feat: remove buildSrc/ and make Gradle build robust

.github/workflows/test.yml

@@ -26,17 +26,16 @@ jobs:
  - name: Compile
  run: |
  make clean
- make check
  make compile
  make compile-with-nextflow
 
+ - name: Test
+ run: make test
+ env:
+ GRADLE_OPTS: '-Dorg.gradle.daemon=false'
+
  - name: Build
  run: make build
 
  - name: Install
  run: make install-local
-
- - name: Test
- run: make test
- env:
- GRADLE_OPTS: '-Dorg.gradle.daemon=false'

Makefile

@@ -1,8 +1,7 @@
 version ?= $(shell grep 'Plugin-Version' plugins/nf-dotenv/src/resources/META-INF/MANIFEST.MF | awk '{ print $$2 }')
 
-.PHONY: check
-check:
- ./gradlew check --warning-mode all
+.PHONY: all
+all: compile build
 
 .PHONY: clean
 clean:

README.md

@@ -1,7 +1,7 @@
 # nf-dotenv
 
 [![CI](https:/fulcrumgenomics/nf-dotenv/actions/workflows/test.yml/badge.svg?branch=main)](https:/fulcrumgenomics/nf-dotenv/actions/workflows/test.yml?query=branch%3Amain)
-[![Nextflow](https://img.shields.io/badge/Nextflow%20DSL2-%E2%89%A522.10.0-blue.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/Nextflow%20DSL2-%E2%89%A522.10.2-blue.svg)](https://www.nextflow.io/)
 [![Java Versions](https://img.shields.io/badge/java-8_|_11_|_17_|_21-blue)](https:/fulcrumgenomics/nf-dotenv)
 
 Automatically source [dotenv](https://hexdocs.pm/dotenvy/dotenv-file-format.html) files into your Nextflow scope.
@@ -119,10 +119,9 @@ samtools 1.16
 
 ## Testing the Plugin Locally
 
-Execute the following to check, compile, and run unit tests for the plugin:
+Execute the following to compile and run unit tests for the plugin:
 
 ```
-make check
 make compile
 make test
 ```

gradle.properties

@@ -0,0 +1,2 @@
+groovyVersion = 3.0.14
+nextflowVersion = 22.10.2

plugins/build.gradle

@@ -12,7 +12,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
 import io.nextflow.gradle.tasks.GithubRepositoryPublisher
 import io.nextflow.gradle.tasks.GithubUploader
 import org.apache.commons.codec.digest.DigestUtils
@@ -22,6 +21,7 @@ import java.time.format.DateTimeFormatter
 
 plugins {
  id "java"
+ id "groovy"
  id "io.nextflow.nf-build-plugin" version "1.0.1"
 }
 
@@ -32,22 +32,25 @@ ext.github_commit_email = project.findProperty('github_commit_email') ?: System.
 
 jar.enabled = false
 
+/** Generate a sha512 hash of the given file. */
 static String computeSha512(File file) {
- if (!file.exists())
+ if (!file.exists()) {
  throw new GradleException("Missing file: $file -- cannot compute SHA-512")
+ }
  return DigestUtils.sha512Hex(file.bytes)
 }
 
+/** The time is now! */
 String now() {
  "${OffsetDateTime.now().format(DateTimeFormatter.ISO_DATE_TIME)}"
 }
 
+/** All the plugins we intend to compile, test, build, install, and publish. */
 List<String> allPlugins() {
- def plugins = []
- new File(rootProject.rootDir, 'plugins') .eachDir { if(it.name.startsWith('nf-')) plugins.add(it.name) }
- return plugins
+ return [new File(rootProject.rootDir, 'plugins/nf-dotenv')] as List<String>
 }
 
+/** Get the metadata for this plugin from the MANIFEST file. */
 static String metaFromManifest(String meta, File file) {
  def str = file.text
  def regex = ~/(?m)^$meta:\s*([\w-\.<>=]+)$/
@@ -71,7 +74,7 @@ subprojects {
  mavenCentral()
  }
 
- version = metaFromManifest('Plugin-Version',file('src/resources/META-INF/MANIFEST.MF'))
+ version = metaFromManifest('Plugin-Version', file('src/resources/META-INF/MANIFEST.MF'))
 
  tasks.withType(Jar).configureEach {
  duplicatesStrategy = DuplicatesStrategy.INCLUDE
@@ -97,7 +100,7 @@ subprojects {
  "requires": "${metaFromManifest('Plugin-Requires', file('src/resources/META-INF/MANIFEST.MF'))}",
  "sha512sum": "${computeSha512(zip)}"
  }
- """.stripIndent()
+ """.stripTrailing().stripIndent()
  file("$buildDir/tmp/makeZip").deleteDir()
  }
  outputs.file("$buildDir/libs/${project.name}-${project.version}.zip")
@@ -107,18 +110,19 @@ subprojects {
  tasks.register('copyPluginLibs', Sync) {
  from configurations.runtimeClasspath
  into 'build/target/libs'
+ duplicatesStrategy 'exclude'
  }
 
  /** Copy the plugin into the project root build/plugins directory. */
  tasks.register('copyPluginZip', Copy) {
- dependsOn project.tasks.findByName('makeZip')
+ dependsOn makeZip
  from makeZip
  into "$rootProject.buildDir/plugins"
  outputs.file("$rootProject.buildDir/plugins/${project.name}-${project.version}.zip")
  doLast {
  ant.unzip(
-  src: "$rootProject.buildDir/plugins/${project.name}-${project.version}.zip",
-  dest: "$rootProject.buildDir/plugins/${project.name}-${project.version}"
+ src: "$rootProject.buildDir/plugins/${project.name}-${project.version}.zip",
+ dest: "$rootProject.buildDir/plugins/${project.name}-${project.version}"
  )
  }
  }
@@ -129,8 +133,10 @@ subprojects {
  tasks.register('uploadPlugin', GithubUploader) {
  dependsOn makeZip
  assets = providers.provider {
- ["$buildDir/libs/${project.name}-${project.version}.zip",
- "$buildDir/libs/${project.name}-${project.version}-meta.json"]
+ [
+ "$buildDir/libs/${project.name}-${project.version}.zip",
+ "$buildDir/libs/${project.name}-${project.version}-meta.json"
+ ]
  }
  release = providers.provider { project.version }
  repo = providers.provider { project.name }
@@ -139,19 +145,6 @@ subprojects {
  authToken = github_access_token
  skipExisting = true
  }
-
- jar {
- from sourceSets.main.allSource
- doLast {
- file("$buildDir/tmp/jar").deleteDir()
- }
- }
-
- tasks.withType(GenerateModuleMetadata).configureEach {
- enabled = false
- }
-
- task upload(dependsOn: [uploadPlugin] ) { }
 }
 
 /** Upload all plugins to the corresponding GitHub repos. */

plugins/nf-dotenv/build.gradle

@@ -12,15 +12,20 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
 plugins {
- // TODO: Figure out how to build all this for cross-Java support without needing ./buildSrc!
- id 'io.nextflow.groovy-library-conventions'
+ id 'groovy'
  id 'idea'
 }
 
 group = 'io.nextflow'
 
+java {
+ toolchain {
+ languageVersion = JavaLanguageVersion.of(11)
+ }
+}
+
+
 idea {
  module.inheritOutputDirs = true
 }
@@ -46,33 +51,31 @@ sourceSets {
  test.resources.srcDirs = ['src/testResources']
 }
 
-ext {
- nextflowVersion = '23.04.0'
-}
-
 dependencies {
  // This dependency is exported to consumers, that is to say, it is found on their compile classpath.
  compileOnly "io.nextflow:nextflow:$nextflowVersion"
- compileOnly 'org.slf4j:slf4j-api:2.0.9'
- compileOnly 'org.pf4j:pf4j:3.10.0'
+ compileOnly 'org.slf4j:slf4j-api:1.7.10'
+ compileOnly 'org.pf4j:pf4j:3.4.1'
 
  // Plugin dependencies.
  implementation 'io.github.cdimascio:dotenv-java:3.0.0'
 
  // Test configuration.
- testImplementation "org.codehaus.groovy:groovy:3.0.19"
- testImplementation "org.codehaus.groovy:groovy-nio:3.0.19"
  testImplementation "io.nextflow:nextflow:$nextflowVersion"
- testImplementation ("org.codehaus.groovy:groovy-test:3.0.19") { exclude group: 'org.codehaus.groovy' }
+ testImplementation "org.codehaus.groovy:groovy:$groovyVersion"
+ testImplementation "org.codehaus.groovy:groovy-nio:$groovyVersion"
+ testImplementation ("org.codehaus.groovy:groovy-test:$groovyVersion") { exclude group: 'org.codehaus.groovy' }
  testImplementation ("cglib:cglib-nodep:3.3.0")
- testImplementation ("org.objenesis:objenesis:3.3")
- testImplementation ("org.spockframework:spock-core:2.3-groovy-3.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
- testImplementation ('org.spockframework:spock-junit4:2.3-groovy-3.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
- testImplementation ('com.google.jimfs:jimfs:1.3.0')
+ testImplementation ("org.objenesis:objenesis:3.1")
+ testImplementation ("org.spockframework:spock-core:2.0-M3-groovy-3.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
+ testImplementation ('org.spockframework:spock-junit4:2.0-M3-groovy-3.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
 
  testImplementation(testFixtures("io.nextflow:nextflow:$nextflowVersion"))
  testImplementation(testFixtures("io.nextflow:nf-commons:$nextflowVersion"))
 
+ testImplementation("org.junit.jupiter:junit-jupiter:5.9.2")
+ testRuntimeOnly("org.junit.platform:junit-platform-launcher")
+
  // 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") }