adding option to input a general transform #1570
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| name: BEAST CI | |
| #on: | |
| # push: | |
| # branches: | |
| # - main | |
| # pull_request: | |
| on: [push] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| BEAGLE_DIR: beagle-lib | |
| BEAGLE_LIB: beagle-lib/usr/local/lib | |
| LD_LIBRARY_PATH: beagle-lib/usr/local/lib | |
| BEAGLE_BRANCH: v4_release | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up JDK 8 | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: "8" | |
| distribution: "adopt" | |
| - name: Setup cmake | |
| uses: lukka/get-cmake@latest | |
| - name: Cache BEAGLE | |
| id: cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ env.BEAGLE_DIR }} | |
| build/dist | |
| key: beagle-beast-${{ hashFiles('**/build_beagle.sh', '**/build.xml') }} | |
| - name: Build BEAGLE | |
| run: | | |
| chmod +x ./.github/scripts/build_beagle.sh | |
| ./.github/scripts/build_beagle.sh | |
| - name: Build BEAST | |
| run: ant dist | |
| - name: Check BEAGLE | |
| run: | | |
| ls ${BEAGLE_LIB} | |
| java -jar -Djava.library.path=${BEAGLE_LIB} build/dist/beast.jar -beagle_info | |
| - name: Set up test matrices | |
| id: set-matrices | |
| run: | | |
| echo "xml-matrix=$(ls tests/TestXML/*.xml | jq -R -s -c 'split("\n")[:-1]')" >> $GITHUB_OUTPUT | |
| echo "xml-load-state-matrix=$(ls tests/TestXMLwithLoadState/*.xml | jq -R -s -c 'split("\n")[:-1]')" >> $GITHUB_OUTPUT | |
| outputs: | |
| xml-matrix: ${{ steps.set-matrices.outputs.xml-matrix }} | |
| xml-load-state-matrix: ${{ steps.set-matrices.outputs.xml-load-state-matrix }} | |
| test-xml: | |
| needs: build | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| file: ${{fromJson(needs.build.outputs.xml-matrix)}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ env.BEAGLE_DIR }} | |
| build/dist | |
| key: beagle-beast-${{ hashFiles('**/build_beagle.sh', '**/build.xml') }} | |
| restore-keys: | | |
| beagle-beast | |
| - name: Rebuild project | |
| run: ant dist | |
| - name: Run test for ${{ matrix.file }} | |
| run: java -Djava.library.path=${BEAGLE_LIB} -jar build/dist/beast.jar -fail_threads -seed 666 -overwrite ${{ matrix.file }} | |
| test-xml-load-state: | |
| needs: build | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| file: ${{fromJson(needs.build.outputs.xml-load-state-matrix)}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ env.BEAGLE_DIR }} | |
| build/dist | |
| key: beagle-beast-${{ hashFiles('**/build_beagle.sh', '**/build.xml') }} | |
| restore-keys: | | |
| beagle-beast | |
| - name: Rebuild project | |
| run: ant dist | |
| - name: Run test with load state for ${{ matrix.file }} | |
| run: | | |
| checkpoint=tests/TestXMLwithLoadState/$(basename ${{ matrix.file }} .xml).chkpt | |
| java -Djava.library.path=${BEAGLE_LIB} -jar build/dist/beast.jar -fail_threads -seed 666 -load_state $checkpoint -overwrite ${{ matrix.file }} | |
| test-junit: | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-java@v4 | |
| with: | |
| java-version: "8" | |
| distribution: "adopt" | |
| - uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ env.BEAGLE_DIR }} | |
| build/dist | |
| key: beagle-beast-${{ hashFiles('**/build_beagle.sh', '**/build.xml') }} | |
| restore-keys: | | |
| beagle-beast | |
| - name: Rebuild project | |
| run: ant dist | |
| - name: Run JUnit tests | |
| run: | | |
| ant -Djava.library.path=${BEAGLE_LIB} junit |