add rstudio bash script #475
Workflow file for this run
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| --- | |
| name: Style | |
| 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 | |
| concurrency: | |
| group: style-${{ 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 style]') | |
| 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" >> $GITHUB_OUTPUT | |
| shell: bash | |
| style: | |
| name: Code Style | |
| runs-on: ubuntu-latest | |
| container: | |
| image: "ghcr.io/pharmaverse/admiralci-${{needs.get_r_version.outputs.r-version}}:latest" | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip style]') | |
| 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: ${{ secrets.GITHUB_TOKEN }} | |
| ##################### END boilerplate steps ##################### | |
| - name: Get changed files | |
| id: changed-files | |
| uses: Ana06/[email protected] | |
| with: | |
| format: csv | |
| filter: | | |
| * | |
| !renv/*.R | |
| - name: Run styler | |
| run: | | |
| changed_files <- unlist(strsplit( | |
| "${{ steps.changed-files.outputs.all }}", | |
| split="," | |
| )) | |
| is_r_file <- function(x) { | |
| ext <- tools::file_ext(x) | |
| ext %in% c("R", "Rmd", "Rnw", "Rmarkdown", "qmd") | |
| } | |
| changed_r_files <- Filter(is_r_file, changed_files) | |
| changed_r_files <- Filter(file.exists, changed_r_files) | |
| detect <- styler::style_file(changed_r_files, dry = "on") | |
| if (TRUE %in% detect$changed) { | |
| problems <- subset(detect$file, detect$changed == T) | |
| cat(paste( | |
| "☠ One or more files had styling errors.", | |
| "Please see the log above for remediations,", | |
| "or simply run the following commands", | |
| "for an immediate fix:\n" | |
| )) | |
| cat("────────────────────────────────────────\n") | |
| cat(paste0( | |
| "styler::style_file(", capture.output(dput(problems)), ")\n" | |
| )) | |
| cat("────────────────────────────────────────\n") | |
| cat("⚠️ Here is the complete git diff for the files that changed:\n") | |
| system("git diff") | |
| cat("────────────────────────────────────────\n") | |
| cat(paste("ℹ️ Version of styler used in this workflow:", packageVersion("styler"))) | |
| quit(status = length(problems)) | |
| } | |
| shell: Rscript {0} |