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]>
Signed-off-by: Edmund Miller <[email protected]>

Author: edmundmiller

README.md

@@ -241,3 +241,4 @@ The `CSVREAD` function provided by the H2 database engine allows you to query an
 Like all dataflow operators in Nextflow, the operators provided by this plugin are executed asynchronously.
 
 In particular, data inserted using the `sqlInsert` operator is _not_ guaranteed to be available to any subsequent queries using the `fromQuery` operator, as it is not possible to make a channel factory operation dependent on some upstream operation.
+

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'