fix: Normalize the option to post coverage as PR comment #1048
Workflow file for this run
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--- | |
name: BiocCheck ☣️ | |
on: | |
push: | |
tags: | |
- "v*" | |
branches: | |
- main | |
pull_request: | |
types: | |
- opened | |
- synchronize | |
- reopened | |
- ready_for_review | |
branches: | |
- main | |
workflow_dispatch: | |
workflow_call: | |
secrets: | |
REPO_GITHUB_TOKEN: | |
description: | | |
Github token with read access to repositories, required for staged.dependencies installation | |
required: false | |
inputs: | |
enable-bioccheck: | |
description: Enable BiocCheck | |
required: false | |
type: boolean | |
default: false | |
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 | |
allow-failure: | |
description: BiocCheck errors will not fail, but will give a warning | |
required: false | |
type: boolean | |
default: false | |
sd-direction: | |
description: The direction to use to install staged dependencies. Choose between 'upstream', 'downstream' and 'all' | |
required: false | |
type: string | |
default: upstream | |
package-subdirectory: | |
description: Subdirectory in the repository, where the R package is located. | |
required: false | |
type: string | |
default: "." | |
concurrency: | |
group: bioccheck-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
jobs: | |
bioccheck: | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
- image: ghcr.io/insightsengineering/rstudio | |
tag: latest | |
name: ${{ matrix.config.image }}, version ${{ matrix.config.tag }} | |
runs-on: ubuntu-latest | |
if: > | |
!contains(github.event.commits[0].message, '[skip bioccheck]') | |
&& contains(inputs.enable-bioccheck, 'true') | |
&& github.event.pull_request.draft == false | |
container: | |
image: ${{ matrix.config.image }}:${{ matrix.config.tag }} | |
steps: | |
- name: Setup token 🔑 | |
id: github-token | |
run: | | |
if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then | |
echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN." | |
echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | |
else | |
echo "Using REPO_GITHUB_TOKEN." | |
echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | |
fi | |
shell: bash | |
- name: Get branch names 🌿 | |
id: branch-name | |
uses: tj-actions/branch-names@v7 | |
- name: Checkout repo (PR) 🛎 | |
uses: actions/checkout@v4 | |
if: github.event_name == 'pull_request' | |
with: | |
ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
path: ${{ github.event.repository.name }} | |
repository: ${{ github.event.pull_request.head.repo.full_name }} | |
- name: Checkout repo 🛎 | |
uses: actions/checkout@v4 | |
if: github.event_name != 'pull_request' | |
with: | |
ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
path: ${{ github.event.repository.name }} | |
- name: Restore SD cache 💰 | |
uses: actions/cache@v4 | |
with: | |
key: sd-${{ runner.os }}-${{ github.event.repository.name }} | |
path: ~/.staged.dependencies | |
- name: Run Staged dependencies 🎦 | |
uses: insightsengineering/staged-dependencies-action@v1 | |
env: | |
GITHUB_PAT: ${{ steps.github-token.outputs.token }} | |
with: | |
path: ${{ github.event.repository.name }} | |
enable-check: ${{ inputs.enable-staged-dependencies-check }} | |
run-system-dependencies: ${{ inputs.install-system-dependencies }} | |
direction: ${{ inputs.sd-direction }} | |
- name: Run BiocCheck ☣️ | |
uses: insightsengineering/bioc-check-action@v1 | |
with: | |
path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} | |
no-check-version-num: true | |
allow-failure: ${{ inputs.allow-failure }} |