@eagleoutice/flowr 2.9.12 → 2.9.13

package/core/steps/pipeline-step.d.ts

@@ -4,7 +4,7 @@
  */
 import type { MergeableRecord } from '../../util/objects';
 import type { InternalStepPrinter, IPipelineStepPrinter, StepOutputFormat } from '../print/print';
-import type { FlowrConfigOptions } from '../../config';
+import type { FlowrConfig } from '../../config';
 /**
  * This represents the format of a step processor which retrieves two things:
  *
@@ -16,7 +16,7 @@ import type { FlowrConfigOptions } from '../../config';
  * list all steps that you require as your {@link IPipelineStepOrder#dependencies|dependencies}, even if they would be
  * already covered transitively.
  */
-export type StepProcessingFunction = (results: Record<string, unknown>, input: Record<string, unknown>, config: FlowrConfigOptions) => unknown;
+export type StepProcessingFunction = (results: Record<string, unknown>, input: Record<string, unknown>, config: FlowrConfig) => unknown;
 /**
  * This represents the required execution frequency of a step.
  */

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

@@ -34,7 +34,7 @@ function getFunctionCallAlias(sourceId, dataflow, environment) {
         return undefined;
     }
     const defs = (0, resolve_by_name_1.resolveByName)(identifier, environment, identifier_1.ReferenceType.Function);
-    if (defs === undefined || defs.length !== 1) {
+    if (defs?.length !== 1) {
         return undefined;
     }
     return [sourceId];
@@ -206,7 +206,7 @@ function trackAliasInEnvironments(identifier, environment, { blocked, idMap, res
             }
         }
     }
-    if (values.size == 0) {
+    if (values.size === 0) {
         return r_value_1.Top;
     }
     return (0, set_constants_1.setFrom)(...values);
@@ -246,18 +246,7 @@ function trackAliasInEnvironments(identifier, environment, { blocked, idMap, res
     }
 });
 function isNestedInLoop(node, ast) {
-    const parent = node?.info.parent;
-    if (node === undefined || !parent) {
-        return false;
-    }
-    const parentNode = ast.get(parent);
-    if (parentNode === undefined) {
-        return false;
-    }
-    if (parentNode.type === type_1.RType.WhileLoop || parentNode.type === type_1.RType.RepeatLoop || parentNode.type === type_1.RType.ForLoop) {
-        return true;
-    }
-    return isNestedInLoop(parentNode, ast);
+    return model_1.RNode.iterateParents(node, ast).some(model_1.RLoopConstructs.is);
 }
 /**
  * Please use {@link resolveIdToValue}
@@ -311,12 +300,14 @@ function trackAliasesInGraph(id, graph, ctx, idMap) {
         }
         const isFn = t === vertex_1.VertexType.FunctionCall;
         const outgoingEdges = graph.outgoingEdges(id) ?? [];
+        let foundRetuns = false;
         // travel all read and defined-by edges
         for (const [targetId, { types }] of outgoingEdges) {
             if (isFn) {
                 if (types === edge_1.EdgeType.Returns || types === edge_1.EdgeType.DefinedByOnCall || types === edge_1.EdgeType.DefinedBy) {
                     queue.add(targetId, baseEnvironment, cleanFingerprint, false);
                 }
+                foundRetuns ||= edge_1.DfEdge.includesType({ types }, edge_1.EdgeType.Returns);
                 continue;
             }
             // currently, they have to be exact!
@@ -324,6 +315,9 @@ function trackAliasesInGraph(id, graph, ctx, idMap) {
                 queue.add(targetId, baseEnvironment, cleanFingerprint, false);
             }
         }
+        if (isFn && !foundRetuns) {
+            return r_value_1.Top;
+        }
     }
     if (forceTop || resultIds.length === 0) {
         return r_value_1.Top;
@@ -332,10 +326,13 @@ function trackAliasesInGraph(id, graph, ctx, idMap) {
     for (const id of resultIds) {
         const node = idMap.get(id);
         if (node !== undefined) {
+            if (node.info.role === "param-v" /* RoleInParent.ParameterDefaultValue */ || model_1.RNode.iterateParents(node, idMap).some(p => p.info.role === "param-v" /* RoleInParent.ParameterDefaultValue */)) {
+                return r_value_1.Top;
+            }
             values.add((0, general_1.valueFromRNodeConstant)(node));
         }
     }
-    return (0, set_constants_1.setFrom)(...values);
+    return values.size === 0 ? r_value_1.Top : (0, set_constants_1.setFrom)(...values);
 }
 /**
  * Please use {@link resolveIdToValue}

package/dataflow/graph/graph.js

@@ -402,17 +402,17 @@ class DataflowGraph {
         to = node_id_1.NodeId.normalize(to);
         const vertex = this.getVertex(from);
         (0, assert_1.guard)(vertex !== undefined, () => `node must be defined for ${from} to add control dependency`);
-        vertex.cds ??= [];
-        let hasControlDependency = false;
-        for (const { id, when: cond } of vertex.cds) {
-            if (id === to && when !== cond) {
-                hasControlDependency = true;
-                break;
+        if (vertex.cds) {
+            for (const { id, when: cond } of vertex.cds) {
+                if (id === to && when !== cond) {
+                    return this;
+                }
             }
         }
-        if (!hasControlDependency) {
-            vertex.cds.push({ id: to, when });
+        else {
+            vertex.cds = [];
         }
+        vertex.cds.push({ id: to, when });
         return this;
     }
     /** Marks the given node as having unknown side effects */

package/dataflow/internal/process/functions/call/built-in/built-in-eval.js

@@ -45,13 +45,13 @@ function processEvalCall(name, args, rootId, data, config) {
         const idGenerator = (0, decorate_1.sourcedDeterministicCountingIdGenerator)(name.lexeme + '::' + rootId, name.location);
         data = {
             ...data,
-            cds: [...(data.cds ?? []), { id: rootId, when: true }]
+            cds: code.length > 1 ? [...(data.cds ?? []), { id: rootId, when: true }] : data.cds
         };
         const originalInfo = { ...information };
         const result = [];
         for (const c of code) {
             const codeRequest = (0, retriever_1.requestFromInput)(c);
-            const r = (0, built_in_source_1.sourceRequest)(rootId, codeRequest, data, originalInfo, idGenerator);
+            const r = (0, built_in_source_1.sourceRequest)(rootId, codeRequest, data, originalInfo, code.length > 1, idGenerator);
             result.push(r);
             // add a returns edge from the eval to the result
             for (const e of r.exitPoints) {

package/dataflow/internal/process/functions/call/built-in/built-in-source.d.ts

@@ -45,7 +45,7 @@ export declare function processSourceCall<OtherInfo>(name: RSymbol<OtherInfo & P
  * Processes a source request with the given dataflow processor information and existing dataflow information
  * Otherwise, this can be an {@link RProjectFile} representing a standalone source file
  */
-export declare function sourceRequest<OtherInfo>(rootId: NodeId, request: RParseRequest | RProjectFile<OtherInfo & ParentInformation>, data: DataflowProcessorInformation<OtherInfo & ParentInformation>, information: DataflowInformation, getId?: IdGenerator<NoInfo>): DataflowInformation;
+export declare function sourceRequest<OtherInfo>(rootId: NodeId, request: RParseRequest | RProjectFile<OtherInfo & ParentInformation>, data: DataflowProcessorInformation<OtherInfo & ParentInformation>, information: DataflowInformation, makeMaybe: boolean, getId?: IdGenerator<NoInfo>): DataflowInformation;
 /**
  * Processes a standalone source file (i.e., not from a source function call)
  */

package/dataflow/internal/process/functions/call/built-in/built-in-source.js

@@ -30,6 +30,7 @@ const r_value_1 = require("../../../../../eval/values/r-value");
 const unknown_side_effect_1 = require("../../../../../graph/unknown-side-effect");
 const alias_tracking_1 = require("../../../../../eval/resolve/alias-tracking");
 const built_in_1 = require("../../../../../environments/built-in");
+const edge_1 = require("../../../../../graph/edge");
 /**
  * Infers working directories based on the given option and reference chain
  */
@@ -117,8 +118,8 @@ function findSource(resolveSource, seed, data) {
             const effectivePath = explore ? path_1.default.join(explore, tryPath) : tryPath;
             const context = data.ctx.files;
             const get = context.exists(effectivePath, capitalization) ?? context.exists(returnPlatformPath(effectivePath), capitalization);
-            if (get && !found.includes(effectivePath)) {
-                found.push(returnPlatformPath(effectivePath));
+            if (get && !found.includes(returnPlatformPath(get))) {
+                found.push(returnPlatformPath(get));
             }
         }
     }
@@ -176,7 +177,7 @@ function processSourceCall(name, args, rootId, data, config) {
                 result = sourceRequest(rootId, {
                     request: 'file',
                     content: f
-                }, data, result, (0, decorate_1.sourcedDeterministicCountingIdGenerator)((findCount > 0 ? findCount + '::' : '') + f, name.location));
+                }, data, result, true, (0, decorate_1.sourcedDeterministicCountingIdGenerator)((findCount > 0 ? findCount + '::' : '') + f, name.location));
             }
             return result;
         }
@@ -189,7 +190,7 @@ function processSourceCall(name, args, rootId, data, config) {
  * Processes a source request with the given dataflow processor information and existing dataflow information
  * Otherwise, this can be an {@link RProjectFile} representing a standalone source file
  */
-function sourceRequest(rootId, request, data, information, getId) {
+function sourceRequest(rootId, request, data, information, makeMaybe, getId) {
     // parse, normalize and dataflow the sourced file
     let dataflow;
     let fst;
@@ -239,11 +240,21 @@ function sourceRequest(rootId, request, data, information, getId) {
     }
     // take the entry point as well as all the written references, and give them a control dependency to the source call to show that they are conditional
     if (!String(rootId).startsWith('file-')) {
-        if (dataflow.graph.hasVertex(dataflow.entryPoint)) {
-            dataflow.graph.addControlDependency(dataflow.entryPoint, rootId, true);
+        if (makeMaybe) {
+            if (dataflow.graph.hasVertex(dataflow.entryPoint)) {
+                dataflow.graph.addControlDependency(dataflow.entryPoint, rootId, true);
+            }
+            for (const out of dataflow.out) {
+                dataflow.graph.addControlDependency(out.nodeId, rootId, true);
+            }
         }
-        for (const out of dataflow.out) {
-            dataflow.graph.addControlDependency(out.nodeId, rootId, true);
+        else {
+            if (dataflow.graph.hasVertex(dataflow.entryPoint)) {
+                dataflow.graph.addEdge(dataflow.entryPoint, rootId, edge_1.EdgeType.Reads);
+            }
+            for (const out of dataflow.out) {
+                dataflow.graph.addEdge(out.nodeId, rootId, edge_1.EdgeType.Reads);
+            }
         }
     }
     data.ctx.files.addConsideredFile(filePath ?? '<inline>');
@@ -272,6 +283,6 @@ function standaloneSourceFile(idx, file, data, information) {
         ...data,
         environment: information.environment,
         referenceChain: [...data.referenceChain, file.filePath]
-    }, information);
+    }, information, false);
 }
 //# sourceMappingURL=built-in-source.js.map

package/documentation/doc-readme.js

@@ -21,7 +21,7 @@ const PublicationsMain = [
         header: 'Statically Analyzing the Dataflow of R Programs (OOPSLA \'25)',
         description: 'Please cite this paper if you are using flowR in your research.',
         doi: 'https://doi.org/10.1145/3763087',
-        bibtex: `@article{10.1145/3763087,
+        bibtex: String.raw `@article{10.1145/3763087,
 	author = {Sihler, Florian and Tichy, Matthias},
 	title = {Statically Analyzing the Dataflow of R Programs},
 	year = {2025},
@@ -32,7 +32,7 @@ const PublicationsMain = [
 	number = {OOPSLA2},
 	url = {https://doi.org/10.1145/3763087},
 	doi = {10.1145/3763087},
-	abstract = {The R programming language is primarily designed for statistical computing and mostly used by researchers without a background in computer science. R provides a wide range of dynamic features and peculiarities that are difficult to analyze statically like dynamic scoping and lazy evaluation with dynamic side effects. At the same time, the R ecosystem lacks sophisticated analysis tools that support researchers in understanding and improving their code.   In this paper, we present a novel static dataflow analysis framework for the R programming language that is capable of handling the dynamic nature of R programs and produces the dataflow graph of given R programs. This graph can be essential in a range of analyses, including program slicing, which we implement as a proof of concept. The core analysis works as a stateful fold over a normalized version of the abstract syntax tree of the R program, which tracks (re-)definitions, values, function calls, side effects, external files, and a dynamic control flow to produce one dataflow graph per program.   We evaluate the correctness of our analysis using output equivalence testing on a manually curated dataset of 779 sensible slicing points from executable real-world R scripts. Additionally, we use a set of systematic test cases based on the capabilities of the R language and the implementation of the R interpreter and measure the runtimes well as the memory consumption on a set of 4,230 real-world R scripts and 20,815 packages available on R’s package manager CRAN.   Furthermore, we evaluate the recall of our program slicer, its accuracy using shrinking, and its improvement over the state of the art. We correctly analyze almost all programs in our equivalence test suite, preserving the identical output for 99.7\\% of the manually curated slicing points. On average, we require 576ms to analyze the dataflow and around 213kB to store the graph of a research script.   This shows that our analysis is capable of analyzing real-world sources quickly and correctly. Our slicer achieves an average reduction of 84.8\\% of tokens indicating its potential to improve program comprehension.},
+	abstract = {The R programming language is primarily designed for statistical computing and mostly used by researchers without a background in computer science. R provides a wide range of dynamic features and peculiarities that are difficult to analyze statically like dynamic scoping and lazy evaluation with dynamic side effects. At the same time, the R ecosystem lacks sophisticated analysis tools that support researchers in understanding and improving their code.   In this paper, we present a novel static dataflow analysis framework for the R programming language that is capable of handling the dynamic nature of R programs and produces the dataflow graph of given R programs. This graph can be essential in a range of analyses, including program slicing, which we implement as a proof of concept. The core analysis works as a stateful fold over a normalized version of the abstract syntax tree of the R program, which tracks (re-)definitions, values, function calls, side effects, external files, and a dynamic control flow to produce one dataflow graph per program.   We evaluate the correctness of our analysis using output equivalence testing on a manually curated dataset of 779 sensible slicing points from executable real-world R scripts. Additionally, we use a set of systematic test cases based on the capabilities of the R language and the implementation of the R interpreter and measure the runtimes well as the memory consumption on a set of 4,230 real-world R scripts and 20,815 packages available on R’s package manager CRAN.   Furthermore, we evaluate the recall of our program slicer, its accuracy using shrinking, and its improvement over the state of the art. We correctly analyze almost all programs in our equivalence test suite, preserving the identical output for 99.7\% of the manually curated slicing points. On average, we require 576ms to analyze the dataflow and around 213kB to store the graph of a research script.   This shows that our analysis is capable of analyzing real-world sources quickly and correctly. Our slicer achieves an average reduction of 84.8\% of tokens indicating its potential to improve program comprehension.},
 	journal = {Proc. ACM Program. Lang.},
 	month = oct,
 	articleno = {309},

package/documentation/wiki-analyzer.js

@@ -29,6 +29,7 @@ const flowr_analyzer_plugin_1 = require("../project/plugins/flowr-analyzer-plugi
 const flowr_analyzer_environment_context_1 = require("../project/context/flowr-analyzer-environment-context");
 const flowr_analyzer_functions_context_1 = require("../project/context/flowr-analyzer-functions-context");
 const flowr_analyzer_meta_context_1 = require("../project/context/flowr-analyzer-meta-context");
+const config_1 = require("../config");
 async function analyzerQuickExample() {
     const analyzer = await new flowr_analyzer_builder_1.FlowrAnalyzerBuilder()
         .setEngine('tree-sitter')
@@ -172,23 +173,24 @@ The following sections highlight some of the most important configuration option
 ${(0, doc_structure_1.section)('Configuring flowR', 3)}
 
 You can fundamentally change the behavior of flowR using the [config file](${doc_files_1.FlowrWikiBaseRef}/Interface#configuring-flowr),
-embedded in the interface ${ctx.link('FlowrConfigOptions')}.
+embedded in the interface ${ctx.link(config_1.FlowrConfig)}.
 With the builder you can either provide a complete configuration or amend the default configuration using:
 
 * ${ctx.linkM(flowr_analyzer_builder_1.FlowrAnalyzerBuilder, 'setConfig')} to set a complete configuration
+* ${ctx.linkM(flowr_analyzer_builder_1.FlowrAnalyzerBuilder, 'configure')} to set the value of a specific key in the config
 * ${ctx.linkM(flowr_analyzer_builder_1.FlowrAnalyzerBuilder, 'amendConfig')} to amend the default configuration
 
-By default, the builder uses flowR's standard configuration obtained with ${ctx.link('defaultConfigOptions')}.
+By default, the builder uses flowR's standard configuration obtained with ${ctx.linkO(config_1.FlowrConfig, 'default')}.
 
 ${(0, doc_structure_1.block)({
             type: 'NOTE',
-            content: `During the analysis with the ${ctx.link(flowr_analyzer_1.FlowrAnalyzer.name)}, you can also access the configuration with
+            content: `During the analysis with the ${ctx.link(flowr_analyzer_1.FlowrAnalyzer)}, you can also access the configuration with
 		 the ${ctx.link(flowr_analyzer_context_1.FlowrAnalyzerContext)}.`
         })}
 
 ${(0, doc_structure_1.section)('Configuring the Engine', 3)}
 
-FlowR supports multiple [engines](${doc_files_1.FlowrWikiBaseRef}/Engines) for parsing and analyzing R code.
+FlowR supports multiple ${ctx.linkPage('wiki/Engines', 'engines')} for parsing and analyzing R code.
 With the builder, you can select the engine to use with:
 
 * ${ctx.linkM(flowr_analyzer_builder_1.FlowrAnalyzerBuilder, 'setEngine')} to set the desired engine.
@@ -292,7 +294,7 @@ ${(0, doc_structure_1.section)('File Loading', 4)}
 
 These plugins register for every file encountered by the [files context](#Files_Context) and determine whether and _how_ they can process the file.
 They are responsible for transforming the raw file content into a representation that flowR can work with during the analysis.
-For example, the ${ctx.link(flowr_analyzer_description_file_plugin_1.FlowrAnalyzerDescriptionFilePlugin.name)} adds support for R \`DESCRIPTION\` files by parsing their content into key-value pairs.
+For example, the ${ctx.link(flowr_analyzer_description_file_plugin_1.FlowrAnalyzerDescriptionFilePlugin)} adds support for R \`DESCRIPTION\` files by parsing their content into key-value pairs.
 These can then be used by other plugins, e.g. the ${ctx.link(flowr_analyzer_package_versions_description_file_plugin_1.FlowrAnalyzerPackageVersionsDescriptionFilePlugin)} that extracts package version information from these files.
 
 If multiple file plugins could apply (${ctx.link('DefaultFlowrAnalyzerFilePlugin::' + flowr_analyzer_file_plugin_1.FlowrAnalyzerFilePlugin.defaultPlugin().applies.name)}) to the same file,

package/documentation/wiki-core.js

@@ -47,9 +47,7 @@ const log_1 = require("../../test/functionality/_helper/log");
 const log_2 = require("../util/log");
 async function makeAnalyzerExample() {
     const analyzer = await new flowr_analyzer_builder_1.FlowrAnalyzerBuilder()
-        .amendConfig(c => {
-        c.ignoreSourceCalls = true;
-    })
+        .configure('ignoreSourceCalls', true)
         .setEngine('tree-sitter')
         .build();
     analyzer.addRequest('x <- 1; y <- x; print(y);');

package/documentation/wiki-dataflow-graph.js

@@ -891,7 +891,7 @@ ${await getVertexExplanations(treeSitter, ctx)}
 
 ${(0, doc_structure_1.section)('Edges', 2, 'edges')}
 
-1. ${(0, doc_data_dfg_util_1.getAllEdges)().map(([k, v], index) => `[\`${k}\` (${v})](#${index + 1}-${k.toLowerCase().replace(/\s/g, '-')}-edge)`).join('\n1. ')}
+1. ${(0, doc_data_dfg_util_1.getAllEdges)().map(([k, v], index) => `[\`${k}\` (${v})](#${index + 1}-${k.toLowerCase().replaceAll(/\s/g, '-')}-edge)`).join('\n1. ')}
 
 ${await getEdgesExplanations(treeSitter, ctx)}
 

package/documentation/wiki-interface.js

@@ -200,7 +200,7 @@ ${await (0, doc_repl_1.documentReplSession)(parser, [{
 For more information on the available queries, please check out the ${ctx.linkPage('wiki/Query API', 'Query API')}.
 `;
 }
-function explainConfigFile() {
+function explainConfigFile(ctx) {
     return `
 
 When running _flowR_, you may want to specify some behaviors with a dedicated configuration file. 
@@ -211,6 +211,8 @@ Within the REPL this works by running the following:
 
 ${(0, doc_code_1.codeBlock)('shell', ':query @config')}
 
+To work with the ${ctx.link(config_1.FlowrConfig)} you can use the provided helper objects alongside its methods like
+${ctx.linkO(config_1.FlowrConfig, 'amend')}.
 The following summarizes the configuration options:
 
 - \`ignoreSourceCalls\`: If set to \`true\`, _flowR_ will ignore source calls when analyzing the code, i.e., ignoring the inclusion of other files.
@@ -298,7 +300,7 @@ ${(0, doc_code_1.codeBlock)('json', JSON.stringify({
 
 <summary style='color:gray'>Full Configuration-File Schema</summary>
 
-${(0, schema_1.describeSchema)(config_1.flowrConfigFileSchema, ansi_1.markdownFormatter)}
+${(0, schema_1.describeSchema)(config_1.FlowrConfig.Schema, ansi_1.markdownFormatter)}
 
 </details>
 
@@ -331,7 +333,7 @@ ${await explainRepl(treeSitter, ctx)}
 <a id='configuring-flowr'></a>
 ## ⚙️ Configuring FlowR
 
-${explainConfigFile()}
+${explainConfigFile(ctx)}
 
 <a id='writing-code'></a>
 ## ⚒️ Writing Code

package/documentation/wiki-linter.js

@@ -46,12 +46,12 @@ function prettyPrintExpectedOutput(expected) {
     //
     lines = expected.trim().replace(/^\s*\[+\s*{*/m, '').replace(/\s*}*\s*]+\s*$/, '').split('\n').filter(l => l.trim() !== '');
     /* take the indentation of the last line and remove it from all but the first: */
-    const indentation = lines[lines.length - 1].match(/^\s*/)?.[0] ?? '';
+    const indentation = lines.at(-1)?.match(/^\s*/)?.[0] ?? '';
     return lines.map((line, i) => {
         if (i === 0) {
             return line;
         }
-        return line.replace(new RegExp('^' + indentation, 'g'), '');
+        return line.replaceAll(new RegExp('^' + indentation, 'g'), '');
     }).join('\n');
 }
 function buildSamplesFromLinterTestCases(_parser, testFile) {
@@ -236,7 +236,7 @@ We use tags to categorize linting rules for users. The following tags are availa
 | Tag/Badge   | Description |
 | --- | :-- |
 ${Object.entries(linter_tags_1.LintingRuleTag).map(([name, tag]) => {
-        return `| <a id="${tag}"></a> ${(makeTagBadge(tag, tagTypes.info))} | ${(0, doc_types_1.getDocumentationForType)('LintingRuleTag::' + name, tagTypes.info).replaceAll(/\n/g, ' ')} (rule${getAllLintingRulesWithTag(tag).length === 1 ? '' : 's'}: ${(0, strings_1.joinWithLast)(getAllLintingRulesWithTag(tag).map(l => linkToRule(l))) || '_none_'}) | `;
+        return `| <a id="${tag}"></a> ${(makeTagBadge(tag, tagTypes.info))} | ${(0, doc_types_1.getDocumentationForType)('LintingRuleTag::' + name, tagTypes.info).replaceAll('\n', ' ')} (rule${getAllLintingRulesWithTag(tag).length === 1 ? '' : 's'}: ${(0, strings_1.joinWithLast)(getAllLintingRulesWithTag(tag).map(l => linkToRule(l))) || '_none_'}) | `;
     }).join('\n')}
 
 ${(0, doc_structure_1.section)('Certainty', 2, 'certainty')}
@@ -248,14 +248,14 @@ ${(0, doc_structure_1.section)('Rule Certainty', 3, 'rule-certainty')}
 | Rule Certainty | Description |
 | -------------- | :---------- |
 ${Object.entries(linter_format_1.LintingRuleCertainty).map(([name, certainty]) => {
-        return `| <a id="${certainty}"></a> \`${certainty}\` | ${(0, doc_types_1.getDocumentationForType)('LintingRuleCertainty::' + name, tagTypes.info).replaceAll(/\n/g, ' ')} (rule${getAllLintingRulesWitCertainty(certainty).length === 1 ? '' : 's'}: ${(0, strings_1.joinWithLast)(getAllLintingRulesWitCertainty(certainty).map(l => linkToRule(l))) || '_none_'}) |`;
+        return `| <a id="${certainty}"></a> \`${certainty}\` | ${(0, doc_types_1.getDocumentationForType)('LintingRuleCertainty::' + name, tagTypes.info).replaceAll('\n', ' ')} (rule${getAllLintingRulesWitCertainty(certainty).length === 1 ? '' : 's'}: ${(0, strings_1.joinWithLast)(getAllLintingRulesWitCertainty(certainty).map(l => linkToRule(l))) || '_none_'}) |`;
     }).join('\n')}
 	
 ${(0, doc_structure_1.section)('Result Certainty', 3, 'result-certainty')}
 
 | Result Certainty | Description |
 | ---------------- | :---------- |
-${Object.entries(linter_format_1.LintingResultCertainty).map(([name, certainty]) => `| <a id="${certainty}"></a> \`${certainty}\` | ${(0, doc_types_1.getDocumentationForType)('LintingResultCertainty::' + name, tagTypes.info).replaceAll(/\n/g, ' ')} |`).join('\n')}
+${Object.entries(linter_format_1.LintingResultCertainty).map(([name, certainty]) => `| <a id="${certainty}"></a> \`${certainty}\` | ${(0, doc_types_1.getDocumentationForType)('LintingResultCertainty::' + name, tagTypes.info).replaceAll('\n', ' ')} |`).join('\n')}
 
 `.trim();
 }

package/documentation/wiki-mk/doc-context.js

@@ -49,8 +49,7 @@ exports.ConstantWikiLinkInfo = {
  */
 function makeDocContextForTypes(shell, ...rootFolders) {
     if (rootFolders.length === 0) {
-        rootFolders.push(path_1.default.resolve(__dirname, '../../../src'));
-        rootFolders.push(path_1.default.resolve(__dirname, '../../../test/functionality'));
+        rootFolders.push(path_1.default.resolve(__dirname, '../../../src'), path_1.default.resolve(__dirname, '../../../test/functionality'));
     }
     const { info, program } = (0, doc_types_1.getTypesFromFolder)({ rootFolder: rootFolders, typeNameForMermaid: undefined });
     return {
@@ -108,10 +107,10 @@ function makeDocContextForTypes(shell, ...rootFolders) {
                 text ??= i.name;
             }
             else {
-                link = `${doc_files_1.FlowrWikiBaseRef}/${pageName.toLowerCase().replace(/ /g, '-')}`;
+                link = `${doc_files_1.FlowrGithubRef}/${pageName.toLowerCase().replaceAll(' ', '-')}`;
             }
             text ??= pageName.split('/').pop() ?? pageName;
-            return `[${text}](${link}${segment ? `#${segment}` : ''})`;
+            return `[${text}](${link}${segment ? '#' + segment : ''})`;
         },
         linkCode(path, lineNumber) {
             const lnk = lineNumber ? `${path.toString()}#L${lineNumber}` : path.toString();

package/engines.d.ts

@@ -1,9 +1,9 @@
-import { type FlowrConfigOptions, type KnownEngines } from './config';
+import { FlowrConfig, type KnownEngines } from './config';
 /**
  * Retrieve all requested engine instance.
  * Please make sure that if this includes the R engine, that you properly shut it down again!
  */
-export declare function retrieveEngineInstances(config: FlowrConfigOptions, defaultOnly?: boolean): Promise<{
+export declare function retrieveEngineInstances(config: FlowrConfig, defaultOnly?: boolean): Promise<{
     engines: KnownEngines;
     default: keyof KnownEngines;
 }>;

package/engines.js

@@ -12,9 +12,9 @@ const log_1 = require("./util/log");
  */
 async function retrieveEngineInstances(config, defaultOnly = false) {
     const engines = {};
-    if ((0, config_1.getEngineConfig)(config, 'r-shell') && (!defaultOnly || config.defaultEngine === 'r-shell')) {
+    if (config_1.FlowrConfig.getForEngine(config, 'r-shell') && (!defaultOnly || config.defaultEngine === 'r-shell')) {
         // we keep an active shell session to allow other parse investigations :)
-        engines['r-shell'] = new shell_1.RShell((0, config_1.getEngineConfig)(config, 'r-shell'), {
+        engines['r-shell'] = new shell_1.RShell(config_1.FlowrConfig.getForEngine(config, 'r-shell'), {
             revive: 2 /* RShellReviveOptions.Always */,
             onRevive: (code, signal) => {
                 const signalText = signal == null ? '' : ` and signal ${signal}`;
@@ -23,8 +23,8 @@ async function retrieveEngineInstances(config, defaultOnly = false) {
             }
         });
     }
-    if ((0, config_1.getEngineConfig)(config, 'tree-sitter') && (!defaultOnly || config.defaultEngine === 'tree-sitter')) {
-        await tree_sitter_executor_1.TreeSitterExecutor.initTreeSitter((0, config_1.getEngineConfig)(config, 'tree-sitter'));
+    if (config_1.FlowrConfig.getForEngine(config, 'tree-sitter') && (!defaultOnly || config.defaultEngine === 'tree-sitter')) {
+        await tree_sitter_executor_1.TreeSitterExecutor.initTreeSitter(config_1.FlowrConfig.getForEngine(config, 'tree-sitter'));
         engines['tree-sitter'] = new tree_sitter_executor_1.TreeSitterExecutor();
     }
     let defaultEngine = config.defaultEngine;

package/linter/rules/dataframe-access-validation.js

@@ -3,7 +3,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.DATA_FRAME_ACCESS_VALIDATION = void 0;
 const shape_inference_1 = require("../../abstract-interpretation/data-frame/shape-inference");
 const satisfiable_domain_1 = require("../../abstract-interpretation/domains/satisfiable-domain");
-const config_1 = require("../../config");
 const cfg_kind_1 = require("../../project/cfg-kind");
 const type_1 = require("../../r-bridge/lang-4.x/ast/model/type");
 const flowr_search_builder_1 = require("../../search/flowr-search-builder");
@@ -13,13 +12,14 @@ const range_1 = require("../../util/range");
 const linter_format_1 = require("../linter-format");
 const linter_tags_1 = require("../linter-tags");
 const identifier_1 = require("../../dataflow/environments/identifier");
+const config_1 = require("../../config");
 exports.DATA_FRAME_ACCESS_VALIDATION = {
     createSearch: () => flowr_search_builder_1.Q.all().with(search_enrichers_1.Enrichment.CallTargets, { onlyBuiltin: true }),
     processSearchResult: async (elements, config, data) => {
         let ctx = data.analyzer.inspectContext();
         ctx = {
             ...ctx,
-            config: (0, config_1.amendConfig)(data.analyzer.flowrConfig, flowrConfig => {
+            config: config_1.FlowrConfig.amend(data.analyzer.flowrConfig, flowrConfig => {
                 if (config.readLoadedData !== undefined) {
                     flowrConfig.abstractInterpretation.dataFrame.readLoadedData.readExternalFiles = config.readLoadedData;
                 }
@@ -61,7 +61,7 @@ exports.DATA_FRAME_ACCESS_VALIDATION = {
             .map(({ nodeId, operand, ...accessed }) => ({
             ...accessed,
             node: data.normalize.idMap.get(nodeId),
-            operand: operand !== undefined ? data.normalize.idMap.get(operand) : undefined,
+            operand: operand === undefined ? undefined : data.normalize.idMap.get(operand),
         }))
             .map(({ node, operand, ...accessed }) => ({
             ...accessed,
@@ -76,10 +76,10 @@ exports.DATA_FRAME_ACCESS_VALIDATION = {
     prettyPrint: {
         [linter_format_1.LintingPrettyPrintContext.Query]: result => `Access of ${result.type} ` +
             (typeof result.accessed === 'string' ? `"${result.accessed}"` : result.accessed) + ' ' +
-            (result.operand !== undefined ? `of \`${result.operand}\`` : `at \`${result.access}\``) + ` at ${range_1.SourceRange.format(result.range)}`,
+            (result.operand === undefined ? `at \`${result.access}\`` : `of \`${result.operand}\``) + ` at ${range_1.SourceRange.format(result.range)}`,
         [linter_format_1.LintingPrettyPrintContext.Full]: result => `Accessed ${result.type} ` +
             (typeof result.accessed === 'string' ? `"${result.accessed}"` : result.accessed) + ' does not exist ' +
-            (result.operand !== undefined ? `in \`${result.operand}\`` : `at \`${result.access}\``) + ` at ${range_1.SourceRange.format(result.range)}`
+            (result.operand === undefined ? `at \`${result.access}\`` : `in \`${result.operand}\``) + ` at ${range_1.SourceRange.format(result.range)}`
     },
     info: {
         name: 'Dataframe Access Validation',

package/linter/rules/naming-convention.d.ts

@@ -53,7 +53,7 @@ export declare function getMostUsedCasing(symbols: {
 /**
  * Attempts to fix the casing of the given identifier to match the provided convention.
  */
-export declare function fixCasing(identifier: string, convention: CasingConvention): string | undefined;
+export declare function fixCasing(identifier: string, convention: CasingConvention, ignorePrefix?: string): string | undefined;
 /**
  * Creates quick fixes for renaming all references to the given node to match the provided replacement.
  */

package/linter/rules/naming-convention.js

@@ -91,11 +91,15 @@ function getMostUsedCasing(symbols) {
 /**
  * Attempts to fix the casing of the given identifier to match the provided convention.
  */
-function fixCasing(identifier, convention) {
+function fixCasing(identifier, convention, ignorePrefix) {
     if (!containsAlpha(identifier)) {
         return undefined;
     }
-    const tokens = identifier.split(/(?=[A-Z])|_/).map(s => s.toLowerCase());
+    if (ignorePrefix) {
+        identifier = identifier.replace(new RegExp(`^(${ignorePrefix})`), '');
+    }
+    const splitOn = identifier.includes('_') ? /_/ : /(?=[A-Z])/;
+    const tokens = identifier.split(splitOn).map(s => s.toLowerCase());
     const firstUp = (s) => {
         if (s.length < 1) {
             return s.toUpperCase();
@@ -167,7 +171,7 @@ exports.NAMING_CONVENTION = {
         const results = symbols
             .filter(m => (m.detectedCasing !== casing) && (!config.ignoreNonAlpha || containsAlpha(m.name)))
             .map(({ id, ...m }) => {
-            const fix = fixCasing(m.name, casing);
+            const fix = fixCasing(m.name, casing, config.ignorePrefix);
             return {
                 ...m,
                 involvedId: id,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@eagleoutice/flowr",
-  "version": "2.9.12",
+  "version": "2.9.13",
   "description": "Static Dataflow Analyzer and Program Slicer for the R Programming Language",
   "types": "dist/src/index.d.ts",
   "repository": {
@@ -178,6 +178,7 @@
     "@types/n-readlines": "^1.0.6",
     "@types/n3": "^1.26.0",
     "@types/object-hash": "^3.0.6",
+    "@types/object-path": "^0.11.4",
     "@types/seedrandom": "^3.0.8",
     "@types/semver": "^7.7.0",
     "@types/tmp": "^0.2.6",
@@ -212,6 +213,7 @@
     "n-readlines": "^1.0.3",
     "n3": "^1.26.0",
     "object-hash": "^3.0.0",
+    "object-path": "^0.11.8",
     "object-sizeof": "^2.6.5",
     "rotating-file-stream": "^3.2.8",
     "seedrandom": "^3.0.5",

package/project/context/flowr-analyzer-context.d.ts

@@ -2,7 +2,7 @@ import { FlowrAnalyzerFilesContext, type RAnalysisRequest, type ReadOnlyFlowrAna
 import { FlowrAnalyzerDependenciesContext, type ReadOnlyFlowrAnalyzerDependenciesContext } from './flowr-analyzer-dependencies-context';
 import { type FlowrAnalyzerPlugin, PluginType } from '../plugins/flowr-analyzer-plugin';
 import type { fileProtocol, RParseRequestFromFile, RParseRequests } from '../../r-bridge/retriever';
-import type { FlowrConfigOptions } from '../../config';
+import { FlowrConfig } from '../../config';
 import type { FlowrFileProvider } from './flowr-file';
 import type { ReadOnlyFlowrAnalyzerEnvironmentContext } from './flowr-analyzer-environment-context';
 import { FlowrAnalyzerEnvironmentContext } from './flowr-analyzer-environment-context';
@@ -34,7 +34,7 @@ export interface ReadOnlyFlowrAnalyzerContext {
     /**
      * The configuration options used by the analyzer.
      */
-    readonly config: FlowrConfigOptions;
+    readonly config: FlowrConfig;
     /**
      * Run all resolution steps that can be done before the main analysis run.
      */
@@ -58,8 +58,8 @@ export declare class FlowrAnalyzerContext implements ReadOnlyFlowrAnalyzerContex
     readonly deps: FlowrAnalyzerDependenciesContext;
     readonly env: FlowrAnalyzerEnvironmentContext;
     private _analyzer;
-    readonly config: FlowrConfigOptions;
-    constructor(config: FlowrConfigOptions, plugins: ReadonlyMap<PluginType, readonly FlowrAnalyzerPlugin[]>);
+    readonly config: FlowrConfig;
+    constructor(config: FlowrConfig, plugins: ReadonlyMap<PluginType, readonly FlowrAnalyzerPlugin[]>);
     /**
      * Provides the analyzer associated with this context, if any.
      * This is usually set when the context is used within an analyzer instance.
@@ -91,7 +91,7 @@ export declare class FlowrAnalyzerContext implements ReadOnlyFlowrAnalyzerContex
  * @see {@link requestFromInput} - for details on how inputs are processed into requests.
  * @see {@link contextFromSources} - to create a context from source code strings directly.
  */
-export declare function contextFromInput(input: `${typeof fileProtocol}${string}` | string | readonly string[] | RParseRequests, config?: FlowrConfigOptions, plugins?: FlowrAnalyzerPlugin[]): FlowrAnalyzerContext;
+export declare function contextFromInput(input: `${typeof fileProtocol}${string}` | string | readonly string[] | RParseRequests, config?: FlowrConfig, plugins?: FlowrAnalyzerPlugin[]): FlowrAnalyzerContext;
 /**
  * Create a {@link FlowrAnalyzerContext} from a set of source code strings.
  * @param sources - A record mapping file paths to their source code content.
@@ -100,4 +100,4 @@ export declare function contextFromInput(input: `${typeof fileProtocol}${string}
  * @see {@link contextFromInput}    - to create a context from input requests.
  * @see {@link FlowrInlineTextFile} - to create inline text files for the sources.
  */
-export declare function contextFromSources(sources: Record<string, string>, config?: FlowrConfigOptions, plugins?: FlowrAnalyzerPlugin[]): FlowrAnalyzerContext;
+export declare function contextFromSources(sources: Record<string, string>, config?: FlowrConfig, plugins?: FlowrAnalyzerPlugin[]): FlowrAnalyzerContext;

package/project/context/flowr-analyzer-context.js

@@ -93,7 +93,7 @@ exports.FlowrAnalyzerContext = FlowrAnalyzerContext;
  * @see {@link requestFromInput} - for details on how inputs are processed into requests.
  * @see {@link contextFromSources} - to create a context from source code strings directly.
  */
-function contextFromInput(input, config = config_1.defaultConfigOptions, plugins) {
+function contextFromInput(input, config = config_1.FlowrConfig.default(), plugins) {
     const context = new FlowrAnalyzerContext(config, (0, arrays_1.arraysGroupBy)(plugins ?? [], (p) => p.type));
     if (typeof input === 'string' || Array.isArray(input) && input.every(i => typeof i === 'string')) {
         const requests = (0, retriever_1.requestFromInput)(input);
@@ -113,7 +113,7 @@ function contextFromInput(input, config = config_1.defaultConfigOptions, plugins
  * @see {@link contextFromInput}    - to create a context from input requests.
  * @see {@link FlowrInlineTextFile} - to create inline text files for the sources.
  */
-function contextFromSources(sources, config = config_1.defaultConfigOptions, plugins) {
+function contextFromSources(sources, config = config_1.FlowrConfig.default(), plugins) {
     const context = new FlowrAnalyzerContext(config, (0, arrays_1.arraysGroupBy)(plugins ?? [], (p) => p.type));
     for (const [p, c] of Object.entries(sources)) {
         context.addFile(new flowr_file_1.FlowrInlineTextFile(p, c));