beast logEvery is int #9 #55
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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-2.7.5.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 |