for dbetabinom and dbetabinomMix, created/edited : test functions and… #27
Workflow file for this run
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| --- | ||
| name: Roxygen 🅾 | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| - pre-release | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| - synchronize | ||
| - reopened | ||
| - ready_for_review | ||
| branches: | ||
| - main | ||
| - pre-release | ||
| workflow_dispatch: | ||
| workflow_call: | ||
| inputs: | ||
| install-system-dependencies: | ||
| description: Check for and install system dependencies | ||
| required: false | ||
| default: false | ||
| type: boolean | ||
| enable-staged-dependencies-check: | ||
| description: Enable staged dependencies YAML check | ||
| required: false | ||
| default: false | ||
| type: boolean | ||
| auto-update: | ||
| description: If man pages are not up-to-date, they will be automatically updated and committed back to the branch. | ||
| required: false | ||
| default: false | ||
| type: boolean | ||
| secrets: | ||
| GITHUB_TOKEN: | ||
| description: | | ||
| Github token with read access to repositories, required for staged.dependencies installation | ||
| required: false | ||
| concurrency: | ||
| group: roxygen-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
| jobs: | ||
| roxygen: | ||
| name: Manual pages check 🏁 | ||
| runs-on: ubuntu-latest | ||
| if: > | ||
| !contains(github.event.commits[0].message, '[skip roxygen]') | ||
| && github.event.pull_request.draft == false | ||
| container: | ||
| image: ghcr.io/insightsengineering/rstudio_4.2.1_bioc_3.15:latest | ||
| steps: | ||
| - name: Get branch names 🌿 | ||
| id: branch-name | ||
| uses: tj-actions/branch-names@v5 | ||
| - name: Checkout repo 🛎 | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
| path: ${{ github.event.repository.name }} | ||
| fetch-depth: 0 | ||
| - name: Run Staged dependencies 🎦 | ||
| uses: insightsengineering/staged-dependencies-action@v1 | ||
| with: | ||
| run-system-dependencies: ${{ inputs.install-system-dependencies }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| SD_REPO_PATH: ${{ github.event.repository.name }} | ||
| SD_ENABLE_CHECK: ${{ inputs.enable-staged-dependencies-check }} | ||
| - name: Generate man pages 📄 | ||
| run: | | ||
| setwd("${{ github.event.repository.name }}") | ||
| logfile <- "roxygen_${{ github.event.repository.name }}.log" | ||
| con <- file(logfile) | ||
| sink(con, append = TRUE, split = TRUE) | ||
| sink(con, append = TRUE, type = "message") | ||
| roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace')) | ||
| sink() | ||
| sink(type = "message") | ||
| logs <- readLines(logfile) | ||
| error_marker <- grep("Error:", logs) | ||
| warnings_marker <- grep("Warning message", logs) | ||
| if (length(warnings_marker) > 0) { | ||
| cat("⚠ One or more warnings were generated during the roxygen build:\n") | ||
| cat(logs[warnings_marker[[1]]:length(logs)], sep = "\n") | ||
| stop("Please 🙏 fix the warnings shown below this message 👇") | ||
| } | ||
| if (length(error_marker) > 0) { | ||
| cat("☠ One or more errors were generated during the roxygen build:\n") | ||
| cat(logs[error_marker[[1]]:length(logs)], sep = "\n") | ||
| stop("Please 🙏 fix the errors shown below this message 👇") | ||
| } | ||
| shell: Rscript {0} | ||
| - name: Roxygen check 🅾 | ||
| run: | | ||
| cd ${{ github.event.repository.name }} | ||
| git status -s | ||
| if [[ -n `git status -s | grep man` ]] | ||
| then { | ||
| ROXYGEN_VERSION="$(Rscript -e 'packageVersion("roxygen2")' | awk '{print $NF}')" | ||
| echo "🙈 Manuals are not up-to-date with roxygen comments!" | ||
| echo "🔀 The following differences were noted:" | ||
| git diff man/* | ||
| if [ "${{ inputs.auto-update }}" == "true" ] | ||
| then { | ||
| echo "Regenerating man pages via auto-update" | ||
| git config --global user.name "github-actions" | ||
| git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com" | ||
| git add man/* | ||
| git commit -m "[skip actions] ROxygen Man Pages Auto Update" | ||
| git pull origin ${GITHUB_HEAD_REF} | ||
| git push -v origin ${GITHUB_HEAD_REF} | ||
| } | ||
| else { | ||
| 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" | ||
| } | ||
| fi | ||
| exit 1 | ||
| } else { | ||
| echo "💚 Manuals are up-to-date with roxygen comments" | ||
| } | ||
| fi | ||
| shell: bash | ||
