Address review feedback: simplify ConfigScope registration

Per Ben's review, only the top-level scope needs @ScopeName, a no-arg
constructor, and extension point registration. Nested scopes are
discovered via fields on the parent class.

- Register CO2FootprintConfig in build.gradle extensionPoints
- Remove @ScopeName from nested scope classes (Trace/Summary/Report/DataFileConfig)
- Remove no-arg constructors from nested scopes and BaseFileConfig
- Remove unnecessary types=[...] from @ConfigOption annotations
  (kept types=[Number, BigDecimal] on ci since it constructs CiRecord from a number)

Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
Signed-off-by: Jonathan Manning <[email protected]>

Author: pinin4fjords

build.gradle

@@ -107,7 +107,8 @@ nextflowPlugin {
     className = 'nextflow.co2footprint.CO2FootprintPlugin'
     extensionPoints = [
             'nextflow.co2footprint.CO2FootprintFactory',
-            'nextflow.co2footprint.CO2FootprintExtension'
+            'nextflow.co2footprint.CO2FootprintExtension',
+            'nextflow.co2footprint.CO2FootprintConfig'
     ]
 
 }

src/main/nextflow/co2footprint/CO2FootprintConfig.groovy

@@ -57,59 +57,59 @@ class CO2FootprintConfig implements ConfigScope {
     private final String timestamp = TraceHelper.launchTimestampFmt()
     private final String executor
 
-    @ConfigOption(types=[Map])
+    @ConfigOption
     @Description('Configuration for the trace file.')
     final TraceFileConfig trace
 
-    @ConfigOption(types=[Map])
+    @ConfigOption
     @Description('Configuration for the summary file.')
     final SummaryFileConfig summary
 
-    @ConfigOption(types=[Map])
+    @ConfigOption
     @Description('Configuration for the report file.')
     final ReportFileConfig report
 
-    @ConfigOption(types=[Map])
+    @ConfigOption
     @Description('Configuration for the data/machine-readable file.')
     final DataFileConfig dataFile
 
-    @ConfigOption(types=[GString])
+    @ConfigOption
     @Description('Location GeoCode from Electricity maps.')
     final String location
 
     @ConfigOption(types=[Number, BigDecimal])
     @Description('Location-based carbon intensity (CI).')
     final CiRecord ci
 
-    @ConfigOption(types=[Number])
+    @ConfigOption
     @Description('Market-based carbon intensity (CI).')
     final BigDecimal ciMarket
 
-    @ConfigOption(types=[GString])
+    @ConfigOption
     @Description('Electricity-maps API token.')
     final String emApiKey
 
-    @ConfigOption(types=[Number])
+    @ConfigOption
     @Description('Power usage effectiveness (PUE) of the data centre.')
     BigDecimal pue
 
-    @ConfigOption(types=[Number])
+    @ConfigOption
     @Description('Power draw of memory [W per GB].')
     final BigDecimal powerdrawMem
 
     @ConfigOption
     @Description('Turns off pattern matching of CPU names.')
     final Boolean ignoreCpuModel
 
-    @ConfigOption(types=[Number])
+    @ConfigOption
     @Description('Default powerdraw of the CPU.')
     final BigDecimal powerdrawCpuDefault
 
-    @ConfigOption(types=[String, GString])
+    @ConfigOption
     @Description('Path to a custom CPU TDP file.')
     final Path customCpuTdpFile
 
-    @ConfigOption(types=[GString])
+    @ConfigOption
     @Description('Type of computer on which the workflow is run [\'local\', \'compute cluster\', \'\'].')
     String machineType
 

src/main/nextflow/co2footprint/Config/BaseFileConfig.groovy

@@ -18,7 +18,7 @@ class BaseFileConfig {
     final String name
     final String ending
 
-    @ConfigOption(types=[String, GString])
+    @ConfigOption
     @Description('Path to the file.')
     final Path file
 
@@ -32,12 +32,6 @@ class BaseFileConfig {
 
     protected final LinkedHashSet<String> usedKeys = [] as LinkedHashSet<String>
 
-    /**
-     * No-arg constructor required by Nextflow's v2 config parser for
-     * subclasses that implement ConfigScope.
-     */
-    protected BaseFileConfig() {}
-
     /**
      * Parses a file-based sub-configuration for nf-co2footprint and sets up defaults and fallbacks.
      *

src/main/nextflow/co2footprint/Config/DataFileConfig.groovy

@@ -3,13 +3,10 @@ package nextflow.co2footprint.Config
 import nextflow.co2footprint.CO2FootprintConfig
 import nextflow.config.spec.ConfigOption
 import nextflow.config.spec.ConfigScope
-import nextflow.config.spec.ScopeName
 import nextflow.script.dsl.Description
 
-@ScopeName('co2footprint.dataFile')
 @Description('The `co2footprint.dataFile` scope allows you to configure the data/machine-actionable file of the `nf-co2footprint` plugin.')
 class DataFileConfig extends BaseFileConfig implements ConfigScope {
-    DataFileConfig() { super() }
 
     @ConfigOption
     @Description('Whether only emission metrics should be reported in the data file.')

src/main/nextflow/co2footprint/Config/ReportFileConfig.groovy

@@ -3,13 +3,10 @@ package nextflow.co2footprint.Config
 import nextflow.co2footprint.CO2FootprintConfig
 import nextflow.config.spec.ConfigOption
 import nextflow.config.spec.ConfigScope
-import nextflow.config.spec.ScopeName
 import nextflow.script.dsl.Description
 
-@ScopeName('co2footprint.report')
 @Description('The `co2footprint.report` scope allows you to configure the report file of the `nf-co2footprint` plugin.')
 class ReportFileConfig extends BaseFileConfig implements ConfigScope{
-    ReportFileConfig() { super() }
 
     @ConfigOption
     @Description('The number of maximum tasks that is displayed in the report.')

src/main/nextflow/co2footprint/Config/SummaryFileConfig.groovy

@@ -2,13 +2,10 @@ package nextflow.co2footprint.Config
 
 import nextflow.co2footprint.CO2FootprintConfig
 import nextflow.config.spec.ConfigScope
-import nextflow.config.spec.ScopeName
 import nextflow.script.dsl.Description
 
-@ScopeName('co2footprint.summary')
 @Description('The `co2footprint.summary` scope allows you to configure the summary file of the `nf-co2footprint` plugin.')
 class SummaryFileConfig extends BaseFileConfig implements ConfigScope{
-    SummaryFileConfig() { super() }
     SummaryFileConfig(Map summaryFileConfig, String timestamp=null) {
         super(summaryFileConfig, timestamp, 'summary', 'txt')
 

src/main/nextflow/co2footprint/Config/TraceFileConfig.groovy

@@ -2,13 +2,10 @@ package nextflow.co2footprint.Config
 
 import nextflow.co2footprint.CO2FootprintConfig
 import nextflow.config.spec.ConfigScope
-import nextflow.config.spec.ScopeName
 import nextflow.script.dsl.Description
 
-@ScopeName('co2footprint.trace')
 @Description('The `co2footprint.trace` scope allows you to configure the trace file of the `nf-co2footprint` plugin.')
 class TraceFileConfig extends BaseFileConfig implements ConfigScope{
-    TraceFileConfig() { super() }
     TraceFileConfig(Map traceFileConfig, String timestamp=null) {
         super(traceFileConfig, timestamp, 'trace', 'txt')