Remove undeclared dependencies from Gradle build

[pjones]

While creating a package for NixOS/nixpkgs I discovered a few undeclared dependencies. Builds using Nix happen in an isolated sandbox with no network connection. Without these dependencies the build would fail.

It's not clear to me why builds succeed for others. Perhaps these dependencies are cached or maybe just downloaded as needed. Either way I thought I'd open a PR.

[bentsherman]

Thanks for digging into this — your diagnosis is right, and I traced where those five modules actually come from.

Nothing in the project requests them. They are pulled in by Gradle's Groovy plugin: GroovyRuntime.inferGroovyClasspath() sees org.apache.groovy:groovy on the compile classpath and assembles a detached configuration with the matching groovy-* companion modules for the compiler itself. Detached configurations belong to no project configuration, which is why ./gradlew dependencies shows no trace of them while a clean build downloads them anyway — presumably also why the Nix prefetch step, which resolves the declared configurations, never records them.

With a scratch GRADLE_USER_HOME so every fetch is logged, on main:

compileJava   -> groovy-json, groovy-yaml                                  (declared deps)
compileGroovy -> groovy-ant, groovy-astbuilder, groovy-datetime,
                 groovy-dateutil, groovy-groovydoc, groovy-docgenerator,
                 groovy-nio, groovy-templates, groovy-xml

compileGroovy fires because of src/test/groovy (Spock) and src/spec/groovy; src/main is pure Java.

The catch with declaring them as implementation is that they land on runtimeClasspath and so go into the shadow JAR. groovy-ant drags in Ant 1.10.15 and groovy-groovydoc drags in javaparser + qdox:

	size	entries
main	15,185,152 (14.5 MiB)	9,134
this PR	19,636,150 (18.7 MiB)	11,482
delta	+4,450,998 (+29%)	+2,348

Since the modules are only needed by the Groovy compiler, the build can just say so and stop inferring. I pushed a commit to this branch that drops the five implementation lines and pins the compiler classpath instead:

configurations {
  groovyCompiler
  nextflowRuntime
}

tasks.withType(GroovyCompile).configureEach {
  groovyClasspath = configurations.groovyCompiler
}

dependencies {
  groovyCompiler 'org.apache.groovy:groovy:4.0.31'
  ...
}

Verified in a clean GRADLE_USER_HOME running shadowJar test: groovy-ant, -astbuilder, -datetime, -dateutil, -groovydoc, -docgenerator, javaparser and qdox are no longer fetched at all, tests pass, and the JAR stays at 15,185,152 bytes. What still gets fetched is genuine: groovy, groovy-json, groovy-nio, groovy-templates, groovy-xml, groovy-yaml, all real dependencies of nf-lang/nextflow or declared runtimeOnly. Ant still appears in the log, but only from plugins.gradle.org as a dependency of the shadow plugin itself, which is equally true on main.

Could you confirm this builds in the Nix sandbox? Nothing undeclared should be requested now, so the packaging shouldn't need the extra dependencies at all.

[bentsherman]

@pjones can you verify that my edits still work in your NixOS environment?

[pjones]

@bentsherman Yes, your changes work in Nix build.

Thank you!