This repository has been archived by the owner on Jan 22, 2024. It is now read-only.
Initialize repo #2
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- | ||
| name: BiocCheck ☣️ | ||
| on: | ||
| push: | ||
| tags: | ||
| - "v*" | ||
| branches: | ||
| - main | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| - synchronize | ||
| - reopened | ||
| - ready_for_review | ||
| branches: | ||
| - main | ||
| workflow_dispatch: | ||
| workflow_call: | ||
| secrets: | ||
| 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 [ "${{ secrets.GITHUB_TOKEN }}" == "" ]; then | ||
| echo "GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN." | ||
| echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | ||
| else | ||
| echo "Using GITHUB_TOKEN." | ||
| echo "token=${{ secrets.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@v3 | ||
| 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: ${{ github.event.repository.name }} | ||
| - name: Restore SD cache 💰 | ||
| uses: actions/cache@v3 | ||
| with: | ||
| key: sd-${{ 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 }} | ||
