Update to plugin registry V1 (#6316)

**RetryConfig Enhancement & Movement:**
- Move RetryConfig from nextflow to nf-commons module for better reusability
- Add support for multiplier parameter in retry configuration
- Replace navigate() dependency with static compilation-friendly getNestedConfig() helper
- Add NXF_RETRY_POLICY_MULTIPLIER environment variable (default: 2.0)

**HTTP Client Modernization:**
- Replace custom HttpRetryableClient with external io.seqera:lib-httpx library
- Update HttpPluginRepository to use HxClient for better reliability
- Enhanced OciAwareFileDownloader with improved authentication and error handling

**Documentation:**
- Add NXF_PLUGINS_REGISTRY_URL and NXF_RETRY_POLICY_MULTIPLIER to env-vars.md
- Document retry policy multiplier configuration for exponential backoff

**Dependencies:**
- Add io.seqera:lib-httpx:1.0.0 and io.seqera:lib-retry:1.2.0
- Remove custom HTTP retry implementation in favor of external libraries

This refactoring improves the plugin system's HTTP infrastructure reliability while
maintaining backward compatibility and adding new configuration flexibility.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

---------

Signed-off-by: jorgee <[email protected]>
Co-authored-by: Paolo Di Tommaso <[email protected]>
Co-authored-by: Claude <[email protected]>

Author: 3 people

docs/reference/env-vars.md

@@ -161,6 +161,11 @@ The following environment variables control the configuration of the Nextflow ru
 `NXF_PLUGINS_DIR`
 : The path where the plugin archives are loaded and stored (default: `$NXF_HOME/plugins`).
 
+`NXF_PLUGINS_REGISTRY_URL`
+: :::{versionadded} 25.08.0-edge
+  :::
+: Specifies the URL of the plugin registry used to download and resolve plugins. This allows using custom or private plugin registries instead of the default public registry.
+
 `NXF_PLUGINS_TEST_REPOSITORY`
 : :::{versionadded} 23.04.0
   :::
@@ -191,6 +196,11 @@ The following environment variables control the configuration of the Nextflow ru
   :::
 : Max delay used for HTTP retryable operations (default: `90s`).
 
+`NXF_RETRY_POLICY_MULTIPLIER`
+: :::{versionadded} 25.08.0-edge
+  :::
+: Delay multiplier used for HTTP retryable operations (default: `2.0`).
+
 `NXF_SCM_FILE`
 : :::{versionadded} 20.10.0
   :::

modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy

@@ -235,7 +235,7 @@ class PublishDir {
     protected void apply0(Set<Path> files) {
         assert path
         // setup the retry policy config to be used
-        this.retryConfig = RetryConfig.config(session)
+        this.retryConfig = RetryConfig.config(session.config)
 
         createPublishDir()
         validatePublishMode()

modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy

@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2024, Seqera Labs
+ * 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.
@@ -18,13 +18,10 @@ package nextflow.util
 
 import java.nio.file.Path
 
-import com.google.common.base.CaseFormat
 import groovy.json.JsonOutput
-import groovy.transform.CompileDynamic
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
-import nextflow.SysEnv
 import nextflow.config.ConfigClosurePlaceholder
 import org.codehaus.groovy.runtime.InvokerHelper
 import org.yaml.snakeyaml.DumperOptions
@@ -370,37 +367,5 @@ class ConfigHelper {
             return value
     }
 
-    static <T> T valueOf(Map config, String name, String prefix, T defValue, Class<T> type)  {
-        assert name, "Argument 'name' cannot be null or empty"
-        assert type, "Argument 'type' cannot be null"
-
-        // try to get the value from the config map
-        final cfg = config?.get(name)
-        if( cfg != null ) {
-            return toType(cfg, type)
-        }
-        // try to fallback to the sys environment
-        if( !prefix.endsWith('_') )
-            prefix += '_'
-        final key = prefix.toUpperCase() + CaseFormat.LOWER_CAMEL.to(CaseFormat.UPPER_UNDERSCORE, name)
-        final env = SysEnv.get(key)
-        if( env != null ) {
-            return toType(env, type)
-        }
-        // return the default value
-        return defValue
-    }
-
-    @CompileDynamic
-    static protected <T> T toType(Object value, Class<T> type)  {
-        if( value == null )
-            return null
-        if( type==Boolean.class ) {
-            return type.cast(Boolean.valueOf(value.toString()))
-        }
-        else {
-            return value.asType(type)
-        }
-    }
 }
 

modules/nextflow/src/main/groovy/nextflow/util/RetryConfig.groovy

@@ -19,11 +19,9 @@ package nextflow.util
 import java.nio.file.Files
 import java.nio.file.Paths
 
-import nextflow.SysEnv
 import nextflow.config.ConfigClosurePlaceholder
 import spock.lang.Specification
 import spock.lang.Unroll
-
 /**
  *
  * @author Paolo Di Tommaso <[email protected]>
@@ -354,72 +352,5 @@ class ConfigHelperTest extends Specification {
         "withName:2foo"     | "'withName:2foo'"     | "withName:'2foo'"
     }
 
-    @Unroll
-    def 'should get config from map' () {
-        given:
-        def NAME = 'foo'
-        def PREFIX = 'P_'
-        and:
-        SysEnv.push(ENV)
-
-        expect:
-        ConfigHelper.valueOf(CONFIG, NAME, PREFIX, DEF_VAL, DEF_TYPE) == EXPECTED
-
-        cleanup:
-        SysEnv.pop()
-
-        where:
-        CONFIG          | ENV           | DEF_VAL       | DEF_TYPE      | EXPECTED
-        null            | [:]           | null          | String        | null
-        [:]             | [:]           | null          | String        | null
-        [:]             | [:]           | 'one'         | String        | 'one'
-        [foo:'two']     | [:]           | 'one'         | String        | 'two'
-        [foo:'']        | [:]           | 'one'         | String        | ''
-        [foo:'two']     | [P_FOO:'bar'] | 'one'         | String        | 'two'
-        [:]             | [P_FOO:'bar'] | 'one'         | String        | 'bar'
-
-        and:
-        null            | [:]           | null          | Integer       | null
-        [:]             | [:]           | null          | Integer       | null
-        [:]             | [:]           | 1             | Integer       | 1
-        [foo:2]         | [:]           | 1             | Integer       | 2
-        [foo:'2']       | [:]           | 1             | Integer       | 2
-        [foo:'2']       | [P_FOO:'3']   | 1             | Integer       | 2
-        [:]             | [P_FOO:'3']   | 1             | Integer       | 3
-
-        and:
-        null            | [:]           | null          | Boolean       | null
-        [:]             | [:]           | true          | Boolean       | true
-        [foo:false]     | [:]           | true          | Boolean       | false
-        [foo:'false']   | [:]           | true          | Boolean       | false
-        [foo:true]      | [:]           | false         | Boolean       | true
-        [foo:'true']    | [:]           | false         | Boolean       | true
-        [foo:'true']    | [P_FOO:'false']| null         | Boolean       | true
-        [:]             | [P_FOO:'false']| null         | Boolean       | false
-        [:]             | [P_FOO:'true'] | null         | Boolean       | true
-
-        and:
-        [:]             | [:]           | Duration.of('1s') | Duration  | Duration.of('1s')
-        [foo:'10ms']    | [:]           | null              | Duration  | Duration.of('10ms')
-        [:]             | [P_FOO:'1s']  | null              | Duration  | Duration.of('1s')
-    }
-
-    def 'should map camelCase to snake uppercase' () {
-        given:
-        SysEnv.push(ENV)
-
-        expect:
-        ConfigHelper.valueOf([:], NAME, PREFIX, null, String) == EXPECTED
-
-        cleanup:
-        SysEnv.pop()
-
-        where:
-        EXPECTED    | PREFIX    | NAME              | ENV
-        null        | 'foo'     | 'bar'             | [:]
-        'one'       | 'foo'     | 'bar'             | [FOO_BAR: 'one']
-        'one'       | 'foo_'    | 'bar'             | [FOO_BAR: 'one']
-        'one'       | 'foo_'    | 'thisAndThat'     | [FOO_THIS_AND_THAT: 'one']
-    }
 
 }

modules/nextflow/src/test/groovy/nextflow/util/ConfigHelperTest.groovy

@@ -34,6 +34,8 @@ dependencies {
     api 'org.pf4j:pf4j:3.12.0'
     api 'org.pf4j:pf4j-update:2.3.0'
     api 'dev.failsafe:failsafe:3.1.0'
+    api 'io.seqera:lib-httpx:1.0.0'
+    api 'io.seqera:lib-retry:1.2.0'
     // patch gson dependency required by pf4j
     api 'com.google.code.gson:gson:2.13.1'