Bump nextflow 25.03.1-edge

Signed-off-by: Ben Sherman <bentshermann@gmail.com>

Author: bentsherman

build.gradle

@@ -27,7 +27,7 @@ test {
 }
 
 dependencies {
-  implementation 'io.nextflow:nf-lang:25.03.0-edge'
+  implementation 'io.nextflow:nf-lang:25.03.1-edge'
   implementation 'org.apache.groovy:groovy:4.0.26'
   implementation 'org.apache.groovy:groovy-json:4.0.26'
   implementation 'org.eclipse.lsp4j:org.eclipse.lsp4j:0.23.0'

src/main/java/nextflow/lsp/compiler/LanguageServerCompiler.java

@@ -21,6 +21,7 @@
 import java.nio.file.Path;
 
 import groovy.lang.GroovyClassLoader;
+import nextflow.config.control.StringReaderSourceWithURI;
 import nextflow.lsp.file.FileCache;
 import nextflow.script.control.Compiler;
 import org.codehaus.groovy.GroovyBugError;

src/main/java/nextflow/lsp/compiler/StringReaderSourceWithURI.java

@@ -0,0 +1,64 @@
+/*
+ * Copyright 2024-2025, 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.
+ */
+package nextflow.lsp.services.config;
+
+import java.net.URI;
+import java.util.Set;
+
+import nextflow.config.ast.ConfigIncludeNode;
+import nextflow.config.control.ResolveIncludeVisitor;
+import org.codehaus.groovy.ast.expr.ConstantExpression;
+import org.codehaus.groovy.control.SourceUnit;
+
+/**
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+public class CachingResolveIncludeVisitor extends ResolveIncludeVisitor {
+
+    private Set<URI> changedUris;
+
+    private boolean changed;
+
+    public CachingResolveIncludeVisitor(SourceUnit sourceUnit, Set<URI> changedUris) {
+        super(sourceUnit);
+        this.changedUris = changedUris;
+    }
+
+    private URI uri() {
+        return getSourceUnit().getSource().getURI();
+    }
+
+    @Override
+    public void visitConfigInclude(ConfigIncludeNode node) {
+        if( !(node.source instanceof ConstantExpression) )
+            return;
+        var source = node.source.getText();
+        var includeUri = getIncludeUri(uri(), source);
+        if( !isIncludeLocal(includeUri) || !isIncludeStale(includeUri) )
+            return;
+        changed = true;
+        super.visitConfigInclude(node);
+    }
+
+    protected boolean isIncludeStale(URI includeUri) {
+        return changedUris.contains(uri()) || changedUris.contains(includeUri);
+    }
+
+    public boolean isChanged() {
+        return changed;
+    }
+}

src/main/java/nextflow/lsp/services/config/CachingResolveIncludeVisitor.java

@@ -31,6 +31,7 @@
 import nextflow.lsp.services.LanguageServerConfiguration;
 import nextflow.script.control.PhaseAware;
 import nextflow.script.control.Phases;
+import nextflow.script.types.Types;
 import org.codehaus.groovy.ast.ASTNode;
 import org.codehaus.groovy.control.CompilerConfiguration;
 import org.codehaus.groovy.control.SourceUnit;
@@ -71,7 +72,7 @@ protected Set<URI> analyze(Set<URI> uris, FileCache fileCache) {
         var changedUris = new HashSet<>(uris);
 
         for( var sourceUnit : getSourceUnits() ) {
-            var visitor = new ResolveIncludeVisitor(sourceUnit, compiler(), uris);
+            var visitor = new CachingResolveIncludeVisitor(sourceUnit, changedUris);
             visitor.visit();
 
             var uri = sourceUnit.getSource().getURI();
@@ -87,7 +88,7 @@ protected Set<URI> analyze(Set<URI> uris, FileCache fileCache) {
             if( sourceUnit == null )
                 continue;
             // phase 3: name checking
-            new ConfigResolveVisitor(sourceUnit, compiler().compilationUnit()).visit();
+            new ConfigResolveVisitor(sourceUnit, compiler().compilationUnit(), Types.DEFAULT_CONFIG_IMPORTS).visit();
             new ConfigSchemaVisitor(sourceUnit, configuration.typeChecking()).visit();
             if( sourceUnit.getErrorCollector().hasErrors() )
                 continue;

src/main/java/nextflow/lsp/services/config/ConfigAstCache.java

@@ -120,7 +120,7 @@ protected Set<URI> analyze(Set<URI> uris, FileCache fileCache) {
             if( sourceUnit == null )
                 continue;
             // phase 3: name checking
-            new ScriptResolveVisitor(sourceUnit, compiler().compilationUnit(), Types.DEFAULT_IMPORTS, libImports).visit();
+            new ScriptResolveVisitor(sourceUnit, compiler().compilationUnit(), Types.DEFAULT_SCRIPT_IMPORTS, libImports).visit();
             new ParameterSchemaVisitor(sourceUnit).visit();
             if( sourceUnit.getErrorCollector().hasErrors() )
                 continue;

src/main/java/nextflow/lsp/services/script/ScriptAstCache.java

@@ -437,7 +437,7 @@ private void populateTypes(String namePrefix, List<CompletionItem> items) {
         populateTypes0(ast.getEnumNodes(uri), namePrefix, items);
 
         // add built-in types
-        populateTypes0(Types.DEFAULT_IMPORTS, namePrefix, items);
+        populateTypes0(Types.DEFAULT_SCRIPT_IMPORTS, namePrefix, items);
     }
 
     private void populateTypes0(Collection<ClassNode> classNodes, String namePrefix, List<CompletionItem> items) {