Address reviewer feedback and simplify build configuration

- Remove unnecessary sourceSets configuration per @bentsherman feedback
- Remove explicit test dependencies (handled by plugin)
- Remove SLF4J and runtime classpath exclusions
- Simplify settings.gradle (remove pluginManagement block)
- Keep only essential database dependencies and Athena tasks
- Update to latest Nextflow Gradle plugin v1.0.0-beta.6
- Maintain full functionality while reducing complexity

All tests pass and plugin builds/installs successfully.

Co-authored-by: Ben Sherman <[email protected]>

Author: edmundmiller

build.gradle

@@ -30,7 +30,7 @@ repositories {
 }
 
 dependencies {
-    // Latest database dependencies from master branch
+    // Database dependencies
     api("org.apache.groovy:groovy-sql:4.0.26") { transitive = false }
     api 'com.h2database:h2:1.4.200'
     api 'mysql:mysql-connector-java:8.0.33'
@@ -45,21 +45,6 @@ dependencies {
 
     //NOTE: Had to remove the slf4j jar due to a conflict
     implementation fileTree(dir: 'src/dist/lib/libs', include: '*.jar')
-
-    // test configuration
-    testImplementation "org.apache.groovy:groovy:4.0.26"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.26"
-    testImplementation ("org.apache.groovy:groovy-test:4.0.26") { exclude group: 'org.apache.groovy' }
-    testImplementation ("cglib:cglib-nodep:3.3.0")
-    testImplementation ("org.objenesis:objenesis:3.1")
-    testImplementation ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation ('com.google.jimfs:jimfs:1.1')
-
-    // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
-    modules {
-        module("commons-logging:commons-logging") { replacedBy("org.slf4j:jcl-over-slf4j") }
-    }
 }
 
 nextflowPlugin {
@@ -107,6 +92,7 @@ task copyAthenDep(dependsOn: unzipAthenDep, type: Copy) {
 // Hook into the new plugin's build process
 compileGroovy.dependsOn('copyAthenDep')
 
-test {
-    useJUnitPlatform()
+// Configure the packagePlugin task to handle duplicates
+tasks.named('packagePlugin') {
+    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
 } 

buildSrc/build.gradle

@@ -1,32 +1,2 @@
-// For the Nextflow plugin Gradle plugin
-pluginManagement {
-    repositories {
-        mavenLocal()
-        gradlePluginPortal()
-    }
-}
-
-/*
- * Copyright 2021, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-plugins {
-    // required to download the toolchain (jdk) from a remote repository
-    // https://github.com/gradle/foojay-toolchains
-    // https://docs.gradle.org/current/userguide/toolchains.html#sub:download_repositories
-    id("org.gradle.toolchains.foojay-resolver-convention") version "0.7.0"
-}
-
 rootProject.name = 'nf-sqldb'