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fix: Normalize the option to post coverage as PR comment #1048

fix: Normalize the option to post coverage as PR comment

fix: Normalize the option to post coverage as PR comment #1048

Workflow file for this run

---
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 }}