@eagleoutice/flowr 2.6.2 → 2.7.0

package/cli/slicer-app.js

@@ -15,7 +15,6 @@ const print_1 = require("../benchmark/stats/print");
 const magic_comments_1 = require("../reconstruct/auto-select/magic-comments");
 const auto_select_defaults_1 = require("../reconstruct/auto-select/auto-select-defaults");
 const config_1 = require("../config");
-const adapter_1 = require("../util/formats/adapter");
 const options = (0, script_1.processCommandLineArgs)('slicer', ['input', 'criterion'], {
     subtitle: 'Slice R code based on a given slicing criterion',
     examples: [
@@ -32,8 +31,8 @@ async function getSlice() {
     (0, assert_1.guard)(options.criterion !== undefined, 'a slicing criterion must be given');
     const config = (0, config_1.getConfig)();
     await slicer.init(options['input-is-text']
-        ? (0, adapter_1.requestFromText)(options.input.replaceAll('\\n', '\n'))
-        : (0, adapter_1.requestFromFile)(options.input), config, options['no-magic-comments'] ? auto_select_defaults_1.doNotAutoSelect : (0, magic_comments_1.makeMagicCommentHandler)(auto_select_defaults_1.doNotAutoSelect));
+        ? { request: 'text', content: options.input.replaceAll('\\n', '\n') }
+        : { request: 'file', content: options.input }, config, options['no-magic-comments'] ? auto_select_defaults_1.doNotAutoSelect : (0, magic_comments_1.makeMagicCommentHandler)(auto_select_defaults_1.doNotAutoSelect));
     let mappedSlices = [];
     let reconstruct = undefined;
     const doSlicing = options.criterion.trim() !== '';
@@ -77,7 +76,7 @@ async function getSlice() {
         if (doSlicing && options.diff) {
             let originalCode = options.input;
             if (!options['input-is-text']) {
-                const request = (0, adapter_1.requestFromFile)(options.input);
+                const request = { request: 'file', content: options.input };
                 originalCode = request.request === 'text' ? request.content : fs_1.default.readFileSync(request.content).toString();
             }
             console.log((0, slice_diff_ansi_1.sliceDiffAnsi)(slice.result, normalize, new Set(mappedSlices.map(({ id }) => id)), originalCode));

package/cli/wiki.d.ts

@@ -0,0 +1,4 @@
+/**
+ * Updates and optionally re-creates all flowR wikis.
+ */
+export declare function makeAllWikis(force: boolean, filter: string[] | undefined): Promise<void>;

package/cli/wiki.js

@@ -0,0 +1,165 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.makeAllWikis = makeAllWikis;
+const doc_context_1 = require("../documentation/wiki-mk/doc-context");
+const shell_1 = require("../r-bridge/shell");
+const tree_sitter_executor_1 = require("../r-bridge/lang-4.x/tree-sitter/tree-sitter-executor");
+const fs_1 = __importDefault(require("fs"));
+const log_1 = require("../../test/functionality/_helper/log");
+const command_line_usage_1 = __importDefault(require("command-line-usage"));
+const command_line_args_1 = __importDefault(require("command-line-args"));
+const version_1 = require("../util/version");
+const wiki_faq_1 = require("../documentation/wiki-faq");
+const ansi_1 = require("../util/text/ansi");
+const documentation_1 = require("../documentation");
+const wiki_cfg_1 = require("../documentation/wiki-cfg");
+const wiki_onboarding_1 = require("../documentation/wiki-onboarding");
+const wiki_analyzer_1 = require("../documentation/wiki-analyzer");
+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 = [
+    new wiki_faq_1.WikiFaq(),
+    new documentation_1.WikiSearch(),
+    new wiki_cfg_1.WikiCfg(),
+    new documentation_1.WikiQuery(),
+    new wiki_onboarding_1.WikiOnboarding(),
+    new wiki_analyzer_1.WikiAnalyzer(),
+    new documentation_1.WikiEngine(),
+    new documentation_1.WikiNormalizedAst(),
+    new documentation_1.WikiCore(),
+    new documentation_1.WikiInterface(),
+    new documentation_1.WikiDataflowGraph(),
+    new documentation_1.WikiLintingAndTesting(),
+    new wiki_linter_1.WikiLinter(),
+    new issue_linting_rule_1.IssueLintingRule(),
+    new doc_readme_1.DocReadme(),
+    new documentation_1.DocCapabilities()
+];
+function sortByLeastRecentChanged(wikis) {
+    return wikis.slice().sort((a, b) => {
+        const aStat = fs_1.default.existsSync(a.getProducer()) ? fs_1.default.statSync(a.getProducer()) : undefined;
+        const bStat = fs_1.default.existsSync(b.getProducer()) ? fs_1.default.statSync(b.getProducer()) : undefined;
+        const aMTime = aStat ? aStat.mtime.getTime() : 0;
+        const bMTime = bStat ? bStat.mtime.getTime() : 0;
+        return bMTime - aMTime;
+    });
+}
+/**
+ * Updates and optionally re-creates all flowR wikis.
+ */
+async function makeAllWikis(force, filter) {
+    const setupStart = new Date();
+    console.log('Setting up wiki generation...');
+    const shell = new shell_1.RShell();
+    console.log('  * R shell initialized');
+    await tree_sitter_executor_1.TreeSitterExecutor.initTreeSitter();
+    const treeSitter = new tree_sitter_executor_1.TreeSitterExecutor();
+    console.log('  * Tree-sitter parser initialized');
+    const ctx = (0, doc_context_1.makeDocContextForTypes)(shell);
+    console.log('  * Wiki context prepared');
+    if (force) {
+        console.log(ansi_1.ansiFormatter.format('Forcing wiki regeneration (existing files will be overwritten)', { style: 1 /* FontStyles.Bold */, color: 3 /* Colors.Yellow */, effect: ansi_1.ColorEffect.Foreground }));
+    }
+    const info = {
+        ctx,
+        shell, treeSitter,
+        force,
+        readFileSync(f) {
+            try {
+                return fs_1.default.readFileSync(f);
+            }
+            catch {
+                return undefined;
+            }
+        },
+        writeFileSync: fs_1.default.writeFileSync
+    };
+    console.log(`Setup for wiki generation took ${(new Date().getTime() - setupStart.getTime())}ms`);
+    const changedWikis = new Set();
+    try {
+        const sortedDocs = sortByLeastRecentChanged(Documents);
+        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';
+            if (filter && !filter.some(f => doc.getTarget().includes(f))) {
+                console.log(`  * Skipping ${type} (filtered out): ${doc.getTarget()}`);
+                continue;
+            }
+            const now = new Date();
+            console.log(ansi_1.ansiFormatter.format(`  [${doc.getTarget()}] Updating ${type}...`, { style: 1 /* FontStyles.Bold */, color: 6 /* Colors.Cyan */, effect: ansi_1.ColorEffect.Foreground }));
+            const changed = await doc.make(info);
+            const text = changed ? `${type} updated` : `${type} identical, no changes made`;
+            if (changed) {
+                changedWikis.add(doc.getTarget());
+            }
+            const color = changed ? 2 /* Colors.Green */ : 7 /* Colors.White */;
+            console.log(ansi_1.ansiFormatter.format(`  [${doc.getTarget()}] ${text}: ${doc.getTarget()} (took ${new Date().getTime() - now.getTime()}ms)`, { color, effect: ansi_1.ColorEffect.Foreground }));
+            for (const out of doc.getWrittenSubfiles()) {
+                changedWikis.add(out);
+                console.log(`    - Also updated: ${out}`);
+            }
+        }
+    }
+    catch (error) {
+        console.error('Error while generating documents:', error);
+    }
+    finally {
+        shell.close();
+    }
+    console.log('All wikis processed in ' + (new Date().getTime() - setupStart.getTime()) + 'ms');
+    console.log(`    * Changed ${changedWikis.size} wiki/doc files.`);
+    // write a temp file in the os temp dir with the changed wikis
+    const filename = `${os_1.default.tmpdir()}/flowr-wiki-changed-files.txt`;
+    fs_1.default.writeFileSync(`${filename}`, Array.from(changedWikis).join('\n'));
+    console.log(`    * List of changed wikis/docs written to ${filename}`);
+}
+if (require.main === module) {
+    const wikiOptions = [
+        { name: 'force', alias: 'F', type: Boolean, description: 'Overwrite existing wiki files, even if nothing changes' },
+        { name: 'filter', alias: 'f', type: String, multiple: true, description: 'Only generate wikis whose target path contains the given string' },
+        { name: 'help', alias: 'h', type: Boolean, description: 'Print this usage guide for the wiki generator' },
+        { name: 'keep-alive', type: Boolean, description: 'Keep-alive wiki generator (only sensible with a reloading script like ts-node-dev)' },
+    ];
+    const optionHelp = [
+        {
+            header: `flowR (version ${(0, version_1.flowrVersion)().toString()})`,
+            content: 'Documentation (wiki, issue, ...) generator for flowR'
+        },
+        {
+            header: 'Synopsis',
+            content: [
+                '$ wiki {bold --help}',
+                '$ wiki {bold --force}',
+                '$ wiki {bold --filter} {italic "dataflow"}'
+            ]
+        },
+        {
+            header: 'Options',
+            optionList: wikiOptions
+        }
+    ];
+    (0, log_1.setMinLevelOfAllLogs)(6 /* LogLevel.Fatal */);
+    // parse args
+    const options = (0, command_line_args_1.default)(wikiOptions);
+    if (options.help) {
+        console.log((0, command_line_usage_1.default)(optionHelp));
+        process.exit(0);
+    }
+    void makeAllWikis(options.force, options.filter).catch(err => {
+        console.error('Error while generating wikis:', err);
+        process.exit(1);
+    }).then(() => {
+        if (options['keep-alive']) {
+            console.log('Wiki generator running in keep-alive mode...');
+            setInterval(() => {
+                // do nothing, just keep alive
+            }, 100);
+        }
+    });
+}
+//# sourceMappingURL=wiki.js.map

package/config.d.ts

@@ -98,6 +98,10 @@ export interface FlowrConfigOptions extends MergeableRecord {
             };
         };
     };
+    readonly project: {
+        /** Whether to resolve unknown paths loaded by the r project disk when trying to source/analyze files */
+        resolveUnknownPathsOnDisk: boolean;
+    };
     /**
      * The engines to use for interacting with R code. Currently, supports {@link TreeSitterEngineConfig} and {@link RShellEngineConfig}.
      * An empty array means all available engines will be used.

package/config.js

@@ -65,6 +65,9 @@ exports.defaultConfigOptions = {
             }
         }
     },
+    project: {
+        resolveUnknownPathsOnDisk: true
+    },
     engines: [],
     defaultEngine: 'tree-sitter',
     solver: {
@@ -103,6 +106,9 @@ exports.flowrConfigFileSchema = joi_1.default.object({
             }).optional().description('Do you want to overwrite (parts) of the builtin definition?')
         }).optional().description('Semantics regarding how to handle the R environment.')
     }).description('Configure language semantics and how flowR handles them.'),
+    project: joi_1.default.object({
+        resolveUnknownPathsOnDisk: joi_1.default.boolean().optional().description('Whether to resolve unknown paths loaded by the r project disk when trying to source/analyze files.')
+    }).description('Project specific configuration options.'),
     engines: joi_1.default.array().items(joi_1.default.alternatives(joi_1.default.object({
         type: joi_1.default.string().required().valid('tree-sitter').description('Use the tree sitter engine.'),
         wasmPath: joi_1.default.string().optional().description('The path to the tree-sitter-r WASM binary to use. If this is undefined, this uses the default path.'),

package/control-flow/cfg-dead-code.js

@@ -54,7 +54,13 @@ class CfgConditionalDeadCodeRemoval extends semantic_cfg_guided_visitor_1.Semant
         }
     }
     handleValuesFor(id, valueId) {
-        const values = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(valueId, { graph: this.config.dfg, full: true, idMap: this.config.normalizedAst.idMap, resolve: this.config.flowrConfig.solver.variables }));
+        const values = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(valueId, {
+            graph: this.config.dfg,
+            full: true,
+            idMap: this.config.normalizedAst.idMap,
+            resolve: this.config.ctx.config.solver.variables,
+            ctx: this.config.ctx,
+        }));
         if (values === undefined || values.elements.length !== 1 || values.elements[0].type != 'logical' || !(0, r_value_1.isValue)(values.elements[0].value)) {
             this.unableToCalculateValue(id);
             return;
@@ -74,7 +80,12 @@ class CfgConditionalDeadCodeRemoval extends semantic_cfg_guided_visitor_1.Semant
         if (data.call.args.length !== 1 || data.call.args[0] === r_function_call_1.EmptyArgument) {
             return undefined;
         }
-        const values = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(data.call.args[0].nodeId, { graph: this.config.dfg, full: true, idMap: this.config.normalizedAst.idMap, resolve: this.config.flowrConfig.solver.variables }));
+        const values = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(data.call.args[0].nodeId, {
+            graph: this.config.dfg,
+            full: true,
+            idMap: this.config.normalizedAst.idMap,
+            ctx: this.config.ctx,
+        }));
         if (values === undefined || values.elements.length !== 1 || values.elements[0].type != 'logical' || !(0, r_value_1.isValue)(values.elements[0].value)) {
             return undefined;
         }
@@ -115,7 +126,7 @@ function cfgAnalyzeDeadCode(cfg, info) {
         controlFlow: cfg,
         normalizedAst: info.ast,
         dfg: info.dfg,
-        flowrConfig: info.config,
+        ctx: info.ctx,
         defaultVisitingOrder: 'forward',
     });
     visitor.start();

package/control-flow/cfg-simplification.d.ts

@@ -3,13 +3,16 @@ import type { NormalizedAst } from '../r-bridge/lang-4.x/ast/model/processing/de
 import type { DataflowGraph } from '../dataflow/graph/graph';
 import type { NodeId } from '../r-bridge/lang-4.x/ast/model/processing/node-id';
 import { cfgAnalyzeDeadCode } from './cfg-dead-code';
-import type { FlowrConfigOptions } from '../config';
+import type { ReadOnlyFlowrAnalyzerContext } from '../project/context/flowr-analyzer-context';
 export interface CfgPassInfo {
     ast?: NormalizedAst;
     dfg?: DataflowGraph;
-    config: FlowrConfigOptions;
+    ctx: ReadOnlyFlowrAnalyzerContext;
 }
 export type CfgSimplificationPass = (cfg: ControlFlowInformation, info: CfgPassInfo) => ControlFlowInformation;
+/**
+ * All available control flow graph simplification passes.
+ */
 export declare const CfgSimplificationPasses: {
     readonly 'unique-cf-sets': typeof uniqueControlFlowSets;
     readonly 'analyze-dead-code': typeof cfgAnalyzeDeadCode;

package/control-flow/cfg-simplification.js

@@ -6,6 +6,9 @@ exports.cfgFindAllReachable = cfgFindAllReachable;
 const cfg_to_basic_blocks_1 = require("./cfg-to-basic-blocks");
 const simple_visitor_1 = require("./simple-visitor");
 const cfg_dead_code_1 = require("./cfg-dead-code");
+/**
+ * All available control flow graph simplification passes.
+ */
 exports.CfgSimplificationPasses = {
     'unique-cf-sets': uniqueControlFlowSets,
     'analyze-dead-code': cfg_dead_code_1.cfgAnalyzeDeadCode,

package/control-flow/extract-cfg.d.ts

@@ -1,24 +1,30 @@
 import { type QuadSerializationConfiguration } from '../util/quads';
+import type { NodeId } from '../r-bridge/lang-4.x/ast/model/processing/node-id';
 import type { NormalizedAst, ParentInformation } from '../r-bridge/lang-4.x/ast/model/processing/decorate';
 import type { DataflowGraph } from '../dataflow/graph/graph';
+import type { DataflowGraphVertexFunctionCall } from '../dataflow/graph/vertex';
 import { type ControlFlowInformation } from './control-flow-graph';
 import { type CfgSimplificationPassName } from './cfg-simplification';
-import type { FlowrConfigOptions } from '../config';
+import type { ReadOnlyFlowrAnalyzerContext } from '../project/context/flowr-analyzer-context';
 /**
  * Given a normalized AST, this approximates the control flow graph of the program.
  * This view is different from the computation of the dataflow graph and may differ,
  * especially because it focuses on intra-procedural analysis.
  * @param ast             - the normalized AST
- * @param config          - the flowR config
+ * @param ctx             - the flowR context
  * @param graph           - additional dataflow facts to consider by the control flow extraction
  * @param simplifications - a list of simplification passes to apply to the control flow graph
  * @see {@link extractCfgQuick} - for a simplified version of this function
  */
-export declare function extractCfg<Info = ParentInformation>(ast: NormalizedAst<Info & ParentInformation>, config: FlowrConfigOptions, graph?: DataflowGraph, simplifications?: readonly CfgSimplificationPassName[]): ControlFlowInformation;
+export declare function extractCfg<Info = ParentInformation>(ast: NormalizedAst<Info & ParentInformation>, ctx: ReadOnlyFlowrAnalyzerContext, graph?: DataflowGraph, simplifications?: readonly CfgSimplificationPassName[]): ControlFlowInformation;
 /**
  * A version of {@link extractCfg} that is much quicker and does not apply any simplifications or dataflow information.
  */
 export declare function extractCfgQuick<Info = ParentInformation>(ast: NormalizedAst<Info>): ControlFlowInformation<import("./control-flow-graph").CfgSimpleVertex>;
+/**
+ * Extracts all function call vertices from the given control flow information and dataflow graph.
+ */
+export declare function getCallsInCfg(cfg: ControlFlowInformation, graph: DataflowGraph): Map<NodeId, Required<DataflowGraphVertexFunctionCall>>;
 export declare const ResolvedCallSuffix = "-resolved-call-exit";
 /**
  * Convert a cfg to RDF quads.

package/control-flow/extract-cfg.js

@@ -3,6 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.ResolvedCallSuffix = void 0;
 exports.extractCfg = extractCfg;
 exports.extractCfgQuick = extractCfgQuick;
+exports.getCallsInCfg = getCallsInCfg;
 exports.cfg2quads = cfg2quads;
 const quads_1 = require("../util/quads");
 const fold_1 = require("../r-bridge/lang-4.x/ast/model/processing/fold");
@@ -56,19 +57,58 @@ function dataflowCfgFolds(dataflowGraph) {
  * This view is different from the computation of the dataflow graph and may differ,
  * especially because it focuses on intra-procedural analysis.
  * @param ast             - the normalized AST
- * @param config          - the flowR config
+ * @param ctx             - the flowR context
  * @param graph           - additional dataflow facts to consider by the control flow extraction
  * @param simplifications - a list of simplification passes to apply to the control flow graph
  * @see {@link extractCfgQuick} - for a simplified version of this function
  */
-function extractCfg(ast, config, graph, simplifications) {
-    return (0, cfg_simplification_1.simplifyControlFlowInformation)((0, fold_1.foldAst)(ast.ast, graph ? dataflowCfgFolds(graph) : cfgFolds), { ast, dfg: graph, config }, simplifications);
+function extractCfg(ast, ctx, graph, simplifications) {
+    return (0, cfg_simplification_1.simplifyControlFlowInformation)(cfgFoldProject(ast.ast, graph ? dataflowCfgFolds(graph) : cfgFolds), { ast, dfg: graph, ctx }, simplifications);
 }
 /**
  * A version of {@link extractCfg} that is much quicker and does not apply any simplifications or dataflow information.
  */
 function extractCfgQuick(ast) {
-    return (0, fold_1.foldAst)(ast.ast, cfgFolds);
+    return cfgFoldProject(ast.ast, cfgFolds);
+}
+/**
+ * Extracts all function call vertices from the given control flow information and dataflow graph.
+ */
+function getCallsInCfg(cfg, graph) {
+    const calls = new Map();
+    for (const vertexId of cfg.graph.vertices().keys()) {
+        const vertex = graph.getVertex(vertexId, true);
+        if ((0, vertex_1.isFunctionCallVertex)(vertex)) {
+            calls.set(vertexId, vertex);
+        }
+    }
+    return calls;
+}
+function cfgFoldProject(proj, folds) {
+    if (proj.files.length === 0) {
+        return (0, control_flow_graph_1.emptyControlFlowInformation)();
+    }
+    else if (proj.files.length === 1) {
+        return (0, fold_1.foldAst)(proj.files[0].root, folds);
+    }
+    const perProject = proj.files.map(file => (0, fold_1.foldAst)(file.root, folds));
+    const finalGraph = perProject[0].graph;
+    for (let i = 1; i < perProject.length; i++) {
+        finalGraph.mergeWith(perProject[i].graph);
+        for (const exitPoint of perProject[i - 1].exitPoints) {
+            for (const entryPoint of perProject[i].entryPoints) {
+                finalGraph.addEdge(entryPoint, exitPoint, { label: 0 /* CfgEdgeType.Fd */ });
+            }
+        }
+    }
+    return {
+        breaks: perProject.flatMap(e => e.breaks),
+        nexts: perProject.flatMap(e => e.nexts),
+        returns: perProject.flatMap(e => e.returns),
+        exitPoints: perProject[perProject.length - 1].exitPoints,
+        entryPoints: perProject[0].entryPoints,
+        graph: finalGraph
+    };
 }
 function cfgLeaf(type) {
     return ({ info: { id } }) => {

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

@@ -13,9 +13,9 @@ import type { NoInfo, RNode } from '../r-bridge/lang-4.x/ast/model/model';
 import type { RSymbol } from '../r-bridge/lang-4.x/ast/model/nodes/r-symbol';
 import type { BuiltInProcessorMapper } from '../dataflow/environments/built-in';
 import type { RExpressionList } from '../r-bridge/lang-4.x/ast/model/nodes/r-expression-list';
-import type { FlowrConfigOptions } from '../config';
+import type { ReadOnlyFlowrAnalyzerContext } from '../project/context/flowr-analyzer-context';
 export interface SemanticCfgGuidedVisitorConfiguration<OtherInfo = NoInfo, ControlFlow extends ControlFlowInformation = ControlFlowInformation, Ast extends NormalizedAst<OtherInfo> = NormalizedAst<OtherInfo>, Dfg extends DataflowGraph = DataflowGraph> extends DataflowCfgGuidedVisitorConfiguration<ControlFlow, Dfg>, SyntaxCfgGuidedVisitorConfiguration<OtherInfo, ControlFlow, Ast> {
-    readonly flowrConfig: FlowrConfigOptions;
+    readonly ctx: ReadOnlyFlowrAnalyzerContext;
 }
 /**
  * This visitor extends on the {@link DataflowAwareCfgGuidedVisitor} by dispatching visitors for separate function calls as well,

package/control-flow/simple-visitor.js

@@ -17,7 +17,7 @@ function visitCfgInReverseOrder(graph, startNodes,
 // eslint-disable-next-line @typescript-eslint/no-invalid-void-type -- void is used to indicate that the return value is ignored/we never stop
 visitor) {
     const visited = new Set();
-    let queue = [...startNodes];
+    let queue = startNodes.slice();
     const hasBb = graph.mayHaveBasicBlocks();
     while (queue.length > 0) {
         const current = queue.pop();
@@ -36,7 +36,7 @@ visitor) {
         }
         const incoming = graph.outgoingEdges(current);
         if (incoming) {
-            queue.push(...incoming.keys());
+            queue = queue.concat(incoming.keys().toArray());
         }
     }
 }

package/control-flow/useless-loop.d.ts

@@ -1,8 +1,8 @@
-import type { FlowrConfigOptions } from '../config';
 import type { DataflowGraph } from '../dataflow/graph/graph';
 import type { NormalizedAst } from '../r-bridge/lang-4.x/ast/model/processing/decorate';
 import type { NodeId } from '../r-bridge/lang-4.x/ast/model/processing/node-id';
 import type { ControlFlowInformation } from './control-flow-graph';
+import type { ReadOnlyFlowrAnalyzerContext } from '../project/context/flowr-analyzer-context';
 export declare const loopyFunctions: Set<"builtin:default" | "builtin:eval" | "builtin:apply" | "builtin:expression-list" | "builtin:source" | "builtin:access" | "builtin:if-then-else" | "builtin:get" | "builtin:rm" | "builtin:library" | "builtin:assignment" | "builtin:special-bin-op" | "builtin:pipe" | "builtin:function-definition" | "builtin:quote" | "builtin:for-loop" | "builtin:repeat-loop" | "builtin:while-loop" | "builtin:replacement" | "builtin:list" | "builtin:vector">;
 /**
  * Checks whether a loop only loops once
@@ -10,7 +10,7 @@ export declare const loopyFunctions: Set<"builtin:default" | "builtin:eval" | "b
  * @param dataflow    - dataflow graph
  * @param controlflow - control flow graph
  * @param ast         - normalized ast
- * @param config      - current flowr config
+ * @param ctx      - current flowr analyzer context
  * @returns true if the given loop only iterates once
  */
-export declare function onlyLoopsOnce(loop: NodeId, dataflow: DataflowGraph, controlflow: ControlFlowInformation, ast: NormalizedAst, config: FlowrConfigOptions): boolean | undefined;
+export declare function onlyLoopsOnce(loop: NodeId, dataflow: DataflowGraph, controlflow: ControlFlowInformation, ast: NormalizedAst, ctx: ReadOnlyFlowrAnalyzerContext): boolean | undefined;

package/control-flow/useless-loop.js

@@ -17,10 +17,10 @@ exports.loopyFunctions = new Set(['builtin:for-loop', 'builtin:while-loop', 'bui
  * @param dataflow    - dataflow graph
  * @param controlflow - control flow graph
  * @param ast         - normalized ast
- * @param config      - current flowr config
+ * @param ctx      - current flowr analyzer context
  * @returns true if the given loop only iterates once
  */
-function onlyLoopsOnce(loop, dataflow, controlflow, ast, config) {
+function onlyLoopsOnce(loop, dataflow, controlflow, ast, ctx) {
     const vertex = dataflow.getVertex(loop);
     if (!vertex) {
         return undefined;
@@ -36,7 +36,12 @@ function onlyLoopsOnce(loop, dataflow, controlflow, ast, config) {
         if (vectorOfLoop === r_function_call_1.EmptyArgument) {
             return undefined;
         }
-        const values = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(vectorOfLoop.nodeId, { graph: dataflow, idMap: dataflow.idMap, resolve: config.solver.variables }));
+        const values = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(vectorOfLoop.nodeId, {
+            graph: dataflow,
+            idMap: dataflow.idMap,
+            resolve: ctx.config.solver.variables,
+            ctx: ctx
+        }));
         if (values === undefined || values.elements.length !== 1 || values.elements[0].type !== 'vector' || !(0, r_value_1.isValue)(values.elements[0].elements)) {
             return undefined;
         }
@@ -49,7 +54,7 @@ function onlyLoopsOnce(loop, dataflow, controlflow, ast, config) {
         controlFlow: controlflow,
         normalizedAst: ast,
         dfg: dataflow,
-        flowrConfig: config,
+        ctx: ctx,
         defaultVisitingOrder: 'forward'
     });
     return visitor.loopsOnlyOnce();
@@ -67,7 +72,13 @@ class CfgSingleIterationLoopDetector extends semantic_cfg_guided_visitor_1.Seman
         if (data.call.args.length !== 1 || data.call.args[0] === r_function_call_1.EmptyArgument) {
             return undefined;
         }
-        const values = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(data.call.args[0].nodeId, { graph: this.config.dfg, full: true, idMap: this.config.normalizedAst.idMap, resolve: this.config.flowrConfig.solver.variables }));
+        const values = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(data.call.args[0].nodeId, {
+            graph: this.config.dfg,
+            full: true,
+            idMap: this.config.normalizedAst.idMap,
+            resolve: this.config.ctx.config.solver.variables,
+            ctx: this.config.ctx
+        }));
         if (values === undefined || values.elements.length !== 1 || values.elements[0].type != 'logical' || !(0, r_value_1.isValue)(values.elements[0].value)) {
             return undefined;
         }

package/core/pipeline-executor.d.ts

@@ -1,6 +1,5 @@
 import { type PipelineStepName, PipelineStepStage } from './steps/pipeline-step';
 import type { Pipeline, PipelineInput, PipelineOutput, PipelinePerRequestInput, PipelineStepOutputWithName } from './steps/pipeline/pipeline';
-import type { FlowrConfigOptions } from '../config';
 /**
  * **Please note:** The {@link PipelineExecutor} is now considered to be a rather low-level API for flowR. While it still works
  * and is the basis for all other layers, we strongly recommend using the {@link FlowrAnalyzer} and its {@link FlowrAnalyzerBuilder|builder}
@@ -93,18 +92,16 @@ export declare class PipelineExecutor<P extends Pipeline> {
     private output;
     private currentExecutionStage;
     private stepCounter;
-    private readonly flowrConfig;
     /**
      * Construct a new pipeline executor.
      * The required additional input is specified by the {@link IPipelineStep#requiredInput|required input configuration} of each step in the `pipeline`.
      *
      * Please see {@link createDataflowPipeline} and friends for engine agnostic shortcuts to create a pipeline executor.
      * And in general, please prefer using the {@link FlowrAnalyzer} and its {@link FlowrAnalyzerBuilder|builder} to create and use an analyzer instance.
-     * @param pipeline - The {@link Pipeline} to execute, probably created with {@link createPipeline}.
-     * @param input    - External {@link PipelineInput|configuration and input} required to execute the given pipeline.
-     * @param flowrConfig   - The flowr config containing the built-in definitions
+     * @param pipeline    - The {@link Pipeline} to execute, probably created with {@link createPipeline}.
+     * @param input       - External {@link PipelineInput|configuration and input} required to execute the given pipeline.
      */
-    constructor(pipeline: P, input: PipelineInput<P>, flowrConfig: FlowrConfigOptions);
+    constructor(pipeline: P, input: PipelineInput<P>);
     /**
      * Retrieve the {@link Pipeline|pipeline} that is currently being.
      */

package/core/pipeline-executor.js

@@ -94,22 +94,19 @@ class PipelineExecutor {
     output = {};
     currentExecutionStage = 0 /* PipelineStepStage.OncePerFile */;
     stepCounter = 0;
-    flowrConfig;
     /**
      * Construct a new pipeline executor.
      * The required additional input is specified by the {@link IPipelineStep#requiredInput|required input configuration} of each step in the `pipeline`.
      *
      * Please see {@link createDataflowPipeline} and friends for engine agnostic shortcuts to create a pipeline executor.
      * And in general, please prefer using the {@link FlowrAnalyzer} and its {@link FlowrAnalyzerBuilder|builder} to create and use an analyzer instance.
-     * @param pipeline - The {@link Pipeline} to execute, probably created with {@link createPipeline}.
-     * @param input    - External {@link PipelineInput|configuration and input} required to execute the given pipeline.
-     * @param flowrConfig   - The flowr config containing the built-in definitions
+     * @param pipeline    - The {@link Pipeline} to execute, probably created with {@link createPipeline}.
+     * @param input       - External {@link PipelineInput|configuration and input} required to execute the given pipeline.
      */
-    constructor(pipeline, input, flowrConfig) {
+    constructor(pipeline, input) {
         this.pipeline = pipeline;
         this.length = pipeline.order.length;
         this.input = input;
-        this.flowrConfig = flowrConfig;
     }
     /**
      * Retrieve the {@link Pipeline|pipeline} that is currently being.
@@ -181,7 +178,7 @@ class PipelineExecutor {
         if (expectedStepName !== undefined) {
             (0, assert_1.guard)(step.name === expectedStepName, () => `Cannot execute next step, expected step ${JSON.stringify(expectedStepName)} but got ${step.name}.`);
         }
-        return [step.name, step.processor(this.output, this.input, this.flowrConfig)];
+        return [step.name, step.processor(this.output, this.input)];
     }
     /**
      * This only makes sense if you have already run a request and want to re-use the per-file results for a new one.

package/core/print/normalize-printer.d.ts

@@ -3,7 +3,7 @@ import type { NormalizedAst } from '../../r-bridge/lang-4.x/ast/model/processing
 /** Should work with larger things as well */
 export declare function normalizedAstToJson(ast: NormalizedAst): string;
 /**
- * Normalized AST to quads serialization
+ * Normalized AST to quads serialization this does not have multi-file support
  * @see {@link serialize2quads}
  * @see {@link QuadSerializationConfiguration}
  * @see {@link normalizedAstToMermaid}

package/core/print/normalize-printer.js

@@ -18,7 +18,7 @@ function normalizedAstToJson(ast) {
     });
 }
 /**
- * Normalized AST to quads serialization
+ * Normalized AST to quads serialization this does not have multi-file support
  * @see {@link serialize2quads}
  * @see {@link QuadSerializationConfiguration}
  * @see {@link normalizedAstToMermaid}
@@ -26,7 +26,7 @@ function normalizedAstToJson(ast) {
  * @see {@link printNormalizedAstToMermaidUrl}
  */
 function normalizedAstToQuads(ast, config) {
-    return (0, quads_1.serialize2quads)(ast.ast, config);
+    return (0, quads_1.serialize2quads)(ast.ast.files[0].root, config);
 }
 /**
  * Serialize the normalized AST to mermaid format

package/core/steps/all/core/00-parse.d.ts

@@ -14,7 +14,7 @@ export declare const PARSE_WITH_R_SHELL_STEP: {
             (value: any, replacer?: (this: any, key: string, value: any) => any, space?: string | number): string;
             (value: any, replacer?: (number | string)[] | null, space?: string | number): string;
         };
-        readonly 5: ({ parsed }: import("../../../../r-bridge/parser").ParseStepOutput<string>, config: QuadSerializationConfiguration) => string;
+        readonly 5: (p: import("../../../../r-bridge/parser").ParseStepOutput<string>, config: QuadSerializationConfiguration) => string;
     };
     readonly dependencies: readonly [];
     readonly requiredInput: ParseRequiredInput<string>;

package/core/steps/all/core/00-parse.js

@@ -13,7 +13,7 @@ exports.PARSE_WITH_R_SHELL_STEP = {
     printer: {
         [0 /* StepOutputFormat.Internal */]: print_1.internalPrinter,
         [2 /* StepOutputFormat.Json */]: JSON.stringify,
-        [5 /* StepOutputFormat.RdfQuads */]: ({ parsed }, config) => (0, parse_printer_1.parseToQuads)(parsed, config)
+        [5 /* StepOutputFormat.RdfQuads */]: (p, config) => (0, parse_printer_1.parseToQuads)(p.files[0].parsed, config)
     },
     dependencies: [],
     requiredInput: undefined