@eagleoutice/flowr 2.7.0 → 2.7.2

package/cli/flowr.d.ts

@@ -1,4 +1,3 @@
-import commandLineUsage from 'command-line-usage';
 export declare const toolName = "flowr";
 export interface FlowrCliOptions {
     'config-file': string;
@@ -32,6 +31,107 @@ export declare const optionHelp: ({
     optionList?: undefined;
 } | {
     header: string;
-    optionList: commandLineUsage.OptionDefinition[];
+    optionList: [{
+        readonly name: "config-file";
+        readonly type: StringConstructor;
+        readonly description: "The name of the configuration file to use";
+        readonly multiple: false;
+    }, {
+        readonly name: "config-json";
+        readonly type: StringConstructor;
+        readonly description: "The flowR configuration to use, as a JSON string";
+        readonly multiple: false;
+    }, {
+        readonly name: "execute";
+        readonly alias: "e";
+        readonly type: StringConstructor;
+        readonly description: "Execute the given command and exit. Use a semicolon \";\" to separate multiple commands.";
+        readonly typeLabel: "{underline command}";
+        readonly multiple: false;
+    }, {
+        readonly name: "help";
+        readonly alias: "h";
+        readonly type: BooleanConstructor;
+        readonly description: "Print this usage guide (or the guide of the corresponding script)";
+    }, {
+        readonly name: "no-ansi";
+        readonly type: BooleanConstructor;
+        readonly description: "Disable ansi-escape-sequences in the output. Useful, if you want to redirect the output to a file.";
+    }, {
+        readonly name: "port";
+        readonly type: NumberConstructor;
+        readonly description: "The port to listen on, if --server is given.";
+        readonly defaultValue: 1042;
+        readonly typeLabel: "{underline port}";
+    }, {
+        readonly name: "r-path";
+        readonly type: StringConstructor;
+        readonly description: "The path to the R executable to use. Defaults to your PATH. This option is being phased out in favor of the engine configuration option \"engine.r-shell.r-path\", which should be used instead.";
+        readonly multiple: false;
+    }, {
+        readonly name: "r-session-access";
+        readonly type: BooleanConstructor;
+        readonly description: "Allow to access the underlying R session when using flowR (security warning: this allows the execution of arbitrary R code!)";
+    }, {
+        readonly name: "script";
+        readonly alias: "s";
+        readonly type: StringConstructor;
+        readonly description: `The sub-script to run (${string})`;
+        readonly multiple: false;
+        readonly defaultOption: true;
+        readonly typeLabel: "{underline files}";
+        readonly defaultValue: undefined;
+    }, {
+        readonly name: "server";
+        readonly type: BooleanConstructor;
+        readonly description: "Do not drop into a repl, but instead start a server on the given port (default: 1042) and listen for messages.";
+    }, {
+        readonly name: "verbose";
+        readonly alias: "v";
+        readonly type: BooleanConstructor;
+        readonly description: "Run with verbose logging (will be passed to the corresponding script)";
+    }, {
+        readonly name: "version";
+        readonly alias: "V";
+        readonly type: BooleanConstructor;
+        readonly description: "Provide information about the version of flowR as well as its underlying R system and exit.";
+    }, {
+        readonly name: "ws";
+        readonly type: BooleanConstructor;
+        readonly description: "If the server flag is set, use websocket for messaging";
+    }, {
+        readonly name: "engine.r-shell.disabled";
+        readonly type: BooleanConstructor;
+        readonly description: "Disable the R shell engine";
+    }, {
+        readonly name: "engine.r-shell.r-path";
+        readonly type: StringConstructor;
+        readonly description: "The path to the R executable to use. Defaults to your PATH.";
+        readonly multiple: false;
+    }, {
+        readonly name: "engine.tree-sitter.disabled";
+        readonly type: BooleanConstructor;
+        readonly description: "Disable the tree-sitter engine";
+    }, {
+        readonly name: "engine.tree-sitter.wasm-path";
+        readonly type: StringConstructor;
+        readonly description: "The path to the tree-sitter-r WASM binary to use. Defaults to the one shipped with flowR.";
+        readonly multiple: false;
+    }, {
+        readonly name: "engine.tree-sitter.tree-sitter-wasm-path";
+        readonly type: StringConstructor;
+        readonly description: "The path to the tree-sitter WASM binary to use. Defaults to the path specified by the tree-sitter package.";
+        readonly multiple: false;
+    }, {
+        readonly name: "engine.tree-sitter.lax";
+        readonly type: BooleanConstructor;
+        readonly description: "Use the lax parser for parsing R code (allowing for syntax errors).";
+        readonly multiple: false;
+    }, {
+        readonly name: "default-engine";
+        readonly type: StringConstructor;
+        readonly description: "The default engine to use for interacting with R code. If this is undefined, an arbitrary engine from the specified list will be used.";
+        readonly multiple: false;
+    }];
     content?: undefined;
 })[];

package/cli/repl/commands/repl-commands.d.ts

@@ -1,5 +1,29 @@
 import type { ReplCodeCommand, ReplCommand } from './repl-main';
+import { scripts } from '../../common/scripts-info';
 export declare const helpCommand: ReplCommand;
+/**
+ * All commands that should be available in the REPL.
+ */
+declare const _commands: {
+    readonly help: ReplCommand;
+    readonly quit: ReplCommand;
+    readonly version: ReplCommand;
+    readonly execute: ReplCommand;
+    readonly parse: ReplCodeCommand;
+    readonly normalize: ReplCodeCommand;
+    readonly 'normalize*': ReplCodeCommand;
+    readonly dataflow: ReplCodeCommand;
+    readonly 'dataflow*': ReplCodeCommand;
+    readonly dataflowsimple: ReplCodeCommand;
+    readonly 'dataflowsimple*': ReplCodeCommand;
+    readonly controlflow: ReplCodeCommand;
+    readonly 'controlflow*': ReplCodeCommand;
+    readonly controlflowbb: ReplCodeCommand;
+    readonly 'controlflowbb*': ReplCodeCommand;
+    readonly query: ReplCodeCommand;
+    readonly 'query*': ReplCodeCommand;
+};
+export type ReplCommandNames = keyof typeof _commands | keyof typeof scripts;
 /**
  * Retrieve all REPL commands (including those generated from master scripts)
  */
@@ -26,3 +50,4 @@ export declare function longestCommandName(): number;
  * @see {@link longestCommandName}
  */
 export declare function padCmd<T>(string: T): string;
+export {};

package/cli/repl/commands/repl-query.js

@@ -1,13 +1,13 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.queryStarCommand = exports.queryCommand = void 0;
-const retriever_1 = require("../../../r-bridge/retriever");
-const args_1 = require("../../../util/text/args");
 const ansi_1 = require("../../../util/text/ansi");
 const schema_1 = require("../../../util/schema");
 const query_1 = require("../../../queries/query");
-const json_1 = require("../../../util/json");
+const retriever_1 = require("../../../r-bridge/retriever");
 const query_print_1 = require("../../../queries/query-print");
+const json_1 = require("../../../util/json");
+const args_1 = require("../../../util/text/args");
 function printHelp(output) {
     output.stderr(`Format: ${(0, ansi_1.italic)(':query "<query>" <code>', output.formatter)}`);
     output.stdout('The query is an array of query objects to represent multiple queries. Each query object may have the following properties:');
@@ -45,8 +45,20 @@ async function processQueryArgs(output, analyzer, remainingArgs) {
         }
         const validationResult = (0, query_1.QueriesSchema)().validate(parsedQuery);
         if (validationResult.error) {
-            output.stderr(`Invalid query: ${validationResult.error.message}`);
-            printHelp(output);
+            output.stderr(`Invalid query: "${output.formatter.format(JSON.stringify(parsedQuery), { style: 3 /* FontStyles.Italic */, color: 3 /* Colors.Yellow */, effect: ansi_1.ColorEffect.Foreground })}"`);
+            for (const line of validationResult.error.details) {
+                const value = line.context?.value ? JSON.stringify(line.context.value) : undefined;
+                output.stderr(` - ${line.message} ${value ? '(' + (0, ansi_1.italic)(value, output.formatter) + ')' : ''}`);
+                const ctx = line.context;
+                for (const detail of ctx?.details?.slice(0, ctx.details.length - 1) ?? []) {
+                    if ('context' in detail && 'message' in detail.context) {
+                        const lines = detail.context.message.split('. ');
+                        for (const l of lines) {
+                            output.stderr(`   - ${l.trim()}`);
+                        }
+                    }
+                }
+            }
             return;
         }
     }

package/cli/wiki.d.ts

@@ -1,3 +1,16 @@
+import { WikiFaq } from '../documentation/wiki-faq';
+import { DocCapabilities, WikiCore, WikiDataflowGraph, WikiEngine, WikiInterface, WikiLintingAndTesting, WikiNormalizedAst, WikiQuery, WikiSearch } from '../documentation';
+import { WikiCfg } from '../documentation/wiki-cfg';
+import { WikiOnboarding } from '../documentation/wiki-onboarding';
+import { WikiAnalyzer } from '../documentation/wiki-analyzer';
+import { IssueLintingRule } from '../documentation/issue-linting-rule';
+import { DocReadme } from '../documentation/doc-readme';
+import { WikiLinter } from '../documentation/wiki-linter';
+import { WikiSetup } from '../documentation/wiki-setup';
+import { WikiOverview } from '../documentation/wiki-overview';
+export declare const AllWikiDocuments: [WikiFaq, WikiSearch, WikiCfg, WikiQuery, WikiOnboarding, WikiAnalyzer, WikiEngine, WikiNormalizedAst, WikiCore, WikiSetup, WikiOverview, WikiInterface, WikiDataflowGraph, WikiLintingAndTesting, WikiLinter, IssueLintingRule, DocReadme, DocCapabilities];
+export type ValidWikiDocumentTargets = ReturnType<typeof AllWikiDocuments[number]['getTarget']>;
+export type ValidWikiDocumentTargetsNoSuffix = ValidWikiDocumentTargets extends `${infer Name}.${string}` ? Name : never;
 /**
  * Updates and optionally re-creates all flowR wikis.
  */

package/cli/wiki.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.AllWikiDocuments = void 0;
 exports.makeAllWikis = makeAllWikis;
 const doc_context_1 = require("../documentation/wiki-mk/doc-context");
 const shell_1 = require("../r-bridge/shell");
@@ -22,7 +23,9 @@ const issue_linting_rule_1 = require("../documentation/issue-linting-rule");
 const doc_readme_1 = require("../documentation/doc-readme");
 const wiki_linter_1 = require("../documentation/wiki-linter");
 const os_1 = __importDefault(require("os"));
-const Documents = [
+const wiki_setup_1 = require("../documentation/wiki-setup");
+const wiki_overview_1 = require("../documentation/wiki-overview");
+exports.AllWikiDocuments = [
     new wiki_faq_1.WikiFaq(),
     new documentation_1.WikiSearch(),
     new wiki_cfg_1.WikiCfg(),
@@ -32,6 +35,8 @@ const Documents = [
     new documentation_1.WikiEngine(),
     new documentation_1.WikiNormalizedAst(),
     new documentation_1.WikiCore(),
+    new wiki_setup_1.WikiSetup(),
+    new wiki_overview_1.WikiOverview(),
     new documentation_1.WikiInterface(),
     new documentation_1.WikiDataflowGraph(),
     new documentation_1.WikiLintingAndTesting(),
@@ -82,7 +87,7 @@ async function makeAllWikis(force, filter) {
     console.log(`Setup for wiki generation took ${(new Date().getTime() - setupStart.getTime())}ms`);
     const changedWikis = new Set();
     try {
-        const sortedDocs = sortByLeastRecentChanged(Documents);
+        const sortedDocs = sortByLeastRecentChanged(exports.AllWikiDocuments);
         console.log(`Generating ${sortedDocs.length} wikis/docs, sorted by most recently updated...`);
         for (const doc of sortedDocs) {
             const type = doc.getTarget().toLowerCase().includes('wiki') ? 'Wiki' : 'Doc';

package/config.d.ts

@@ -152,6 +152,10 @@ export interface FlowrConfigOptions extends MergeableRecord {
      * Configuration options for abstract interpretation
      */
     readonly abstractInterpretation: {
+        /**
+         * The threshold for the number of visitations of a node at which widening should be performed to ensure the termination of the fixpoint iteration
+         */
+        readonly wideningThreshold: number;
         /**
          * The configuration of the shape inference for data frames
          */
@@ -160,10 +164,6 @@ export interface FlowrConfigOptions extends MergeableRecord {
              * The maximum number of columns names to infer for data frames before over-approximating the column names to top
              */
             readonly maxColNames: number;
-            /**
-             * The threshold for the number of visitations of a node at which widening should be performed to ensure the termination of the fixpoint iteration
-             */
-            readonly wideningThreshold: number;
             /**
              * Configuration options for reading data frame shapes from loaded external data files, such as CSV files
              */

package/config.js

@@ -86,9 +86,9 @@ exports.defaultConfigOptions = {
         }
     },
     abstractInterpretation: {
+        wideningThreshold: 4,
         dataFrame: {
             maxColNames: 50,
-            wideningThreshold: 4,
             readLoadedData: {
                 readExternalFiles: true,
                 maxReadLines: 1e6

package/control-flow/basic-cfg-guided-visitor.js

@@ -30,19 +30,18 @@ class BasicCfgGuidedVisitor {
         return true;
     }
     startVisitor(start) {
-        const g = this.config.controlFlow.graph;
-        const n = this.config.defaultVisitingOrder === 'forward' ?
-            (n) => g.ingoingEdges(n) :
-            (n) => g.outgoingEdges(n);
+        const graph = this.config.controlFlow.graph;
+        const getNext = this.config.defaultVisitingOrder === 'forward' ?
+            (node) => graph.ingoingEdges(node)?.keys().toArray().toReversed() :
+            (node) => graph.outgoingEdges(node)?.keys().toArray();
         const stack = [...start];
         while (stack.length > 0) {
-            const current = stack.shift();
+            const current = stack.pop();
             if (!this.visitNode(current)) {
                 continue;
             }
-            const outgoing = n(current) ?? [];
-            for (const [to] of outgoing) {
-                stack.unshift(to);
+            for (const next of getNext(current) ?? []) {
+                stack.push(next);
             }
         }
     }

package/control-flow/control-flow-graph.d.ts

@@ -103,7 +103,7 @@ export interface ReadOnlyControlFlowGraph {
     readonly rootIds: () => ReadonlySet<NodeId>;
     /**
      * Provide a view of all vertices in the graph.
-     * @param includeBasicBlockElements - if true, the elements of basic block elements are included in the result, otherwise this will only the basic blocks themselves
+     * @param includeBasicBlockElements - if true, the elements of basic block elements are included in the result, otherwise only the basic blocks themselves are included
      * @see {@link ReadOnlyControlFlowGraph#rootVertexIds|rootVertexIds()} - for a way to get the root vertices of the graph.
      * @see {@link ReadOnlyControlFlowGraph#getVertex|getVertex()} - for a way to get a specific vertex by its id.
      * @see {@link ReadOnlyControlFlowGraph#edges|edges()} - for a way to get all edges in the graph.

package/control-flow/semantic-cfg-guided-visitor.d.ts

@@ -205,7 +205,7 @@ export declare class SemanticCfgGuidedVisitor<OtherInfo = NoInfo, ControlFlow ex
      * @protected
      */
     protected onUnnamedCall(_data: {
-        vertex: DataflowGraphVertexFunctionCall;
+        call: DataflowGraphVertexFunctionCall;
     }): void;
     /**
      * This event triggers for every function call that is not handled by a specific overload,

package/control-flow/semantic-cfg-guided-visitor.js

@@ -115,7 +115,7 @@ class SemanticCfgGuidedVisitor extends dfg_cfg_guided_visitor_1.DataflowAwareCfg
     visitFunctionCall(vertex) {
         super.visitFunctionCall(vertex);
         if (vertex.origin === 'unnamed') {
-            this.onUnnamedCall({ vertex });
+            this.onUnnamedCall({ call: vertex });
         }
         else {
             this.onDispatchFunctionCallOrigins(vertex, vertex.origin);

package/dataflow/eval/resolve/alias-tracking.js

@@ -92,7 +92,7 @@ function getAliases(sourceIds, dataflow, environment) {
             definitions.add(def);
         }
     }
-    return [...definitions];
+    return Array.from(definitions);
 }
 /**
  * Evaluates the value of a node in the set domain.

package/dataflow/internal/linker.d.ts

@@ -19,6 +19,8 @@ export declare function findNonLocalReads(graph: DataflowGraph, ignore: readonly
 export declare function produceNameSharedIdMap(references: IdentifierReference[]): NameIdMap;
 /**
  * Links the given arguments to the given parameters within the given graph.
+ * This follows the `pmatch` semantics of R
+ * @see https://cran.r-project.org/doc/manuals/R-lang.html#Argument-matching
  */
 export declare function linkArgumentsOnCall(args: FunctionArgument[], params: RParameter<ParentInformation>[], graph: DataflowGraph): void;
 /**

package/dataflow/internal/linker.js

@@ -79,27 +79,28 @@ function produceNameSharedIdMap(references) {
 }
 /**
  * Links the given arguments to the given parameters within the given graph.
+ * This follows the `pmatch` semantics of R
+ * @see https://cran.r-project.org/doc/manuals/R-lang.html#Argument-matching
  */
 function linkArgumentsOnCall(args, params, graph) {
     const nameArgMap = new Map(args.filter(graph_1.isNamedArgument).map(a => [a.name, a]));
-    const nameParamMap = new Map(params.filter(p => p?.name?.content !== undefined).map(p => [p.name.content, p]));
+    const nameParamMap = new Map(params.filter(p => p?.name?.content !== undefined)
+        .map(p => [p.name.content, p]));
     const specialDotParameter = params.find(p => p.special);
     // all parameters matched by name
     const matchedParameters = new Set();
     // first map names
-    for (const [name, arg] of nameArgMap) {
+    for (const [name, { nodeId: argId }] of nameArgMap) {
         const pmatchName = (0, prefix_1.findByPrefixIfUnique)(name, nameParamMap.keys()) ?? name;
         const param = nameParamMap.get(pmatchName);
         if (param?.name) {
-            logger_1.dataflowLogger.trace(`mapping named argument "${name}" to parameter "${param.name.content}"`);
-            graph.addEdge(arg.nodeId, param.name.info.id, edge_1.EdgeType.DefinesOnCall);
-            graph.addEdge(param.name.info.id, arg.nodeId, edge_1.EdgeType.DefinedByOnCall);
+            graph.addEdge(argId, param.name.info.id, edge_1.EdgeType.DefinesOnCall);
+            graph.addEdge(param.name.info.id, argId, edge_1.EdgeType.DefinedByOnCall);
             matchedParameters.add(name);
         }
         else if (specialDotParameter?.name) {
-            logger_1.dataflowLogger.trace(`mapping named argument "${name}" to dot-dot-dot parameter`);
-            graph.addEdge(arg.nodeId, specialDotParameter.name.info.id, edge_1.EdgeType.DefinesOnCall);
-            graph.addEdge(specialDotParameter.name.info.id, arg.nodeId, edge_1.EdgeType.DefinedByOnCall);
+            graph.addEdge(argId, specialDotParameter.name.info.id, edge_1.EdgeType.DefinesOnCall);
+            graph.addEdge(specialDotParameter.name.info.id, argId, edge_1.EdgeType.DefinedByOnCall);
         }
     }
     const remainingParameter = params.filter(p => !p?.name || !matchedParameters.has(p.name.content));
@@ -107,12 +108,10 @@ function linkArgumentsOnCall(args, params, graph) {
     for (let i = 0; i < remainingArguments.length; i++) {
         const arg = remainingArguments[i];
         if (arg === r_function_call_1.EmptyArgument) {
-            logger_1.dataflowLogger.trace(`skipping value argument for ${i}`);
             continue;
         }
         if (remainingParameter.length <= i) {
             if (specialDotParameter !== undefined) {
-                logger_1.dataflowLogger.trace(`mapping unnamed argument ${i} (id: ${arg.nodeId}) to dot-dot-dot parameter`);
                 graph.addEdge(arg.nodeId, specialDotParameter.name.info.id, edge_1.EdgeType.DefinesOnCall);
                 graph.addEdge(specialDotParameter.name.info.id, arg.nodeId, edge_1.EdgeType.DefinedByOnCall);
             }
@@ -133,14 +132,13 @@ function linkFunctionCallArguments(targetId, idMap, functionCallName, functionRo
     // we get them by just choosing the rhs of the definition
     const linkedFunction = idMap.get(targetId);
     if (linkedFunction === undefined) {
-        logger_1.dataflowLogger.trace(`no function definition found for ${functionCallName} (${functionRootId})`);
+        logger_1.dataflowLogger.trace(`no fdef found for ${functionCallName} (${functionRootId})`);
         return;
     }
     if (linkedFunction.type !== type_1.RType.FunctionDefinition) {
         logger_1.dataflowLogger.trace(`function call definition base ${functionCallName} does not lead to a function definition (${functionRootId}) but got ${linkedFunction.type}`);
         return;
     }
-    (0, log_1.expensiveTrace)(logger_1.dataflowLogger, () => `linking arguments for ${functionCallName} (${functionRootId}) to ${JSON.stringify(linkedFunction.location)}`);
     linkArgumentsOnCall(callArgs, linkedFunction.parameters, finalGraph);
 }
 /**

package/documentation/doc-capabilities.d.ts

@@ -3,7 +3,7 @@ import { DocMaker } from './wiki-mk/doc-maker';
 /**
  * https://github.com/flowr-analysis/flowr/wiki/Capabilities
  */
-export declare class DocCapabilities extends DocMaker {
+export declare class DocCapabilities extends DocMaker<'wiki/Capabilities.md'> {
     constructor();
     protected text({ treeSitter }: DocMakerArgs): Promise<string>;
 }

package/documentation/doc-readme.d.ts

@@ -3,7 +3,7 @@ import { DocMaker } from './wiki-mk/doc-maker';
 /**
  * https://github.com/flowr-analysis/flowr/blob/main/README.md
  */
-export declare class DocReadme extends DocMaker {
+export declare class DocReadme extends DocMaker<'README.md'> {
     constructor();
     text({ treeSitter }: DocMakerArgs): Promise<string>;
 }

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

@@ -30,7 +30,7 @@ async function getCfg(parser, code, simplifications = [], useDfg = true) {
  */
 function printCfg(cfg, ast, prefix = 'flowchart BT\n', simplify = false) {
     return `
-${(0, doc_code_1.codeBlock)('mermaid', (0, cfg_1.cfgToMermaid)(cfg, ast, prefix, simplify))}
+${(0, doc_code_1.codeBlock)('mermaid', (0, cfg_1.cfgToMermaid)(cfg, ast, { prefix, simplify }))}
 	`;
 }
 /**

package/documentation/doc-util/doc-cli-option.d.ts

@@ -1,17 +1,17 @@
 /** Automatically provides hover over with the documentation for these! */
 import { scripts } from '../../cli/common/scripts-info';
 import { flowrMainOptionDefinitions } from '../../cli/flowr-main-options';
-type ScriptOptions<Type extends keyof typeof scripts | 'flowr'> = Type extends keyof typeof scripts ? typeof scripts[Type]['options'][number]['name'] : Type extends 'flowr' ? typeof flowrMainOptionDefinitions[number]['name'] : never;
+import type { ReplCommandNames } from '../../cli/repl/commands/repl-commands';
+export type ScriptOptions<Type extends keyof typeof scripts | 'flowr'> = Type extends keyof typeof scripts ? typeof scripts[Type]['options'][number]['name'] : Type extends 'flowr' ? typeof flowrMainOptionDefinitions[number]['name'] : never;
 /**
- *
+ * Produce the documentation string for a CLI long option
  */
 export declare function getCliLongOptionOf<ScriptName extends keyof typeof scripts | 'flowr', OptionName extends ScriptOptions<ScriptName>>(scriptName: ScriptName, optionName: OptionName, withAlias?: boolean, quote?: boolean): string;
 /**
- *
+ * Produce the documentation string for multiple CLI long options
  */
 export declare function multipleCliOptions<ScriptName extends keyof typeof scripts | 'flowr', OptionName extends ScriptOptions<ScriptName>>(scriptName: ScriptName, ...options: OptionName[]): string;
 /**
- *
+ * Produce the documentation string for a REPL command
  */
-export declare function getReplCommand(commandName: string, quote?: boolean, showStar?: boolean): string;
-export {};
+export declare function getReplCommand(commandName: ReplCommandNames | string, quote?: boolean, showStar?: boolean): string;

package/documentation/doc-util/doc-cli-option.js

@@ -11,7 +11,7 @@ const flowr_main_options_1 = require("../../cli/flowr-main-options");
 const repl_commands_1 = require("../../cli/repl/commands/repl-commands");
 const doc_escape_1 = require("./doc-escape");
 /**
- *
+ * Produce the documentation string for a CLI long option
  */
 function getCliLongOptionOf(scriptName, optionName, withAlias = false, quote = true) {
     const script = scriptName === 'flowr' ? flowr_main_options_1.flowrMainOptionDefinitions : scripts_info_1.scripts[scriptName].options;
@@ -26,13 +26,13 @@ function getCliLongOptionOf(scriptName, optionName, withAlias = false, quote = t
     return (0, html_hover_over_1.textWithTooltip)(`${char}-${ligatureBreaker}-${optionName}${char}`, 'Description (Command Line Argument): ' + description) + alias;
 }
 /**
- *
+ * Produce the documentation string for multiple CLI long options
  */
 function multipleCliOptions(scriptName, ...options) {
     return options.map(o => getCliLongOptionOf(scriptName, o, false, true)).join(' ');
 }
 /**
- *
+ * Produce the documentation string for a REPL command
  */
 function getReplCommand(commandName, quote = true, showStar = false) {
     const availableNames = (0, repl_commands_1.getReplCommands)();

package/documentation/doc-util/doc-dfg.d.ts

@@ -1,8 +1,8 @@
 import type { DataflowGraph, UnknownSideEffect } from '../../dataflow/graph/graph';
-import { type MermaidMarkdownMark } from '../../util/mermaid/dfg';
 import type { DEFAULT_DATAFLOW_PIPELINE } from '../../core/steps/pipeline/default-pipelines';
 import type { PipelineOutput } from '../../core/steps/pipeline/pipeline';
 import type { KnownParser } from '../../r-bridge/parser';
+import type { MermaidMarkdownMark } from '../../util/mermaid/info';
 /**
  * Visualizes the dataflow graph as a mermaid graph inside a markdown code block.
  * Please use this only for documentation purposes, for programmatic usage use {@link graphToMermaid} directly.

package/documentation/doc-util/doc-files.d.ts

@@ -3,11 +3,14 @@ export declare const FlowrGithubBaseRef = "https://github.com/flowr-analysis";
 export declare const FlowrSiteBaseRef = "https://flowr-analysis.github.io/flowr";
 export declare const RemoteFlowrFilePathBaseRef = "https://github.com/flowr-analysis/flowr/tree/main/";
 export declare const FlowrWikiBaseRef = "https://github.com/flowr-analysis/flowr/wiki";
+export declare const FlowrGithubRef: string;
 export declare const FlowrNpmRef = "https://www.npmjs.com/package/@eagleoutice/flowr";
 export declare const FlowrDockerRef = "https://hub.docker.com/r/eagleoutice/flowr";
 export declare const FlowrCodecovRef = "https://app.codecov.io/gh/flowr-analysis/flowr";
 export declare const FlowrVsCode = "https://marketplace.visualstudio.com/items?itemName=code-inspect.vscode-flowr";
 export declare const FlowrPositron = "https://open-vsx.org/extension/code-inspect/vscode-flowr";
+export declare const FlowrRStudioAddin = "https://github.com/flowr-analysis/rstudio-addin-flowr";
+export declare const FlowrRAdapter = "https://github.com/flowr-analysis/flowr-r-adapter";
 /**
  * Returns a markdown link to the given file path relative to the project root.
  */

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

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.FlowrPositron = exports.FlowrVsCode = exports.FlowrCodecovRef = exports.FlowrDockerRef = exports.FlowrNpmRef = exports.FlowrWikiBaseRef = exports.RemoteFlowrFilePathBaseRef = exports.FlowrSiteBaseRef = exports.FlowrGithubBaseRef = exports.FlowrGithubGroupName = void 0;
+exports.FlowrRAdapter = exports.FlowrRStudioAddin = exports.FlowrPositron = exports.FlowrVsCode = exports.FlowrCodecovRef = exports.FlowrDockerRef = exports.FlowrNpmRef = exports.FlowrGithubRef = exports.FlowrWikiBaseRef = exports.RemoteFlowrFilePathBaseRef = exports.FlowrSiteBaseRef = exports.FlowrGithubBaseRef = exports.FlowrGithubGroupName = void 0;
 exports.getFilePathMd = getFilePathMd;
 exports.getFileContentFromRoot = getFileContentFromRoot;
 exports.linkFlowRSourceFile = linkFlowRSourceFile;
@@ -13,11 +13,14 @@ exports.FlowrGithubBaseRef = `https://github.com/${exports.FlowrGithubGroupName}
 exports.FlowrSiteBaseRef = `https://${exports.FlowrGithubGroupName}.github.io/flowr`;
 exports.RemoteFlowrFilePathBaseRef = `${exports.FlowrGithubBaseRef}/flowr/tree/main/`;
 exports.FlowrWikiBaseRef = `${exports.FlowrGithubBaseRef}/flowr/wiki`;
+exports.FlowrGithubRef = exports.FlowrGithubBaseRef + '/flowr';
 exports.FlowrNpmRef = 'https://www.npmjs.com/package/@eagleoutice/flowr';
 exports.FlowrDockerRef = 'https://hub.docker.com/r/eagleoutice/flowr';
 exports.FlowrCodecovRef = `https://app.codecov.io/gh/${exports.FlowrGithubGroupName}/flowr`;
 exports.FlowrVsCode = 'https://marketplace.visualstudio.com/items?itemName=code-inspect.vscode-flowr';
 exports.FlowrPositron = 'https://open-vsx.org/extension/code-inspect/vscode-flowr';
+exports.FlowrRStudioAddin = `${exports.FlowrGithubBaseRef}/rstudio-addin-flowr`;
+exports.FlowrRAdapter = `${exports.FlowrGithubBaseRef}/flowr-r-adapter`;
 /**
  * Returns a markdown link to the given file path relative to the project root.
  */

package/documentation/doc-util/doc-normalized-ast.js

@@ -19,7 +19,7 @@ const flowr_analyzer_context_1 = require("../../project/context/flowr-analyzer-c
 function printNormalizedAst(ast, prefix = 'flowchart TD\n') {
     return `
 \`\`\`mermaid
-${(0, ast_1.normalizedAstToMermaid)(ast, prefix)}
+${(0, ast_1.normalizedAstToMermaid)(ast, { prefix })}
 \`\`\`
 	`;
 }
@@ -50,7 +50,7 @@ ${code}
 <summary style="color:gray">Mermaid Code</summary>
 
 \`\`\`
-${(0, ast_1.normalizedAstToMermaid)(result.normalize.ast, prefix)}
+${(0, ast_1.normalizedAstToMermaid)(result.normalize.ast, { prefix })}
 \`\`\`
 
 </details>

package/documentation/issue-linting-rule.d.ts

@@ -3,7 +3,7 @@ import { DocMaker } from './wiki-mk/doc-maker';
 /**
  * https://github.com/flowr-analysis/flowr/blob/main/.github/ISSUE_TEMPLATE/linting-rule.yaml
  */
-export declare class IssueLintingRule extends DocMaker {
+export declare class IssueLintingRule extends DocMaker<'.github/ISSUE_TEMPLATE/linting-rule.yaml'> {
     constructor();
     text({ ctx }: DocMakerArgs): string;
 }

package/documentation/wiki-analyzer.d.ts

@@ -3,7 +3,7 @@ import { DocMaker } from './wiki-mk/doc-maker';
 /**
  * https://github.com/flowr-analysis/flowr/wiki/Analyzer
  */
-export declare class WikiAnalyzer extends DocMaker {
+export declare class WikiAnalyzer extends DocMaker<'wiki/Analyzer.md'> {
     constructor();
     text({ ctx }: DocMakerArgs): string;
 }

package/documentation/wiki-cfg.d.ts

@@ -3,7 +3,7 @@ import { DocMaker } from './wiki-mk/doc-maker';
 /**
  * https://github.com/flowr-analysis/flowr/wiki/Control-Flow-Graph
  */
-export declare class WikiCfg extends DocMaker {
+export declare class WikiCfg extends DocMaker<'wiki/Control Flow Graph.md'> {
     constructor();
     text({ ctx, shell }: DocMakerArgs): Promise<string>;
 }

package/documentation/wiki-core.d.ts

@@ -8,7 +8,7 @@ export declare function inspectContextExample(analyzer: FlowrAnalyzer): void;
 /**
  * https://github.com/flowr-analysis/flowr/wiki/Core
  */
-export declare class WikiCore extends DocMaker {
+export declare class WikiCore extends DocMaker<'wiki/Core.md'> {
     constructor();
     text({ shell, treeSitter, ctx }: DocMakerArgs): Promise<string>;
 }

package/documentation/wiki-dataflow-graph.d.ts

@@ -3,7 +3,7 @@ import { DocMaker } from './wiki-mk/doc-maker';
 /**
  * https://github.com/flowr-analysis/flowr/wiki/Dataflow-Graph
  */
-export declare class WikiDataflowGraph extends DocMaker {
+export declare class WikiDataflowGraph extends DocMaker<'wiki/Dataflow Graph.md'> {
     constructor();
     protected text({ ctx, treeSitter }: DocMakerArgs): Promise<string>;
 }