all updated and refreshed into final report-tlf-pilot3.pdf #52
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| on: | |
| workflow_dispatch: | |
| workflow_call: | |
| inputs: | |
| r-version: | |
| description: 'The version of R to use' | |
| default: '4.2' | |
| required: false | |
| type: string | |
| lint-all-files: | |
| description: 'Lint all files every time' | |
| default: 'false' | |
| required: false | |
| type: string | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| name: Check 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 [ "$R_VERSION" == "" ] | |
| then { | |
| R_VERSION="4.2" | |
| } | |
| fi | |
| echo "R_VERSION=$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/branch-names@v5.4 | |
| - 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 [ "$R_VERSION" == "" ] | |
| then { | |
| R_VERSION="4.2" | |
| } | |
| fi | |
| echo "R_VERSION=$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: ${{ secrets.GITHUB_TOKEN }} | |
| ##################### END boilerplate steps ##################### | |
| - name: Changed files | |
| id: files | |
| uses: Ana06/get-changed-files@v2.2.0 | |
| with: | |
| format: 'json' | |
| filter: '*' | |
| - name: Lint | |
| run: | | |
| install.packages("lintr") | |
| exclusions_list <- NULL | |
| if (!identical("${{ 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_dir(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} |