Update build convention and make file

Signed-off-by: Paolo Di Tommaso <[email protected]>

Author: pditommaso

Makefile

@@ -1,7 +1,71 @@
+config ?= compileClasspath
+
+ifdef module 
+mm = :${module}:
+else 
+mm = 
+endif 
+
+clean:
+	rm -rf .nextflow*
+	rm -rf work
+	rm -rf build
+	rm -rf plugins/*/build
+	./gradlew clean
+
+compile:
+	./gradlew compileGroovy
+	@echo "DONE `date`"
+
+
+check:
+	./gradlew check
+
+
 #
 # Show dependencies try `make deps config=runtime`, `make deps config=google`
 #
-deps: FORCE
-	./gradlew -q :plugins:nf-sqldb:dependencies --configuration runtimeClasspath
+deps:
+	./gradlew -q ${mm}dependencies --configuration ${config}
+
+deps-all:
+	./gradlew -q dependencyInsight --configuration ${config} --dependency ${module}
+
+#
+# Refresh SNAPSHOTs dependencies
+#
+refresh:
+	./gradlew --refresh-dependencies 
+
+#
+# Run all tests or selected ones
+#
+test:
+ifndef class
+	./gradlew ${mm}test
+else
+	./gradlew ${mm}test --tests ${class}
+endif
+
+assemble:
+	./gradlew assemble
+
+#
+# generate build zips under build/plugins
+# you can install the plugin copying manually these files to $HOME/.nextflow/plugins
+#
+buildPlugins:
+	./gradlew copyPluginZip
+
+#
+# Upload JAR artifacts to Maven Central
+#
+upload:
+	./gradlew upload
+
+
+upload-plugins:
+	./gradlew plugins:upload
 
-FORCE: ;
+publish-index:
+	./gradlew plugins:publishIndex

README.md

@@ -6,7 +6,6 @@ The following databases are currently supported:
 
 * [AWS Athena](https://aws.amazon.com/athena/) (Setup guide [here](docs/aws-athena.md))
 * [DuckDB](https://duckdb.org/)
-* [Google BigQuery](https://cloud.google.com/bigquery) (Setup guide [here](docs/google-bigquery.md))
 * [H2](https://www.h2database.com)
 * [MySQL](https://www.mysql.com/)
 * [MariaDB](https://mariadb.org/)
@@ -25,13 +24,6 @@ plugins {
 }
 ```
 
-Support for BigQuery is provided in a separate plugin:
-
-```groovy
-plugins {
-    id 'nf-bigquery'
-}
-```
 
 ## Configuration
 

buildSrc/src/main/groovy/io.nextflow.groovy-common-conventions.gradle

@@ -14,17 +14,17 @@ repositories {
 
 java {
     toolchain {
-        languageVersion = JavaLanguageVersion.of(19)
+        languageVersion = JavaLanguageVersion.of(21)
     }
 }
 
 compileJava {
-    options.release.set(11)
+    options.release.set(17)
 }
 
 tasks.withType(GroovyCompile) {
-    sourceCompatibility = '11'
-    targetCompatibility = '11'
+    sourceCompatibility = 17
+    targetCompatibility = 17
 }
 
 tasks.withType(Test) {

plugins/nf-sqldb/src/main/nextflow/sql/SqlPlugin.groovy

@@ -17,6 +17,7 @@
 
 package nextflow.sql
 
+import groovy.transform.CompileStatic
 import nextflow.plugin.BasePlugin
 import org.pf4j.PluginWrapper
 
@@ -25,6 +26,7 @@ import org.pf4j.PluginWrapper
  *
  * @author Paolo Di Tommaso <[email protected]>
  */
+@CompileStatic
 class SqlPlugin extends BasePlugin {
 
     SqlPlugin(PluginWrapper wrapper) {

plugins/nf-sqldb/src/resources/META-INF/MANIFEST.MF

@@ -3,4 +3,4 @@ Plugin-Class: nextflow.sql.SqlPlugin
 Plugin-Id: nf-sqldb
 Plugin-Provider: Seqera Labs
 Plugin-Version: 0.6.0
-Plugin-Requires: >=24.01.0-edge
+Plugin-Requires: >=24.04.0

plugins/nf-sqldb/src/test/nextflow/sql/SqlDslTest.groovy

@@ -32,7 +32,7 @@ import spock.lang.Requires
 import spock.lang.Shared
 import spock.lang.Timeout
 import test.Dsl2Spec
-import test.MockScriptRunner
+import test.helpers.MockScriptRunner
 
 import java.nio.file.Path
 

plugins/nf-sqldb/src/test/test/MockHelpers.groovy renamed to plugins/nf-sqldb/src/test/test/helpers/MockHelpers.groovy

@@ -15,7 +15,7 @@
  *
  */
 
-package test
+package test.helpers
 
 import java.nio.file.Paths
 
@@ -147,13 +147,13 @@ class MockMonitor implements TaskMonitor {
      *
      * @param handler A not null {@code TaskHandler} instance
      */
-    boolean evict(TaskHandler handler) { }
+    boolean evict(TaskHandler handler) { return null }
 
     /**
      * Start the monitoring activity for the queued tasks
      * @return The instance itself, useful to chain methods invocation
      */
-    TaskMonitor start() { }
+    TaskMonitor start() { return null }
 
     /**
      * Notify when a task terminates
@@ -190,9 +190,11 @@ class MockTaskHandler extends TaskHandler {
 
     @Override
     boolean checkIfCompleted() {
-        true
+        return true
     }
 
+    protected void killTask() { }
+
     @Override
     void kill() { }
 

plugins/nf-sqldb/src/test/test/TestHelper.groovy renamed to plugins/nf-sqldb/src/test/test/helpers/TestHelper.groovy

@@ -15,7 +15,7 @@
  *
  */
 
-package test
+package test.helpers
 import java.nio.file.Files
 import java.nio.file.Path
 import java.util.zip.GZIPInputStream