Merge branch 'contents' of https://github.com/Genentech/phase1b into … #7
Workflow file for this run
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| --- | ||
| name: BiocCheck ☣️ | ||
| on: | ||
| push: | ||
| tags: | ||
| - "v*" | ||
| branches: | ||
| - main | ||
| - pre-release | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| - synchronize | ||
| - reopened | ||
| - ready_for_review | ||
| branches: | ||
| - main | ||
| - pre-release | ||
| 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: true | ||
| type: boolean | ||
| allow-failure: | ||
| description: BiocCheck errors will not fail, but will give a warning. | ||
| required: false | ||
| type: boolean | ||
| default: false | ||
| 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_4.2.1_bioc_3.15 | ||
| 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: Get branch names 🌿 | ||
| id: branch-name | ||
| uses: tj-actions/branch-names@v5 | ||
| - name: Checkout repo 🛎 | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
| path: ${{ github.event.repository.name }} | ||
| - name: Run Staged dependencies 🎦 | ||
| uses: insightsengineering/staged-dependencies-action@v1 | ||
| with: | ||
| run-system-dependencies: ${{ inputs.install-system-dependencies }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| SD_REPO_PATH: ${{ github.event.repository.name }} | ||
| SD_ENABLE_CHECK: ${{ inputs.enable-staged-dependencies-check }} | ||
| - name: Run BiocCheck ☣️ | ||
| uses: insightsengineering/bioc-check-action@v1 | ||
| with: | ||
| path: ${{ github.event.repository.name }} | ||
| no-check-version-num: true | ||
| allow-failure: ${{ inputs.allow-failure }} | ||
