| "Repository" = "CRAN", | |
| "Requirements" = requirements[[dep_name]] | |
| ) | |
| } else { | |
| renv_lock[["Packages"]][[dep_name]] <- list( | |
| "Package" = dep_name, | |
| "Version" = dep_version, | |
| "Source" = "Repository", | |
| "Repository" = "CRAN" | |
| ) | |
| } | |
| } | |
| } | |
| # Write the list to a JSON file (renv.lock) | |
| writeLines(jsonlite::toJSON(renv_lock, pretty = TRUE, auto_unbox = TRUE), "renv-${{ matrix.r_version }}.lock") | |
| print("generated renv.lock content") | |
| system("cat renv-${{ matrix.r_version }}.lock") | |
| shell: Rscript {0} | |
| - name: Upload deps.csv and renv.lock artifacts | |
| uses: actions/upload-artifact@v4 | |
| if: | | |
| (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') || | |
| matrix.r_version != 'devel' | |
| with: | |
| name: deps-${{ matrix.r_version }} | |
| path: | | |
| /workspace/tmp/ | |
| - name: Check Version | |
| id: check_version | |
| if: | | |
| (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') || | |
| matrix.r_version != 'devel' | |
| run: | | |
| maintenance_version="F" | |
| description_dat <- readLines("DESCRIPTION") | |
| for (i in seq_along(description_dat)) { | |
| if (grepl("^Version:", description_dat[i])) { | |
| current_version <- sub("^Version: ", "", description_dat[i]) | |
| version_parts <- strsplit(current_version, "\\.")[[1]] | |
| # check if maintenance version | |
| if (length(version_parts) == 4) { | |
| print("Maintenance version detected (format X.Y.Z.M with M >= 9000)") | |
| maintenance_version="T" | |
| } | |
| } | |
| } | |
| cat(sprintf("maintenance_version=%s", maintenance_version), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE) | |
| shell: Rscript {0} | |
| - name: Check | |
| if: | | |
| (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') || | |
| matrix.r_version != 'devel' | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| run: | | |
| unlink("tmp",recursive=TRUE) | |
| if ("${{ steps.check_version.outputs.maintenance_version }}" == "T"){ | |
| Sys.setenv("_R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_" = TRUE) | |
| } | |
| if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck") | |
| options(crayon.enabled = TRUE) | |
| check_error_on <- "error" | |
| if (check_error_on == "") { | |
| check_error_on <- "note" | |
| } | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-manual", "--as-cran"), | |
| error_on = check_error_on, | |
| check_dir = "check" | |
| ) | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: r${{ matrix.r_version }}-results | |
| path: check | |