test #1331
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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: "." | |
| deps-installation-method: | |
| description: | | |
| Which method for installing R package dependencies to use? Supported values are: | |
| staged-dependencies | |
| setup-r-dependencies | |
| required: false | |
| type: string | |
| default: staged-dependencies | |
| lookup-refs: | |
| description: | | |
| List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'. | |
| 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/[email protected] | |
| 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/[email protected] | |
| if: github.event_name != 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| path: ${{ github.event.repository.name }} | |
| - name: Check commit message 💬 | |
| run: | | |
| git config --global --add safe.directory $(pwd) | |
| export head_commit_message="$(git show -s --format=%B | tr '\r\n' ' ' | tr '\n' ' ')" | |
| echo "head_commit_message = $head_commit_message" | |
| if [[ $head_commit_message == *"$SKIP_INSTRUCTION"* ]]; then | |
| echo "Skip instruction detected - cancelling the workflow." | |
| exit 1 | |
| fi | |
| shell: bash | |
| working-directory: ${{ github.event.repository.name }} | |
| env: | |
| SKIP_INSTRUCTION: "[skip bioccheck]" | |
| - name: Restore SD cache 💰 | |
| if: >- | |
| inputs.deps-installation-method == 'staged-dependencies' | |
| uses: actions/cache@v4 | |
| with: | |
| key: sd-${{ runner.os }}-${{ github.event.repository.name }} | |
| path: ~/.staged.dependencies | |
| - name: Run Staged dependencies 🎦 | |
| if: >- | |
| inputs.deps-installation-method == 'staged-dependencies' | |
| uses: insightsengineering/staged-dependencies-action@v2 | |
| 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: Setup R dependencies 🎦 | |
| if: >- | |
| inputs.deps-installation-method == 'setup-r-dependencies' | |
| uses: insightsengineering/setup-r-dependencies@v1 | |
| env: | |
| GITHUB_PAT: ${{ steps.github-token.outputs.token }} | |
| with: | |
| lookup-refs: ${{ inputs.lookup-refs }} | |
| repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} | |
| - 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 }} |