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test for dbetabinom.R #14

test for dbetabinom.R

test for dbetabinom.R #14

Workflow file for this run

---
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 πŸ” 
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 πŸ›Ž
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 πŸ‘š
run: |
install.packages("styler", repos = "https://cloud.r-project.org")
shell: Rscript {0}
- name: Get changed files πŸ—ž
id: changed-files
uses: tj-actions/changed-files@v20
with:
path: ${{ github.event.repository.name }}
separator: ","
files: |
**.R
**.Rmd
**.Rnw
**.Rmarkdown
**.qmd
- name: Run styler πŸ‘Ÿ
run: |
setwd("${{ 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 πŸ…Ύ
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}