From b44345638a5fb8b4450c828b1f309cd4752eb22b Mon Sep 17 00:00:00 2001 From: HenrikSpiegel <49019622+HenrikSpiegel@users.noreply.github.com> Date: Thu, 18 Apr 2024 09:15:54 +0200 Subject: [PATCH] New CI flow: Check package against specific CRAN snapshot(s). (#25) * Adds a new subflow which checks the package against specific cran snapshot(s) * Adds CI-CD badges. --- .../actions/setup-r-dependencies/action.yaml | 220 ++++++++++++++++++ .github/workflows/Check-package.yaml | 17 +- .github/workflows/R-CMD-check-versions.yaml | 74 ++++++ .github/workflows/R-CMD-check.yaml | 4 +- .github/workflows/Release-package.yaml | 4 + DESCRIPTION | 2 +- README.Rmd | 9 + README.md | 9 + vignettes/ep_overview.Rmd | 4 +- 9 files changed, 333 insertions(+), 10 deletions(-) create mode 100644 .github/actions/setup-r-dependencies/action.yaml create mode 100644 .github/workflows/R-CMD-check-versions.yaml diff --git a/.github/actions/setup-r-dependencies/action.yaml b/.github/actions/setup-r-dependencies/action.yaml new file mode 100644 index 0000000..30dee9e --- /dev/null +++ b/.github/actions/setup-r-dependencies/action.yaml @@ -0,0 +1,220 @@ +name: 'setup-r-dependencies' +description: 'Action to setup installation tools and install R dependencies' +author: 'Jim Hester (modified by Henrik Spiegelhauer)' +inputs: + cache: + description: 'A boolean value indicating whether packages should be cached from one to the other' + required: true + default: true + cache-version: + description: 'The version of the cache, change this from the default (1) to start over with a fresh cache. Ignored if cache: false' + required: true + default: 1 + extra-packages: + description: 'Any extra packages to install outside of the packages listed in the dependencies' + needs: + description: 'Any extra Config/Needs fields which need to be included when installing dependencies' + packages: + description: 'Which package(s) to install.' + default: 'deps::., any::sessioninfo' + pak-version: + description: 'Which pak version to use. Possible values are "stable", "rc" and "devel".' + default: 'stable' + working-directory: + description: 'Using the working-directory keyword, you can specify the working directory of where "pkg_deps" command searches for dependencies in the "DESCRIPTION" file.' + default: '.' + dependencies: + description: 'Types of dependencies to install. Must be an R expression. Note that it often needs to be quoted in YAML, see the README for details.' + default: '"all"' + dependency_repo: + description: 'Overwrite the default CRAN-like reposity' + default: 'NULL' + upgrade: + description: 'Whether to install the latest available versions of the dependencies. Must be an R expression. See the README for details if you need quoting.' + default: 'FALSE' + lockfile-create-lib: + description: 'The package library to consider when creating the pak lockfile. This is passed to the `lib` argument of `pak::lockfile_create()`. Defaults to an empty library, for reproducibility. Must be an R expression. Note that it often needs to be quoted in YAML, see the README for details.' + default: 'NULL' + install-pandoc: + description: 'Whether to install pandoc. By default it is installed if it is not on the PATH and the local package suggests or depends on the rmarkdown package.' + pandoc-version: + description: 'Pandoc version to install.' + default: '3.1.11' +runs: + using: "composite" + steps: + - name: Set site library path + run: | + # Set site library path + cat("::group::Set site library path\n") + if (Sys.getenv("RENV_PROJECT") != "") { + message("renv project detected, no need to set R_LIBS_SITE") + cat(sprintf("R_LIB_FOR_PAK=%s\n", .libPaths()[1]), file = Sys.getenv("GITHUB_ENV"), append = TRUE) + q("no") + } + lib <- Sys.getenv("R_LIBS_SITE") + if (lib == "") { + lib <- file.path(dirname(.Library), "site-library") + cat(sprintf("R_LIBS_SITE=%s\n", lib), file = Sys.getenv("GITHUB_ENV"), append = TRUE) + cat(sprintf("R_LIB_FOR_PAK=%s\n", lib), file = Sys.getenv("GITHUB_ENV"), append = TRUE) + message("Setting R_LIBS_SITE to ", lib) + } else { + message("R_LIBS_SITE is already set to ", lib) + cat(sprintf("R_LIB_FOR_PAK=%s\n", strsplit(lib, .Platform$path.sep)[[1]][[1]]), file = Sys.getenv("GITHUB_ENV"), append = TRUE) + } + cat("::endgroup::\n") + shell: Rscript {0} + + - name: Install pak (Windows) + if: runner.os == 'Windows' + run: | + # Install pak + cat("::group::Install pak\n") + lib <- Sys.getenv("R_LIB_FOR_PAK") + dir.create(lib, showWarnings = FALSE, recursive = TRUE) + install.packages("pak", lib = lib, repos = sprintf( + "https://r-lib.github.io/p/pak/%s/%s/%s/%s", + "${{ inputs.pak-version }}", + .Platform$pkgType, + R.Version()$os, + R.Version()$arch + )) + cat("::endgroup::\n") + shell: Rscript {0} + + - name: Install pak (Unix) + if: runner.os != 'Windows' + run: | + # Install pak + echo "::group::Install pak" + if which sudo >/dev/null; then SUDO="sudo -E --preserve-env=PATH env"; else SUDO=""; fi + $SUDO R -q -e 'dir.create(Sys.getenv("R_LIB_FOR_PAK"), recursive = TRUE, showWarnings = FALSE)' + $SUDO R -q -e 'install.packages("pak", lib = Sys.getenv("R_LIB_FOR_PAK"), repos = sprintf("https://r-lib.github.io/p/pak/%s/%s/%s/%s", "${{ inputs.pak-version }}", .Platform$pkgType, R.Version()$os, R.Version()$arch))' + echo "::endgroup::" + shell: bash + + - name: Query dependencies + id: install + run: | + # Override the default CRAN-like repository + if ("${{ inputs.dependency_repo }}" != "NULL") { + options(repos = c(CRAN = "${{ inputs.dependency_repo }}")) + } + + # Dependency resolution + cat("::group::Dependency resolution\n") + cat("os-version=", sessionInfo()$running, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE) + r_version <- + if (grepl("development", R.version.string)) { + pdf(tempfile()) + ge_ver <- attr(recordPlot(), "engineVersion") + dev.off() + paste0("R version ", getRversion(), " (ge:", ge_ver, "; iid:", .Internal(internalsID()), ")") + } else { + R.version.string + } + cat("r-version=", r_version, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE) + needs <- sprintf("Config/Needs/%s", strsplit("${{ inputs.needs }}", "[[:space:],]+")[[1]]) + deps <- strsplit("${{ inputs.packages }}", "[[:space:],]+")[[1]] + extra_deps <- strsplit("${{ inputs.extra-packages }}", "[[:space:],]+")[[1]] + dir.create(".github", showWarnings=FALSE) + Sys.setenv("PKGCACHE_HTTP_VERSION" = "2") + library(pak, lib.loc = Sys.getenv("R_LIB_FOR_PAK")) + pak::lockfile_create( + c(deps, extra_deps), + lockfile = ".github/pkg.lock", + upgrade = (${{ inputs.upgrade }}), + dependencies = c(needs, (${{ inputs.dependencies }})), + lib = ${{ inputs.lockfile-create-lib }} + ) + cat("::endgroup::\n") + cat("::group::Show Lockfile\n") + writeLines(readLines(".github/pkg.lock")) + cat("::endgroup::\n") + shell: Rscript {0} + working-directory: ${{ inputs.working-directory }} + + - name: Restore R package cache + if: inputs.cache == 'true' + uses: actions/cache@v4 + with: + path: | + ${{ env.R_LIBS_USER }}/* + !${{ env.R_LIBS_USER }}/pak + key: ${{ format('{0}-{1}-{2}-{3}', steps.install.outputs.os-version, steps.install.outputs.r-version, inputs.cache-version, inputs.dependency_repo, hashFiles(format('{0}/.github/pkg.lock', inputs.working-directory ))) }} + restore-keys: ${{ steps.install.outputs.os-version }}-${{ steps.install.outputs.r-version }}-${{inputs.cache-version }}-${{inputs.dependency_repo }} + + - name: Install dependencies + run: | + # Override the default CRAN-like repository + if ("${{ inputs.dependency_repo }}" != "NULL") { + options(repos = c(CRAN = "${{ inputs.dependency_repo }}")) + } + + # Install/Update packages + cat("::group::Install/update packages\n") + Sys.setenv("PKGCACHE_HTTP_VERSION" = "2") + library(pak, lib.loc = Sys.getenv("R_LIB_FOR_PAK")) + pak::lockfile_install(".github/pkg.lock") + ## Clean up lock file + unlink(".github/pkg.lock") + cat("::endgroup::\n") + shell: Rscript {0} + working-directory: ${{ inputs.working-directory }} + + - name: Check whether pandoc needs to be installed + id: check-pandoc + run: | + cat("::group::Check if package needs pandoc\n") + o <- '${{ inputs.install-pandoc }}' + if (! o %in% c('true', 'false')) { + if (Sys.which("pandoc") != "") { + o <- 'false' + } else if (file.exists("DESCRIPTION")) { + deptypes <- list(direct = "all", indirect = character()) + deps <- pak::pkg_deps(".", dependencies = deptypes) + if ("rmarkdown" %in% deps$package) { + o <- 'true' + } else { + o <- 'false' + } + } else { + o <- 'false' + } + } + cat("install=", o, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE) + cat("::endgroup::\n") + shell: Rscript {0} + working-directory: ${{ inputs.working-directory }} + + - name: Install pandoc if needed + if: ${{ steps.check-pandoc.outputs.install == 'true' }} + uses: r-lib/actions/setup-pandoc@v2 + with: + pandoc-version: ${{ inputs.pandoc-version }} + + - name: Session info + run: | + # Session info + cat("::group::Session info\n") + if (requireNamespace("sessioninfo", quietly = TRUE)) { + if (packageVersion("sessioninfo") >= "1.2.1") { + sessioninfo::session_info(pkgs = "installed", include_base = TRUE) + } else { + options(width = 200) + sessioninfo::session_info(rownames(installed.packages()), include_base=TRUE) + } + } else { + sessionInfo() + } + cat("::endgroup::\n") + shell: Rscript {0} + working-directory: ${{ inputs.working-directory }} + + - name: Don't use tar 1.30 from Rtools35 to store the cache + if: runner.os == 'Windows' + shell: bash + run: | + if command -v /c/Rtools/bin/tar && /c/Rtools/bin/tar --version | grep -q 'tar (GNU tar) 1.30' + then echo 'C:/Program Files/Git/usr/bin' >> $GITHUB_PATH + fi diff --git a/.github/workflows/Check-package.yaml b/.github/workflows/Check-package.yaml index 627d8cf..b6771d2 100644 --- a/.github/workflows/Check-package.yaml +++ b/.github/workflows/Check-package.yaml @@ -10,6 +10,10 @@ on: workflow_dispatch: workflow_call: +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + name: Check Package 📦 jobs: @@ -23,10 +27,15 @@ jobs: name: License Check 🃏 uses: insightsengineering/r.pkg.template/.github/workflows/licenses.yaml@main - # Runs R CMD check using the local R-CMD-check.yaml workflow - check: - name: RMD check 📦 - uses: ./.github/workflows/R-CMD-check.yaml + # # Runs R CMD check using the local R-CMD-check.yaml workflow + # check: + # name: RMD check 📦 + # uses: ./.github/workflows/R-CMD-check.yaml + + # Runs R CMD check with specific version(s) of R and cran-snapshot + check-versions: + name: RMD check versions 📜 + uses: ./.github/workflows/R-CMD-check-versions.yaml # Runs unittests while capturing code:cov and uploads to Codecov io. See local subflow test: diff --git a/.github/workflows/R-CMD-check-versions.yaml b/.github/workflows/R-CMD-check-versions.yaml new file mode 100644 index 0000000..f89b50d --- /dev/null +++ b/.github/workflows/R-CMD-check-versions.yaml @@ -0,0 +1,74 @@ +--- +# R-CMD check which allows you to lock the R version and date of the CRAN snapshot. +# This is particularly helpful for ensuring that the package works with internal systems. + on: + workflow_dispatch: + workflow_call: + + name: R-CMD-check-versions + + jobs: + R-CMD-check: + runs-on: ${{ matrix.os }} + name: ${{ matrix.os }} (R ${{ matrix.config.r }}, CRAN ${{ matrix.config.date }}) + strategy: + fail-fast: false + matrix: + os: + - macos-latest + - windows-latest + - ubuntu-latest + config: + - date: 'latest' + r: 'release' + - date: 2023-10-25 # Lock the date of the CRAN snapshot + r: 4.3.1 + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v4 + - uses: r-lib/actions/setup-pandoc@v2 + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + use-public-rspm: false + + - name: Determine the CRAN image to use + id: cran-image + run: | + if [ "${{ matrix.config.date }}" == "latest" ]; then + echo "image=https://cloud.r-project.org" >> $GITHUB_OUTPUT + else + echo "image=https://packagemanager.posit.co/cran/${{ matrix.config.date }}" >> $GITHUB_OUTPUT + fi + shell: bash + + - name: Debug image + run: | + echo ${{ steps.cran-image.outputs.image }} + shell: bash + + - name: Install R dependencies (custom) + uses: ./.github/actions/setup-r-dependencies + with: + cache: true + dependency_repo: ${{ steps.cran-image.outputs.image }} + working-directory: ${{ github.workspace }} + extra-packages: any::rcmdcheck + + - name: Session info + run: | + sessionInfo() + installed.packages()[,c("Package", "Version")] + + shell: Rscript {0} + + - uses: r-lib/actions/check-r-package@v2 + with: + args: 'c("--no-manual", "--as-cran")' + upload-snapshots: true + error-on: '"error"' + check-dir: '"check"' + upload-results: true diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 0fdf02d..1a7864b 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -18,8 +18,8 @@ jobs: matrix: config: - {os: ubuntu-latest, r: 'release'} - - {os: windows-latest, r: 'release'} - - {os: macos-latest, r: 'release'} + #- {os: windows-latest, r: 'release'} + #- {os: macos-latest, r: 'release'} # - {os: ubuntu-latest, r: 'oldrel-1'} # - {os: ubuntu-latest, r: 'oldrel-2'} # - {os: ubuntu-latest, r: 'oldrel-3'} diff --git a/.github/workflows/Release-package.yaml b/.github/workflows/Release-package.yaml index fafaf60..b7518b4 100644 --- a/.github/workflows/Release-package.yaml +++ b/.github/workflows/Release-package.yaml @@ -10,6 +10,10 @@ workflow_dispatch: workflow_call: + concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + name: Release Package 🚀 jobs: diff --git a/DESCRIPTION b/DESCRIPTION index 279f647..49e1d1f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -22,7 +22,7 @@ Suggests: usethis, rmarkdown, testthat (>= 3.0.0), - kableExtra (>= 1.4), + kableExtra, testr, tidyr, pharmaverseadam diff --git a/README.Rmd b/README.Rmd index 9697f7d..2caa6d3 100644 --- a/README.Rmd +++ b/README.Rmd @@ -3,6 +3,15 @@ always_allow_html: true --- + + +[![Check Package +📦](https://github.com/hta-pharma/ramnog/actions/workflows/Check-package.yaml/badge.svg)](https://github.com/hta-pharma/ramnog/actions/workflows/Check-package.yaml) +[![Release Package +🚀](https://github.com/hta-pharma/ramnog/actions/workflows/Release-package.yaml/badge.svg)](https://github.com/hta-pharma/ramnog/actions/workflows/Release-package.yaml) +[![codecov.io](https://img.shields.io/codecov/c/gh/hta-pharma/ramnog?style=plastic&label=codecov.io)]((https://app.codecov.io/github/hta-pharma/ramnog?branch=main)) + + # ramnog ramnog website # R packages for AMNOG analyses ramnog website diff --git a/README.md b/README.md index fcfb8fb..9785594 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,13 @@ + + +[![Check Package +📦](https://github.com/hta-pharma/ramnog/actions/workflows/Check-package.yaml/badge.svg)](https://github.com/hta-pharma/ramnog/actions/workflows/Check-package.yaml) +[![Release Package +🚀](https://github.com/hta-pharma/ramnog/actions/workflows/Release-package.yaml/badge.svg)](https://github.com/hta-pharma/ramnog/actions/workflows/Release-package.yaml) +[![codecov.io](https://img.shields.io/codecov/c/gh/hta-pharma/ramnog?style=plastic&label=codecov.io)]((https://app.codecov.io/github/hta-pharma/ramnog?branch=main)) + + # ramnog ramnog website # R packages for AMNOG analyses ramnog website diff --git a/vignettes/ep_overview.Rmd b/vignettes/ep_overview.Rmd index f2e5726..5a46c3c 100644 --- a/vignettes/ep_overview.Rmd +++ b/vignettes/ep_overview.Rmd @@ -1,8 +1,6 @@ --- title: "Endpoint Specification" -output: - rmarkdown::html_vignette: - toc: true +output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Endpoint Specification} %\VignetteEncoding{UTF-8}