Move CLI into nf-cli module

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

build.gradle

@@ -237,7 +237,7 @@ task compile {
 
 def getRuntimeConfigs() {
     def names = subprojects
-            .findAll { prj -> prj.name in ['nextflow','nf-commons','nf-httpfs','nf-lang'] }
+            .findAll { prj -> prj.name in ['nextflow','nf-cli-v1','nf-commons','nf-httpfs','nf-lang'] }
             .collect { it.name }
 
     FileCollection result = null
@@ -262,8 +262,10 @@ task exportClasspath {
     doLast {
         def home = System.getProperty('user.home')
         def all = getRuntimeConfigs()
-        def libs = all.collect { File file ->  /*println file.canonicalPath.replace(home, '$HOME');*/ file.canonicalPath;  }
-        ['nextflow','nf-commons','nf-httpfs','nf-lang'].each {libs << file("modules/$it/build/libs/${it}-${version}.jar").canonicalPath }
+        def libs = all.collect { File file -> file.canonicalPath }
+        ['nextflow','nf-cli-v1','nf-commons','nf-httpfs','nf-lang'].each {
+            libs << file("modules/$it/build/libs/${it}-${version}.jar").canonicalPath
+        }
         file('.launch.classpath').text = libs.unique().join(':')
     }
 }
@@ -276,7 +278,7 @@ ext.nexusEmail = project.findProperty('nexusEmail')
 // `signing.keyId` property needs to be defined in the `gradle.properties` file
 ext.enableSignArchives = project.findProperty('signing.keyId')
 
-ext.coreProjects = projects( ':nextflow', ':nf-commons', ':nf-httpfs', ':nf-lang' )
+ext.coreProjects = projects( ':nextflow', ':nf-cli-v1', ':nf-commons', ':nf-httpfs', ':nf-lang' )
 
 configure(coreProjects) {
     group = 'io.nextflow'

modules/nextflow/build.gradle

@@ -1,8 +1,19 @@
-plugins {
-    id "com.gradleup.shadow" version "8.3.5"
-}
+/*
+ * Copyright 2013-2025, 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.
+ */
 apply plugin: 'groovy'
-apply plugin: 'application'
 
 sourceSets {
     main.java.srcDirs = []
@@ -13,10 +24,6 @@ sourceSets {
     test.resources.srcDirs = ['src/test/resources']
 }
 
-compileGroovy {
-    options.compilerArgs = ['-XDignore.symbol.file']
-}
-
 dependencies {
     api(project(':nf-commons'))
     api(project(':nf-httpfs'))
@@ -37,14 +44,13 @@ dependencies {
     api "commons-lang:commons-lang:2.6"
     api "commons-codec:commons-codec:1.15"
     api "commons-io:commons-io:2.15.1"
-    api "com.beust:jcommander:1.35"
     api("com.esotericsoftware.kryo:kryo:2.24.0") { exclude group: 'com.esotericsoftware.minlog', module: 'minlog' }
-    api('org.iq80.leveldb:leveldb:0.12')
-    api('org.eclipse.jgit:org.eclipse.jgit:7.1.0.202411261347-r')
-    api ('javax.activation:activation:1.1.1')
-    api ('javax.mail:mail:1.4.7')
-    api ('org.yaml:snakeyaml:2.2')
-    api ('org.jsoup:jsoup:1.15.4')
+    api 'org.iq80.leveldb:leveldb:0.12'
+    api 'org.eclipse.jgit:org.eclipse.jgit:7.1.0.202411261347-r'
+    api 'javax.activation:activation:1.1.1'
+    api 'javax.mail:mail:1.4.7'
+    api 'org.yaml:snakeyaml:2.2'
+    api 'org.jsoup:jsoup:1.15.4'
     api 'jline:jline:2.9'
     api 'org.pf4j:pf4j:3.12.0'
     api 'dev.failsafe:failsafe:3.1.0'
@@ -59,28 +65,4 @@ dependencies {
     testFixturesApi ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy' }
     testFixturesApi ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy' }
     testFixturesApi 'com.google.jimfs:jimfs:1.2'
-
-}
-
-
-test {
-    minHeapSize = "512m"
-    maxHeapSize = "4096m"
-}
-
-application {
-    mainClass = 'nextflow.cli.Launcher'
-}
-
-run{
-    args( (project.hasProperty("runCmd") ? project.findProperty("runCmd") : "set a cmd to run").split(' ') )
-}
-
-shadowJar {
-    archiveClassifier='one'
-    manifest {
-        attributes 'Main-Class': "$mainClassName"
-    }
-    mergeServiceFiles()
-    mergeGroovyExtensionModules()
 }

modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy

@@ -27,7 +27,6 @@ import groovy.transform.PackageScope
 import groovy.transform.ToString
 import groovy.transform.TupleConstructor
 import groovy.util.logging.Slf4j
-import nextflow.cli.HubOptions
 import nextflow.config.ConfigParserFactory
 import nextflow.config.Manifest
 import nextflow.exception.AbortOperationException
@@ -98,12 +97,12 @@ class AssetManager {
      *
      * @param pipeline The pipeline to be managed by this manager e.g. {@code nextflow-io/hello}
      */
-    AssetManager( String pipelineName, HubOptions cliOpts = null) {
+    AssetManager( String pipelineName, HubOptions hubOpts = null) {
         assert pipelineName
         // read the default config file (if available)
         def config = ProviderConfig.getDefault()
         // build the object
-        build(pipelineName, config, cliOpts)
+        build(pipelineName, config, hubOpts)
     }
 
     AssetManager( String pipelineName, Map config ) {
@@ -117,19 +116,19 @@ class AssetManager {
      *
      * @param pipelineName A project name or a project repository Git URL
      * @param config A {@link Map} holding the configuration properties defined in the {@link ProviderConfig#DEFAULT_SCM_FILE} file
-     * @param cliOpts User credentials provided on the command line. See {@link HubOptions} trait
+     * @param hubOpts User credentials provided on the command line. See {@link HubOptions} trait
      * @return The {@link AssetManager} object itself
      */
     @PackageScope
-    AssetManager build( String pipelineName, Map config = null, HubOptions cliOpts = null ) {
+    AssetManager build( String pipelineName, Map config = null, HubOptions hubOpts = null ) {
 
         this.providerConfigs = ProviderConfig.createFromMap(config)
 
         this.project = resolveName(pipelineName)
         this.localPath = checkProjectDir(project)
-        this.hub = checkHubProvider(cliOpts)
+        this.hub = checkHubProvider(hubOpts)
         this.provider = createHubProvider(hub)
-        setupCredentials(cliOpts)
+        setupCredentials(hubOpts)
         validateProjectDir()
 
         return this
@@ -152,14 +151,14 @@ class AssetManager {
     /**
      * Sets the user credentials on the {@link RepositoryProvider} object
      *
-     * @param cliOpts The user credentials specified on the program command line. See {@code HubOptions}
+     * @param hubOpts The user credentials specified on the program command line. See {@code HubOptions}
      */
     @PackageScope
-    void setupCredentials( HubOptions cliOpts ) {
-        if( cliOpts?.hubUser ) {
-            cliOpts.hubProvider = hub
-            final user = cliOpts.getHubUser()
-            final pwd = cliOpts.getHubPassword()
+    void setupCredentials( HubOptions hubOpts ) {
+        if( hubOpts.user() ) {
+            hubOpts = new HubOptions(hub, hubOpts.user())
+            final user = hubOpts.getUser()
+            final pwd = hubOpts.getPassword()
             provider.setCredentials(user, pwd)
         }
     }
@@ -214,15 +213,15 @@ class AssetManager {
      * Find out the "hub provider" (i.e. the platform on which the remote repository is stored
      * for example: github, bitbucket, etc) and verifies that it is a known provider.
      *
-     * @param cliOpts The user hub info provider as command line options. See {@link HubOptions}
+     * @param hubOpts The user hub info provider as command line options. See {@link HubOptions}
      * @return The name of hub name e.g. {@code github}, {@code bitbucket}, etc.
      */
     @PackageScope
-    String checkHubProvider( HubOptions cliOpts ) {
+    String checkHubProvider( HubOptions hubOpts ) {
 
         def result = hub
         if( !result )
-            result = cliOpts?.getHubProvider()
+            result = hubOpts.provider()
         if( !result )
             result = guessHubProviderFromGitConfig()
         if( !result )

modules/nextflow/src/main/groovy/nextflow/scm/HubOptions.groovy

@@ -0,0 +1,54 @@
+/*
+ * Copyright 2013-2024, 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.
+ */
+
+package nextflow.scm
+
+import groovy.transform.CompileStatic
+/**
+ * Options for interacting with a git repository provider i.e. GitHub or BitBucket
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+@CompileStatic
+record HubOptions(
+    String provider,
+    String user
+) {
+
+    String getPassword() {
+        if( !user )
+            return null
+
+        final p = user.indexOf(':')
+        if( p != -1 )
+            return user.substring(p + 1)
+
+        final console = System.console()
+        if( !console )
+            return null
+
+        print "Enter your $provider password: "
+        return new String(console.readPassword())
+    }
+
+    String getUser() {
+        if( !user )
+            return user
+
+        final p = user.indexOf(':')
+        return p != -1 ? user.substring(0, p) : user
+    }
+}

modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy

@@ -25,10 +25,10 @@ import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.transform.ToString
 import groovy.util.logging.Slf4j
+import nextflow.Const
 import nextflow.NF
 import nextflow.NextflowMeta
 import nextflow.Session
-import nextflow.config.ConfigBuilder
 import nextflow.config.Manifest
 import nextflow.exception.WorkflowScriptErrorException
 import nextflow.trace.WorkflowStats
@@ -265,7 +265,7 @@ class WorkflowMetadata {
         this.outputDir = session.outputDir
         this.workDir = session.workDir
         this.launchDir = Paths.get('.').complete()
-        this.profile = session.profile ?: ConfigBuilder.DEFAULT_PROFILE
+        this.profile = session.profile ?: Const.DEFAULT_PROFILE
         this.sessionId = session.uniqueId
         this.resume = session.resumeMode
         this.stubRun = session.stubRun