fix: add stop codon substitution conditional branch to protein-variant #356
Workflow file for this run
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: build | |
| on: [push, pull_request] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| java: ['8', '11', '17'] | |
| clojure: ['1.8', '1.9', '1.10', '1.11'] | |
| name: Test with Java ${{ matrix.java }} and Clojure ${{ matrix.clojure }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.m2/repository | |
| key: ${{ runner.os }}-lein-${{ hashFiles('**/project.clj') }} | |
| restore-keys: | | |
| ${{ runner.os }}-lein- | |
| - name: Setup Java | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'adopt' | |
| java-version: ${{ matrix.java }} | |
| - name: Setup Clojure | |
| uses: DeLaGuardo/setup-clojure@13.1 | |
| with: | |
| lein: latest | |
| - name: Install dependencies | |
| run: lein deps | |
| - name: Run tests | |
| run: lein with-profile +${{ matrix.clojure }} test | |
| coverage: | |
| needs: [test] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.m2/repository | |
| key: ${{ runner.os }}-lein-${{ hashFiles('**/project.clj') }} | |
| restore-keys: | | |
| ${{ runner.os }}-lein- | |
| - name: Setup Java | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'adopt' | |
| java-version: '17' | |
| - name: Setup Clojure | |
| uses: DeLaGuardo/setup-clojure@13.1 | |
| with: | |
| lein: latest | |
| - name: Install dependencies | |
| run: lein deps | |
| - name: Generate code coverage | |
| run: lein cloverage --codecov | |
| - uses: codecov/codecov-action@v3 | |
| with: | |
| files: ./target/coverage/codecov.json | |
| get-version: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| version: ${{ steps.get-version.outputs.version }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Get version | |
| id: get-version | |
| run: | | |
| echo "version=$(head -n 1 project.clj | sed -e 's/^(defproject.*"\(.*\)"$/\1/')" >> $GITHUB_OUTPUT | |
| deploy: | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/master' | |
| needs: [test, get-version] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Java | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'adopt' | |
| java-version: '17' | |
| - name: Setup Clojure | |
| uses: DeLaGuardo/setup-clojure@13.1 | |
| with: | |
| lein: latest | |
| - name: Deploy | |
| if: endsWith(needs.get-version.outputs.version, '-SNAPSHOT') | |
| env: | |
| CLOJARS_USERNAME: ${{ secrets.CLOJARS_USERNAME }} | |
| CLOJARS_PASSWORD: ${{ secrets.CLOJARS_PASSWORD }} | |
| run: lein deploy snapshots |