Enable v2 syntax parser by default (#6643)

Author: bentsherman

docs/reference/feature-flags.md

@@ -23,6 +23,8 @@ Feature flags with the `nextflow.preview` prefix can cause pipelines run with ne
 : When `true`, enables the use of modules with binary scripts. See {ref}`module-binaries` for more information.
 
 `nextflow.enable.strict`
+: :::{deprecated} 26.04.0
+  :::
 : When `true`, executes the pipeline in "strict" mode, which introduces the following rules:
 
   - When reading a params file, Nextflow will fail if a dynamic param value references an undefined variable

docs/strict-syntax.md

@@ -16,6 +16,10 @@ export NXF_SYNTAX_PARSER=v2
 ```
 :::
 
+:::{versionchanged} 26.04.0
+The strict syntax is enabled by default. You can disable it by setting the environment variable `NXF_SYNTAX_PARSER=v1`.
+:::
+
 ## Overview
 
 The strict syntax is a subset of DSL2. While DSL2 allows any Groovy syntax, the strict syntax allows only a subset of Groovy syntax for Nextflow scripts and config files. This new specification enables more specific error reporting, ensures more consistent code, and will allow the Nextflow language to evolve independently of Groovy.

modules/nextflow/src/main/groovy/nextflow/NF.groovy

@@ -33,7 +33,7 @@ class NF {
     }
 
     static String getSyntaxParserVersion() {
-        return SysEnv.get('NXF_SYNTAX_PARSER', 'v1')
+        return SysEnv.get('NXF_SYNTAX_PARSER', 'v2')
     }
 
     static boolean isSyntaxParserV2() {

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

@@ -492,8 +492,9 @@ class CmdRun extends CmdBase implements HubOptions {
     }
 
     static void detectStrictFeature(ConfigMap config, Map sysEnv) {
+        if( NF.isSyntaxParserV2() )
+            return
         final defStrict = sysEnv.get('NXF_ENABLE_STRICT') ?: false
-        log
         final strictMode = config.navigate('nextflow.enable.strict', defStrict)
         if( strictMode ) {
             log.debug "Enabling nextflow strict mode"
@@ -522,8 +523,10 @@ class CmdRun extends CmdBase implements HubOptions {
     }
 
     static String detectDslMode(ConfigMap config, String scriptText, Map sysEnv) {
-        // -- try determine DSL version from config file
+        if( NF.isSyntaxParserV2() )
+            return DSL2
 
+        // -- try determine DSL version from config file
         final dsl = config.navigate('nextflow.enable.dsl') as String
 
         // -- script can still override the DSL version

modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy

@@ -85,7 +85,7 @@ class ConfigBuilder {
 
     List<String> warnings = new ArrayList<>(10)
 
-    Map<String,Object> declaredParams = [:]
+    Map<String,Object> declaredParams
 
     ConfigBuilder() {
         setHomeDir(Const.APP_HOME_DIR)
@@ -407,6 +407,7 @@ class ConfigBuilder {
                 checkValidProfile(parser.getDeclaredProfiles())
             }
 
+            this.declaredParams = parser.getDeclaredParams()
         }
 
         // guarantee top scopes
@@ -438,7 +439,6 @@ class ConfigBuilder {
         final config = parse0(parser, entry)
         if( NF.getSyntaxParserVersion() == 'v1' )
             validate(config, entry)
-        declaredParams.putAll(parser.getDeclaredParams())
         result.merge(config)
     }
 

modules/nextflow/src/main/groovy/nextflow/config/parser/v2/ConfigDsl.groovy

@@ -19,6 +19,7 @@ package nextflow.config.parser.v2
 import java.nio.file.NoSuchFileException
 import java.nio.file.Path
 
+import groovy.transform.CompileDynamic
 import groovy.transform.CompileStatic
 import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
@@ -42,13 +43,15 @@ class ConfigDsl extends Script {
 
     private boolean strict
 
+    private boolean stripSecrets
+
     private Path configPath
 
-    private Map paramOverrides
+    private Map cliParams
 
     private List<String> profiles
 
-    private Map target = [:]
+    private Map target = [params: [:]]
 
     private Set<String> declaredProfiles = []
 
@@ -66,13 +69,21 @@ class ConfigDsl extends Script {
         this.strict = value
     }
 
+    void setStripSecrets(boolean value) {
+        this.stripSecrets = value
+    }
+
     void setConfigPath(Path path) {
         this.configPath = path
     }
 
-    void setParams(Map paramOverrides) {
-        this.paramOverrides = paramOverrides
-        target.params = paramOverrides
+    void setParams(Map params) {
+        this.cliParams = params
+        (target.params as Map).putAll(params)
+    }
+
+    void setConfigParams(Map params) {
+        (target.params as Map).putAll(params)
     }
 
     void setProfiles(List<String> profiles) {
@@ -120,7 +131,7 @@ class ConfigDsl extends Script {
     void assign(List<String> names, Object value) {
         if( names.size() == 2 && names.first() == 'params' ) {
             declareParam(names.last(), value)
-            if( paramOverrides.containsKey(names.last()) )
+            if( cliParams.containsKey(names.last()) )
                 return
         }
         navigate(names.init()).put(names.last(), value)
@@ -195,8 +206,10 @@ class ConfigDsl extends Script {
                 .setIgnoreIncludes(ignoreIncludes)
                 .setRenderClosureAsString(renderClosureAsString)
                 .setStrict(strict)
+                .setStripSecrets(stripSecrets)
                 .setBinding(binding.getVariables())
-                .setParams(target.params as Map)
+                .setParams(cliParams)
+                .setConfigParams(target.params as Map)
                 .setProfiles(profiles)
         final config = parser.parse(configText, includePath)
         declaredProfiles.addAll(parser.getDeclaredProfiles())
@@ -213,6 +226,7 @@ class ConfigDsl extends Script {
      * @param includePath
      */
     @Memoized
+    @CompileDynamic // required to support ProviderPath::getText() over NioExtensions::getText()
     protected static String readConfigFile(Path includePath) {
         try {
             return includePath.getText()

modules/nextflow/src/main/groovy/nextflow/config/parser/v2/ConfigParserV2.groovy

@@ -18,6 +18,7 @@ package nextflow.config.parser.v2
 
 import java.nio.file.Path
 
+import groovy.transform.CompileDynamic
 import groovy.transform.CompileStatic
 import nextflow.config.ConfigParser
 import nextflow.exception.ConfigParseException
@@ -36,7 +37,9 @@ class ConfigParserV2 implements ConfigParser {
 
     private Map bindingVars = [:]
 
-    private Map paramOverrides = [:]
+    private Map cliParams = [:]
+
+    private Map configParams = [:]
 
     private boolean ignoreIncludes = false
 
@@ -48,9 +51,9 @@ class ConfigParserV2 implements ConfigParser {
 
     private List<String> appliedProfiles
 
-    private Set<String> declaredProfiles
+    private Set<String> declaredProfiles = []
 
-    private Map<String,Object> declaredParams
+    private Map<String,Object> declaredParams = [:]
 
     private GroovyShell groovyShell
 
@@ -79,7 +82,7 @@ class ConfigParserV2 implements ConfigParser {
     }
 
     @Override
-    ConfigParser setStripSecrets(boolean value) {
+    ConfigParserV2 setStripSecrets(boolean value) {
         this.stripSecrets = value
         return this
     }
@@ -91,10 +94,15 @@ class ConfigParserV2 implements ConfigParser {
     }
 
     @Override
-    ConfigParserV2 setParams(Map vars) {
-        // deep clone the map to prevent side-effect
+    ConfigParserV2 setParams(Map params) {
+        // deep clone the map to prevent side effects with nested params
         // see https://github.com/nextflow-io/nextflow/issues/1923
-        this.paramOverrides = Bolts.deepClone(vars)
+        this.cliParams = Bolts.deepClone(params)
+        return this
+    }
+
+    ConfigParserV2 setConfigParams(Map params) {
+        this.configParams = params
         return this
     }
 
@@ -127,14 +135,17 @@ class ConfigParserV2 implements ConfigParser {
             if( path )
                 script.setConfigPath(path)
             script.setIgnoreIncludes(ignoreIncludes)
-            script.setParams(paramOverrides)
-            script.setProfiles(appliedProfiles)
             script.setRenderClosureAsString(renderClosureAsString)
+            script.setStrict(strict)
+            script.setStripSecrets(stripSecrets)
+            script.setParams(cliParams)
+            script.setConfigParams(configParams)
+            script.setProfiles(appliedProfiles)
             script.run()
 
             final target = script.getTarget()
-            declaredProfiles = script.getDeclaredProfiles()
-            declaredParams = script.getDeclaredParams()
+            declaredProfiles.addAll(script.getDeclaredProfiles())
+            declaredParams.putAll(script.getDeclaredParams())
             return Bolts.toConfigObject(target)
         }
         catch( CompilationFailedException e ) {
@@ -168,8 +179,9 @@ class ConfigParserV2 implements ConfigParser {
     }
 
     @Override
+    @CompileDynamic // required to support ProviderPath::getText() over NioExtensions::getText()
     ConfigObject parse(Path path) {
-        return parse(path.text, path)
+        return parse(path.getText(), path)
     }
 
     private ConfigCompiler compiler

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

@@ -20,6 +20,7 @@ import java.nio.file.LinkOption
 import java.nio.file.Path
 import java.nio.file.Paths
 
+import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode
 import groovy.transform.Memoized
 import groovy.transform.PackageScope
@@ -39,6 +40,7 @@ import groovy.util.logging.Slf4j
  */
 @EqualsAndHashCode
 @Slf4j
+@CompileStatic
 class ProviderPath implements Path {
 
     @PackageScope
@@ -59,18 +61,27 @@ class ProviderPath implements Path {
         this.delegate = path
     }
 
+    @Override
+    Path relativize(Path other) {
+        new ProviderPath(provider, delegate.relativize(other))
+    }
+
+    @Override
     Path resolveSibling(Path other) {
         new ProviderPath(provider, delegate.resolveSibling(other.toString()))
     }
 
+    @Override
     Path resolveSibling(String other) {
         new ProviderPath(provider, delegate.resolveSibling(other))
     }
 
+    @Override
     Path resolve(Path other) {
         new ProviderPath(provider, delegate.resolve(other.toString()))
     }
 
+    @Override
     Path resolve(String other) {
         new ProviderPath(provider, delegate.resolve(other))
     }
@@ -97,10 +108,16 @@ class ProviderPath implements Path {
         provider.readText(delegate.toString())
     }
 
+    @Override
+    URI toUri() {
+        URI.create(toUriString())
+    }
+
     String toUriString() {
         provider.getContentUrl(delegate.toString())
     }
 
+    @Override
     String toString() {
         final base = provider.getRepositoryUrl()
         final file = delegate.toString()
@@ -110,20 +127,23 @@ class ProviderPath implements Path {
     /**
      * @return the path itself because it's absolute by definition being a remote file
      */
+    @Override
     Path toAbsolutePath() {
         return this
     }
 
     /**
      * @return {@code true} because it's absolute by definition being a remote file
      */
+    @Override
     boolean isAbsolute() {
         return true
     }
 
     /**
      * @return the path itself because it's absolute by definition being a remote file
      */
+    @Override
     Path normalize() {
         return this
     }

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

@@ -40,16 +40,12 @@ abstract class BaseScript extends Script implements ExecutionContext {
 
     private Session session
 
-    private ProcessFactory processFactory
-
     private ScriptMeta meta
 
     private WorkflowDef entryFlow
 
     private OutputDef publisher
 
-    @Lazy InputStream stdin = { System.in }()
-
     BaseScript() {
         meta = ScriptMeta.register(this)
     }
@@ -90,7 +86,6 @@ abstract class BaseScript extends Script implements ExecutionContext {
     private void setup() {
         binding.owner = this
         session = binding.getSession()
-        processFactory = session.newProcessFactory(this)
 
         binding.setVariable( 'baseDir', session.baseDir )
         binding.setVariable( 'projectDir', session.baseDir )

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

@@ -25,5 +25,5 @@ class BaseScriptConsts {
 
     public static Object[] EMPTY_ARGS = [] as Object[]
 
-    public static List<String> PRIVATE_NAMES = ['session','processFactory','taskProcessor','meta','entryFlow', 'publisher']
+    public static List<String> PRIVATE_NAMES = ['session','meta','entryFlow', 'publisher']
 }