chore: upgrade gradle, increase memory for tests, improve logging if …

…tests fail

.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()

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:[email protected]: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
@@ -131,15 +137,17 @@ 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 {
   manifest {
     attributes 'Implementation-Title': project.name
     attributes 'Implementation-Version': project.version
   }
+  archiveBaseName = project.ext.archiveBaseName
 }
 
 tasks.withType(Javadoc).configureEach {

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

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
@@ -130,26 +131,29 @@ 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.
 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
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
         # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045
+        # shellcheck disable=SC2039,SC3045
         ulimit -n "$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" \

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"
+    }
+  }
+}