@eagleoutice/flowr 2.6.3 → 2.7.2

package/dataflow/internal/process/process-value.js

@@ -7,18 +7,18 @@ const identifier_1 = require("../../environments/identifier");
 /**
  *
  */
-function processValue({ info: { id } }, data) {
+function processValue({ info: { id } }, { controlDependencies, completeAst: { idMap }, ctx: { env }, environment }) {
     return {
         unknownReferences: [],
-        in: [{ nodeId: id, name: undefined, controlDependencies: data.controlDependencies, type: identifier_1.ReferenceType.Constant }],
+        in: [{ nodeId: id, name: undefined, controlDependencies, type: identifier_1.ReferenceType.Constant }],
         out: [],
-        environment: data.environment,
-        graph: new graph_1.DataflowGraph(data.completeAst.idMap).addVertex({
+        environment,
+        graph: new graph_1.DataflowGraph(idMap).addVertex({
             tag: vertex_1.VertexType.Value,
             id: id,
-            cds: data.controlDependencies
-        }),
-        exitPoints: [{ nodeId: id, type: 0 /* ExitPointType.Default */, controlDependencies: data.controlDependencies }],
+            cds: controlDependencies
+        }, env.makeCleanEnv()),
+        exitPoints: [{ nodeId: id, type: 0 /* ExitPointType.Default */, controlDependencies }],
         entryPoint: id
     };
 }

package/dataflow/processor.d.ts

@@ -3,7 +3,7 @@
  */
 import type { ControlDependency, DataflowInformation } from './info';
 import type { NormalizedAst, ParentInformation, RNodeWithParent } from '../r-bridge/lang-4.x/ast/model/processing/decorate';
-import type { IEnvironment, REnvironmentInformation } from './environments/environment';
+import type { REnvironmentInformation } from './environments/environment';
 import type { RNode } from '../r-bridge/lang-4.x/ast/model/model';
 import type { KnownParserType, Parser } from '../r-bridge/parser';
 import type { FlowrAnalyzerContext } from '../project/context/flowr-analyzer-context';
@@ -31,10 +31,6 @@ export interface DataflowProcessorInformation<OtherInfo> {
      * The chain of control-flow {@link NodeId}s that lead to the current node (e.g., of known ifs).
      */
     readonly controlDependencies: ControlDependency[] | undefined;
-    /**
-     * The built-in environment
-     */
-    readonly builtInEnvironment: IEnvironment;
     /**
      * The flowr context used for environment seeding, files, and precision control, ...
      */

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-dfg.js

@@ -82,13 +82,14 @@ ${switchCodeAndGraph ? dfGraph : codeText}
 }
 /** returns resolved expected df graph */
 async function verifyExpectedSubgraph(parser, code, expectedSubgraph) {
+    const context = (0, flowr_analyzer_context_1.contextFromInput)(code);
     /* we verify that we get what we want first! */
     const info = await (0, default_pipelines_1.createDataflowPipeline)(parser, {
-        context: (0, flowr_analyzer_context_1.contextFromInput)(code),
+        context: context,
         getId: (0, decorate_1.deterministicCountingIdGenerator)(0)
     }).allRemainingSteps();
     expectedSubgraph.setIdMap(info.normalize.idMap);
-    expectedSubgraph = (0, resolve_graph_1.resolveDataflowGraph)(expectedSubgraph);
+    expectedSubgraph = (0, resolve_graph_1.resolveDataflowGraph)(expectedSubgraph, context);
     const report = (0, diff_dataflow_graph_1.diffOfDataflowGraphs)({ name: 'expected', graph: expectedSubgraph }, { name: 'got', graph: info.dataflow.graph }, {
         leftIsSubgraph: true
     });

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>
@@ -64,12 +64,13 @@ ${(0, ast_1.normalizedAstToMermaid)(result.normalize.ast, prefix)}
  */
 async function verifyExpectedSubgraph(shell, code, expectedSubgraph) {
     /* we verify that we get what we want first! */
+    const context = (0, flowr_analyzer_context_1.contextFromInput)(code);
     const info = await (0, default_pipelines_1.createDataflowPipeline)(shell, {
-        context: (0, flowr_analyzer_context_1.contextFromInput)(code),
+        context: context,
         getId: (0, decorate_1.deterministicCountingIdGenerator)(0)
     }).allRemainingSteps();
     expectedSubgraph.setIdMap(info.normalize.idMap);
-    expectedSubgraph = (0, resolve_graph_1.resolveDataflowGraph)(expectedSubgraph);
+    expectedSubgraph = (0, resolve_graph_1.resolveDataflowGraph)(expectedSubgraph, context);
     const report = (0, diff_dataflow_graph_1.diffOfDataflowGraphs)({ name: 'expected', graph: expectedSubgraph }, { name: 'got', graph: info.dataflow.graph }, {
         leftIsSubgraph: true
     });

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

@@ -133,7 +133,7 @@ export interface FnElementInfo {
 export declare function printCodeOfElement({ program, info, dropLinesEnd, dropLinesStart, doNotAutoGobble, hideDefinedAt }: FnElementInfo, name: string): string;
 /**
  * Create a short link to a type in the documentation.
- * If you create a wiki, please refer to the functions provided by the {@link GeneralWikiContext}.
+ * If you create a wiki, please refer to the functions provided by the {@link GeneralDocContext}.
  * @param name      - The name of the type, e.g. `MyType`, may include a container, e.g.,`MyContainer::MyType` (this works with function nestings too)
  *                    Use `:::` if you want to access a scoped function, but the name should be displayed without the scope
  * @param hierarchy - The hierarchy of types to search in

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

@@ -477,7 +477,7 @@ function printCodeOfElement({ program, info, dropLinesEnd = 0, dropLinesStart =
         const lines = code.replaceAll('\t', '    ').split(/\n/g);
         let gobble = Number.POSITIVE_INFINITY;
         for (const line of lines) {
-            const match = line.match(/^(\s+)\S+/);
+            const match = line.match(/^(\s*)\S+/);
             if (match) {
                 gobble = Math.min(gobble, match[1].length);
             }
@@ -523,7 +523,7 @@ function retrieveNode(name, hierarchy, fuzzy = false, type = undefined) {
 }
 /**
  * Create a short link to a type in the documentation.
- * If you create a wiki, please refer to the functions provided by the {@link GeneralWikiContext}.
+ * If you create a wiki, please refer to the functions provided by the {@link GeneralDocContext}.
  * @param name      - The name of the type, e.g. `MyType`, may include a container, e.g.,`MyContainer::MyType` (this works with function nestings too)
  *                    Use `:::` if you want to access a scoped function, but the name should be displayed without the scope
  * @param hierarchy - The hierarchy of types to search in

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-analyzer.js

@@ -26,6 +26,7 @@ const flowr_analyzer_plugin_defaults_1 = require("../project/plugins/flowr-analy
 const doc_maker_1 = require("./wiki-mk/doc-maker");
 const flowr_analyzer_rmd_file_plugin_1 = require("../project/plugins/file-plugins/notebooks/flowr-analyzer-rmd-file-plugin");
 const flowr_analyzer_plugin_1 = require("../project/plugins/flowr-analyzer-plugin");
+const flowr_analyzer_environment_context_1 = require("../project/context/flowr-analyzer-environment-context");
 async function analyzerQuickExample() {
     const analyzer = await new flowr_analyzer_builder_1.FlowrAnalyzerBuilder()
         .setEngine('tree-sitter')
@@ -78,7 +79,8 @@ ${(0, doc_structure_1.collapsibleToc)({
             'Context Information': {
                 'Files Context': undefined,
                 'Loading Order Context': undefined,
-                'Dependencies Context': undefined
+                'Dependencies Context': undefined,
+                'Environment Context': undefined
             },
             'Caching': undefined
         })}
@@ -396,6 +398,17 @@ Probably the most important method is
 ${ctx.linkM(flowr_analyzer_dependencies_context_1.FlowrAnalyzerDependenciesContext, 'getDependency', { codeFont: true, realNameWrapper: 'i' })}
 that allows you to query for a specific dependency by name.
 
+${(0, doc_structure_1.section)('Environment Context', 3)}
+
+Here is the structure of the ${ctx.link(flowr_analyzer_environment_context_1.FlowrAnalyzerEnvironmentContext)} that provides access to the built-in environment:
+
+${ctx.hierarchy(flowr_analyzer_environment_context_1.FlowrAnalyzerEnvironmentContext, { showImplSnippet: false })}
+
+The environment context provides access to the built-in environment via
+${ctx.linkM(flowr_analyzer_environment_context_1.FlowrAnalyzerEnvironmentContext, 'makeCleanEnv', { codeFont: true, realNameWrapper: 'i' })}.
+It also provides the empty built-in environment, which only contains primitives, via
+${ctx.linkM(flowr_analyzer_environment_context_1.FlowrAnalyzerEnvironmentContext, 'makeCleanEnvWithEmptyBuiltIns', { codeFont: true, realNameWrapper: 'i' })}.
+
 ${(0, doc_structure_1.section)('Caching', 2)}
 
 To speed up analyses, flowR provides a caching mechanism that stores intermediate results of the analysis.

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>;
 }

package/documentation/wiki-dataflow-graph.js

@@ -195,7 +195,7 @@ However, in general, flowR may use any fitting handler as an origin. For example
 ${(0, doc_structure_1.details)('Example: Simple Function Call (unresolved)', await (async () => {
                 const code = 'foo(x,3,y=3,)';
                 const [text, info] = await (0, doc_dfg_1.printDfGraphForCode)(parser, code, { mark: new Set([8]), exposeResult: true });
-                const callInfo = [...info.dataflow.graph.vertices(true)].find(([, vertex]) => vertex.tag === vertex_1.VertexType.FunctionCall && vertex.name === 'foo');
+                const callInfo = info.dataflow.graph.vertices(true).find(([, vertex]) => vertex.tag === vertex_1.VertexType.FunctionCall && vertex.name === 'foo');
                 (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]));
@@ -308,7 +308,7 @@ Consider a case in which you have a built-in function (like the assignment opera
 
 ${await (async () => {
                     const [text, info] = await (0, doc_dfg_1.printDfGraphForCode)(parser, 'x <- 2\nif(u) `<-` <- `*`\nx <- 3', { switchCodeAndGraph: true, mark: new Set([9, '9->0', '9->10']), exposeResult: true });
-                    const interestingUseOfAssignment = [...info.dataflow.graph.vertices(true)].find(([, vertex]) => vertex.id === 11);
+                    const interestingUseOfAssignment = info.dataflow.graph.vertices(true).find(([, vertex]) => vertex.id === 11);
                     (0, assert_1.guard)(interestingUseOfAssignment !== undefined, () => 'Could not find interesting assignment vertex for the code');
                     const [id, interestingVertex] = interestingUseOfAssignment;
                     const env = interestingVertex.environment;
@@ -333,7 +333,7 @@ Hence, trying to re-resolve the call using ${ctx.link(linker_1.getAllFunctionCal
 the following target ids: { \`${[...(0, linker_1.getAllFunctionCallTargets)(id, info.dataflow.graph)].join('`, `')}\` }.
 This way we know that the call may refer to the built-in assignment operator or to the multiplication.
 Similarly, trying to resolve the name with ${ctx.link(resolve_by_name_1.resolveByName)}\` using the environment attached to the call vertex (filtering for any reference type) returns (in a similar fashion): 
-{ \`${(0, resolve_by_name_1.resolveByName)(name, env)?.map(d => d.nodeId).join('`, `')}\` } (however, the latter will not trace aliases).
+{ \`${(0, resolve_by_name_1.resolveByNameAnyType)(name, env)?.map(d => d.nodeId).join('`, `')}\` } (however, the latter will not trace aliases).
 
 	`;
                 })()}
@@ -449,8 +449,7 @@ vertices of function definitions or not (e.g., \`${new graph_1.DataflowGraph(und
 
 ${(0, doc_structure_1.details)('Example: Nested Function Definitions', await (async () => {
                     const [text, info] = await (0, doc_dfg_1.printDfGraphForCode)(parser, 'f <- function() { g <- function() 3 }', { mark: new Set([9, 6]), exposeResult: true });
-                    const definitions = info.dataflow.graph.vertices(true)
-                        .filter(([, vertex]) => vertex.tag === vertex_1.VertexType.FunctionDefinition)
+                    const definitions = info.dataflow.graph.verticesOfType(vertex_1.VertexType.FunctionDefinition)
                         .map(([id, vertex]) => `| \`${id}\` | { \`${[...vertex.subflow.graph].join('`, `')}\` } |`)
                         .toArray();
                     return `
@@ -740,7 +739,7 @@ class WikiDataflowGraph extends doc_maker_1.DocMaker {
         return `
 This page briefly summarizes flowR's dataflow graph, represented by the ${ctx.link(graph_1.DataflowGraph)} class within the code.
 In case you want to manually build such a graph (e.g., for testing), you can use the ${ctx.link(dataflowgraph_builder_1.DataflowGraphBuilder)}.
-If you are interested in which features we support and which features are still to be worked on, please refer to our [capabilities](${doc_files_1.FlowrWikiBaseRef}/Capabilities) page.
+If you are interested in which features we support and which features are still to be worked on, please refer to our ${ctx.linkPage('wiki/Capabilities')} page.
 In summary, we discuss the following topics:
 
 - [Vertices](#vertices)
@@ -759,12 +758,12 @@ wiki page if you are unsure.
 
 > [!TIP]
 > If you want to investigate the dataflow graph,
-> you can either use the [Visual Studio Code extension](${doc_files_1.FlowrGithubBaseRef}/vscode-flowr) or the ${(0, doc_cli_option_1.getReplCommand)('dataflow*')}
-> command in the REPL (see the [Interface wiki page](${doc_files_1.FlowrWikiBaseRef}/Interface) for more information). 
-> There is also a simplified perspective available with ${(0, doc_cli_option_1.getReplCommand)('dataflowsimple*')} that does not show everything but is easier to read.
+> you can either use the [Visual Studio Code extension](${doc_files_1.FlowrVsCode}) or the ${ctx.replCmd('dataflow*')}
+> command in the REPL (see the ${ctx.linkPage('wiki/Interface', 'Interface wiki page')} for more information). 
+> There is also a simplified perspective available with ${ctx.replCmd('dataflowsimple*')} that does not show everything but is easier to read.
 > When using _flowR_ as a library, you may use the functions in ${(0, doc_files_1.getFilePathMd)('../util/mermaid/dfg.ts')}.
 > 
-> If you receive a dataflow graph in its serialized form (e.g., by talking to a [_flowR_ server](${doc_files_1.FlowrWikiBaseRef}/Interface)), you can use ${ctx.link(`${graph_1.DataflowGraph.name}::${graph_1.DataflowGraph.fromJson.name}`, { realNameWrapper: 'i', codeFont: true })} to retrieve the graph from the JSON representation.
+> If you receive a dataflow graph in its serialized form (e.g., by talking to a [_flowR_ server](${doc_files_1.FlowrWikiBaseRef}/Interface)), you can use ${ctx.linkM(graph_1.DataflowGraph, 'fromJson', { realNameWrapper: 'i', codeFont: true })} to retrieve the graph from the JSON representation.
 >
 > Also, check out the [${doc_files_1.FlowrGithubGroupName}/sample-analyzer-df-diff](${doc_files_1.FlowrGithubBaseRef}/sample-analyzer-df-diff) repository for a complete example project creating and comparing dataflow graphs.
 
@@ -774,7 +773,7 @@ ${await (0, doc_dfg_1.printDfGraphForCode)(treeSitter, 'x <- 3\ny <- x + 1\ny')}
 The above dataflow graph showcases the general gist. We define a dataflow graph as a directed graph G = (V, E), differentiating between ${(0, doc_data_dfg_util_1.getAllVertices)().length} types of vertices V and
 ${(0, doc_data_dfg_util_1.getAllEdges)().length} types of edges E allowing each vertex to have a single, and each edge to have multiple distinct types.
 Additionally, every node may have links to its [control dependencies](#control-dependencies) (which you may view as a ${(0, text_1.nth)((0, doc_data_dfg_util_1.getAllEdges)().length + 1)} edge type, 
-although they are explicitly no data dependency and relate to the [Control Flow Graph](${doc_files_1.FlowrWikiBaseRef}/Control%20Flow%20Graph)).
+although they are explicitly no data dependency and relate to the ${ctx.linkPage('wiki/Control Flow Graph')}. 
 
 <details open>
 

package/documentation/wiki-engine.d.ts

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

package/documentation/wiki-engine.js

@@ -5,7 +5,6 @@ const shell_1 = require("../r-bridge/shell");
 const shell_executor_1 = require("../r-bridge/shell-executor");
 const tree_sitter_executor_1 = require("../r-bridge/lang-4.x/tree-sitter/tree-sitter-executor");
 const doc_files_1 = require("./doc-util/doc-files");
-const doc_cli_option_1 = require("./doc-util/doc-cli-option");
 const doc_structure_1 = require("./doc-util/doc-structure");
 const doc_maker_1 = require("./wiki-mk/doc-maker");
 /**
@@ -30,13 +29,13 @@ we provide the concept of engines.
 Engines can be loaded with [flowR's configuration file](${doc_files_1.FlowrWikiBaseRef}/Interface#configuring-flowr). Additionally, they
 are exposed with some command line options (e.g., when using the docker image of flowR):
 
-- ${(0, doc_cli_option_1.getCliLongOptionOf)('flowr', 'engine.r-shell.disabled', false)} to disable the ${ctx.link(shell_1.RShell)} engine
-- ${(0, doc_cli_option_1.getCliLongOptionOf)('flowr', 'engine.r-shell.r-path', false)} (which is the canonical version of ${(0, doc_cli_option_1.getCliLongOptionOf)('flowr', 'r-path')})
-- ${(0, doc_cli_option_1.getCliLongOptionOf)('flowr', 'engine.tree-sitter.disabled', false)} to disable the ${ctx.link(tree_sitter_executor_1.TreeSitterExecutor)} engine
-- ${(0, doc_cli_option_1.getCliLongOptionOf)('flowr', 'engine.tree-sitter.lax', false)} to use lax parsing with tree-sitter
-- ${(0, doc_cli_option_1.getCliLongOptionOf)('flowr', 'engine.tree-sitter.wasm-path', false)} pass the path to the wasm of the r grammar of tree-sitter (see [below](#tree-sitter))
-- ${(0, doc_cli_option_1.getCliLongOptionOf)('flowr', 'engine.tree-sitter.tree-sitter-wasm-path', false)} pass the path to the wasm of tree-sitter (see [below](#tree-sitter))
-- ${(0, doc_cli_option_1.getCliLongOptionOf)('flowr', 'default-engine', false)} to set the default engine to use
+- ${ctx.cliOption('flowr', 'engine.r-shell.disabled', false)} to disable the ${ctx.link(shell_1.RShell)} engine
+- ${ctx.cliOption('flowr', 'engine.r-shell.r-path', false)} (which is the canonical version of ${ctx.cliOption('flowr', 'r-path')})
+- ${ctx.cliOption('flowr', 'engine.tree-sitter.disabled', false)} to disable the ${ctx.link(tree_sitter_executor_1.TreeSitterExecutor)} engine
+- ${ctx.cliOption('flowr', 'engine.tree-sitter.lax', false)} to use lax parsing with tree-sitter
+- ${ctx.cliOption('flowr', 'engine.tree-sitter.wasm-path', false)} pass the path to the wasm of the r grammar of tree-sitter (see [below](#tree-sitter))
+- ${ctx.cliOption('flowr', 'engine.tree-sitter.tree-sitter-wasm-path', false)} pass the path to the wasm of tree-sitter (see [below](#tree-sitter))
+- ${ctx.cliOption('flowr', 'default-engine', false)} to set the default engine to use
 
 <a id="tree-sitter"></a>
 ## Dealing with the Tree-Sitter Engine
@@ -47,8 +46,8 @@ ${(0, doc_structure_1.block)({
         })}
 
 In general, there is no need for you to pass custom paths using either
-${(0, doc_cli_option_1.getCliLongOptionOf)('flowr', 'engine.tree-sitter.wasm-path', false)} or
-${(0, doc_cli_option_1.getCliLongOptionOf)('flowr', 'engine.tree-sitter.tree-sitter-wasm-path', false)}.
+${ctx.cliOption('flowr', 'engine.tree-sitter.wasm-path', false)} or
+${ctx.cliOption('flowr', 'engine.tree-sitter.tree-sitter-wasm-path', false)}.
 However, you may want to experiment with the R grammar or provide a newer
 one in case that of _flowR_ is outdated.
 

package/documentation/wiki-faq.d.ts

@@ -2,7 +2,7 @@ import { DocMaker } from './wiki-mk/doc-maker';
 /**
  * https://github.com/flowr-analysis/flowr/wiki/FAQ
  */
-export declare class WikiFaq extends DocMaker {
+export declare class WikiFaq extends DocMaker<'wiki/FAQ.md'> {
     constructor();
     text(): string;
 }

package/documentation/wiki-faq.js

@@ -14,7 +14,6 @@ class WikiFaq extends doc_maker_1.DocMaker {
         const faqs = (0, faqs_1.registerFaqs)();
         return `
 	${faqs.toMarkdown()}
-
     `.trim();
     }
 }

package/documentation/wiki-interface.d.ts

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

package/documentation/wiki-interface.js

@@ -94,11 +94,11 @@ with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
 
 `;
 }
-async function explainRepl(parser) {
+async function explainRepl(parser, ctx) {
     return `
 > [!NOTE]
-> To execute arbitrary R commands with a repl request, _flowR_ has to be started explicitly with ${(0, doc_cli_option_1.getCliLongOptionOf)('flowr', 'r-session-access')}.
-> Please be aware that this introduces a security risk and note that this relies on the [\`r-shell\` engine](${doc_files_1.FlowrWikiBaseRef}/Engines).
+> To execute arbitrary R commands with a repl request, _flowR_ has to be started explicitly with ${ctx.cliOption('flowr', 'r-session-access')}.
+> Please be aware that this introduces a security risk and note that this relies on the ${ctx.linkPage('wiki/Engines', '`r-shell` engine')} .
 
 Although primarily meant for users to explore, 
 there is nothing which forbids simply calling _flowR_ as a subprocess to use standard-in, -output, and -error 
@@ -108,8 +108,8 @@ with the [REPL Request](#message-request-repl-execution) message).
 The read-eval-print loop (REPL) works relatively simple.
 You can submit an expression (using <kbd>Enter</kbd>),
 which is interpreted as an R&nbsp;expression by default but interpreted as a *command* if it starts with a colon (\`:\`).
-The best command to get started with the REPL is ${(0, doc_cli_option_1.getReplCommand)('help')}.
-Besides, you can leave the REPL either with the command ${(0, doc_cli_option_1.getReplCommand)('quit')} or by pressing <kbd>Ctrl</kbd>+<kbd>C</kbd> twice.
+The best command to get started with the REPL is ${ctx.replCmd('help')}.
+Besides, you can leave the REPL either with the command ${ctx.replCmd('quit')} or by pressing <kbd>Ctrl</kbd>+<kbd>C</kbd> twice.
 When writing a *command*, you may press <kbd>Tab</kbd> to get a list of completions, if available.
 Multiple commands can be entered in a single line by separating them with a semicolon (\`;\`), e.g. \`:parse "x<-2"; :df*\`.
 If a command is given without R code, the REPL will re-use R code given in a previous command. 
@@ -142,20 +142,20 @@ the REPL will re-use previously obtained information and not re-parse the code a
 ### Example: Retrieving the Dataflow Graph
 
 To retrieve a URL to the [mermaid](https://mermaid.js.org/) diagram of the dataflow of a given expression, 
-use ${(0, doc_cli_option_1.getReplCommand)('dataflow*')} (or ${(0, doc_cli_option_1.getReplCommand)('dataflow')} to get the mermaid code in the cli):
+use ${ctx.replCmd('dataflow*')} (or ${ctx.replCmd('dataflow')} to get the mermaid code in the cli):
 
 ${await (0, doc_repl_1.documentReplSession)(parser, [{
             command: ':dataflow* y <- 1 + x',
             description: `Retrieve the dataflow graph of the expression \`y <- 1 + x\`. It looks like this:\n${await (0, doc_dfg_1.printDfGraphForCode)(parser, 'y <- 1 + x')}`
         }])}
 
-For the slicing with ${(0, doc_cli_option_1.getReplCommand)('slicer')}, you have access to the same [magic comments](#slice-magic-comments) as with the [slice request](#message-request-slice).
+For the slicing with ${ctx.replCmd('slicer')}, you have access to the same [magic comments](#slice-magic-comments) as with the [slice request](#message-request-slice).
 
 ### Example: Interfacing with the File System
 
-Many commands that allow for an R-expression (like ${(0, doc_cli_option_1.getReplCommand)('dataflow*')}) allow for a file as well 
+Many commands that allow for an R-expression (like ${ctx.replCmd('dataflow*')}) allow for a file as well 
 if the argument starts with \`${retriever_1.fileProtocol}\`. 
-If you are working from the root directory of the _flowR_ repository, the following gives you the parsed AST of the example file using the ${(0, doc_cli_option_1.getReplCommand)('parse')} command:
+If you are working from the root directory of the _flowR_ repository, the following gives you the parsed AST of the example file using the ${ctx.replCmd('parse')} command:
 
 ${await (0, doc_repl_1.documentReplSession)(parser, [{
             command: `:parse ${retriever_1.fileProtocol}test/testfiles/example.R`,
@@ -232,9 +232,9 @@ ${(0, doc_code_1.codeBlock)('json', JSON.stringify({
             }
         },
         abstractInterpretation: {
+            wideningThreshold: 4,
             dataFrame: {
                 maxColNames: 20,
-                wideningThreshold: 4,
                 readLoadedData: {
                     readExternalFiles: true,
                     maxReadLines: 1_000_000
@@ -436,8 +436,7 @@ class WikiInterface extends doc_maker_1.DocMaker {
     }
     async text({ shell, ctx, treeSitter }) {
         return `
-Although far from being as detailed as the in-depth explanation of
-[_flowR_](${doc_files_1.FlowrWikiBaseRef}/Core),
+Although far from being as detailed as the in-depth explanation of ${ctx.linkPage('wiki/Core', '_flowR_')},
 this wiki page explains how to interface with _flowR_ in more detail.
 In general, command line arguments and other options provide short descriptions on hover over.
 
@@ -454,7 +453,7 @@ ${await explainServer(shell)}
 <a id='using-the-repl'></a>
 ## 💻 Using the REPL
 
-${await explainRepl(treeSitter)}
+${await explainRepl(treeSitter, ctx)}
 
 <a id='configuring-flowr'></a>
 ## ⚙️ Configuring FlowR

package/documentation/wiki-linter.d.ts

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

package/documentation/wiki-linter.js

@@ -144,7 +144,7 @@ df[6, "value"]
         const certaintyText = `\`${(0, html_hover_over_1.textWithTooltip)(rule.info.certainty, certaintyDoc)}\``;
         if (format === 'short') {
             ruleExplanations.set(name, () => Promise.resolve(`
-	**[${rule.info.name}](${doc_files_1.FlowrWikiBaseRef}/${getPageNameForLintingRule(name)}):** ${rule.info.description} [see ${(0, doc_types_1.shortLinkFile)(ruleType, types)}]\\
+	**[${rule.info.name}](${doc_files_1.FlowrWikiBaseRef}/${encodeURIComponent(getPageNameForLintingRule(name))}):** ${rule.info.description} [see ${(0, doc_types_1.shortLinkFile)(ruleType, types)}]\\
 	${tags}
 
 		`.trim()));

package/documentation/wiki-linting-and-testing.d.ts

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