diff --git a/.github/workflows/ci-pharmcat.yml b/.github/workflows/ci-pharmcat.yml index 59befedf1..469969bf3 100644 --- a/.github/workflows/ci-pharmcat.yml +++ b/.github/workflows/ci-pharmcat.yml @@ -37,7 +37,14 @@ jobs: cache: 'gradle' - name: Run PharmCAT tests - run: ./gradlew test --no-daemon + run: ./gradlew test --no-daemon --info --scan + + - uses: actions/upload-artifact@v4 + if: failure() + with: + name: ci-pharmcat-tests-jdk17 + path: build/reports/tests/test/index.html + if-no-files-found: ignore - uses: actions/upload-artifact@v4 if: failure() @@ -47,7 +54,14 @@ jobs: if-no-files-found: ignore - name: Run PharmCAT tests on Java 21 - run: ./gradlew testOnJava21 --no-daemon + run: ./gradlew testOnJava21 --no-daemon --info --scan + + - uses: actions/upload-artifact@v4 + if: failure() + with: + name: ci-pharmcat-tests-jdk21 + path: build/reports/tests/test/index.html + if-no-files-found: ignore - uses: actions/upload-artifact@v4 if: failure() diff --git a/build.gradle b/build.gradle index 02c335cc8..77512a871 100644 --- a/build.gradle +++ b/build.gradle @@ -25,12 +25,8 @@ def getVersionName() { } -sourceCompatibility = 17 -targetCompatibility = 17 project.group = 'org.pharmgkb' project.version = getVersionName() -archivesBaseName = "pharmcat" -mainClassName = "org.pharmgkb.pharmcat.PharmCAT" ext { moduleName = 'org.pharmgkb.pharmcat' @@ -39,6 +35,8 @@ ext { scm = 'scm:git@github.com:PharmGKB/PharmCAT.git' orgName = 'PharmGKB' orgUrl = 'https://www.pharmgkb.org' + mainClassName = "org.pharmgkb.pharmcat.PharmCAT" + archiveBaseName = "pharmcat" } def dataDir = System.env.PHARMCAT_DATA_DIR == null ? 'build' : System.env.PHARMCAT_DATA_DIR @@ -87,6 +85,8 @@ clean.dependsOn(tasks.cleanTestOutput) test.dependsOn(tasks.cleanTestOutput) java { + sourceCompatibility = JavaVersion.VERSION_17 + targetCompatibility = JavaVersion.VERSION_17 toolchain { languageVersion = JavaLanguageVersion.of(17) } @@ -96,7 +96,13 @@ tasks.withType(JavaCompile).configureEach { options.encoding = 'UTF-8' } +application { + mainClass = project.ext.mainClassName +} + tasks.withType(Test).configureEach { + minHeapSize = "512m" + maxHeapSize = "1024m" useJUnitPlatform() testLogging { // set options for log level LIFECYCLE @@ -131,8 +137,9 @@ jar { attributes 'Automatic-Module-Name': project.ext.moduleName attributes 'Implementation-Title': project.name attributes 'Implementation-Version': project.version - attributes 'Main-Class': mainClassName + attributes 'Main-Class': project.ext.mainClassName } + archiveBaseName = project.ext.archiveBaseName } shadowJar { @@ -140,6 +147,7 @@ shadowJar { attributes 'Implementation-Title': project.name attributes 'Implementation-Version': project.version } + archiveBaseName = project.ext.archiveBaseName } tasks.withType(Javadoc).configureEach { diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar index c1962a79e..7f93135c4 100644 Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 744c64d12..1af9e0930 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,6 +1,7 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip networkTimeout=10000 +validateDistributionUrl=true zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew index aeb74cbb4..1aa94a426 100755 --- a/gradlew +++ b/gradlew @@ -83,7 +83,8 @@ done # This is normally unused # shellcheck disable=SC2034 APP_BASE_NAME=${0##*/} -APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit +# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036) +APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit # Use the maximum available, or set MAX_FD != -1 to use that value. MAX_FD=maximum @@ -130,10 +131,13 @@ location of your Java installation." fi else JAVACMD=java - which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. + if ! command -v java >/dev/null 2>&1 + then + die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. Please set the JAVA_HOME variable in your environment to match the location of your Java installation." + fi fi # Increase the maximum file descriptors if we can. @@ -141,7 +145,7 @@ if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then case $MAX_FD in #( max*) # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked. - # shellcheck disable=SC3045 + # shellcheck disable=SC2039,SC3045 MAX_FD=$( ulimit -H -n ) || warn "Could not query maximum file descriptor limit" esac @@ -149,7 +153,7 @@ if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then '' | soft) :;; #( *) # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked. - # shellcheck disable=SC3045 + # shellcheck disable=SC2039,SC3045 ulimit -n "$MAX_FD" || warn "Could not set maximum file descriptor limit to $MAX_FD" esac @@ -198,11 +202,11 @@ fi # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' -# Collect all arguments for the java command; -# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of -# shell script including quotes and variable substitutions, so put them in -# double quotes to make sure that they get re-expanded; and -# * put everything else in single quotes, so that it's not re-expanded. +# Collect all arguments for the java command: +# * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments, +# and any embedded shellness will be escaped. +# * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be +# treated as '${Hostname}' itself on the command line. set -- \ "-Dorg.gradle.appname=$APP_BASE_NAME" \ diff --git a/settings.gradle b/settings.gradle index 522e08e66..fc123e9f6 100644 --- a/settings.gradle +++ b/settings.gradle @@ -1 +1,15 @@ +plugins { + id("com.gradle.enterprise") version("3.16.1") +} + rootProject.name = 'PharmCAT' + +gradleEnterprise { + if (System.getenv("CI") != null) { + buildScan { + publishAlways() + termsOfServiceUrl = "https://gradle.com/terms-of-service" + termsOfServiceAgree = "yes" + } + } +}