update to QuPath 0.6.*

.github/workflows/build_jar.yml

@@ -10,15 +10,15 @@
      runs-on: ubuntu-latest
      steps:
      - uses: actions/checkout@v2
-     - name: Set up JDK 11
+     - name: Set up JDK 21
        uses: actions/setup-java@v2
        with:
-         java-version: '11'
+         java-version: '21'
          distribution: 'adopt-hotspot'
      - name: Grant execute permission for gradlew
        run: chmod +x gradlew
      - name: Build with Gradle
-       run: ./gradlew build -P toolchain=11
+       run: ./gradlew build -P toolchain=21
      - uses: actions/upload-artifact@v2
        with:
          name: jar

.github/workflows/gradle.yml

@@ -10,12 +10,12 @@
      runs-on: ubuntu-latest
      steps:
      - uses: actions/checkout@v2
-     - name: Set up JDK 11
+     - name: Set up JDK 21
        uses: actions/setup-java@v2
        with:
-         java-version: '11'
+         java-version: '21'
          distribution: 'adopt-hotspot'
      - name: Grant execute permission for gradlew
        run: chmod +x gradlew
      - name: Build with Gradle
-       run: ./gradlew build -P toolchain=11
+       run: ./gradlew build -P toolchain=21

.github/workflows/publish-release.yml

@@ -14,12 +14,12 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-java@v2
         with:
-          java-version: '11'
+          java-version: '21'
           distribution: 'adopt-hotspot'
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
       - name: Publish package
-        run: ./gradlew publish -P toolchain=11 -P release=true
+        run: ./gradlew publish -P toolchain=21 -P release=true
         env:
           MAVEN_USER: ${{ secrets.MAVEN_USER }}
           MAVEN_PASS: ${{ secrets.MAVEN_PASS }}

.github/workflows/publish-snapshot.yml

@@ -14,12 +14,12 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-java@v2
         with:
-          java-version: '11'
+          java-version: '21'
           distribution: 'adopt-hotspot'
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
       - name: Publish package
-        run: ./gradlew publish -P toolchain=11
+        run: ./gradlew publish -P toolchain=21
         env:
           MAVEN_USER: ${{ secrets.MAVEN_USER }}
           MAVEN_PASS: ${{ secrets.MAVEN_PASS }}

build.gradle.kts

@@ -0,0 +1,60 @@
+plugins {
+    // To optionally create a shadow/fat jar that bundle up any non-core dependencies
+    id("com.gradleup.shadow") version "8.3.5"
+    // QuPath Gradle extension convention plugin
+    id("qupath-conventions")
+    `maven-publish`
+}
+
+qupathExtension {
+    name = "qupath-extension-abba"
+    group = "ch.epfl.biop"
+    version = "0.4.0-SNAPSHOT"
+    description = "QuPath extension to use Aligning Big Brain and Atlases"
+    automaticModule = "qupath.ext.biop.abba"
+}
+
+dependencies {
+    // Main dependencies for most QuPath extensions
+    shadow(libs.bundles.qupath)
+    shadow(libs.bundles.logging)
+    shadow(libs.qupath.fxtras)
+
+    implementation("commons-io:commons-io:2.11.0")
+    implementation("net.imglib2:imglib2-realtransform:4.0.3")
+    implementation("qupath.ext.warpy:qupath-extension-warpy:0.3.1")
+    // implementation("qupath.ext.warpy:qupath-extension-warpy:0.4.0") // supports QP 0.6.*
+}
+
+
+
+publishing {
+    repositories {
+        maven {
+            name = "scijava"
+            //credentials(PasswordCredentials::class)
+            url = if (version.toString().endsWith("SNAPSHOT")) {
+                uri("https://maven.scijava.org/content/repositories/snapshots")
+            } else {
+                uri("https://maven.scijava.org/content/repositories/releases")
+            }
+            credentials {
+                username = System.getenv("MAVEN_USER")
+                password = System.getenv("MAVEN_PASS")
+            }
+        }
+    }
+
+    publications {
+        create<MavenPublication>("mavenJava") {
+            pom {
+                licenses {
+                    license {
+                        name = "GNU General Public License, Version 3"
+                        url = "https://www.gnu.org/licenses/gpl-3.0.txt"
+                    }
+                }
+            }
+        }
+    }
+}

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.12-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

gradlew

@@ -15,6 +15,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+# SPDX-License-Identifier: Apache-2.0
+#
 
 ##############################################################################
 #
@@ -55,7 +57,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -84,7 +86,8 @@ done
 # shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
 # Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
-APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
+APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s
+' "$PWD" ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -145,15 +148,15 @@ 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
@@ -202,11 +205,11 @@ 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" \