Upgrade pandoc to v2 in code-coverage job. #477
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| on: | |
| workflow_dispatch: | |
| workflow_call: | |
| inputs: | |
| r-version: | |
| description: 'The version of R to use' | |
| default: '4.1' | |
| required: false | |
| type: string | |
| lint-all-files: | |
| description: 'Lint all files every time' | |
| default: 'false' | |
| required: false | |
| type: string | |
| push: | |
| branches: | |
| - main | |
| - devel | |
| - pre-release | |
| pull_request: | |
| branches: | |
| - main | |
| - devel | |
| - pre-release | |
| name: Lint | |
| concurrency: | |
| group: lint-${{ 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" >> $GITHUB_OUTPUT | |
| shell: bash | |
| lint: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| container: | |
| image: "ghcr.io/pharmaverse/admiralci-${{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: ${{ secrets.GITHUB_TOKEN }} | |
| ##################### END boilerplate steps ##################### | |
| - name: Changed files | |
| id: files | |
| uses: Ana06/[email protected] | |
| with: | |
| format: 'json' | |
| filter: '*' | |
| - name: Lint | |
| run: | | |
| exclusions_list <- NULL | |
| if (!identical("${{ inputs.lint-all-files }}", "true")) { | |
| changed_files <- jsonlite::fromJSON('${{ steps.files.outputs.added_modified }}') | |
| all_files <- list.files(recursive = TRUE) | |
| exclusions_list <- if (any(changed_files %in% c(".lintr", "renv.lock"))) { | |
| as.list(setdiff(all_files, changed_files)) | |
| } else { | |
| NULL | |
| } | |
| } | |
| lints <- lintr::lint_package(exclusions = exclusions_list) | |
| saveRDS(lints, file = "lints.rds") | |
| shell: Rscript {0} | |
| - name: Error if lints are detected | |
| run: | | |
| lints <- readRDS("lints.rds") | |
| if (length(lints) > 0L) { | |
| print(lints) | |
| stop("Lints detected. Please review and adjust code according to the comments provided.", call. = FALSE) | |
| } | |
| shell: Rscript {0} |