fix dir #1524
Workflow file for this run
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| name: unit tests | |
| on: [push, pull_request] | |
| concurrency: | |
| group: unittest-${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Unit Tests | |
| runs-on: ubuntu-24.04 | |
| environment: github-actions | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| lfs: true | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| - name: Setup Scala | |
| uses: olafurpg/setup-scala@v12 | |
| with: | |
| java-version: adopt-openj9@1.8.0-292 | |
| - name: Cache .ivy2 | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.ivy2 | |
| key: ${{ runner.os }}-ivy2-${{ hashFiles('**/build.sbt') }} | |
| - name: Cache .sbt | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.sbt | |
| key: ${{ runner.os }}-sbt-${{ hashFiles('**/build.properties') }} | |
| - name: Unit Tests | |
| run: | | |
| set -e | |
| sbt +clean coverage +test && sbt coverageReport coverageAggregate && (find $HOME/.sbt -name "*.lock" | xargs rm) && (find $HOME/.ivy2 -name "ivydata-*.properties" | xargs rm) | |
| - name: Code Coverage | |
| uses: codecov/codecov-action@v5.1.1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| flags: unittests # optional | |
| fail_ci_if_error: true # optional (default = false) | |
| verbose: true # optional (default = false) | |
| release: | |
| if: ${{ github.repository == 'fulcrumgenomics/fgbio' && github.ref == 'refs/heads/main' }} | |
| needs: test | |
| runs-on: ubuntu-24.04 | |
| environment: github-actions | |
| env: | |
| SONATYPE_USER: ${{ secrets.SONATYPE_USER }} | |
| SONATYPE_PASS: ${{ secrets.SONATYPE_PASS }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup Scala | |
| uses: olafurpg/setup-scala@v12 | |
| with: | |
| java-version: adopt-openj9@1.8.0-292 | |
| - name: Upload to Sonatype | |
| run: | | |
| sbt +publish | |
| docs: | |
| name: Generate tool and metric markdown docs | |
| needs: test | |
| runs-on: ubuntu-latest | |
| if: ${{ github.event_name == 'pull_request' || (github.repository == 'fulcrumgenomics/fgbio' && github.ref == 'refs/heads/main') }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| # To work with the `pull_request` or any other non-`push` even with git-auto-commit | |
| ref: ${{ github.head_ref }} | |
| - name: Generate the docs | |
| uses: ./.github/actions/docs/ | |
| with: | |
| build-dir: ./build | |
| latest: ${{ github.event_name == 'pull_request' }} | |
| - name: Generate gh-pages preview (pull request only) | |
| uses: rossjrw/pr-preview-action@df22037db54ab6ee34d3c1e2b8810ac040a530c6 # v1.6.0 | |
| if: ${{ github.event_name == 'pull_request' }} | |
| with: | |
| source-dir: ./build | |
| - name: Commit generated docs (main only) | |
| uses: nick-fields/retry@v3 | |
| #i.e. if: ${{ github.event_name != 'pull_request' }} | |
| if: ${{ github.repository == 'fulcrumgenomics/fgbio' && github.ref == 'refs/heads/main' }} | |
| with: | |
| shell: bash -l {0} | |
| max_attempts: 5 | |
| retry_on: error | |
| polling_interval_seconds: 5 | |
| timeout_minutes: 5 | |
| command: | | |
| pushd gh-pages | |
| git add tools metrics index.md | |
| git config --global user.name "Github Actions" | |
| git config --global user.email "nobody@fulcrumgenomics.com" | |
| git commit --all --message "devel: ${{ github.head_ref }}" --author "Nobody <nobody@fulcrumgenomics.com>" || echo "nothing to commit" | |
| git rebase origin/gh-pages | |
| git fetch origin | |
| git push --atomic --set-upstream origin gh-pages | |
| popd |