51 documentation updates v01 #121
Workflow file for this run
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| on: | |
| pull_request: | |
| branches: | |
| - main | |
| paths: | |
| - .github/workflows/r-renv-lock.yml | |
| - DESCRIPTION | |
| name: Generate renv.lock | |
| concurrency: | |
| group: r-renv-lock-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| r-renv-lock-gen: | |
| if: github.event.pull_request.draft == false | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| max-parallel: 1 | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: ubuntu-20.04, r: '4.2', repos: 'https://packagemanager.posit.co/cran/2023-03-15/'} | |
| - {os: ubuntu-20.04, r: '4.3', repos: 'https://packagemanager.posit.co/cran/2023-04-20/'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: true | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| R_CRAN_REPO: ${{ matrix.config.repos }} | |
| RENV_PROFILE_NAME: ${{ matrix.config.r }} | |
| R_RELEASE_LAGACY: ${{ matrix.config.legacy || false }} | |
| steps: | |
| - name: Get branch names | |
| id: branch-name | |
| uses: tj-actions/[email protected] | |
| - name: Checkout repo (PR) 🛎 | |
| uses: actions/checkout@v3 | |
| 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: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - name: Install system dependencies | |
| run: sudo apt update && sudo apt install libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libgit2-dev -y | |
| - name: Collect dependencies | |
| run: | | |
| Sys.setenv("RENV_CONFIG_SANDBOX_ENABLED" = FALSE) | |
| Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE) | |
| source("renv/activate.R") | |
| lock_gen_version <- "0.1.0" | |
| legacy <- identical(Sys.getenv("R_RELEASE_LAGACY"), "true") | |
| renv_profile <- Sys.getenv("RENV_PROFILE_NAME", "dev") | |
| if (legacy) renv_profile <- paste0(renv_profile, "_legacy") | |
| cran_r_release <- Sys.getenv("R_CRAN_REPO", "https://packagemanager.posit.co/cran/2023-03-15/") | |
| cran_latest <- Sys.getenv("CRAN_R_LATEST", "https://packagemanager.posit.co/cran/latest") | |
| unlink(file.path("renv", "profiles", renv_profile), recursive = TRUE) | |
| cat("\n==================================\n") | |
| cat("Create renv.lock files\n") | |
| cat(paste("renv_profile: \"", renv_profile, "\"\n", sep = "")) | |
| cat(paste("cran_r_release: \"", cran_r_release, "\"\n", sep = "")) | |
| cat(paste("cran_latest: \"", cran_latest, "\"\n", sep = "")) | |
| cat("==================================\n") | |
| renv::activate(profile = renv_profile) | |
| renv::settings$snapshot.type("custom") | |
| .get_dependencies <- function(project_dir) { | |
| dependencies <- renv::dependencies("DESCRIPTION", dev = TRUE)$Package | |
| c( | |
| project_dir, | |
| dependencies, | |
| "devtools", | |
| "staged.dependencies", | |
| "styler" | |
| ) |> | |
| unique() |> | |
| renv:::renv_package_dependencies() |> | |
| names() | |
| } | |
| options(renv.snapshot.filter = .get_dependencies) | |
| # CRAN repo from R release | |
| options("repos" = c("RSPM" = cran_r_release)) | |
| renv::install("openpharma/staged.dependencies", repos = options("repos")) | |
| renv::install("devtools", repos = options("repos")) | |
| # Packages from stage dependencies to ignore | |
| renv::settings$ignored.packages(c("admiraldev")) | |
| # Install dependencies | |
| renv::settings$snapshot.type("explicit") | |
| renv::install(repos = options("repos")) | |
| # Set newest CRAN for few packages upgrade | |
| options("repos" = c( | |
| "CRAN" = cran_latest, | |
| "RSPM" = cran_r_release | |
| )) | |
| # Install latest remotes version | |
| renv::install("remotes", repos = cran_latest) | |
| install_min_version <- function(pkg, version) { | |
| upgrade <- try(packageVersion(pkg) >= version, silent = TRUE) | |
| if (!isTRUE(upgrade)) { | |
| message("Upgrade `", pkg, "` to `", version, "`") | |
| renv::install(paste0(pkg, "@", version), dependencies = "none") | |
| } | |
| } | |
| renv::install("R.cache", dependencies = "Imports") | |
| install_min_version("vctrs", "0.4.1") | |
| install_min_version("rlang", "1.0.6") | |
| renv::install("[email protected]", dependencies = "none") | |
| renv::install("[email protected]", dependencies = "none") | |
| renv::settings$snapshot.type("custom") | |
| renv::snapshot(force = TRUE, prompt = FALSE) | |
| if (identical(renv_profile, "4.3")) { | |
| file.copy(renv::paths$lockfile(), "renv.lock", overwrite = TRUE) | |
| } | |
| shell: Rscript --vanilla {0} | |
| - name: Commit and push changes | |
| uses: stefanzweifel/git-auto-commit-action@v4 | |
| with: | |
| commit_message: Automatic renv profile update. | |
| file_pattern: 'renv.lock renv/profiles/*' | |
| commit_user_name: pharmaverse-bot | |
| commit_user_email: [email protected] | |
| create_branch: true |