Closes #143 and modifies #139 for removal of admiral.test and adding pharmaverse sdtm #464
Workflow file for this run
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| on: | |
| workflow_dispatch: | |
| workflow_call: | |
| inputs: | |
| r-version: | |
| description: 'The version of R to use' | |
| default: '4.1' | |
| required: false | |
| type: string | |
| push: | |
| branches: | |
| - main | |
| - devel | |
| - pre-release | |
| pull_request: | |
| branches: | |
| - main | |
| - devel | |
| - pre-release | |
| name: Man Pages | |
| concurrency: | |
| group: roxygen-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| get_r_version: | |
| name: Get R version | |
| runs-on: ubuntu-latest | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip lint]') | |
| outputs: | |
| r-version: ${{ steps.normalizer.outputs.R_VERSION }} | |
| steps: | |
| - name: Normalize inputs | |
| id: normalizer | |
| run: | | |
| R_VERSION="${{ inputs.r-version }}" | |
| if [ "$R_VERSION" == "" ] | |
| then { | |
| R_VERSION="4.1" | |
| } | |
| fi | |
| echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT | |
| shell: bash | |
| lint: | |
| name: Roxygen | |
| runs-on: ubuntu-latest | |
| container: | |
| image: "ghcr.io/pharmaverse/admiralci-${{needs.get_r_version.outputs.r-version}}:latest" | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip lint]') | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| needs: get_r_version | |
| steps: | |
| ##################### BEGIN boilerplate 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: Checkout repository | |
| uses: actions/checkout@v3 | |
| if: github.event_name != 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| - name: Normalize inputs | |
| id: normalizer | |
| run: | | |
| R_VERSION="${{ inputs.r-version }}" | |
| if [ "$R_VERSION" == "" ] | |
| then { | |
| R_VERSION="4.1" | |
| } | |
| fi | |
| echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - name: Restore cache | |
| uses: actions/cache@v3 | |
| 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 | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| ##################### END boilerplate steps ##################### | |
| - name: Generate man pages | |
| run: roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace')) | |
| shell: Rscript {0} | |
| - name: Set-up safe dir | |
| run: git config --global --add safe.directory "${GITHUB_WORKSPACE}" | |
| shell: bash | |
| - name: Roxygen check | |
| if: "!startsWith(github.event.comment.body, '/roxygenize')" | |
| 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 |