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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,41 +1,127 @@ | ||
| 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 | ||
| env: | ||
| BEAGLE_DIR: beagle-lib | ||
| BEAGLE_LIB: beagle-lib/usr/local/lib | ||
| LD_LIBRARY_PATH: beagle-lib/usr/local/lib | ||
| BEAGLE_BRANCH: v4_release | ||
| 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 }} | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Set up JDK 8 | ||
| uses: actions/setup-java@v2 | ||
| with: | ||
| java-version: '8' | ||
| distribution: 'adopt' | ||
| - name: Setup cmake | ||
| uses: lukka/get-cmake@latest | ||
| # - name: Build BEAGLE | ||
| # - run: git clone -b $BEAGLE_BRANCH --depth 1 https://github.com/beagle-dev/beagle-lib.git $BEAGLE_DIR | ||
| # - run: cd $BEAGLE_DIR | ||
| # - run: mkdir build | ||
| # - run: cd build | ||
| # - run: echo $PWD | ||
| # - run: cmake -DBUILD_CUDA=OFF -DBUILD_OPENCL=OFF .. | ||
| # - run: make DESTDIR=BEAGLE_DIR | ||
| - run: chmod +x ci/build_beagle.sh | ||
| - run: ci/build_beagle.sh | ||
| - run: ant dist | ||
| - run: ls ${BEAGLE_LIB} | ||
| - run: java -jar -Djava.library.path=${BEAGLE_LIB} build/dist/beast.jar -beagle_info | ||
| - run: chmod +x ci/test.sh | ||
| - run: ci/test.sh | ||
| # - run: chmod +x ci/test_with_load_state.sh | ||
| # - run: ci/test_with_load_state.sh | ||
| - run: ant -Djava.library.path=${BEAGLE_LIB} junit | ||
| 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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -13,7 +13,7 @@ out/ | |
| *.tree | ||
| *.xml | ||
| !examples/**/*.xml | ||
| !ci/**/*.xml | ||
| !tests/**/*.xml | ||
|
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| zig_zag | ||
| src/revision.txt | ||
|
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