real fix #3
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| name: nf-scil checks | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request_target: | |
| branches: | |
| - main | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v3 | |
| - uses: pre-commit/[email protected] | |
| # FIXME Flip this off once we get to less than a couple hundred. Adding | |
| # this so it will only run against changed files. It'll make it much | |
| # easier to fix these as they come up rather than everything at once. | |
| with: | |
| extra_args: "" | |
| prettier: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Install NodeJS | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: Install Prettier | |
| run: npm install -g prettier | |
| - name: Run Prettier --check | |
| run: prettier --check . | |
| editorconfig: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: Install editorconfig-checker | |
| run: npm install -g editorconfig-checker | |
| - name: Run ECLint check | |
| run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) | |
| failing-modules: | |
| name: failing-modules | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'modules' output variable | |
| modules: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Get branch names. | |
| id: branch-names | |
| uses: tj-actions/branch-names@v8 | |
| - uses: SamhammerAG/last-successful-build-action@v5 | |
| id: successful-ref | |
| with: | |
| branch: ${{ steps.branch-names.outputs.current_branch }} | |
| token: ${{ github.token }} | |
| workflow: "Modules Tests" | |
| # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
| - uses: mirpedrol/paths-filter@main | |
| id: filter | |
| with: | |
| filters: "tests/config/pytest_modules.yml" | |
| token: "" | |
| base: ${{ steps.successful-ref.outputs.commit_hash }} | |
| lint-modules: | |
| name: lint-modules | |
| needs: [failing-modules] | |
| if: needs.failing-modules.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| module: ["${{ fromJson(needs.failing-modules.outputs.modules) }}"] | |
| uses: ./.github/workflows/lint_module.yml | |
| with: | |
| module: ${{ matrix.module }} | |
| secrets: inherit | |
| test-modules: | |
| name: test-modules | |
| needs: [failing-modules] | |
| if: needs.failing-modules.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| module: ["${{ fromJson(needs.failing-modules.outputs.modules) }}"] | |
| profile: ["docker", "singularity"] | |
| exclude: | |
| - module: "nf-test" | |
| uses: ./.github/workflows/test_module.yml | |
| with: | |
| module: ${{ matrix.module }} | |
| profile: ${{ matrix.profile }} | |
| secrets: inherit | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: [prettier, editorconfig, failing-modules, lint-modules, test-modules] | |
| if: ${{ !cancelled() }} | |
| steps: | |
| - name: All tests ok | |
| if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: ${{ !cancelled() }} | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |