@eagleoutice/flowr 2.9.11 → 2.9.13

package/documentation/wiki-engine.js

@@ -37,6 +37,19 @@ are exposed with some command line options (e.g., when using the docker image of
 - ${ctx.cliOption('flowr', 'engine.tree-sitter.tree-sitter-wasm-path', false)} pass the path to the wasm of tree-sitter (see [below](#tree-sitter))
 - ${ctx.cliOption('flowr', 'default-engine', false)} to set the default engine to use
 
+<a id="r-shell"></a>
+## Dealing with the R Shell Engine
+
+The ${ctx.link(shell_1.RShell)} engine is the original engine of flowR and is still available today.
+It provides a powerful interface to the R interpreter, allowing for complex interactions and the execution of R code.
+There are two interfaces available: 
+
+* The ${ctx.link(shell_1.RShell)} which is asynchronous and allows for non-blocking interactions with the R interpreter. This is the default engine.
+* The ${ctx.link(shell_executor_1.RShellExecutor)} which is synchronous and blocks the execution until the R code is executed. This can be useful for certain use cases where you want to ensure that the R code is executed before proceeding with the analysis.
+
+Please note, that these classes are available to you even if you do not use/enable the R shell engine.
+The selection and preparation of the engine just reflects what the flowR analysis will use. 
+
 <a id="tree-sitter"></a>
 ## Dealing with the Tree-Sitter Engine
 
@@ -59,6 +72,11 @@ you first must build the new wasm file. For this you have to:
 3. Pass the \`tree-sitter-r.wasm\` to flowR. 
 
 For tree-sitter, please rely on the [releases](https://github.com/tree-sitter/tree-sitter/releases).
+
+${(0, doc_structure_1.block)({
+            type: 'NOTE',
+            content: 'The tree-sitter grammar may not be able to parse all valid R code due to some bugs in the parser grammar. In that case, please report these to the [tree-sitter-r repository](https://github.com/r-lib/tree-sitter-r).'
+        })}
 `;
     }
 }

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.d.ts

@@ -47,17 +47,50 @@ type StaticKeys<T> = T extends {
     prototype: infer P;
 } ? Exclude<keyof T, keyof P> : never;
 export declare const ConstantWikiLinkInfo: {
-    readonly 'flowr:npm': "https://www.npmjs.com/package/@eagleoutice/flowr";
-    readonly 'flowr:github': string;
-    readonly 'flowr:wiki': "https://github.com/flowr-analysis/flowr/wiki";
-    readonly 'flowr:docker': "https://hub.docker.com/r/eagleoutice/flowr";
-    readonly 'flowr:vscode': "https://marketplace.visualstudio.com/items?itemName=code-inspect.vscode-flowr";
-    readonly 'flowr:positron': "https://open-vsx.org/extension/code-inspect/vscode-flowr";
-    readonly 'flowr:rstudio-addin': "https://github.com/flowr-analysis/rstudio-addin-flowr";
-    readonly 'flowr:radapter': "https://github.com/flowr-analysis/flowr-r-adapter";
-    readonly 'flowr:benchmarks': "https://flowr-analysis.github.io/flowr/wiki/stats/benchmark";
-    readonly 'flowr:docs': "https://flowr-analysis.github.io/flowr/docs";
-    readonly 'flowr:zenodo': "https://zenodo.org/doi/10.5281/zenodo.13319290";
+    readonly 'flowr:npm': {
+        readonly url: "https://www.npmjs.com/package/@eagleoutice/flowr";
+        readonly name: "flowR on npm";
+    };
+    readonly 'flowr:github': {
+        readonly url: string;
+        readonly name: "flowR's GitHub";
+    };
+    readonly 'flowr:wiki': {
+        readonly url: "https://github.com/flowr-analysis/flowr/wiki";
+        readonly name: "flowR's wiki";
+    };
+    readonly 'flowr:docker': {
+        readonly url: "https://hub.docker.com/r/eagleoutice/flowr";
+        readonly name: "flowR's Docker Image";
+    };
+    readonly 'flowr:vscode': {
+        readonly url: "https://marketplace.visualstudio.com/items?itemName=code-inspect.vscode-flowr";
+        readonly name: "flowR extension for VS Code";
+    };
+    readonly 'flowr:positron': {
+        readonly url: "https://open-vsx.org/extension/code-inspect/vscode-flowr";
+        readonly name: "flowR extension for Positron";
+    };
+    readonly 'flowr:rstudio-addin': {
+        readonly url: "https://github.com/flowr-analysis/rstudio-addin-flowr";
+        readonly name: "flowR RStudio Addin";
+    };
+    readonly 'flowr:radapter': {
+        readonly url: "https://github.com/flowr-analysis/flowr-r-adapter";
+        readonly name: "flowR R Adapter";
+    };
+    readonly 'flowr:benchmarks': {
+        readonly url: "https://flowr-analysis.github.io/flowr/wiki/stats/benchmark";
+        readonly name: "flowR benchmark page";
+    };
+    readonly 'flowr:docs': {
+        readonly url: "https://flowr-analysis.github.io/flowr/docs";
+        readonly name: "flowR code docs";
+    };
+    readonly 'flowr:zenodo': {
+        readonly url: "https://zenodo.org/doi/10.5281/zenodo.13319290";
+        readonly name: "flowR on Zenodo";
+    };
 };
 /**
  * Provides methods to generate links, code snippets, and documentation for code elements.

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

@@ -23,17 +23,17 @@ function getNameFromElementIdOrRef(element) {
     }
 }
 exports.ConstantWikiLinkInfo = {
-    'flowr:npm': doc_files_1.FlowrNpmRef,
-    'flowr:github': doc_files_1.FlowrGithubRef,
-    'flowr:wiki': doc_files_1.FlowrWikiBaseRef,
-    'flowr:docker': doc_files_1.FlowrDockerRef,
-    'flowr:vscode': doc_files_1.FlowrVsCode,
-    'flowr:positron': doc_files_1.FlowrPositron,
-    'flowr:rstudio-addin': doc_files_1.FlowrRStudioAddin,
-    'flowr:radapter': doc_files_1.FlowrRAdapter,
-    'flowr:benchmarks': 'https://flowr-analysis.github.io/flowr/wiki/stats/benchmark',
-    'flowr:docs': 'https://flowr-analysis.github.io/flowr/docs',
-    'flowr:zenodo': 'https://zenodo.org/doi/10.5281/zenodo.13319290'
+    'flowr:npm': { url: doc_files_1.FlowrNpmRef, name: 'flowR on npm' },
+    'flowr:github': { url: doc_files_1.FlowrGithubRef, name: 'flowR\'s GitHub' },
+    'flowr:wiki': { url: doc_files_1.FlowrWikiBaseRef, name: 'flowR\'s wiki' },
+    'flowr:docker': { url: doc_files_1.FlowrDockerRef, name: 'flowR\'s Docker Image' },
+    'flowr:vscode': { url: doc_files_1.FlowrVsCode, name: 'flowR extension for VS Code' },
+    'flowr:positron': { url: doc_files_1.FlowrPositron, name: 'flowR extension for Positron' },
+    'flowr:rstudio-addin': { url: doc_files_1.FlowrRStudioAddin, name: 'flowR RStudio Addin' },
+    'flowr:radapter': { url: doc_files_1.FlowrRAdapter, name: 'flowR R Adapter' },
+    'flowr:benchmarks': { url: 'https://flowr-analysis.github.io/flowr/wiki/stats/benchmark', name: 'flowR benchmark page' },
+    'flowr:docs': { url: 'https://flowr-analysis.github.io/flowr/docs', name: 'flowR code docs' },
+    'flowr:zenodo': { url: 'https://zenodo.org/doi/10.5281/zenodo.13319290', name: 'flowR on Zenodo' },
 };
 /**
  * Creates a wiki context for generating documentation for code elements.
@@ -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 {
@@ -100,15 +99,18 @@ function makeDocContextForTypes(shell, ...rootFolders) {
             });
         },
         linkPage(pageName, linkText, segment) {
-            const text = linkText ?? pageName.split('/').pop() ?? pageName;
             let link;
+            let text = linkText;
             if (pageName in exports.ConstantWikiLinkInfo) {
-                link = exports.ConstantWikiLinkInfo[pageName];
+                const i = exports.ConstantWikiLinkInfo[pageName];
+                link = i.url;
+                text ??= i.name;
             }
             else {
-                link = `${doc_files_1.FlowrWikiBaseRef}/${pageName.toLowerCase().replace(/ /g, '-')}`;
+                link = `${doc_files_1.FlowrGithubRef}/${pageName.toLowerCase().replaceAll(' ', '-')}`;
             }
-            return `[${text}](${link}${segment ? `#${segment}` : ''})`;
+            text ??= pageName.split('/').pop() ?? pageName;
+            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": "2.9.11",
+  "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));

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

@@ -59,7 +59,7 @@ export interface ReadOnlyFlowrAnalyzerFilesContext {
     /**
      * Check if the context has a file with the given path.
      * Please note, that this may also check the file system, depending on the configuration
-     * (see {@link FlowrConfigOptions.project.resolveUnknownPathsOnDisk}).
+     * (see {@link FlowrConfig.project.resolveUnknownPathsOnDisk}).
      * @param path - The path to the file.
      *
      * If you do not know the exact path or, e.g., casing of the file, use {@link exists} instead.
@@ -70,7 +70,7 @@ export interface ReadOnlyFlowrAnalyzerFilesContext {
      * @param path - The path to the file.
      * @param ignoreCase - Whether to ignore case when checking for the file.
      *
-     * Please note that this method checks the file system based on the configuration (see {@link FlowrConfigOptions.project.resolveUnknownPathsOnDisk}).
+     * Please note that this method checks the file system based on the configuration (see {@link FlowrConfig.project.resolveUnknownPathsOnDisk}).
      * @returns The actual path of the file if it exists, otherwise `undefined`.
      */
     exists(path: string, ignoreCase: boolean): string | undefined;

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

@@ -129,19 +129,39 @@ class FlowrAnalyzerFilesContext extends abstract_flowr_analyzer_context_1.Abstra
             if (!ignoreCase) {
                 return this.hasFile(p) ? p : undefined;
             }
+            if (this.hasFile(p)) {
+                return p;
+            }
             // walk the directory and find the first match
             const dir = path_1.default.dirname(p);
-            const file = path_1.default.basename(p);
+            const file = path_1.default.basename(p).toLowerCase();
             // try to find in local known files first
-            const localFound = Array.from(this.files.keys()).find(f => {
-                return path_1.default.dirname(f) === dir && path_1.default.basename(f).toLowerCase() === file.toLowerCase();
-            });
-            if (localFound) {
-                return localFound;
+            for (const f of this.files.keys()) {
+                if (path_1.default.dirname(f).toLowerCase() !== dir.toLowerCase()) {
+                    continue;
+                }
+                const lf = path_1.default.basename(f).toLowerCase();
+                if (file === lf) {
+                    return f;
+                }
             }
             if (this.ctx.config.project.resolveUnknownPathsOnDisk) {
-                const files = fs_1.default.readdirSync(dir);
-                const found = files.find(f => f.toLowerCase() === file.toLowerCase());
+                let files;
+                if (fs_1.default.existsSync(dir)) {
+                    files = fs_1.default.readdirSync(dir);
+                }
+                else {
+                    // try to find a dir in parent
+                    const parentDir = path_1.default.dirname(dir);
+                    if (fs_1.default.existsSync(parentDir)) {
+                        const parentFiles = fs_1.default.readdirSync(parentDir);
+                        const foundDir = parentFiles.find(f => f.toLowerCase() === path_1.default.basename(dir).toLowerCase());
+                        if (foundDir) {
+                            files = fs_1.default.readdirSync(path_1.default.join(parentDir, foundDir));
+                        }
+                    }
+                }
+                const found = files?.find(f => f.toLowerCase() === file);
                 return found ? path_1.default.join(dir, found) : undefined;
             }
             return undefined;

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

@@ -1,10 +1,11 @@
-import { type EngineConfig, type FlowrConfigOptions } from '../config';
-import type { DeepWritable } from 'ts-essentials';
+import { type EngineConfig, FlowrConfig } from '../config';
+import type { DeepWritable, PathValue } from 'ts-essentials';
 import { FlowrAnalyzer } from './flowr-analyzer';
 import type { KnownParser } from '../r-bridge/parser';
 import type { FlowrAnalyzerPlugin } from './plugins/flowr-analyzer-plugin';
 import type { NormalizeRequiredInput } from '../core/steps/all/core/10-normalize';
 import type { BuiltInFlowrPluginName, PluginToRegister } from './plugins/plugin-registry';
+import type { AutocompletablePaths } from '../util/objects';
 /**
  * Builder for the {@link FlowrAnalyzer}, use it to configure all analysis aspects before creating the analyzer instance
  * with {@link FlowrAnalyzerBuilder#build|`.build()`} or {@link FlowrAnalyzerBuilder#buildSync|`.buildSync()`}.
@@ -32,7 +33,7 @@ export declare class FlowrAnalyzerBuilder {
     private flowrConfig;
     private parser?;
     private input?;
-    private plugins;
+    private readonly plugins;
     /**
      * Creates a new builder for the {@link FlowrAnalyzer}.
      * By default, the standard set of plugins as returned by {@link FlowrAnalyzerPluginDefaults} are registered.
@@ -44,15 +45,18 @@ export declare class FlowrAnalyzerBuilder {
     constructor(withDefaultPlugins?: boolean);
     /**
      * Apply an amendment to the configuration the builder currently holds.
-     * Per default, the {@link defaultConfigOptions} are used.
+     * This is mostly intended for more complex logic to transform the config.
+     * Please consider using {@link FlowrAnalyzerBuilder.configure} to set/amend individual values
+     * Per default, the value returned by {@link FlowrConfig.default} is used.
      * @param func - Receives the current configuration of the builder and allows for amendment.
      */
-    amendConfig(func: (config: DeepWritable<FlowrConfigOptions>) => FlowrConfigOptions | void): this;
+    amendConfig(func: (config: DeepWritable<FlowrConfig>) => FlowrConfig | void): this;
     /**
      * Overwrite the configuration used by the resulting analyzer.
      * @param config - The new configuration.
      */
-    setConfig(config: FlowrConfigOptions): this;
+    setConfig(config: FlowrConfig): this;
+    configure<K extends AutocompletablePaths<FlowrConfig>>(key: K, value: PathValue<FlowrConfig, K>): this;
     /**
      * Set the parser instance used by the analyzer.
      * This is an alternative to {@link FlowrAnalyzerBuilder#setEngine} if you already have a parser instance.

package/project/flowr-analyzer-builder.js

@@ -33,7 +33,7 @@ const plugin_registry_1 = require("./plugins/plugin-registry");
  * @see https://github.com/flowr-analysis/flowr/wiki/Analyzer
  */
 class FlowrAnalyzerBuilder {
-    flowrConfig = (0, config_1.cloneConfig)(config_1.defaultConfigOptions);
+    flowrConfig = config_1.FlowrConfig.default();
     parser;
     input;
     plugins = new Map();
@@ -52,12 +52,14 @@ class FlowrAnalyzerBuilder {
     }
     /**
      * Apply an amendment to the configuration the builder currently holds.
-     * Per default, the {@link defaultConfigOptions} are used.
+     * This is mostly intended for more complex logic to transform the config.
+     * Please consider using {@link FlowrAnalyzerBuilder.configure} to set/amend individual values
+     * Per default, the value returned by {@link FlowrConfig.default} is used.
      * @param func - Receives the current configuration of the builder and allows for amendment.
      */
     // eslint-disable-next-line @typescript-eslint/no-invalid-void-type
     amendConfig(func) {
-        this.flowrConfig = (0, config_1.amendConfig)(this.flowrConfig, func);
+        this.flowrConfig = config_1.FlowrConfig.amend(this.flowrConfig, func);
         return this;
     }
     /**
@@ -68,6 +70,13 @@ class FlowrAnalyzerBuilder {
         this.flowrConfig = config;
         return this;
     }
+    /**
+     * Set a specific value in the configuration used by the resulting analyzer.
+     */
+    configure(key, value) {
+        config_1.FlowrConfig.setInConfigInPlace(this.flowrConfig, key, value);
+        return this;
+    }
     /**
      * Set the parser instance used by the analyzer.
      * This is an alternative to {@link FlowrAnalyzerBuilder#setEngine} if you already have a parser instance.

package/project/flowr-analyzer.d.ts

@@ -1,4 +1,4 @@
-import type { FlowrConfigOptions } from '../config';
+import type { FlowrConfig } from '../config';
 import type { KnownParser, KnownParserInformation } from '../r-bridge/parser';
 import { type Queries, type QueryResults, type SupportedQueryTypes } from '../queries/query';
 import type { ControlFlowInformation } from '../control-flow/control-flow-graph';
@@ -139,7 +139,7 @@ export interface ReadonlyFlowrAnalysisProvider<Parser extends KnownParser = Know
      */
     runFull(force?: boolean): Promise<void>;
     /** This is the config used for the analyzer */
-    flowrConfig: FlowrConfigOptions;
+    flowrConfig: FlowrConfig;
 }
 /**
  * Central class for conducting analyses with FlowR.
@@ -165,7 +165,7 @@ export declare class FlowrAnalyzer<Parser extends KnownParser = KnownParser> imp
      * @param cache  - The caching layer to use for storing analysis results.
      */
     constructor(parser: Parser, ctx: FlowrAnalyzerContext, cache: FlowrAnalyzerCache<Parser>);
-    get flowrConfig(): FlowrConfigOptions;
+    get flowrConfig(): FlowrConfig;
     context(): FlowrAnalyzerContext;
     parserInformation(): KnownParserInformation;
     inspectContext(): ReadOnlyFlowrAnalyzerContext;