Personal tool to split up large intervals in an interval list. #1980
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| name: unit tests | |
| on: | |
| push: | |
| pull_request: | |
| workflow_call: | |
| secrets: | |
| CODECOV_TOKEN: | |
| required: true | |
| SONATYPE_USER: | |
| required: false | |
| SONATYPE_PASS: | |
| required: false | |
| concurrency: | |
| group: unittest-${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Unit Tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| jvm: ["temurin:1.8.0-442", "temurin:1.11.0.27", "temurin:1.17.0.15", "temurin:1.21.0.7", "temurin:1.22.0.2"] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
| with: | |
| fetch-depth: 0 | |
| lfs: true | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| - name: Setup cache | |
| uses: coursier/cache-action@4e2615869d13561d626ed48655e1a39e5b192b3c # v6.4.7 | |
| - name: setup Scala | |
| uses: coursier/setup-action@039f736548afa5411c1382f40a5bd9c2d30e0383 # v1.3.9 | |
| with: | |
| apps: scala:2.13.14 scalac:2.13.14 scaladoc:2.13.14 sbt:1.11.2 | |
| jvm: ${{ matrix.jvm }} | |
| - name: Unit Tests | |
| run: | | |
| set -e | |
| sbt clean coverage test | |
| sbt coverageReport coverageAggregate | |
| - name: Code Coverage | |
| uses: codecov/codecov-action@ad3126e916f78f00edff4ed0317cf185271ccc2d # v5.4.2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| flags: unittests # optional | |
| fail_ci_if_error: true # optional (default = false) | |
| verbose: true # optional (default = false) | |
| # while the "docs" job below tests building the online docs, this is added here | |
| # to fail-fast when docs are not correctly written. | |
| - name: Ensure docs will compile (fast-fail) | |
| run: | | |
| set -e | |
| sbt doc | |
| release: | |
| if: ${{ github.repository == 'fulcrumgenomics/fgbio' && github.ref == 'refs/heads/main' && github.event_name != 'workflow_call' }} | |
| needs: test | |
| runs-on: ubuntu-latest | |
| environment: github-actions | |
| env: | |
| SONATYPE_USER: ${{ secrets.SONATYPE_USER }} | |
| SONATYPE_PASS: ${{ secrets.SONATYPE_PASS }} | |
| PGP_PASSPHRASE: ${{ secrets.PGP_PASSPHRASE }} | |
| PGP_SECRET: ${{ secrets.PGP_SECRET }} | |
| steps: | |
| - name: Check for secrets.SONATYPE_USER | |
| if: ${{ env.SONATYPE_USER == '' }} | |
| run: | | |
| echo '"SONATYPE_USER" secret not set' | |
| echo 'please go to "settings > secrets > actions" to create it' | |
| - name: Check for secrets.SONATYPE_PASS | |
| if: ${{ env.SONATYPE_PASS == '' }} | |
| run: | | |
| echo '"SONATYPE_PASS" secret not set' | |
| echo 'please go to "settings > secrets > actions" to create it' | |
| - name: Check for secrets.PGP_PASSPHRASE | |
| if: ${{ env.PGP_PASSPHRASE== '' }} | |
| run: | | |
| echo '"PGP_PASSPHRASE" secret not set' | |
| echo 'please go to "settings > secrets > actions" to create it' | |
| - name: Check for secrets.PGP_SECRET | |
| if: ${{ env.PGP_SECRET== '' }} | |
| run: | | |
| echo '"PGP_SECRET" secret not set' | |
| echo 'please go to "settings > secrets > actions" to create it' | |
| - name: Export tty | |
| run: | | |
| echo "GPG_TTY=$(tty)" >> $GITHUB_ENV | |
| - name: Setup GPG | |
| shell: bash -l {0} | |
| run: | | |
| echo "$PGP_SECRET" | base64 --decode | gpg --import --batch --yes | |
| - name: Checkout | |
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
| 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: Setup cache | |
| uses: coursier/cache-action@4e2615869d13561d626ed48655e1a39e5b192b3c # v6.4.7 | |
| - name: setup Scala | |
| uses: coursier/setup-action@039f736548afa5411c1382f40a5bd9c2d30e0383 # v1.3.9 | |
| with: | |
| apps: scala:2.13.14 scalac:2.13.14 scaladoc:2.13.14 sbt:1.11.2 | |
| jvm: "temurin:1.8.0-442" | |
| - name: Build and sign artifacts | |
| shell: bash -l {0} | |
| run: | | |
| sbt +publishSigned | |
| docs: | |
| name: Generate tool and metric markdown docs | |
| needs: test | |
| runs-on: ubuntu-latest | |
| if: ${{ github.event_name != 'workflow_call' && (github.event_name == 'pull_request' || (github.repository == 'fulcrumgenomics/fgbio' && github.ref == 'refs/heads/main')) }} | |
| steps: | |
| - name: Checkout | |
| id: checkout | |
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
| with: | |
| # 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: false | |
| - name: Generate gh-pages preview (pull request only) | |
| uses: rossjrw/pr-preview-action@2fb559e4766555e23d07b73d313fe97c4f8c3cfe # v1.6.1 | |
| if: ${{ github.event_name == 'pull_request' }} | |
| with: | |
| source-dir: ./build | |
| - name: Commit generated docs (main only) | |
| uses: nick-fields/retry@ce71cc2ab81d554ebbe88c79ab5975992d79ba08 # v3.0.2 | |
| #i.e. if: ${{ github.event_name != 'pull_request' }} | |
| if: ${{ github.repository == 'fulcrumgenomics/fgbio' && github.ref == 'refs/heads/main' }} | |
| with: | |
| max_attempts: 5 | |
| retry_on: error | |
| polling_interval_seconds: 5 | |
| timeout_minutes: 5 | |
| command: | | |
| set -euo pipefail | |
| pushd ./build | |
| git add tools metrics index.md | |
| git config --global user.name "Github Actions" | |
| git config --global user.email "[email protected]" | |
| git commit --all --message "devel: ${{ steps.checkout.outputs.ref }}" --author "Nobody <[email protected]>" || echo "nothing to commit" | |
| git fetch origin gh-pages | |
| git rebase -X ours origin/gh-pages | |
| git push --atomic --set-upstream origin gh-pages | |
| popd | |
| new_command_on_retry: | | |
| set -euo pipefail | |
| pushd ./build | |
| git fetch origin gh-pages | |
| git rebase --abort | |
| git rebase -X ours origin/gh-pages | |
| git push --atomic --set-upstream origin gh-pages | |
| popd |