test for dbetabinom.R #14
Workflow file for this run
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| --- | |
| name: Style | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - pre-release | |
| pull_request: | |
| types: | |
| - opened | |
| - synchronize | |
| - reopened | |
| - ready_for_review | |
| branches: | |
| - main | |
| - pre-release | |
| workflow_dispatch: | |
| workflow_call: | |
| inputs: | |
| auto-update: | |
| description: If R code style is not up-to-date, styling will automatically be applied and restyled files will be automatically committed o the branch. | |
| required: false | |
| default: false | |
| type: boolean | |
| concurrency: | |
| group: style-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| style: | |
| name: Check code style 🔠 | |
| runs-on: ubuntu-latest | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip style]') | |
| && github.event.pull_request.draft == false | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio_4.2.1_bioc_3.15:latest | |
| steps: | |
| - name: Checkout Code 🛎 | |
| uses: actions/checkout@v3 | |
| with: | |
| path: ${{ github.event.repository.name }} | |
| fetch-depth: 0 | |
| - name: Get branch names 🌿 | |
| if: inputs.auto-update | |
| id: branch-name | |
| uses: tj-actions/branch-names@v5 | |
| - name: Install styler 👚 | |
| run: | | |
| install.packages("styler", repos = "https://cloud.r-project.org") | |
| shell: Rscript {0} | |
| - name: Get changed files 🗞 | |
| id: changed-files | |
| uses: tj-actions/changed-files@v20 | |
| with: | |
| path: ${{ github.event.repository.name }} | |
| separator: "," | |
| files: | | |
| **.R | |
| **.Rmd | |
| **.Rnw | |
| **.Rmarkdown | |
| **.qmd | |
| - name: Run styler 👟 | |
| run: | | |
| setwd("${{ github.event.repository.name }}") | |
| changed_files <- unlist(strsplit( | |
| "${{ steps.changed-files.outputs.all_changed_files }}", | |
| split="," | |
| )) | |
| is_r_file <- function(x) { | |
| ext <- tools::file_ext(x) | |
| ext %in% c("R", "Rmd", "Rnw", "Rmarkdown", "qmd") | |
| } | |
| changed_r_files <- Filter(is_r_file, changed_files) | |
| dry <- if(isTRUE(as.logical("${{ inputs.auto-update }}"))) "off" else "on" | |
| detect <- styler::style_file(changed_r_files, dry = dry) | |
| if (TRUE %in% detect$changed) { | |
| problems <- subset(detect$file, detect$changed == TRUE) | |
| dput(problems, file = "/tmp/style-problems.R") | |
| writeLines( | |
| problems, | |
| con = "/tmp/style-problems.txt", | |
| sep = " " | |
| ) | |
| } | |
| shell: Rscript {0} | |
| - name: Check file existence | |
| id: check_files | |
| uses: andstor/file-existence-action@v1 | |
| with: | |
| files: "/tmp/style-problems.R, /tmp/style-problems.txt" | |
| - name: Get problematic files | |
| id: problem-files | |
| if: steps.check_files.outputs.files_exists == 'true' | |
| run: | | |
| perl -p -i -e 's/\R//g;' /tmp/style-problems.R | |
| echo "::set-output name=unstyled-files::$(cat /tmp/style-problems.txt)" | |
| shell: bash | |
| - name: Autocommit styled files | |
| if: > | |
| inputs.auto-update | |
| && steps.check_files.outputs.files_exists == 'true' | |
| run: | | |
| cd ${{ github.event.repository.name }} | |
| git config --global user.name 'github-actions' | |
| git config --global user.email '41898282+github-actions[bot]@users.noreply.github.com' | |
| git add ${{ steps.problem-files.outputs.unstyled-files }} | |
| git commit -m '[skip actions] Restyle files' | |
| git pull origin ${{ steps.branch-name.outputs.head_ref_branch }} | |
| git push -v origin HEAD:${{ steps.branch-name.outputs.head_ref_branch }} | |
| shell: bash | |
| - name: Styler check summary 🅾 | |
| if: > | |
| inputs.auto-update != true | |
| && steps.check_files.outputs.files_exists == 'true' | |
| run: | | |
| 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(", | |
| readLines("/tmp/style-problems.R", warn=FALSE), | |
| ")\n" | |
| )) | |
| cat("────────────────────────────────────────\n") | |
| quit(status = 1) | |
| shell: Rscript {0} |