done #10 #63
Workflow file for this run
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| name: LPhy BEAST Ext tests | |
| on: [ push, pull_request, workflow_dispatch ] | |
| jobs: | |
| test-lphybeast: | |
| runs-on: ubuntu-latest | |
| steps: | |
| # must under LPhyBeast folder, otherwise build will fail | |
| - name: Checkout main | |
| uses: actions/checkout@v3 | |
| with: | |
| path: LPhyBeastExt | |
| - name: Set up JDK 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: 17 | |
| distribution: 'adopt' | |
| cache: 'gradle' | |
| # pwd /home/runner/work/LPhyBeast/LPhyBeast | |
| # PWD=$(pwd) | |
| # package path /home/runner/.beast/2.7 | |
| - name: Set environmental variables | |
| run: | | |
| mkdir /home/runner/.beast | |
| mkdir /home/runner/.beast/2.7 | |
| ls LPhyBeastExt | |
| find . -name "lib" | |
| echo "BEAST_LIB=LPhyBeastExt/lphybeast-ext/lib" >> $GITHUB_ENV | |
| echo "LAUNCHER=launcher-2.7.6.jar" >> $GITHUB_ENV | |
| echo "REPO_DIR=/home/runner/.beast/2.7" >> $GITHUB_ENV | |
| echo $REPO_DIR | |
| # /home/runner/.beast/2.7 | |
| - name: Install packages | |
| run: | | |
| ls $BEAST_LIB/$LAUNCHER | |
| ls $REPO_DIR | |
| java -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/$LAUNCHER" beast.pkgmgmt.PackageManager -add bdtree | |
| java -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/$LAUNCHER" beast.pkgmgmt.PackageManager -add BEAST_CLASSIC | |
| java -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/$LAUNCHER" beast.pkgmgmt.PackageManager -add BEASTLabs | |
| java -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/$LAUNCHER" beast.pkgmgmt.PackageManager -add FastRelaxedClockLogNormal | |
| java -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/$LAUNCHER" beast.pkgmgmt.PackageManager -add feast | |
| java -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/$LAUNCHER" beast.pkgmgmt.PackageManager -add SSM | |
| java -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/$LAUNCHER" beast.pkgmgmt.PackageManager -add Mascot | |
| java -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/$LAUNCHER" beast.pkgmgmt.PackageManager -add MM | |
| java -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/$LAUNCHER" beast.pkgmgmt.PackageManager -add SA | |
| # https://github.com/CompEvol/beast2/issues/1078 | |
| - name: Install beast2 base | |
| run: | | |
| ls $REPO_DIR | |
| mkdir $REPO_DIR/BEAST.base | |
| cp $BEAST_LIB/BEAST.base.version.xml $REPO_DIR/BEAST.base/version.xml | |
| mkdir $REPO_DIR/BEAST.base/lib | |
| cp $BEAST_LIB/BEAST.base-*.jar $REPO_DIR/BEAST.base/lib | |
| - name: Check file paths | |
| run: | | |
| find . -name "lib" | |
| ls LPhyBeastExt/lphybeast-ext | |
| - name: Check all packages | |
| run: ls $REPO_DIR/*/lib | |
| - name: Install lphybeast | |
| # change working dir, so gradle will work | |
| working-directory: ./LPhyBeastExt | |
| # gradle will download lphybeast from Maven repo database | |
| run: | | |
| ./gradlew build -x test --no-daemon | |
| pwd | |
| ls lphybeast-ext/build | |
| ls lphybeast-ext/build/lphybeast | |
| - name: Run unit tests | |
| # change working dir, so gradle will work | |
| working-directory: ./LPhyBeastExt | |
| # run test | |
| run: ./gradlew test --no-daemon | |
| - name: Publish unit test results | |
| uses: EnricoMi/publish-unit-test-result-action@v2 | |
| if: always() | |
| with: | |
| files: ./LPhyBeastExt/*/build/test-results/**/*.xml |