make jcc2Fasta.lphy working in lphybeat LinguaPhylo/linguaPhylo#437 #464
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| name: Lphy BEAST 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: LPhyBeast | |
| # - name: Checkout Lphy | |
| # uses: actions/checkout@v3 | |
| # with: | |
| # repository: LinguaPhylo/linguaPhylo | |
| # path: linguaPhylo | |
| - name: Set up JDK 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: 17 | |
| distribution: 'adopt' | |
| cache: 'gradle' | |
| - name: Setup Gradle | |
| uses: gradle/gradle-build-action@v2 | |
| with: | |
| gradle-version: 7.6 | |
| # pwd /home/runner/work/LPhyBeast/LPhyBeast | |
| # PWD=$(pwd) | |
| # package path /home/runner/.beast/2.7 | |
| - name: Set environmental variables | |
| run: | | |
| mkdir /home/runner/.beast | |
| rm -rf /home/runner/.beast/2.7 | |
| mkdir /home/runner/.beast/2.7 | |
| ls LPhyBeast | |
| find . -name "lib" | |
| echo "BEAST_LIB=LPhyBeast/lphybeast/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 | |
| # https://github.com/CompEvol/beast2/issues/1078 | |
| - name: Install beast2 base | |
| run: | | |
| find $REPO_DIR -type d | |
| 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 | |
| #./linguaPhylo/lphy/lib | |
| #./LPhyBeast/lphybeast/lib | |
| - name: Check all packages | |
| run: | | |
| ls $REPO_DIR/*/lib | |
| - name: Run unit tests | |
| # change working dir, so gradle will work | |
| working-directory: ./LPhyBeast | |
| # only available in lphy at the moment | |
| # temp disable test because of github issue | |
| run: ./gradlew build | |
| - name: Publish unit test results | |
| uses: EnricoMi/publish-unit-test-result-action@v2 | |
| if: always() | |
| with: | |
| files: ./LPhyBeast/*/build/test-results/**/*.xml |