Remove test constructors or mark as TestOnly (#5216)

---------

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

Author: bentsherman

modules/nextflow/src/main/groovy/nextflow/cli/CmdPull.groovy

@@ -22,6 +22,7 @@ import groovy.util.logging.Slf4j
 import nextflow.exception.AbortOperationException
 import nextflow.plugin.Plugins
 import nextflow.scm.AssetManager
+import nextflow.util.TestOnly
 /**
  * CLI sub-command PULL
  *
@@ -49,7 +50,7 @@ class CmdPull extends CmdBase implements HubOptions {
     @Override
     final String getName() { NAME }
 
-    /* only for testing purpose */
+    @TestOnly
     protected File root
 
     @Override
@@ -64,7 +65,6 @@ class CmdPull extends CmdBase implements HubOptions {
             return
         }
 
-        /* only for testing purpose */
         if( root ) {
             AssetManager.root = root
         }

modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy

@@ -33,6 +33,7 @@ import nextflow.file.FileMutex
 import nextflow.util.CacheHelper
 import nextflow.util.Duration
 import nextflow.util.Escape
+import nextflow.util.TestOnly
 /**
  * Handle Conda environment creation and caching
  *
@@ -86,9 +87,8 @@ class CondaCache {
         return "conda"
     }
 
-    /** Only for testing purpose - do not use */
-    @PackageScope
-    CondaCache() {}
+    @TestOnly
+    protected CondaCache() {}
 
     /**
      * Create a Conda env cache object

modules/nextflow/src/main/groovy/nextflow/container/ApptainerCache.groovy

@@ -27,9 +27,6 @@ import groovy.transform.CompileStatic
 @CompileStatic
 class ApptainerCache extends SingularityCache {
 
-    /** only for testing */
-    protected ApptainerCache() {}
-
     ApptainerCache(ContainerConfig config, Map<String,String> env=null) {
         super(config, env)
     }

modules/nextflow/src/main/groovy/nextflow/container/CharliecloudCache.groovy

@@ -29,6 +29,7 @@ import groovyx.gpars.dataflow.LazyDataflowVariable
 import nextflow.Global
 import nextflow.file.FileMutex
 import nextflow.util.Duration
+import nextflow.util.TestOnly
 /**
  * Handle caching of remote Charliecloud images
  *
@@ -52,7 +53,7 @@ class CharliecloudCache {
 
     private String registry
 
-    /** Only for debugging purpose - do not use */
+    @TestOnly
     @PackageScope
     CharliecloudCache() {}
 

modules/nextflow/src/main/groovy/nextflow/container/SingularityCache.groovy

@@ -52,10 +52,6 @@ class SingularityCache {
 
     private Duration pullTimeout = Duration.of('20min')
 
-    /** Only for debugging purpose - do not use */
-    @PackageScope
-    SingularityCache() {}
-
     protected String getBinaryName() { return 'singularity' }
 
     protected String getAppName() { getBinaryName().capitalize() }

modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy

@@ -39,6 +39,7 @@ import nextflow.processor.TaskRun
 import nextflow.secret.SecretsLoader
 import nextflow.util.Escape
 import nextflow.util.MemoryUnit
+import nextflow.util.TestOnly
 /**
  * Builder to create the Bash script which is used to
  * wrap and launch the user task
@@ -124,8 +125,8 @@ class BashWrapperBuilder {
         this.copyStrategy = strategy ?: new SimpleFileCopyStrategy(bean)
     }
 
-    /** only for testing -- do not use */
-    protected BashWrapperBuilder() { }
+    @TestOnly
+    protected BashWrapperBuilder() {}
 
     /**
      * @return The bash script fragment to change to the 'scratch' directory if it has been specified in the task configuration

modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy

@@ -44,6 +44,7 @@ import nextflow.processor.TaskRun
 import nextflow.trace.TraceRecord
 import nextflow.util.CmdLineHelper
 import nextflow.util.Duration
+import nextflow.util.TestOnly
 import nextflow.util.Throttle
 /**
  * Handles a job execution in the underlying grid platform
@@ -83,7 +84,7 @@ class GridTaskHandler extends TaskHandler implements FusionAwareTask {
 
     BatchCleanup batch
 
-    /** only for testing purpose */
+    @TestOnly
     protected GridTaskHandler() {}
 
     GridTaskHandler( TaskRun task, AbstractGridExecutor executor ) {

modules/nextflow/src/main/groovy/nextflow/extension/DumpOp.groovy

@@ -63,10 +63,6 @@ class DumpOp {
         return this
     }
 
-    /** Only for testing -- do not use */
-    protected DumpOp() {}
-
-
     boolean isEnabled() {
         if( !dumpNames )
             return false

modules/nextflow/src/main/groovy/nextflow/extension/TransposeOp.groovy

@@ -22,6 +22,7 @@ import groovyx.gpars.dataflow.DataflowReadChannel
 import groovyx.gpars.dataflow.DataflowWriteChannel
 import nextflow.Channel
 import nextflow.util.CheckHelper
+import nextflow.util.TestOnly
 /**
  * Implements channel transpose operator
  *
@@ -48,9 +49,7 @@ class TransposeOp {
         this.remainder = params?.remainder as Boolean
     }
 
-    /**
-     * Only for test -- do not use
-     */
+    @TestOnly
     @PackageScope
     TransposeOp() {}
 

modules/nextflow/src/main/groovy/nextflow/file/DirWatcher.groovy

@@ -33,6 +33,7 @@ import java.nio.file.attribute.BasicFileAttributes
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+import nextflow.util.TestOnly
 import nextflow.util.Threads
 
 /**
@@ -79,7 +80,7 @@ class DirWatcher implements DirListener {
 
     private volatile boolean terminated
 
-    /* only for testing */
+    @TestOnly
     protected DirWatcher() {}
 
     DirWatcher(String syntax, String folder, String pattern, boolean skipHidden, String events, FileSystem fs) {

modules/nextflow/src/main/groovy/nextflow/file/DirWatcherV2.groovy

@@ -27,6 +27,7 @@ import java.nio.file.WatchEvent
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.util.Duration
+import nextflow.util.TestOnly
 import org.apache.commons.io.monitor.FileAlterationListener
 import org.apache.commons.io.monitor.FileAlterationMonitor
 import org.apache.commons.io.monitor.FileAlterationObserver
@@ -73,7 +74,8 @@ class DirWatcherV2 implements DirListener, FileAlterationListener {
 
     private FileAlterationMonitor monitor
 
-    protected DirWatcherV2() { }
+    @TestOnly
+    protected DirWatcherV2() {}
 
     DirWatcherV2(String syntax, String folder, String pattern, boolean skipHidden, String events, FileSystem fs) {
         assert syntax in ['regex','glob']

modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy

@@ -41,9 +41,6 @@ class FusionScriptLauncher extends BashWrapperBuilder {
     private Path remoteWorkDir
     private Map<String,String> env
 
-    /* ONLY FOR TESTING - DO NOT USE */
-    protected FusionScriptLauncher() { }
-
     static FusionScriptLauncher create(TaskBean bean, String scheme) {
 
         final remoteWorkDir = bean.workDir

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

@@ -34,6 +34,7 @@ import nextflow.Global
 import nextflow.exception.ProcessException
 import nextflow.script.ScriptBinding
 import nextflow.util.KryoHelper
+import nextflow.util.TestOnly
 /**
  * Map used to delegate variable resolution to script scope
  *
@@ -91,7 +92,7 @@ class TaskContext implements Map<String,Object>, Cloneable {
         log.trace "Binding names for '$name' > $variableNames"
     }
 
-    /** ONLY FOR TEST PURPOSE -- do not use */
+    @TestOnly
     protected TaskContext() { }
 
     TaskContext clone() {

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

@@ -25,6 +25,7 @@ import groovy.transform.CompileDynamic
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.trace.TraceRecord
+import nextflow.util.TestOnly
 /**
  * Actions to handle the underlying job running the user task.
  *
@@ -44,8 +45,8 @@ abstract class TaskHandler {
         this.task = task
     }
 
-    /** Only for testing purpose */
-    protected TaskHandler() { }
+    @TestOnly
+    protected TaskHandler() {}
 
     /**
      * The task managed by this handler

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

@@ -284,8 +284,8 @@ class TaskProcessor {
         currentProcessor0 = this
     }
 
-    /* for testing purpose - do not remove */
-    protected TaskProcessor() { }
+    @TestOnly
+    protected TaskProcessor() {}
 
     /**
      * Create and initialize the processor object

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

@@ -71,9 +71,6 @@ class IncludeDef {
         this.modules = new ArrayList<>(modules)
     }
 
-    /** only for testing purpose -- do not use */
-    protected IncludeDef() { }
-
     IncludeDef from(Object path) {
         this.path = path
         return this

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

@@ -49,6 +49,7 @@ import nextflow.script.params.TupleInParam
 import nextflow.script.params.TupleOutParam
 import nextflow.script.params.ValueInParam
 import nextflow.script.params.ValueOutParam
+import nextflow.util.TestOnly
 
 /**
  * Holds the process configuration properties
@@ -180,9 +181,8 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
         this.processName = name
     }
 
-    /* Only for testing purpose */
-    @PackageScope
-    ProcessConfig( Map delegate ) {
+    @TestOnly
+    protected ProcessConfig( Map delegate ) {
         configProperties = delegate
     }
 

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

@@ -40,9 +40,6 @@ class ProcessFactory {
 
     private ExecutorFactory executorFactory
 
-    /* only for test -- do not use */
-    protected ProcessFactory() { }
-
     ProcessFactory( BaseScript ownerScript, Session session ) {
         this.owner = ownerScript
         this.session = session

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

@@ -133,9 +133,6 @@ class ScriptMeta {
         }
     }
 
-    /** only for testing */
-    protected ScriptMeta() {}
-
     void setScriptPath(Path path) {
         scriptsByPath.put(path, script)
         scriptPath = path

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

@@ -24,6 +24,7 @@ import nextflow.exception.MissingProcessException
 import nextflow.exception.MissingValueException
 import nextflow.exception.ScriptRuntimeException
 import nextflow.extension.CH
+import nextflow.util.TestOnly
 /**
  * Models a script workflow component
  *
@@ -67,7 +68,7 @@ class WorkflowDef extends BindableDef implements ChainableDef, IterableDef, Exec
         this.variableNames = getVarNames0()
     }
 
-    /* ONLY FOR TESTING PURPOSE */
+    @TestOnly
     protected WorkflowDef() {}
 
     WorkflowDef clone() {

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

@@ -33,6 +33,7 @@ import nextflow.config.Manifest
 import nextflow.exception.WorkflowScriptErrorException
 import nextflow.trace.WorkflowStats
 import nextflow.util.Duration
+import nextflow.util.TestOnly
 import org.codehaus.groovy.runtime.InvokerHelper
 /**
  * Models workflow metadata properties and notification handler
@@ -292,11 +293,8 @@ class WorkflowMetadata {
        return config.isEnabled() ? config.getEngine() : null
     }
 
-    /**
-     * Only for testing purpose -- do not use
-     */
-    @PackageScope
-    WorkflowMetadata() {}
+    @TestOnly
+    protected WorkflowMetadata() {}
 
     /**
      * Implements the following idiom in the pipeline script:

modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy

@@ -26,6 +26,7 @@ import nextflow.exception.IllegalFileException
 import nextflow.file.FilePatternSplitter
 import nextflow.script.TokenVar
 import nextflow.util.BlankSeparatedList
+import nextflow.util.TestOnly
 /**
  * Model a process *file* output parameter
  *
@@ -35,9 +36,7 @@ import nextflow.util.BlankSeparatedList
 @InheritConstructors
 class FileOutParam extends BaseOutParam implements OutParam, ArityParam, OptionalParam, PathQualifier {
 
-    /**
-     * ONLY FOR TESTING DO NOT USE
-     */
+    @TestOnly
     protected FileOutParam(Map params) {
         super(new Binding(), [])
     }

modules/nextflow/src/main/groovy/nextflow/spack/SpackCache.groovy

@@ -32,6 +32,7 @@ import nextflow.file.FileMutex
 import nextflow.util.CacheHelper
 import nextflow.util.Duration
 import nextflow.util.Escape
+import nextflow.util.TestOnly
 import org.yaml.snakeyaml.Yaml
 /**
  * Handle Spack environment creation and caching
@@ -71,9 +72,8 @@ class SpackCache {
 
     @PackageScope Path getConfigCacheDir0() { configCacheDir0 }
 
-    /** Only for testing purpose - do not use */
-    @PackageScope
-    SpackCache() {}
+    @TestOnly
+    protected SpackCache() {}
 
     /**
      * Create a Spack env cache object

modules/nextflow/src/main/groovy/nextflow/trace/TraceHelper.groovy

@@ -30,6 +30,7 @@ import java.time.format.DateTimeFormatter
 import groovy.transform.CompileStatic
 import groovy.transform.Memoized
 import nextflow.exception.AbortOperationException
+import nextflow.util.TestOnly
 
 /**
  * Helper methods for trace and observer feature
@@ -39,7 +40,7 @@ import nextflow.exception.AbortOperationException
 @CompileStatic
 class TraceHelper {
 
-    /* only for testing -- do not use */
+    @TestOnly
     static protected String testTimestampFmt
 
     static public final Instant launchTimestamp = Instant.now()