@eagleoutice/flowr 2.9.12 → 2.9.13

package/README.md

@@ -24,7 +24,7 @@ It offers a wide variety of features, for example:
     
     ```shell
     $ docker run -it --rm eagleoutice/flowr # or npm run flowr 
-    flowR repl using flowR v2.9.11, R grammar v14 (tree-sitter engine)
+    flowR repl using flowR v2.9.12, R grammar v14 (tree-sitter engine)
     R> :query @linter "read.csv(\"/root/x.txt\")"
     ```
     
@@ -33,19 +33,19 @@ It offers a wide variety of features, for example:
     
     
     ```text
-    Query: linter (2 ms)
+    Query: linter (3 ms)
        ╰ Deprecated Functions (deprecated-functions):
-           ╰ Metadata: totalCalls: 0, totalFunctionDefinitions: 0, searchTimeMs: 1, processTimeMs: 0
+           ╰ Metadata: totalCalls: 0, totalFunctionDefinitions: 0, searchTimeMs: 0, processTimeMs: 0
        ╰ File Path Validity (file-path-validity):
            ╰ certain:
                ╰ Path `/root/x.txt` at 1.1-23
-           ╰ Metadata: totalReads: 1, totalUnknown: 0, totalWritesBeforeAlways: 0, totalValid: 0, searchTimeMs: 0, processTimeMs: 0
+           ╰ Metadata: totalReads: 1, totalUnknown: 0, totalWritesBeforeAlways: 0, totalValid: 0, searchTimeMs: 1, processTimeMs: 0
        ╰ Seeded Randomness (seeded-randomness):
            ╰ Metadata: consumerCalls: 0, callsWithFunctionProducers: 0, callsWithAssignmentProducers: 0, callsWithNonConstantProducers: 0, callsWithOtherBranchProducers: 0, searchTimeMs: 0, processTimeMs: 0
        ╰ Absolute Paths (absolute-file-paths):
            ╰ certain:
                ╰ Path `/root/x.txt` at 1.1-23
-           ╰ Metadata: totalConsidered: 1, totalUnknown: 0, searchTimeMs: 0, processTimeMs: 0
+           ╰ Metadata: totalConsidered: 1, totalUnknown: 0, searchTimeMs: 1, processTimeMs: 0
        ╰ Unused Definitions (unused-definitions):
            ╰ Metadata: totalConsidered: 0, searchTimeMs: 0, processTimeMs: 0
        ╰ Naming Convention (naming-convention):
@@ -58,7 +58,7 @@ It offers a wide variety of features, for example:
            ╰ Metadata: consideredNodes: 5, searchTimeMs: 0, processTimeMs: 0
        ╰ Useless Loops (useless-loop):
            ╰ Metadata: numOfUselessLoops: 0, searchTimeMs: 0, processTimeMs: 0
-    All queries together required ≈2 ms (1ms accuracy, total 2 ms)
+    All queries together required ≈3 ms (1ms accuracy, total 3 ms)
     ```
     
     
@@ -82,17 +82,17 @@ It offers a wide variety of features, for example:
     
     Query: **linter** (2 ms)\
        ╰ **Deprecated Functions** (deprecated-functions):\
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>totalCalls: 0, totalFunctionDefinitions: 0, searchTimeMs: 1, processTimeMs: 0</code>\
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>totalCalls: 0, totalFunctionDefinitions: 0, searchTimeMs: 0, processTimeMs: 0</code>\
     &nbsp;&nbsp;&nbsp;╰ **File Path Validity** (file-path-validity):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ certain:\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ Path `/root/x.txt` at 1.1-23\
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>totalReads: 1, totalUnknown: 0, totalWritesBeforeAlways: 0, totalValid: 0, searchTimeMs: 0, processTimeMs: 0</code>\
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>totalReads: 1, totalUnknown: 0, totalWritesBeforeAlways: 0, totalValid: 0, searchTimeMs: 1, processTimeMs: 0</code>\
     &nbsp;&nbsp;&nbsp;╰ **Seeded Randomness** (seeded-randomness):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>consumerCalls: 0, callsWithFunctionProducers: 0, callsWithAssignmentProducers: 0, callsWithNonConstantProducers: 0, callsWithOtherBranchProducers: 0, searchTimeMs: 0, processTimeMs: 0</code>\
     &nbsp;&nbsp;&nbsp;╰ **Absolute Paths** (absolute-file-paths):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ certain:\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ Path `/root/x.txt` at 1.1-23\
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>totalConsidered: 1, totalUnknown: 0, searchTimeMs: 1, processTimeMs: 0</code>\
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>totalConsidered: 1, totalUnknown: 0, searchTimeMs: 0, processTimeMs: 0</code>\
     &nbsp;&nbsp;&nbsp;╰ **Unused Definitions** (unused-definitions):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>totalConsidered: 0, searchTimeMs: 0, processTimeMs: 0</code>\
     &nbsp;&nbsp;&nbsp;╰ **Naming Convention** (naming-convention):\
@@ -100,7 +100,7 @@ It offers a wide variety of features, for example:
     &nbsp;&nbsp;&nbsp;╰ **Network Functions** (network-functions):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>totalCalls: 0, totalFunctionDefinitions: 0, searchTimeMs: 0, processTimeMs: 0</code>\
     &nbsp;&nbsp;&nbsp;╰ **Dataframe Access Validation** (dataframe-access-validation):\
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>numOperations: 0, numAccesses: 0, totalAccessed: 0, searchTimeMs: 0, processTimeMs: 0</code>\
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>numOperations: 0, numAccesses: 0, totalAccessed: 0, searchTimeMs: 0, processTimeMs: 1</code>\
     &nbsp;&nbsp;&nbsp;╰ **Dead Code** (dead-code):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>consideredNodes: 5, searchTimeMs: 0, processTimeMs: 0</code>\
     &nbsp;&nbsp;&nbsp;╰ **Useless Loops** (useless-loop):\
@@ -109,7 +109,7 @@ It offers a wide variety of features, for example:
     
     <details> <summary style="color:gray">Show Detailed Results as Json</summary>
     
-    The analysis required _2.2 ms_ (including parsing and normalization and the query) within the generation environment.
+    The analysis required _2.1 ms_ (including parsing and normalization and the query) within the generation environment.
     
     In general, the JSON contains the Ids of the nodes in question as they are present in the normalized AST or the dataflow graph of flowR.
     Please consult the [Interface](https://github.com/flowr-analysis/flowr/wiki/Interface) wiki page for more information on how to get those.
@@ -126,7 +126,7 @@ It offers a wide variety of features, for example:
             ".meta": {
               "totalCalls": 0,
               "totalFunctionDefinitions": 0,
-              "searchTimeMs": 1,
+              "searchTimeMs": 0,
               "processTimeMs": 0
             }
           },
@@ -149,7 +149,7 @@ It offers a wide variety of features, for example:
               "totalUnknown": 0,
               "totalWritesBeforeAlways": 0,
               "totalValid": 0,
-              "searchTimeMs": 0,
+              "searchTimeMs": 1,
               "processTimeMs": 0
             }
           },
@@ -181,7 +181,7 @@ It offers a wide variety of features, for example:
             ".meta": {
               "totalConsidered": 1,
               "totalUnknown": 0,
-              "searchTimeMs": 1,
+              "searchTimeMs": 0,
               "processTimeMs": 0
             }
           },
@@ -218,7 +218,7 @@ It offers a wide variety of features, for example:
               "numAccesses": 0,
               "totalAccessed": 0,
               "searchTimeMs": 0,
-              "processTimeMs": 0
+              "processTimeMs": 1
             }
           },
           "dead-code": {
@@ -308,7 +308,7 @@ It offers a wide variety of features, for example:
     
     ```shell
     $ docker run -it --rm eagleoutice/flowr # or npm run flowr 
-    flowR repl using flowR v2.9.11, R grammar v14 (tree-sitter engine)
+    flowR repl using flowR v2.9.12, R grammar v14 (tree-sitter engine)
     R> :query @static-slice (11@sum) file://test/testfiles/example.R
     ```
     
@@ -322,7 +322,7 @@ It offers a wide variety of features, for example:
     N <- 10
     for(i in 1:(N-1)) sum <- sum + i + w
     sum
-    All queries together required ≈2 ms (1ms accuracy, total 2 ms)
+    All queries together required ≈3 ms (1ms accuracy, total 4 ms)
     ```
     
     
@@ -338,7 +338,7 @@ It offers a wide variety of features, for example:
         
 
 * 📚 **dependency analysis**\
-  Given your analysis project, flowR offers a plethora of so-called [queries](https://github.com/flowr-analysis/flowr/wiki/wiki/query-api) to get more information about your code.
+  Given your analysis project, flowR offers a plethora of so-called [queries](https://github.com/flowr-analysis/flowr/wiki/query-api) to get more information about your code.
   An important query is the [dependencies query](https://github.com/flowr-analysis/flowr/wiki/Query-API#dependencies-query), which shows you the library your project needs,
   the data files it reads, the scripts it sources, and the data it outputs.
   
@@ -356,16 +356,16 @@ It offers a wide variety of features, for example:
          
 
 * 🚀 **fast call-graph, data-, and control-flow graphs**\
-  Within just [<i><span title="This measurement is automatically fetched from the latest benchmark!">98.9 ms</span></i> (as of Feb 18, 2026)](https://flowr-analysis.github.io/flowr/wiki/stats/benchmark), 
+  Within just [<i><span title="This measurement is automatically fetched from the latest benchmark!">97.7 ms</span></i> (as of Feb 19, 2026)](https://flowr-analysis.github.io/flowr/wiki/stats/benchmark), 
   _flowR_ can analyze the data- and control-flow of the average real-world R&nbsp;script. See the [benchmarks](https://flowr-analysis.github.io/flowr/wiki/stats/benchmark) for more information,
-  and consult the [wiki pages](https://github.com/flowr-analysis/flowr/wiki/wiki/dataflow-graph) for more details on the [dataflow graphs](https://github.com/flowr-analysis/flowr/wiki/wiki/dataflow-graph) as well as [call graphs](https://github.com/flowr-analysis/flowr/wiki/wiki/dataflow-graph#perspectives-cg).
+  and consult the [wiki pages](https://github.com/flowr-analysis/flowr/wiki/dataflow-graph) for more details on the [dataflow graphs](https://github.com/flowr-analysis/flowr/wiki/dataflow-graph) as well as [call graphs](https://github.com/flowr-analysis/flowr/wiki/dataflow-graph#perspectives-cg).
 
     
     <details><summary>Example: Generating a dataflow graph with flowR</summary>
     
     
     You can investigate flowR's analyses using the [REPL](https://github.com/flowr-analysis/flowr/wiki/Interface#using-the-repl).
-    Commands like <span title="Description (Repl Command, starred version): Returns the URL to mermaid.live; Base Command: Get mermaid code for the dataflow graph, start with 'file://' to indicate a file (aliases: :d*, :df*)">`:dataflow*`</span> allow you to view a [dataflow graph](https://github.com/flowr-analysis/flowr/wiki/wiki/dataflow-graph) for a given R script.
+    Commands like <span title="Description (Repl Command, starred version): Returns the URL to mermaid.live; Base Command: Get mermaid code for the dataflow graph, start with 'file://' to indicate a file (aliases: :d*, :df*)">`:dataflow*`</span> allow you to view a [dataflow graph](https://github.com/flowr-analysis/flowr/wiki/dataflow-graph) for a given R script.
     
     Let's have a look at the following example:
     
@@ -386,13 +386,13 @@ It offers a wide variety of features, for example:
     ```
     
     
-    To get the [dataflow graph](https://github.com/flowr-analysis/flowr/wiki/wiki/dataflow-graph) for this script, you can use the following command:
+    To get the [dataflow graph](https://github.com/flowr-analysis/flowr/wiki/dataflow-graph) for this script, you can use the following command:
     
     
     
     ```shell
     $ docker run -it --rm eagleoutice/flowr # or npm run flowr 
-    flowR repl using flowR v2.9.11, R grammar v14 (tree-sitter engine)
+    flowR repl using flowR v2.9.12, R grammar v14 (tree-sitter engine)
     R> :dataflow* test/testfiles/example.R
     ```
     
@@ -700,7 +700,7 @@ It offers a wide variety of features, for example:
     ```
     
     	
-    (The analysis required _1.6 ms_ (including parse and normalize, using the [tree-sitter](https://github.com/flowr-analysis/flowr/wiki/Engines) engine) within the generation environment.)
+    (The analysis required _1.5 ms_ (including parse and normalize, using the [tree-sitter](https://github.com/flowr-analysis/flowr/wiki/Engines) engine) within the generation environment.)
     
     
     
@@ -727,8 +727,8 @@ If you are already using flowR and want to give feedback, please consider fillin
  
 ## ⭐ Getting Started
 
-To get started with _flowR_ and its features, please check out the [Overview](https://github.com/flowr-analysis/flowr/wiki/wiki/overview) wiki page. 
-The [Setup](https://github.com/flowr-analysis/flowr/wiki/wiki/setup) wiki page explains how you can download and setup _flowR_ on your system. 
+To get started with _flowR_ and its features, please check out the [Overview](https://github.com/flowr-analysis/flowr/wiki/overview) wiki page. 
+The [Setup](https://github.com/flowr-analysis/flowr/wiki/setup) wiki page explains how you can download and setup _flowR_ on your system. 
 With docker&nbsp;🐳️, the following line should be enough (and drop you directly into the read-eval-print loop):
 
 
@@ -865,7 +865,7 @@ please check out the following publications (if you find that a paper is missing
 
 ## 🚀 Contributing
 
-We welcome every contribution! Please check out the [developer onboarding](https://github.com/flowr-analysis/flowr/wiki/wiki/onboarding) section in the wiki for all the information you will need.
+We welcome every contribution! Please check out the [developer onboarding](https://github.com/flowr-analysis/flowr/wiki/onboarding) section in the wiki for all the information you will need.
 
 ### Contributors
 

package/benchmark/slicer.d.ts

@@ -13,7 +13,7 @@ import { type RParseRequestFromFile, type RParseRequestFromText } from '../r-bri
 import { type SlicingCriteriaFilter } from '../slicing/criterion/collect-all';
 import type { AutoSelectPredicate } from '../reconstruct/auto-select/auto-select-defaults';
 import type { KnownParserName } from '../r-bridge/parser';
-import { type FlowrConfigOptions } from '../config';
+import { FlowrConfig } from '../config';
 /**
  * The logger to be used for benchmarking as a global object.
  */
@@ -63,6 +63,7 @@ export declare class BenchmarkSlicer {
     private dataflow;
     private normalizedAst;
     private controlFlow;
+    private callGraph;
     private totalStopwatch;
     private finished;
     private executor;
@@ -72,7 +73,7 @@ export declare class BenchmarkSlicer {
      * Initialize the slicer on the given request.
      * Can only be called once for each instance.
      */
-    init(request: RParseRequestFromFile | RParseRequestFromText, config: FlowrConfigOptions, autoSelectIf?: AutoSelectPredicate, threshold?: number): Promise<void>;
+    init(request: RParseRequestFromFile | RParseRequestFromText, config: FlowrConfig, autoSelectIf?: AutoSelectPredicate, threshold?: number): Promise<void>;
     private calculateStatsAfterInit;
     /**
      * Slice for the given {@link SlicingCriteria}.
@@ -84,6 +85,7 @@ export declare class BenchmarkSlicer {
      * Extract the control flow graph using {@link extractCFG}
      */
     extractCFG(): void;
+    extractCG(): void;
     /**
      * Infer the shape of data frames using abstract interpretation with {@link inferDataFrameShapes}
      * @returns The statistics of the data frame shape inference

package/benchmark/slicer.js

@@ -31,6 +31,7 @@ const fs_1 = __importDefault(require("fs"));
 const flowr_analyzer_context_1 = require("../project/context/flowr-analyzer-context");
 const r_project_1 = require("../r-bridge/lang-4.x/ast/model/nodes/r-project");
 const r_comment_1 = require("../r-bridge/lang-4.x/ast/model/nodes/r-comment");
+const call_graph_1 = require("../dataflow/graph/call-graph");
 /**
  * The logger to be used for benchmarking as a global object.
  */
@@ -47,6 +48,7 @@ class BenchmarkSlicer {
     dataflow;
     normalizedAst;
     controlFlow;
+    callGraph;
     totalStopwatch;
     finished = false;
     // Yes, this is unclean, but we know that we assign the executor during the initialization and this saves us from having to check for nullability every time
@@ -65,10 +67,10 @@ class BenchmarkSlicer {
         // we know these are in sync so we just cast to one of them
         this.parser = await this.commonMeasurements.measure('initialize R session', async () => {
             if (this.parserName === 'r-shell') {
-                return new shell_1.RShell((0, config_1.getEngineConfig)(config, 'r-shell'));
+                return new shell_1.RShell(config_1.FlowrConfig.getForEngine(config, 'r-shell'));
             }
             else {
-                await tree_sitter_executor_1.TreeSitterExecutor.initTreeSitter((0, config_1.getEngineConfig)(config, 'tree-sitter'));
+                await tree_sitter_executor_1.TreeSitterExecutor.initTreeSitter(config_1.FlowrConfig.getForEngine(config, 'tree-sitter'));
                 return new tree_sitter_executor_1.TreeSitterExecutor();
             }
         });
@@ -228,6 +230,13 @@ class BenchmarkSlicer {
         const ast = this.normalizedAst;
         this.controlFlow = this.measureSimpleStep('extract control flow graph', () => (0, extract_cfg_1.extractCfg)(ast, this.context, undefined, undefined, true));
     }
+    extractCG() {
+        exports.benchmarkLogger.trace('try to extract the call graph');
+        this.guardActive();
+        const g = this.dataflow?.graph;
+        (0, assert_1.guard)(g !== undefined, 'dataflow should be defined for call graph extraction');
+        this.callGraph = this.measureSimpleStep('extract call graph', () => (0, call_graph_1.computeCallGraph)(g));
+    }
     /**
      * Infer the shape of data frames using abstract interpretation with {@link inferDataFrameShapes}
      * @returns The statistics of the data frame shape inference
@@ -422,6 +431,7 @@ class BenchmarkSlicer {
         const normalizeTime = Number(this.stats.commonMeasurements.get('normalize R AST'));
         const dataflowTime = Number(this.stats.commonMeasurements.get('produce dataflow information'));
         const controlFlowTime = Number(this.stats.commonMeasurements.get('extract control flow graph'));
+        const callGraphTime = Number(this.stats.commonMeasurements.get('extract call graph'));
         const dataFrameShapeTime = Number(this.stats.commonMeasurements.get('infer data frame shapes'));
         this.stats.retrieveTimePerToken = {
             raw: retrieveTime / this.stats.input.numberOfRTokens,
@@ -439,14 +449,18 @@ class BenchmarkSlicer {
             raw: (retrieveTime + normalizeTime + dataflowTime) / this.stats.input.numberOfRTokens,
             normalized: (retrieveTime + normalizeTime + dataflowTime) / this.stats.input.numberOfNormalizedTokens
         };
-        this.stats.controlFlowTimePerToken = !isNaN(controlFlowTime) ? {
+        this.stats.controlFlowTimePerToken = Number.isNaN(controlFlowTime) ? undefined : {
             raw: controlFlowTime / this.stats.input.numberOfRTokens,
             normalized: controlFlowTime / this.stats.input.numberOfNormalizedTokens,
-        } : undefined;
-        this.stats.dataFrameShapeTimePerToken = !isNaN(dataFrameShapeTime) ? {
+        };
+        this.stats.callGraphTimePerToken = Number.isNaN(callGraphTime) ? undefined : {
+            raw: callGraphTime / this.stats.input.numberOfRTokens,
+            normalized: callGraphTime / this.stats.input.numberOfNormalizedTokens,
+        };
+        this.stats.dataFrameShapeTimePerToken = Number.isNaN(dataFrameShapeTime) ? undefined : {
             raw: dataFrameShapeTime / this.stats.input.numberOfRTokens,
             normalized: dataFrameShapeTime / this.stats.input.numberOfNormalizedTokens,
-        } : undefined;
+        };
         return {
             stats: this.stats,
             parse: typeof this.loadedXml === 'string' ? this.loadedXml : JSON.stringify(this.loadedXml),

package/benchmark/stats/print.js

@@ -104,6 +104,12 @@ Total common time per R token:        ${formatNanoseconds(stats.totalCommonTimeP
 Control flow extraction:              ${print(stats.commonMeasurements, 'extract control flow graph')}
 Control flow extraction per token:    ${formatNanoseconds(stats.controlFlowTimePerToken.normalized)}
 Control flow extraction per R token:  ${formatNanoseconds(stats.controlFlowTimePerToken.raw)}`;
+    }
+    if (stats.commonMeasurements.has('extract call graph') && stats.callGraphTimePerToken !== undefined) {
+        result += `
+Call graph extraction:                ${print(stats.commonMeasurements, 'extract call graph')}
+Call graph extraction per token:      ${formatNanoseconds(stats.callGraphTimePerToken.normalized)}
+Call graph extraction per R token:    ${formatNanoseconds(stats.callGraphTimePerToken.raw)}`;
     }
     if (stats.commonMeasurements.has('infer data frame shapes') && stats.dataFrameShapeTimePerToken !== undefined) {
         result += `
@@ -210,6 +216,12 @@ Total common time per R token:        ${formatSummarizedTimeMeasure(stats.totalC
 Control flow extraction:              ${formatSummarizedTimeMeasure(stats.commonMeasurements.get('extract control flow graph'))}
 Control flow extraction per token:    ${formatSummarizedTimeMeasure(stats.controlFlowTimePerToken.normalized)}
 Control flow extraction per R token:  ${formatSummarizedTimeMeasure(stats.controlFlowTimePerToken.raw)}`;
+    }
+    if (stats.commonMeasurements.has('extract call graph') && stats.callGraphTimePerToken !== undefined) {
+        result += `
+Call graph extraction:                ${formatSummarizedTimeMeasure(stats.commonMeasurements.get('extract call graph'))}
+Call graph extraction per token:      ${formatSummarizedTimeMeasure(stats.callGraphTimePerToken.normalized)}
+Call graph extraction per R token:    ${formatSummarizedTimeMeasure(stats.callGraphTimePerToken.raw)}`;
     }
     if (stats.commonMeasurements.has('infer data frame shapes') && stats.dataFrameShapeTimePerToken !== undefined) {
         result += `

package/benchmark/stats/stats.d.ts

@@ -6,8 +6,8 @@ import type { TimePerToken } from '../summarizer/data';
 import type { MergeableRecord } from '../../util/objects';
 import type { DataFrameOperationName } from '../../abstract-interpretation/data-frame/semantics';
 export declare const RequiredSlicerMeasurements: readonly ["initialize R session", "retrieve AST from R code", "normalize R AST", "produce dataflow information", "close R session", "total"];
-export declare const OptionalSlicerMeasurements: readonly ["extract control flow graph", "infer data frame shapes"];
-export declare const CommonSlicerMeasurements: readonly ["initialize R session", "retrieve AST from R code", "normalize R AST", "produce dataflow information", "close R session", "total", "extract control flow graph", "infer data frame shapes"];
+export declare const OptionalSlicerMeasurements: readonly ["extract control flow graph", "infer data frame shapes", "extract call graph"];
+export declare const CommonSlicerMeasurements: readonly ["initialize R session", "retrieve AST from R code", "normalize R AST", "produce dataflow information", "close R session", "total", "extract control flow graph", "infer data frame shapes", "extract call graph"];
 export type CommonSlicerMeasurements = typeof CommonSlicerMeasurements[number];
 export declare const PerSliceMeasurements: readonly ["static slicing", "reconstruct code", "total"];
 export type PerSliceMeasurements = typeof PerSliceMeasurements[number];
@@ -91,5 +91,6 @@ export interface SlicerStats {
     dataflowTimePerToken: TimePerToken<number>;
     totalCommonTimePerToken: TimePerToken<number>;
     controlFlowTimePerToken?: TimePerToken<number>;
+    callGraphTimePerToken?: TimePerToken<number>;
     dataFrameShapeTimePerToken?: TimePerToken<number>;
 }

package/benchmark/stats/stats.js

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PerSliceMeasurements = exports.CommonSlicerMeasurements = exports.OptionalSlicerMeasurements = exports.RequiredSlicerMeasurements = void 0;
 exports.RequiredSlicerMeasurements = ['initialize R session', 'retrieve AST from R code', 'normalize R AST', 'produce dataflow information', 'close R session', 'total'];
-exports.OptionalSlicerMeasurements = ['extract control flow graph', 'infer data frame shapes'];
+exports.OptionalSlicerMeasurements = ['extract control flow graph', 'infer data frame shapes', 'extract call graph'];
 exports.CommonSlicerMeasurements = [...exports.RequiredSlicerMeasurements, ...exports.OptionalSlicerMeasurements];
 exports.PerSliceMeasurements = ['static slicing', 'reconstruct code', 'total'];
 //# sourceMappingURL=stats.js.map

package/benchmark/summarizer/data.d.ts

@@ -65,6 +65,7 @@ export interface UltimateSlicerStats {
     dataflowTimePerToken: TimePerToken;
     totalCommonTimePerToken: TimePerToken;
     controlFlowTimePerToken?: TimePerToken;
+    callGraphTimePerToken?: TimePerToken;
     dataFrameShapeTimePerToken?: TimePerToken;
     sliceTimePerToken: TimePerToken;
     reconstructTimePerToken: TimePerToken;

package/benchmark/summarizer/second-phase/process.js

@@ -25,6 +25,7 @@ function summarizeAllSummarizedStats(stats) {
     const dataflowTimesPerToken = [];
     const totalCommonTimesPerToken = [];
     const controlFlowTimePerToken = [];
+    const callGraphTimePerToken = [];
     const dataFrameShapeTimePerToken = [];
     const memory = new defaultmap_1.DefaultMap(() => []);
     const reductions = [];
@@ -52,6 +53,9 @@ function summarizeAllSummarizedStats(stats) {
         if (stat.controlFlowTimePerToken !== undefined) {
             controlFlowTimePerToken.push(stat.controlFlowTimePerToken);
         }
+        if (stat.callGraphTimePerToken !== undefined) {
+            callGraphTimePerToken.push(stat.callGraphTimePerToken);
+        }
         if (stat.dataFrameShapeTimePerToken !== undefined) {
             dataFrameShapeTimePerToken.push(stat.dataFrameShapeTimePerToken);
         }
@@ -82,6 +86,7 @@ function summarizeAllSummarizedStats(stats) {
         dataflowTimePerToken: (0, process_1.summarizeTimePerToken)(dataflowTimesPerToken),
         totalCommonTimePerToken: (0, process_1.summarizeTimePerToken)(totalCommonTimesPerToken),
         controlFlowTimePerToken: controlFlowTimePerToken.length > 0 ? (0, process_1.summarizeTimePerToken)(controlFlowTimePerToken) : undefined,
+        callGraphTimePerToken: callGraphTimePerToken.length > 0 ? (0, process_1.summarizeTimePerToken)(callGraphTimePerToken) : undefined,
         dataFrameShapeTimePerToken: dataFrameShapeTimePerToken.length > 0 ? (0, process_1.summarizeTimePerToken)(dataFrameShapeTimePerToken) : undefined,
         failedToRepParse,
         timesHitThreshold,

package/cli/benchmark-app.d.ts

@@ -16,4 +16,5 @@ export interface BenchmarkCliOptions {
     'per-file-time-limit'?: number;
     'sampling-strategy': string;
     cfg?: boolean;
+    cg?: boolean;
 }

package/cli/benchmark-app.js

@@ -75,6 +75,7 @@ async function benchmark() {
         '--sampling-strategy', options['sampling-strategy'],
         ...(options.seed ? ['--seed', options.seed] : []),
         ...(options.cfg ? ['--cfg'] : []),
+        ...(options.cg ? ['--cg'] : [])
     ]);
     const runs = options.runs ?? 1;
     for (let i = 1; i <= runs; i++) {

package/cli/benchmark-helper-app.d.ts

@@ -10,7 +10,8 @@ export interface SingleBenchmarkCliOptions {
     parser: KnownParserName;
     'dataframe-shape-inference': boolean;
     'max-slices': number;
-    'cfg': boolean;
+    cfg: boolean;
+    cg: boolean;
     threshold?: number;
     'sampling-strategy': string;
     seed?: string;

package/cli/benchmark-helper-app.js

@@ -31,14 +31,14 @@ async function benchmark() {
     (0, assert_1.guard)(options.output !== undefined, 'No output file given');
     (0, assert_1.guard)((options['file-id'] === undefined) === (options['run-num'] === undefined), 'When giving a file-id or run-num, both have to be given');
     // prefix for printing to console, includes file id and run number if present
-    const prefix = `[${options.input}${options['file-id'] !== undefined ? ` (file ${options['file-id']}, run ${options['run-num']})` : ''}]`;
+    const prefix = `[${options.input}${options['file-id'] === undefined ? '' : ` (file ${options['file-id']}, run ${options['run-num']})`}]`;
     console.log(`${prefix} Appending output to ${options.output}`);
     const directory = path_1.default.parse(options.output).dir;
     // ensure the directory exists if the path contains one
     if (directory !== '') {
         fs_1.default.mkdirSync(directory, { recursive: true });
     }
-    const config = (0, config_1.getConfig)();
+    const config = config_1.FlowrConfig.fromFile();
     // ensure the file exists
     const fileStat = fs_1.default.statSync(options.input);
     (0, assert_1.guard)(fileStat.isFile(), `File ${options.input} does not exist or is no file`);
@@ -58,7 +58,7 @@ async function benchmark() {
             console.log(`${prefix} Skipping Slicing due to --slice=${options.slice}`);
         }
         else {
-            const limit = parseInt(options.slice);
+            const limit = Number.parseInt(options.slice);
             console.log(`${prefix} Slicing up to ${limit} possible slices`);
             const count = await slicer.sliceForAll(all_variables_1.DefaultAllVariablesFilter, (i, total, arr) => console.log(`${prefix} Slicing ${i + 1}/${total} [${JSON.stringify(arr[i])}]`), { sampleCount: limit, maxSliceCount: maxSlices, sampleStrategy: options['sampling-strategy'], seed: options.seed });
             console.log(`${prefix} Completed Slicing`);
@@ -68,6 +68,9 @@ async function benchmark() {
         if (options['cfg'] || options['dataframe-shape-inference']) {
             slicer.extractCFG();
         }
+        if (options['cg']) {
+            slicer.extractCG();
+        }
         if (options['dataframe-shape-inference']) {
             console.log(`${prefix} Performing shape inference for data frames`);
             slicer.inferDataFrameShapes();

package/cli/common/options.d.ts

@@ -105,6 +105,10 @@ export declare const benchmarkOptions: [{
     readonly alias: "c";
     readonly type: BooleanConstructor;
     readonly description: "Extract the control flow graph of the file (benchmark it too)";
+}, {
+    readonly name: "cg";
+    readonly type: BooleanConstructor;
+    readonly description: "Extract the call graph of the file (benchmark it too)";
 }];
 export declare const benchmarkHelperOptions: [{
     readonly name: "verbose";
@@ -146,6 +150,10 @@ export declare const benchmarkHelperOptions: [{
     readonly alias: "c";
     readonly type: BooleanConstructor;
     readonly description: "Extract the control flow graph of the file (benchmark it too)";
+}, {
+    readonly name: "cg";
+    readonly type: BooleanConstructor;
+    readonly description: "Extract the call graph of the file (benchmark it too)";
 }, {
     readonly name: "output";
     readonly alias: "o";

package/cli/common/options.js

@@ -27,7 +27,8 @@ exports.benchmarkOptions = [
     { name: 'threshold', alias: 't', type: Number, description: 'How many re-visits of the same node are ok?', defaultValue: undefined, typeLabel: '{underline number}' },
     { name: 'per-file-time-limit', type: Number, description: 'Time limit in milliseconds to process single file (disabled by default)', defaultValue: undefined, typeLabel: '{underline number}' },
     { name: 'sampling-strategy', type: String, description: 'Which strategy to use, when sampling is enabled', defaultValue: 'random', typeLabel: '{underline random/equidistant}' },
-    { name: 'cfg', alias: 'c', type: Boolean, description: 'Extract the control flow graph of the file (benchmark it too)' }
+    { name: 'cfg', alias: 'c', type: Boolean, description: 'Extract the control flow graph of the file (benchmark it too)' },
+    { name: 'cg', type: Boolean, description: 'Extract the call graph of the file (benchmark it too)' }
 ];
 exports.benchmarkHelperOptions = [
     { name: 'verbose', alias: 'v', type: Boolean, description: 'Run with verbose logging [do not use for the real benchmark as this affects the time measurements, but only to find errors]' },
@@ -37,6 +38,7 @@ exports.benchmarkHelperOptions = [
     { name: 'run-num', alias: 'r', type: Number, description: 'The n-th time that the file with the given file-id is being benchmarked' },
     { name: 'slice', alias: 's', type: String, description: 'Automatically slice for *all* variables (default) or *no* slicing and only parsing/dataflow construction. Numbers will indicate: sample X random slices from all.', defaultValue: 'all', typeLabel: '{underline all/no}' },
     { name: 'cfg', alias: 'c', type: Boolean, description: 'Extract the control flow graph of the file (benchmark it too)' },
+    { name: 'cg', type: Boolean, description: 'Extract the call graph of the file (benchmark it too)' },
     { name: 'output', alias: 'o', type: String, description: 'File to write the measurements to (appends a single line in JSON format)', typeLabel: '{underline file}' },
     { name: 'parser', type: String, description: 'The parser to use for the benchmark', defaultValue: 'r-shell', typeLabel: '{underline parser}' },
     { name: 'dataframe-shape-inference', type: Boolean, description: 'Infer the shape of data frames using abstract interpretation (includes control flow graph extraction)', defaultValue: false },

package/cli/common/scripts-info.d.ts

@@ -192,6 +192,10 @@ declare const _scripts: {
             readonly alias: "c";
             readonly type: BooleanConstructor;
             readonly description: "Extract the control flow graph of the file (benchmark it too)";
+        }, {
+            readonly name: "cg";
+            readonly type: BooleanConstructor;
+            readonly description: "Extract the call graph of the file (benchmark it too)";
         }];
     };
     'benchmark-helper': {
@@ -239,6 +243,10 @@ declare const _scripts: {
             readonly alias: "c";
             readonly type: BooleanConstructor;
             readonly description: "Extract the control flow graph of the file (benchmark it too)";
+        }, {
+            readonly name: "cg";
+            readonly type: BooleanConstructor;
+            readonly description: "Extract the call graph of the file (benchmark it too)";
         }, {
             readonly name: "output";
             readonly alias: "o";

package/cli/export-quads-app.js

@@ -18,7 +18,7 @@ const options = (0, script_1.processCommandLineArgs)('export-quads', [], {
         '{bold --help}'
     ]
 });
-const shell = new shell_1.RShell((0, config_1.getEngineConfig)((0, config_1.getConfig)(), 'r-shell'));
+const shell = new shell_1.RShell(config_1.FlowrConfig.getForEngine(config_1.FlowrConfig.fromFile(), 'r-shell'));
 async function writeQuadForSingleFile(request, output) {
     const normalized = await (0, retriever_1.retrieveNormalizedAstFromRCode)(request, shell);
     const serialized = (0, quads_1.serialize2quads)(normalized.ast.files[0].root, { context: request.content });

package/cli/flowr.js

@@ -54,7 +54,7 @@ if (options['no-ansi']) {
 function createConfig() {
     let config;
     if (options['config-json']) {
-        const passedConfig = (0, config_1.parseConfig)(options['config-json']);
+        const passedConfig = config_1.FlowrConfig.parse(options['config-json']);
         if (passedConfig) {
             log_1.log.info(`Using passed config ${JSON.stringify(passedConfig)}`);
             config = passedConfig;
@@ -68,10 +68,10 @@ function createConfig() {
                 process.exit(1);
             }
         }
-        config = (0, config_1.getConfig)(options['config-file'] ?? flowr_main_options_1.defaultConfigFile);
+        config = config_1.FlowrConfig.fromFile(options['config-file'] ?? flowr_main_options_1.defaultConfigFile);
     }
     // for all options that we manually supply that have a config equivalent, set them in the config
-    config = (0, config_1.amendConfig)(config, c => {
+    config = config_1.FlowrConfig.amend(config, c => {
         c.engines ??= [];
         if (!options['engine.r-shell.disabled']) {
             c.engines.push({ type: 'r-shell', rPath: options['r-path'] || options['engine.r-shell.r-path'] });

package/cli/repl/core.d.ts

@@ -1,7 +1,7 @@
 import * as readline from 'readline';
 import { type ReplOutput } from './commands/repl-main';
 import type { MergeableRecord } from '../../util/objects';
-import type { FlowrConfigOptions } from '../../config';
+import type { FlowrConfig } from '../../config';
 import type { FlowrAnalyzer } from '../../project/flowr-analyzer';
 /**
  * Completion suggestions for a specific REPL command
@@ -18,11 +18,11 @@ export interface CommandCompletions {
 /**
  * Used by the repl to provide automatic completions for a given (partial) input line
  */
-export declare function replCompleter(line: string, config: FlowrConfigOptions): [string[], string];
+export declare function replCompleter(line: string, config: FlowrConfig): [string[], string];
 /**
  * Produces default readline options for the flowR REPL
  */
-export declare function makeDefaultReplReadline(config: FlowrConfigOptions): readline.ReadLineOptions;
+export declare function makeDefaultReplReadline(config: FlowrConfig): readline.ReadLineOptions;
 /**
  * Handles a string input for the REPL, returning the parsed string and any remaining input.
  */

package/cli/repl/server/connection.d.ts

@@ -3,7 +3,7 @@ import { type TREE_SITTER_DATAFLOW_PIPELINE, DEFAULT_SLICING_PIPELINE } from '..
 import type { PipelineOutput } from '../../../core/steps/pipeline/pipeline';
 import type { DeepPartial } from 'ts-essentials';
 import type { KnownParser, ParseStepOutput } from '../../../r-bridge/parser';
-import type { FlowrConfigOptions } from '../../../config';
+import type { FlowrConfig } from '../../../config';
 import type { NormalizedAst } from '../../../r-bridge/lang-4.x/ast/model/processing/decorate';
 import type { DataflowInformation } from '../../../dataflow/info';
 import type { Tree } from 'web-tree-sitter';
@@ -19,7 +19,7 @@ export declare class FlowRServerConnection {
     private readonly allowRSessionAccess;
     private readonly config;
     private readonly fileMap;
-    constructor(socket: Socket, name: string, parser: KnownParser, allowRSessionAccess: boolean, config: FlowrConfigOptions);
+    constructor(socket: Socket, name: string, parser: KnownParser, allowRSessionAccess: boolean, config: FlowrConfig);
     private currentMessageBuffer;
     private handleData;
     private handleFileAnalysisRequest;

package/cli/repl/server/server.d.ts

@@ -1,6 +1,6 @@
 import { type Server } from './net';
 import { FlowrLogger } from '../../../util/log';
-import type { FlowrConfigOptions, KnownEngines } from '../../../config';
+import type { FlowrConfig, KnownEngines } from '../../../config';
 export declare const serverLog: FlowrLogger;
 /**
  * This class controls the TCP server, which can be started by calling {@link start}.
@@ -17,7 +17,7 @@ export declare class FlowRServer {
     /** maps names to the respective connection */
     private readonly connections;
     private nameCounter;
-    constructor(engines: KnownEngines, defaultEngine: keyof KnownEngines, allowRSessionAccess: boolean, config: FlowrConfigOptions, server?: Server);
+    constructor(engines: KnownEngines, defaultEngine: keyof KnownEngines, allowRSessionAccess: boolean, config: FlowrConfig, server?: Server);
     start(port: number): Promise<void>;
     private onConnect;
 }