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fixup workflows #3
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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: | ||
| 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 }} | ||
