beast logEvery is int #9 #55
This file contains 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: 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-2.7.5.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 |