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finish test for logit #19

finish test for logit

finish test for logit #19

Workflow file for this run

---
name: Roxygen πŸ…Ύ
on:
push:
branches:
- main
- pre-release
pull_request:
types:
- opened
- synchronize
- reopened
- ready_for_review
branches:
- main
- pre-release
workflow_dispatch:
workflow_call:
inputs:
install-system-dependencies:
description: Check for and install system dependencies
required: false
default: false
type: boolean
enable-staged-dependencies-check:
description: Enable staged dependencies YAML check
required: false
default: false
type: boolean
auto-update:
description: If man pages are not up-to-date, they will be automatically updated and committed back to the branch.
required: false
default: false
type: boolean
secrets:
GITHUB_TOKEN:

Check failure on line 37 in .github/workflows/roxygen.yaml

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GitHub Actions / .github/workflows/roxygen.yaml

Invalid workflow file

secret name `GITHUB_TOKEN` within `workflow_call` can not be used since it would collide with system reserved name
description: |
Github token with read access to repositories, required for staged.dependencies installation
required: false
concurrency:
group: roxygen-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
jobs:
roxygen:
name: Manual pages check 🏁
runs-on: ubuntu-latest
if: >
!contains(github.event.commits[0].message, '[skip roxygen]')
&& github.event.pull_request.draft == false
container:
image: ghcr.io/insightsengineering/rstudio_4.2.1_bioc_3.15:latest
steps:
- name: Get branch names 🌿
id: branch-name
uses: tj-actions/branch-names@v5
- name: Checkout repo πŸ›Ž
uses: actions/checkout@v3
with:
ref: ${{ steps.branch-name.outputs.head_ref_branch }}
path: ${{ github.event.repository.name }}
fetch-depth: 0
- name: Run Staged dependencies 🎦
uses: insightsengineering/staged-dependencies-action@v1
with:
run-system-dependencies: ${{ inputs.install-system-dependencies }}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
SD_REPO_PATH: ${{ github.event.repository.name }}
SD_ENABLE_CHECK: ${{ inputs.enable-staged-dependencies-check }}
- name: Generate man pages πŸ“„
run: |
setwd("${{ github.event.repository.name }}")
logfile <- "roxygen_${{ github.event.repository.name }}.log"
con <- file(logfile)
sink(con, append = TRUE, split = TRUE)
sink(con, append = TRUE, type = "message")
roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))
sink()
sink(type = "message")
logs <- readLines(logfile)
error_marker <- grep("Error:", logs)
warnings_marker <- grep("Warning message", logs)
if (length(warnings_marker) > 0) {
cat("⚠ One or more warnings were generated during the roxygen build:\n")
cat(logs[warnings_marker[[1]]:length(logs)], sep = "\n")
stop("Please πŸ™ fix the warnings shown below this message πŸ‘‡")
}
if (length(error_marker) > 0) {
cat("☠ One or more errors were generated during the roxygen build:\n")
cat(logs[error_marker[[1]]:length(logs)], sep = "\n")
stop("Please πŸ™ fix the errors shown below this message πŸ‘‡")
}
shell: Rscript {0}
- name: Roxygen check πŸ…Ύ
run: |
cd ${{ github.event.repository.name }}
git status -s
if [[ -n `git status -s | grep man` ]]
then {
ROXYGEN_VERSION="$(Rscript -e 'packageVersion("roxygen2")' | awk '{print $NF}')"
echo "πŸ™ˆ Manuals are not up-to-date with roxygen comments!"
echo "πŸ”€ The following differences were noted:"
git diff man/*
if [ "${{ inputs.auto-update }}" == "true" ]
then {
echo "Regenerating man pages via auto-update"
git config --global user.name "github-actions"
git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
git add man/*
git commit -m "[skip actions] ROxygen Man Pages Auto Update"
git pull origin ${GITHUB_HEAD_REF}
git push -v origin ${GITHUB_HEAD_REF}
}
else {
echo -e "\nπŸ’» Please rerun the following command on your workstation and push your changes"
echo "--------------------------------------------------------------------"
echo "roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))"
echo "--------------------------------------------------------------------"
echo "β„Ή roxygen2 version that was used in this workflow: $ROXYGEN_VERSION"
echo "πŸ™ Please ensure that the 'RoxygenNote' field in the DESCRIPTION file matches this version"
}
fi
exit 1
} else {
echo "πŸ’š Manuals are up-to-date with roxygen comments"
}
fi
shell: bash