@eagleoutice/flowr 2.2.14 → 2.2.16

package/documentation/doc-util/doc-types.js

@@ -4,14 +4,21 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.mermaidHide = void 0;
+exports.getTypeScriptSourceFiles = getTypeScriptSourceFiles;
+exports.dropGenericsFromTypeName = dropGenericsFromTypeName;
+exports.removeCommentSymbolsFromTypeScriptComment = removeCommentSymbolsFromTypeScriptComment;
+exports.getTextualCommentsFromTypeScript = getTextualCommentsFromTypeScript;
+exports.getStartLineOfTypeScriptNode = getStartLineOfTypeScriptNode;
 exports.getType = getType;
 exports.followTypeReference = followTypeReference;
+exports.getTypePathForTypeScript = getTypePathForTypeScript;
 exports.getTypePathLink = getTypePathLink;
-exports.getTypesFromFolderAsMermaid = getTypesFromFolderAsMermaid;
+exports.getTypesFromFolder = getTypesFromFolder;
 exports.implSnippet = implSnippet;
 exports.printHierarchy = printHierarchy;
 exports.printCodeOfElement = printCodeOfElement;
 exports.shortLink = shortLink;
+exports.shortLinkFile = shortLinkFile;
 exports.getDocumentationForType = getDocumentationForType;
 const typescript_1 = __importDefault(require("typescript"));
 const assert_1 = require("../../util/assert");
@@ -23,7 +30,7 @@ const doc_code_1 = require("./doc-code");
 const doc_structure_1 = require("./doc-structure");
 const html_hover_over_1 = require("../../util/html-hover-over");
 const doc_general_1 = require("./doc-general");
-function getSourceFiles(fileNames) {
+function getTypeScriptSourceFiles(fileNames) {
     try {
         const program = typescript_1.default.createProgram(fileNames, { target: typescript_1.default.ScriptTarget.ESNext });
         return { program, files: fileNames.map(fileName => program.getSourceFile(fileName)).filter(file => !!file) };
@@ -33,7 +40,7 @@ function getSourceFiles(fileNames) {
         return { files: [], program: undefined };
     }
 }
-function dropGenericsFromType(type) {
+function dropGenericsFromTypeName(type) {
     let previous;
     do {
         previous = type;
@@ -41,7 +48,7 @@ function dropGenericsFromType(type) {
     } while (type !== previous);
     return type;
 }
-function removeCommentSymbols(comment) {
+function removeCommentSymbolsFromTypeScriptComment(comment) {
     return comment
         // remove '/** \n * \n */...
         .replace(/^\/\*\*?/gm, '').replace(/^\s*\*\s*/gm, '').replace(/\*\/$/gm, '').replace(/^\s*\*/gm, '')
@@ -49,22 +56,22 @@ function removeCommentSymbols(comment) {
         .replace(/\{@[a-zA-Z]+ ([^}]+\|)?(?<name>[^}]+)}/gm, '<code>$<name></code>')
         .trim();
 }
-function getTextualComments(node) {
+function getTextualCommentsFromTypeScript(node) {
     const comments = typescript_1.default.getJSDocCommentsAndTags(node);
     const out = [];
     for (const { comment } of comments) {
         if (typeof comment === 'string') {
-            out.push(removeCommentSymbols(comment));
+            out.push(removeCommentSymbolsFromTypeScriptComment(comment));
         }
         else if (comment !== undefined) {
             for (const c of comment) {
-                out.push(removeCommentSymbols(c.getText(c.getSourceFile())));
+                out.push(removeCommentSymbolsFromTypeScriptComment(c.getText(c.getSourceFile())));
             }
         }
     }
     return out;
 }
-function getStartLine(node, sourceFile) {
+function getStartLineOfTypeScriptNode(node, sourceFile) {
     const lineStart = sourceFile.getLineAndCharacterOfPosition(node.getStart(sourceFile)).line;
     return lineStart + 1;
 }
@@ -97,17 +104,17 @@ function collectHierarchyInformation(sourceFiles, options) {
             const interfaceName = node.name?.getText(sourceFile) ?? '';
             const baseTypes = node.heritageClauses?.flatMap(clause => clause.types
                 .map(type => type.getText(sourceFile) ?? '')
-                .map(dropGenericsFromType)) ?? [];
+                .map(dropGenericsFromTypeName)) ?? [];
             const generics = node.typeParameters?.map(param => param.getText(sourceFile) ?? '') || [];
             hierarchyList.push({
-                name: dropGenericsFromType(interfaceName),
+                name: dropGenericsFromTypeName(interfaceName),
                 node,
                 kind: 'interface',
                 extends: baseTypes,
                 generics,
-                comments: getTextualComments(node),
+                comments: getTextualCommentsFromTypeScript(node),
                 filePath: sourceFile.fileName,
-                lineNumber: getStartLine(node, sourceFile),
+                lineNumber: getStartLineOfTypeScriptNode(node, sourceFile),
                 properties: node.members.map(member => {
                     const name = member.name?.getText(sourceFile) ?? '';
                     return `${name}${(0, mermaid_1.escapeMarkdown)(': ' + getType(member, typeChecker))}`;
@@ -121,55 +128,69 @@ function collectHierarchyInformation(sourceFiles, options) {
                 baseTypes = node.type.types
                     .filter(typeNode => typescript_1.default.isTypeReferenceNode(typeNode))
                     .flatMap(typeName => followTypeReference(typeName, sourceFile))
-                    .map(dropGenericsFromType);
+                    .map(dropGenericsFromTypeName);
             }
             else if (typescript_1.default.isTypeReferenceNode(node.type)) {
-                baseTypes = [...followTypeReference(node.type, sourceFile)].map(dropGenericsFromType);
+                baseTypes = [...followTypeReference(node.type, sourceFile)].map(dropGenericsFromTypeName);
             }
             const generics = node.typeParameters?.map(param => param.getText(sourceFile) ?? '') ?? [];
             hierarchyList.push({
-                name: dropGenericsFromType(typeName),
+                name: dropGenericsFromTypeName(typeName),
                 node,
                 kind: 'type',
                 extends: baseTypes,
-                comments: getTextualComments(node),
+                comments: getTextualCommentsFromTypeScript(node),
                 generics,
                 filePath: sourceFile.fileName,
-                lineNumber: getStartLine(node, sourceFile),
+                lineNumber: getStartLineOfTypeScriptNode(node, sourceFile),
             });
         }
         else if (typescript_1.default.isEnumDeclaration(node)) {
             const enumName = node.name?.getText(sourceFile) ?? '';
             hierarchyList.push({
-                name: dropGenericsFromType(enumName),
+                name: dropGenericsFromTypeName(enumName),
                 node,
                 kind: 'enum',
                 extends: [],
-                comments: getTextualComments(node),
+                comments: getTextualCommentsFromTypeScript(node),
                 generics: [],
                 filePath: sourceFile.fileName,
-                lineNumber: getStartLine(node, sourceFile),
+                lineNumber: getStartLineOfTypeScriptNode(node, sourceFile),
                 properties: node.members.map(member => {
                     const name = member.name?.getText(sourceFile) ?? '';
                     return `${name}${(0, mermaid_1.escapeMarkdown)(': ' + getType(member, typeChecker))}`;
                 })
             });
         }
+        else if (typescript_1.default.isEnumMember(node)) {
+            const typeName = node.parent.name?.getText(sourceFile) ?? '';
+            const enumName = dropGenericsFromTypeName(typeName);
+            hierarchyList.push({
+                name: dropGenericsFromTypeName(node.name.getText(sourceFile)),
+                node,
+                kind: 'enum',
+                extends: [enumName],
+                comments: getTextualCommentsFromTypeScript(node),
+                generics: [],
+                filePath: sourceFile.fileName,
+                lineNumber: getStartLineOfTypeScriptNode(node, sourceFile),
+            });
+        }
         else if (typescript_1.default.isClassDeclaration(node)) {
             const className = node.name?.getText(sourceFile) ?? '';
             const baseTypes = node.heritageClauses?.flatMap(clause => clause.types
                 .map(type => type.getText(sourceFile) ?? '')
-                .map(dropGenericsFromType)) ?? [];
+                .map(dropGenericsFromTypeName)) ?? [];
             const generics = node.typeParameters?.map(param => param.getText(sourceFile) ?? '') ?? [];
             hierarchyList.push({
-                name: dropGenericsFromType(className),
+                name: dropGenericsFromTypeName(className),
                 node,
                 kind: 'class',
                 extends: baseTypes,
-                comments: getTextualComments(node),
+                comments: getTextualCommentsFromTypeScript(node),
                 generics,
                 filePath: sourceFile.fileName,
-                lineNumber: getStartLine(node, sourceFile),
+                lineNumber: getStartLineOfTypeScriptNode(node, sourceFile),
                 properties: node.members.map(member => {
                     const name = member.name?.getText(sourceFile) ?? '';
                     return `${name}${(0, mermaid_1.escapeMarkdown)(': ' + getType(member, typeChecker))}`;
@@ -178,16 +199,16 @@ function collectHierarchyInformation(sourceFiles, options) {
         }
         else if (typescript_1.default.isVariableDeclaration(node) || typescript_1.default.isExportDeclaration(node) || typescript_1.default.isExportAssignment(node) || typescript_1.default.isDeclarationStatement(node)) {
             const name = node.name?.getText(sourceFile) ?? '';
-            const comments = getTextualComments(node);
+            const comments = getTextualCommentsFromTypeScript(node);
             hierarchyList.push({
-                name: dropGenericsFromType(name),
+                name: dropGenericsFromTypeName(name),
                 node,
                 kind: 'variable',
                 extends: [],
                 comments,
                 generics: [],
                 filePath: sourceFile.fileName,
-                lineNumber: getStartLine(node, sourceFile),
+                lineNumber: getStartLineOfTypeScriptNode(node, sourceFile),
             });
         }
         else if (typescript_1.default.isPropertyAssignment(node) || typescript_1.default.isPropertyDeclaration(node) || typescript_1.default.isPropertySignature(node)
@@ -199,16 +220,16 @@ function collectHierarchyInformation(sourceFiles, options) {
                 parent = parent.parent;
             }
             if (typeof parent === 'object' && 'name' in parent) {
-                const comments = getTextualComments(node);
+                const comments = getTextualCommentsFromTypeScript(node);
                 hierarchyList.push({
-                    name: dropGenericsFromType(name),
+                    name: dropGenericsFromTypeName(name),
                     node,
                     kind: 'variable',
                     extends: [parent.name?.getText(sourceFile) ?? ''],
                     comments,
                     generics: [],
                     filePath: sourceFile.fileName,
-                    lineNumber: getStartLine(node, sourceFile),
+                    lineNumber: getStartLineOfTypeScriptNode(node, sourceFile),
                 });
             }
         }
@@ -219,9 +240,12 @@ function collectHierarchyInformation(sourceFiles, options) {
     });
     return hierarchyList;
 }
-function getTypePathLink({ filePath, lineNumber }, prefix = doc_files_1.RemoteFlowrFilePathBaseRef) {
-    const fromSource = filePath.replace(/^.*\/src\//, 'src/').replace(/^.*\/test\//, 'test/');
-    return `${prefix}/${fromSource}#L${lineNumber}`;
+function getTypePathForTypeScript({ filePath }) {
+    return filePath.replace(/^.*\/src\//, 'src/').replace(/^.*\/test\//, 'test/');
+}
+function getTypePathLink(elem, prefix = doc_files_1.RemoteFlowrFilePathBaseRef) {
+    const fromSource = getTypePathForTypeScript(elem);
+    return `${prefix}/${fromSource}#L${elem.lineNumber}`;
 }
 function generateMermaidClassDiagram(hierarchyList, rootName, options, visited = new Set()) {
     const collect = { nodeLines: [], edgeLines: [] };
@@ -261,10 +285,10 @@ function generateMermaidClassDiagram(hierarchyList, rootName, options, visited =
             }
             else {
                 if (node.kind === 'type' || hierarchyList.find(h => h.name === baseType)?.kind === 'type') {
-                    collect.edgeLines.push(`${dropGenericsFromType(baseType)} .. ${node.name}`);
+                    collect.edgeLines.push(`${dropGenericsFromTypeName(baseType)} .. ${node.name}`);
                 }
                 else {
-                    collect.edgeLines.push(`${dropGenericsFromType(baseType)} <|-- ${node.name}`);
+                    collect.edgeLines.push(`${dropGenericsFromTypeName(baseType)} <|-- ${node.name}`);
                 }
                 const { nodeLines, edgeLines } = generateMermaidClassDiagram(hierarchyList, baseType, options, visited);
                 collect.nodeLines.push(...nodeLines);
@@ -275,7 +299,10 @@ function generateMermaidClassDiagram(hierarchyList, rootName, options, visited =
     return collect;
 }
 function visualizeMermaidClassDiagram(hierarchyList, options) {
-    const { nodeLines, edgeLines } = generateMermaidClassDiagram(hierarchyList, options.typeName, options);
+    if (!options.typeNameForMermaid) {
+        return undefined;
+    }
+    const { nodeLines, edgeLines } = generateMermaidClassDiagram(hierarchyList, options.typeNameForMermaid, options);
     return nodeLines.length === 0 && edgeLines.length === 0 ? '' : `
 classDiagram
 direction RL
@@ -284,17 +311,20 @@ ${edgeLines.join('\n')}
 `;
 }
 function getTypesFromFileAsMermaid(fileNames, options) {
-    const { files, program } = getSourceFiles(fileNames);
+    const { files, program } = getTypeScriptSourceFiles(fileNames);
     (0, assert_1.guard)(files.length > 0, () => `No source files found for ${JSON.stringify(fileNames)}`);
     const withProgram = { ...options, program };
     const hierarchyList = collectHierarchyInformation(files, withProgram);
     return {
-        text: visualizeMermaidClassDiagram(hierarchyList, withProgram),
+        mermaid: visualizeMermaidClassDiagram(hierarchyList, withProgram),
         info: hierarchyList,
         program
     };
 }
-function getTypesFromFolderAsMermaid(options) {
+/**
+ * Inspect typescript source code for types and return a report.
+ */
+function getTypesFromFolder(options) {
     (0, assert_1.guard)(options.rootFolder !== undefined || options.files !== undefined, 'Either rootFolder or files must be provided');
     const files = [...options.files ?? []];
     if (options.rootFolder) {
@@ -356,17 +386,22 @@ function printCodeOfElement({ program, info }, name) {
     const code = node.node.getFullText(program.getSourceFile(node.node.getSourceFile().fileName));
     return `${(0, doc_code_1.codeBlock)('ts', code)}\n<i>Defined at <a href="${getTypePathLink(node)}">${getTypePathLink(node, '.')}</a></i>\n`;
 }
-function retrieveNode(name, hierarchy) {
+function fuzzyCompare(a, b) {
+    const aStr = a.toLowerCase().replace(/[^a-z0-9]/g, '-').trim();
+    const bStr = b.toLowerCase().replace(/[^a-z0-9]/g, '-').trim();
+    return aStr === bStr || aStr.includes(bStr) || bStr.includes(aStr);
+}
+function retrieveNode(name, hierarchy, fuzzy = false) {
     let container = undefined;
     if (name.includes('::')) {
         [container, name] = name.split(/:::?/);
     }
-    let node = hierarchy.filter(e => e.name === name);
+    let node = hierarchy.filter(e => fuzzy ? fuzzyCompare(e.name, name) : e.name === name);
     if (node.length === 0) {
         return undefined;
     }
     else if (container) {
-        node = node.filter(n => n.extends.includes(container));
+        node = node.filter(n => fuzzy ? n.extends.some(n => fuzzyCompare(n, container)) : n.extends.includes(container));
         if (node.length === 0) {
             return undefined;
         }
@@ -393,11 +428,20 @@ function shortLink(name, hierarchy, codeStyle = true, realNameWrapper = 'b') {
         pkg = undefined;
     }
     const comments = node.comments?.join('\n').replace(/\\?\n|```[a-zA-Z]*|\s\s*/g, ' ').replace(/<\/?code>|`/g, '').replace(/<\/?p\/?>/g, ' ').replace(/"/g, '\'') ?? '';
-    return `[${codeStyle ? '<code>' : ''}${(node.comments?.length ?? 0) > 0 ?
-        (0, html_hover_over_1.textWithTooltip)(pkg ? `${pkg}::<${realNameWrapper}>${mainName}</${realNameWrapper}>` : mainName, comments.length > 400 ? comments.slice(0, 400) + '...' : comments) : node.name}${codeStyle ? '</code>' : ''}](${getTypePathLink(node)})`;
+    return `<a href="${getTypePathLink(node)}">${codeStyle ? '<code>' : ''}${(node.comments?.length ?? 0) > 0 ?
+        (0, html_hover_over_1.textWithTooltip)(pkg ? `${pkg}::<${realNameWrapper}>${mainName}</${realNameWrapper}>` : mainName, comments.length > 400 ? comments.slice(0, 400) + '...' : comments) : node.name}${codeStyle ? '</code>' : ''}</a>`;
 }
-function getDocumentationForType(name, hierarchy, prefix = '') {
+function shortLinkFile(name, hierarchy) {
     const res = retrieveNode(name, hierarchy);
+    if (!res) {
+        console.error(`Could not find node ${name} when resolving short link!`);
+        return '';
+    }
+    const [, , node] = res;
+    return `<a href="${getTypePathLink(node)}">${getTypePathForTypeScript(node)}</a>`;
+}
+function getDocumentationForType(name, hierarchy, prefix = '', fuzzy = false) {
+    const res = retrieveNode(name, hierarchy, fuzzy);
     if (!res) {
         return '';
     }

package/documentation/print-cfg-wiki.js

@@ -32,6 +32,7 @@ const semantic_cfg_guided_visitor_1 = require("../control-flow/semantic-cfg-guid
 const doc_issue_1 = require("./doc-util/doc-issue");
 const edge_1 = require("../dataflow/graph/edge");
 const assert_1 = require("../util/assert");
+const config_1 = require("../config");
 const CfgLongExample = `f <- function(a, b = 3) {
  if(a > b) {
  	return(a * b);
@@ -89,10 +90,10 @@ class CollectNumbersSyntaxVisitor extends syntax_cfg_guided_visitor_1.SyntaxAwar
 class CollectNumbersDataflowVisitor extends dfg_cfg_guided_visitor_1.DataflowAwareCfgGuidedVisitor {
     numbers = [];
     constructor(controlFlow, dataflow) {
-        super({ controlFlow, dataflow, defaultVisitingOrder: 'forward' });
+        super({ controlFlow, dfg: dataflow, defaultVisitingOrder: 'forward' });
     }
     visitValue(node) {
-        const astNode = this.config.dataflow.graph.idMap?.get(node.id);
+        const astNode = this.config.dfg.idMap?.get(node.id);
         if ((0, r_number_1.isRNumber)(astNode)) {
             this.numbers.push(astNode.content);
         }
@@ -103,8 +104,8 @@ class CollectNumbersDataflowVisitor extends dfg_cfg_guided_visitor_1.DataflowAwa
 }
 class CollectSourcesSemanticVisitor extends semantic_cfg_guided_visitor_1.SemanticCfgGuidedVisitor {
     sources = [];
-    constructor(controlFlow, normalizedAst, dataflow) {
-        super({ controlFlow, normalizedAst, dataflow, defaultVisitingOrder: 'forward' });
+    constructor(controlFlow, normalizedAst, dataflow, config) {
+        super({ controlFlow, normalizedAst, dfg: dataflow, flowrConfig: config, defaultVisitingOrder: 'forward' });
     }
     onAssignmentCall({ source }) {
         if (source) {
@@ -117,14 +118,12 @@ class CollectSourcesSemanticVisitor extends semantic_cfg_guided_visitor_1.Semant
 }
 async function getText(shell) {
     const rversion = (await shell.usedRVersion())?.format() ?? 'unknown';
-    const types = (0, doc_types_1.getTypesFromFolderAsMermaid)({
+    const types = (0, doc_types_1.getTypesFromFolder)({
         rootFolder: path_1.default.resolve('./src'),
-        typeName: 'RNode',
         inlineTypes: doc_types_1.mermaidHide
     });
-    const testTypes = (0, doc_types_1.getTypesFromFolderAsMermaid)({
+    const testTypes = (0, doc_types_1.getTypesFromFolder)({
         rootFolder: path_1.default.resolve('./test'),
-        typeName: 'assertCfg',
         inlineTypes: doc_types_1.mermaidHide
     });
     return `${(0, doc_auto_gen_1.autoGenHeader)({ filename: module.filename, purpose: 'control flow graph', rVersion: rversion })}
@@ -206,7 +205,7 @@ ${(0, doc_structure_1.section)('Structure of the Control Flow Graph', 2, 'cfg-st
 You can produce your very own control flow graph with ${(0, doc_types_1.shortLink)(extract_cfg_1.extractCfg.name, types.info)}.
 The ${(0, doc_types_1.shortLink)(control_flow_graph_1.ControlFlowGraph.name, types.info)} class describes everything required to model the control flow graph, with its edge types described by
  ${(0, doc_types_1.shortLink)('CfgEdge', types.info)} and its vertices by ${(0, doc_types_1.shortLink)('CfgSimpleVertex', types.info)}.
-However, you should be aware of the ${(0, doc_types_1.shortLink)('ControlFlowInformation', types.info)} interface which adds some additional information the the CFG
+However, you should be aware of the ${(0, doc_types_1.shortLink)('ControlFlowInformation', types.info)} interface which adds some additional information the CFG
 (and is used during the construction of the CFG as well):
 
 ${(0, doc_types_1.printHierarchy)({ info: types.info, root: 'ControlFlowInformation', program: types.program, openTop: true })}
@@ -475,7 +474,7 @@ Again, executing it with the CFG and Dataflow of the expression \`x - 1 + 2L * 3
 
 ${await (async () => {
         const res = await (0, doc_cfg_1.getCfg)(shell, 'x - 1 + 2L * 3');
-        const visitor = new CollectNumbersDataflowVisitor(res.info, res.dataflow);
+        const visitor = new CollectNumbersDataflowVisitor(res.info, res.dataflow.graph);
         visitor.start();
         const collected = visitor.getNumbers();
         return collected.map(n => '\n- `' + JSON.stringify(n) + '`').join('');
@@ -500,7 +499,7 @@ Executing it with the CFG and Dataflow of the expression \`x <- 2; 3 -> x; assig
 
 ${await (async () => {
         const res = await (0, doc_cfg_1.getCfg)(shell, 'x <- 2; 3 -> x; assign("x", 42 + 21)');
-        const visitor = new CollectSourcesSemanticVisitor(res.info, res.ast, res.dataflow);
+        const visitor = new CollectSourcesSemanticVisitor(res.info, res.ast, res.dataflow.graph, config_1.defaultConfigOptions);
         visitor.start();
         const collected = visitor.getSources();
         return collected.map(n => '\n- `' + n + '`').join('');

package/documentation/print-core-wiki.js

@@ -42,12 +42,12 @@ const normalize_for_1 = require("../r-bridge/lang-4.x/ast/parser/main/internal/l
 const doc_issue_1 = require("./doc-util/doc-issue");
 const pipeline_executor_1 = require("../core/pipeline-executor");
 const pipeline_1 = require("../core/steps/pipeline/pipeline");
+const config_1 = require("../config");
 async function getText(shell) {
     const rversion = (await shell.usedRVersion())?.format() ?? 'unknown';
     const sampleCode = 'x <- 1; print(x)';
-    const { info, program } = (0, doc_types_1.getTypesFromFolderAsMermaid)({
+    const { info, program } = (0, doc_types_1.getTypesFromFolder)({
         rootFolder: path_1.default.resolve('./src'),
-        typeName: shell_1.RShell.name,
         inlineTypes: doc_types_1.mermaidHide
     });
     return `${(0, doc_auto_gen_1.autoGenHeader)({ filename: module.filename, purpose: 'core', rVersion: rversion })}
@@ -112,7 +112,7 @@ const result = await executor.allRemainingSteps();
 `)}
 
 This is, roughly, what the ${(0, doc_types_1.shortLink)('replGetDataflow', info)} function does for the ${(0, doc_cli_option_1.getReplCommand)('dataflow')} REPL command when using the [\`tree-sitter\` engine](${doc_files_1.FlowrWikiBaseRef}/Engines).
-We create a new ${(0, doc_types_1.shortLink)(pipeline_executor_1.PipelineExecutor.name, info)} with the ${(0, doc_types_1.shortLink)('TREE_SITTER_DATAFLOW_PIPELINE', info)} and then use ${(0, doc_types_1.shortLink)(`${pipeline_executor_1.PipelineExecutor.name}::${new pipeline_executor_1.PipelineExecutor(default_pipelines_1.TREE_SITTER_PARSE_PIPELINE, { parser: new tree_sitter_executor_1.TreeSitterExecutor(), request: (0, retriever_1.requestFromInput)('') }).allRemainingSteps.name}`, info)} 
+We create a new ${(0, doc_types_1.shortLink)(pipeline_executor_1.PipelineExecutor.name, info)} with the ${(0, doc_types_1.shortLink)('TREE_SITTER_DATAFLOW_PIPELINE', info)} and then use ${(0, doc_types_1.shortLink)(`${pipeline_executor_1.PipelineExecutor.name}::${new pipeline_executor_1.PipelineExecutor(default_pipelines_1.TREE_SITTER_PARSE_PIPELINE, { parser: new tree_sitter_executor_1.TreeSitterExecutor(), request: (0, retriever_1.requestFromInput)('') }, config_1.defaultConfigOptions).allRemainingSteps.name}`, info)} 
 to cause the execution of all contained steps (in general, pipelines can be executed step-by-step, but this is usually not required if you just want the result).
 ${(0, doc_types_1.shortLink)(retriever_1.requestFromInput.name, info)} is merely a convenience function to create a request object from a code string.
 
@@ -254,7 +254,7 @@ While looking at the mermaid visualization of such an AST is nice and usually su
 
 Let's have a look at the normalized AST for the sample code \`${sampleCode}\` (please refer to the [normalized AST](${doc_files_1.FlowrWikiBaseRef}/Normalized-AST) wiki page for more information):
 
-${(0, doc_structure_1.details)('Normalized AST for <code>x <- 1; print(x)</code>', (0, doc_code_1.codeBlock)('json', JSON.stringify((await (0, default_pipelines_1.createNormalizePipeline)(shell, { request: (0, retriever_1.requestFromInput)(sampleCode) }).allRemainingSteps()).normalize.ast, json_1.jsonReplacer, 4)))}
+${(0, doc_structure_1.details)('Normalized AST for <code>x <- 1; print(x)</code>', (0, doc_code_1.codeBlock)('json', JSON.stringify((await (0, default_pipelines_1.createNormalizePipeline)(shell, { request: (0, retriever_1.requestFromInput)(sampleCode) }, config_1.defaultConfigOptions).allRemainingSteps()).normalize.ast, json_1.jsonReplacer, 4)))}
 
 This is… a lot! We get the type from the ${(0, doc_types_1.shortLink)('RType', info)} enum, the lexeme, location information, an id, the children of the node, and their parents.
 While the [normalized AST](${doc_files_1.FlowrWikiBaseRef}/Normalized-AST) wiki page provides you with information on how to interpret this data, we will focus on how we get it from the
@@ -275,7 +275,7 @@ For single nodes, we use ${(0, doc_types_1.shortLink)(normalize_single_node_1.no
 
 The output of just this pass is listed below (using the ${(0, doc_types_1.shortLink)(parser_2.normalizeButNotDecorated.name, info)} function):
 
-${(0, doc_structure_1.details)('Ast for <code>x <- 1; print(x)</code> after the first normalization', (0, doc_code_1.codeBlock)('json', JSON.stringify((0, parser_2.normalizeButNotDecorated)((await (0, default_pipelines_1.createParsePipeline)(shell, { request: (0, retriever_1.requestFromInput)(sampleCode) }).allRemainingSteps()).parse), json_1.jsonReplacer, 4)))}
+${(0, doc_structure_1.details)('Ast for <code>x <- 1; print(x)</code> after the first normalization', (0, doc_code_1.codeBlock)('json', JSON.stringify((0, parser_2.normalizeButNotDecorated)((await (0, default_pipelines_1.createParsePipeline)(shell, { request: (0, retriever_1.requestFromInput)(sampleCode) }, config_1.defaultConfigOptions).allRemainingSteps()).parse), json_1.jsonReplacer, 4)))}
 
 
 #### Decorating the AST

package/documentation/print-dataflow-graph-wiki.js

@@ -34,9 +34,11 @@ const linker_1 = require("../dataflow/internal/linker");
 const doc_normalized_ast_1 = require("./doc-util/doc-normalized-ast");
 const dfg_get_origin_1 = require("../dataflow/origin/dfg-get-origin");
 const identify_link_to_last_call_relation_1 = require("../queries/catalog/call-context-query/identify-link-to-last-call-relation");
+const alias_tracking_1 = require("../dataflow/eval/resolve/alias-tracking");
 const doc_issue_1 = require("./doc-util/doc-issue");
 const unnamed_call_handling_1 = require("../dataflow/internal/process/functions/call/unnamed-call-handling");
 const environment_builder_1 = require("../../test/functionality/_helper/dataflow/environment-builder");
+const config_1 = require("../config");
 async function subExplanation(shell, { description, code, expectedSubgraph }) {
     expectedSubgraph = await (0, doc_dfg_1.verifyExpectedSubgraph)(shell, code, expectedSubgraph);
     const marks = [];
@@ -203,9 +205,8 @@ ${(0, doc_structure_1.details)('Example: Simple Function Call (unresolved)', awa
                 (0, assert_1.guard)(callInfo !== undefined, () => `Could not find call vertex for ${code}`);
                 const [callId, callVert] = callInfo;
                 const inverseMapReferenceTypes = Object.fromEntries(Object.entries(identifier_1.ReferenceType).map(([k, v]) => [v, k]));
-                const identifierType = (0, doc_types_1.getTypesFromFolderAsMermaid)({
+                const identifierType = (0, doc_types_1.getTypesFromFolder)({
                     files: [path_1.default.resolve('./src/dataflow/environments/identifier.ts')],
-                    typeName: 'IdentifierReference',
                     inlineTypes: ['ControlDependency']
                 });
                 return `
@@ -744,21 +745,21 @@ async function dummyDataflow() {
     const result = await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_DATAFLOW_PIPELINE, {
         parser: shell,
         request: (0, retriever_1.requestFromInput)('x <- 1\nx + 1')
-    }).allRemainingSteps();
+    }, config_1.defaultConfigOptions).allRemainingSteps();
     shell.close();
     return result;
 }
 async function getText(shell) {
     const rversion = (await shell.usedRVersion())?.format() ?? 'unknown';
     /* we collect type information on the graph */
-    const vertexType = (0, doc_types_1.getTypesFromFolderAsMermaid)({
+    const vertexType = (0, doc_types_1.getTypesFromFolder)({
         rootFolder: path_1.default.resolve('./src/'),
-        typeName: 'DataflowGraphVertexInfo',
+        typeNameForMermaid: 'DataflowGraphVertexInfo',
         inlineTypes: ['MergeableRecord']
     });
-    const edgeType = (0, doc_types_1.getTypesFromFolderAsMermaid)({
+    const edgeType = (0, doc_types_1.getTypesFromFolder)({
         files: [path_1.default.resolve('./src/dataflow/graph/edge.ts'), path_1.default.resolve('./src/dataflow/graph/graph.ts'), path_1.default.resolve('./src/dataflow/environments/identifier.ts'), path_1.default.resolve('./src/dataflow/info.ts')],
-        typeName: 'EdgeType',
+        typeNameForMermaid: 'EdgeType',
         inlineTypes: ['MergeableRecord']
     });
     return `${(0, doc_auto_gen_1.autoGenHeader)({ filename: module.filename, purpose: 'dataflow graph', rVersion: rversion })}
@@ -806,7 +807,7 @@ The following vertices types exist:
 
 1. ${(0, doc_data_dfg_util_1.getAllVertices)().map(([k, v], index) => `[\`${k}\`](#${index + 1}-${v.toLowerCase().replace(/\s/g, '-')}-vertex)`).join('\n1. ')}
 
-${vertexType.text.trim().length > 0 ? (0, doc_structure_1.details)('Class Diagram', 'All boxes should link to their respective implementation:\n' + (0, doc_code_1.codeBlock)('mermaid', vertexType.text)) : ''}
+${vertexType.mermaid.trim().length > 0 ? (0, doc_structure_1.details)('Class Diagram', 'All boxes should link to their respective implementation:\n' + (0, doc_code_1.codeBlock)('mermaid', vertexType.mermaid)) : ''}
 
 </details>
 
@@ -818,7 +819,7 @@ The following edges types exist, internally we use bitmasks to represent multipl
 
 1. ${(0, doc_data_dfg_util_1.getAllEdges)().map(([k, v], index) => `[\`${k}\` (${v})](#${index + 1}-${k.toLowerCase().replace(/\s/g, '-')}-edge)`).join('\n1. ')}
 
-${edgeType.text.trim().length > 0 ? (0, doc_structure_1.details)('Class Diagram', 'All boxes should link to their respective implementation:\n' + (0, doc_code_1.codeBlock)('mermaid', edgeType.text)) : ''}
+${edgeType.mermaid.trim().length > 0 ? (0, doc_structure_1.details)('Class Diagram', 'All boxes should link to their respective implementation:\n' + (0, doc_code_1.codeBlock)('mermaid', edgeType.mermaid)) : ''}
 
 </details>
 
@@ -977,7 +978,7 @@ Depending on what you are interested in, there exists a plethora of functions an
 * The **[Query API](${doc_files_1.FlowrWikiBaseRef}/Query%20API)** provides many functions to query the dataflow graph for specific information (dependencies, calls, slices, clusters, ...)
 * The **[Search API](${doc_files_1.FlowrWikiBaseRef}/Search%20API)** allows you to search for specific vertices or edges in the dataflow graph or the original program
 * ${(0, doc_types_1.shortLink)(node_id_1.recoverName.name, vertexType.info)} and ${(0, doc_types_1.shortLink)(node_id_1.recoverContent.name, vertexType.info)} to get the name or content of a vertex in the dataflow graph
-* ${(0, doc_types_1.shortLink)(resolve_by_name_1.resolveValueOfVariable.name, vertexType.info)} and ${(0, doc_types_1.shortLink)(resolve_by_name_1.resolveIdToValue.name, vertexType.info)} to resolve the value of a variable or id (if possible, see [below](#dfg-resolving-values))
+* ${(0, doc_types_1.shortLink)(alias_tracking_1.resolveIdToValue.name, vertexType.info)} to resolve the value of a variable or id (if possible, see [below](#dfg-resolving-values))
 * ${(0, doc_types_1.shortLink)(edge_1.edgeIncludesType.name, vertexType.info)} to check if an edge includes a specific type and ${(0, doc_types_1.shortLink)(edge_1.splitEdgeTypes.name, vertexType.info)} to split the bitmask of edges into its types (see [below](#dfg-resolving-values))
 * ${(0, doc_types_1.shortLink)(identify_link_to_last_call_relation_1.getValueOfArgument.name, vertexType.info)} to get the (syntactical) value of an argument in a function call 
 * ${(0, doc_types_1.shortLink)(dfg_get_origin_1.getOriginInDfg.name, vertexType.info)} to get information about where a read, call, ... comes from (see [below](#dfg-resolving-values))
@@ -989,8 +990,8 @@ ${(0, doc_structure_1.section)('Resolving Values', 3, 'dfg-resolving-values')}
 FlowR supports a [configurable](${doc_files_1.FlowrWikiBaseRef}/Interface#configuring-flowr) level of value tracking&mdash;all with the goal of knowing the static value domain of a variable.
 These capabilities are exposed by the [resolve value Query](${doc_files_1.FlowrWikiBaseRef}/Query-API#resolve-value-query) and backed by two important functions:
 
-${(0, doc_types_1.shortLink)(resolve_by_name_1.resolveValueOfVariable.name, vertexType.info)} provides an environment-sensitive (see ${(0, doc_types_1.shortLink)('REnvironmentInformation', vertexType.info)})
-value resolution, while ${(0, doc_types_1.shortLink)(resolve_by_name_1.resolveIdToValue.name, vertexType.info)} provides a more general, but potentially less precise resolution independent of the current state.
+${(0, doc_types_1.shortLink)(alias_tracking_1.resolveIdToValue.name, vertexType.info)} provides an environment-sensitive (see ${(0, doc_types_1.shortLink)('REnvironmentInformation', vertexType.info)})
+value resolution depending on if the environment is provided.
 
 ${(0, doc_structure_1.section)('Assessing Edges', 3, 'dfg-assess-edge')}
 
@@ -1004,7 +1005,7 @@ Retrieving the _types_ of the edge from the print call to its argument returns:
 ${await (async () => {
             const dfg = await (0, default_pipelines_1.createDataflowPipeline)(shell, {
                 request: (0, retriever_1.requestFromInput)('print(x)')
-            }).allRemainingSteps();
+            }, config_1.defaultConfigOptions).allRemainingSteps();
             const edge = dfg.dataflow.graph.outgoingEdges(3);
             if (edge) {
                 const wanted = edge.get(1);

package/documentation/print-engines-wiki.js

@@ -15,10 +15,9 @@ const doc_cli_option_1 = require("./doc-util/doc-cli-option");
 const doc_structure_1 = require("./doc-util/doc-structure");
 async function getText(shell) {
     const rversion = (await shell.usedRVersion())?.format() ?? 'unknown';
-    const types = (0, doc_types_1.getTypesFromFolderAsMermaid)({
+    const types = (0, doc_types_1.getTypesFromFolder)({
         rootFolder: path_1.default.resolve('src/r-bridge/lang-4.x/tree-sitter/'),
         files: [path_1.default.resolve('./src/config.ts'), path_1.default.resolve('./src/r-bridge/shell.ts'), path_1.default.resolve('./src/r-bridge/shell-executor.ts')],
-        typeName: 'FlowrConfigOptions',
         inlineTypes: doc_types_1.mermaidHide
     });
     return `${(0, doc_auto_gen_1.autoGenHeader)({ filename: module.filename, purpose: 'engines', rVersion: rversion })}
@@ -49,7 +48,7 @@ are exposed with some command line options (e.g., when using the docker image of
 
 ${(0, doc_structure_1.block)({
         type: 'WARNING',
-        content: 'As the tree-sitter engine is only for parsing, it cannot execute R code.'
+        content: 'As the tree-sitter engine is only for parsing, it cannot execute R code. This engine is now the default.'
     })}
 
 In general, there is no need for you to pass custom paths using either 

package/documentation/print-faq-wiki.js

@@ -24,14 +24,20 @@ There are several ways to generate mermaid diagrams based on the input data that
 
 ${qAndA('How do I create new wiki pages?', `
 To create an automatically generated wiki page, you can follow these steps:
-- Createa a new file in \`src/documentation\` with a name like \`print-my-page-wiki.ts\`.
+- Create a new file in \`src/documentation\` with a name like \`print-my-page-wiki.ts\`.
 - Add a new wiki generation script to the ${(0, doc_files_1.getFilePathMd)('../../package.json')}. You can copy one of the existing ones of the form \`"wiki:my-page": "ts-node src/documentation/print-my-page-wiki.ts"\`.
 - Add the wiki generation script to the \`broken-links-and-wiki.yml\` GitHub workflow file to enable automatic generation through the CI. You can copy one of the existing ones of the form \`update_page wiki/"My page" wiki:my-page\`.
 
 You can test your page by piping the wiki generation script to a file. For example, you can run the following command:
 ${(0, doc_code_1.codeBlock)('shell', 'npm run --silent wiki:my-page > __my-page.md')}
-`)}
+
 Remember not to commit this file, as it's only meant for testing.
+`)}
+
+${qAndA('Why can\'t I pass arguments when running flowR with npm?', `
+With \`npm\` you have to pass arguments in a specific way. The \`--\` operator is used to separate the \`npm\` arguments from the script arguments. For example, if you want to run \`flowR\` with the \`--help\` argument, you can use the following command:
+${(0, doc_code_1.codeBlock)('shell', 'npm run flowR -- --help')}
+`)}
 
 ## 🇷 R FAQ
 

package/documentation/print-interface-wiki.js

@@ -249,10 +249,9 @@ ${(0, schema_1.describeSchema)(config_1.flowrConfigFileSchema, ansi_1.markdownFo
 	`;
 }
 function explainWritingCode(shell) {
-    const types = (0, doc_types_1.getTypesFromFolderAsMermaid)({
+    const types = (0, doc_types_1.getTypesFromFolder)({
         rootFolder: path_1.default.resolve('./src/'),
         files: [path_1.default.resolve('./src/core/pipeline-executor.ts'), path_1.default.resolve('./src/core/steps/pipeline/default-pipelines.ts')],
-        typeName: 'RShell',
         inlineTypes: doc_types_1.mermaidHide
     });
     return `

package/documentation/print-linter-issue.d.ts

@@ -0,0 +1 @@
+export {};