@eagleoutice/flowr 2.7.6 → 2.8.0

package/documentation/wiki-query.js

@@ -35,6 +35,10 @@ const inspect_higher_order_query_executor_1 = require("../queries/catalog/inspec
 const doc_escape_1 = require("./doc-util/doc-escape");
 const doc_maker_1 = require("./wiki-mk/doc-maker");
 const files_query_executor_1 = require("../queries/catalog/files-query/files-query-executor");
+const call_graph_query_executor_1 = require("../queries/catalog/call-graph-query/call-graph-query-executor");
+const inspect_recursion_query_executor_1 = require("../queries/catalog/inspect-recursion-query/inspect-recursion-query-executor");
+const does_call_query_executor_1 = require("../queries/catalog/does-call-query/does-call-query-executor");
+const inspect_exception_query_executor_1 = require("../queries/catalog/inspect-exceptions-query/inspect-exception-query-executor");
 (0, doc_query_1.registerQueryDocumentation)('call-context', {
     name: 'Call-Context Query',
     type: 'active',
@@ -124,6 +128,47 @@ ${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
 		`;
     }
 });
+(0, doc_query_1.registerQueryDocumentation)('call-graph', {
+    name: 'Call-Graph Query',
+    type: 'active',
+    shortDescription: 'Returns the call graph of the given code.',
+    functionName: call_graph_query_executor_1.executeCallGraphQuery.name,
+    functionFile: '../queries/catalog/call-graph-query/call-graph-query-executor.ts',
+    buildExplanation: async (shell, ctx) => {
+        const exampleCode = 'x + 1';
+        return `
+This query calculates and returns the ${ctx.linkPage('wiki/Dataflow Graph', 'call graph', 'perspectives-cg')} of the given code.
+
+Using the example code \`${exampleCode}\`, the following query returns the dataflow graph of the code:
+${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
+                type: 'call-graph'
+            }], { showCode: true, collapseQuery: true })}
+		`;
+    }
+});
+(0, doc_query_1.registerQueryDocumentation)('does-call', {
+    name: 'Does-Call Query',
+    type: 'active',
+    shortDescription: 'Checks whether a function calls another function matching given constraints.',
+    functionName: does_call_query_executor_1.executeDoesCallQuery.name,
+    functionFile: '../queries/catalog/does-call-query/does-call-query-executor.ts',
+    buildExplanation: async (shell) => {
+        const exampleCode = 'f <- function(x) { eval(x) };\nf("1 + 1")';
+        return `
+This query checks whether a function calls another function matching given constraints.
+
+Using the example code:
+${(0, doc_code_1.codeBlock)('r', exampleCode)}
+the following query checks whether the call to \`f\` calls \`eval\`:
+${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
+                type: 'does-call',
+                queryId: 'calls-eval',
+                call: '2@f',
+                calls: { type: 'name', name: 'eval', nameExact: true }
+            }], { showCode: true, collapseQuery: false, shorthand: '(2@f:"eval")' })}
+		`;
+    }
+});
 (0, doc_query_1.registerQueryDocumentation)('files', {
     name: 'Files Query',
     type: 'active',
@@ -239,7 +284,67 @@ Please note, that functions that are just identities (e.g., \`function(x) x\`) a
 Using the example code \`${exampleCode}\` the following query returns the information for all identified function definitions whether they are higher-order functions:
 ${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
                 type: 'inspect-higher-order',
-            }], { showCode: true })}
+            }], { showCode: true, collapseQuery: true })}
+
+This query also supports a slicing criterion based query mode that only returns information for functions matching the given criteria:
+${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
+                type: 'inspect-higher-order',
+                filter: ['1@function']
+            }], { showCode: false, shorthand: (0, doc_query_1.sliceQueryShorthand)(['1@function'], (0, doc_escape_1.escapeNewline)(exampleCode)) })}
+		`;
+    }
+});
+(0, doc_query_1.registerQueryDocumentation)('inspect-recursion', {
+    name: 'Inspect Recursive Functions Query',
+    type: 'active',
+    shortDescription: 'Determine whether functions are recursive',
+    functionName: inspect_recursion_query_executor_1.executeRecursionQuery.name,
+    functionFile: '../queries/catalog/inspect-recursion-query/inspect-recursion-query-executor.ts',
+    buildExplanation: async (shell) => {
+        const exampleCode = 'fact <- function(n) { if(n <= 1) 1 else n * fact(n - 1) }';
+        return `
+With this query you can identify which functions in the code are recursive.
+Please note, that functions that *may* be recursive due to indirect calls are also considered recursive.
+
+Using the example code \`${exampleCode}\` the following query returns the information for all identified function definitions whether they are recursive:
+${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
+                type: 'inspect-recursion',
+            }], { showCode: true, collapseQuery: true })}
+
+This query also supports a slicing criterion based query mode that only returns information for functions matching the given criteria:
+${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
+                type: 'inspect-recursion',
+                filter: ['1@function']
+            }], { showCode: true, shorthand: (0, doc_query_1.sliceQueryShorthand)(['1@function'], (0, doc_escape_1.escapeNewline)(exampleCode)) })}
+		`;
+    }
+});
+(0, doc_query_1.registerQueryDocumentation)('inspect-exception', {
+    name: 'Inspect Exceptions of Functions Query',
+    type: 'active',
+    shortDescription: 'Determine whether functions throw exceptions (known to flowR)',
+    functionName: inspect_exception_query_executor_1.executeExceptionQuery.name,
+    functionFile: '../queries/catalog/inspect-exceptions-query/inspect-exception-query-executor.ts',
+    buildExplanation: async (shell) => {
+        const exampleCode = `mayFail <- function(x) {
+  if(x < 0) stop("Negative value!")
+  else sqrt(x)
+}
+safeFail <- function(x) {
+  tryCatch(
+    mayFail(x),
+    error = function(e) { NA }
+  )
+}`;
+        return `
+With this query you can identify which functions in the code throw exceptions (known to flowR).
+
+Using the following example code:
+${(0, doc_code_1.codeBlock)('r', exampleCode)}
+the following query returns the information for all identified function definitions whether they throw exceptions:
+${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
+                type: 'inspect-exception',
+            }], { showCode: true, collapseQuery: true })}
 		`;
     }
 });
@@ -350,6 +455,9 @@ ${await (0, doc_repl_1.documentReplSession)(shell, [
                 description: 'Set the slicing threshold to 10,000.'
             }
         ])}
+
+One of the most useful options to change on-the-fly are probably those under \`repl\`. For example, setting \`repl.quickStats=true\`
+enables quick statistics after each REPL command.
 `;
     }
 });

package/linter/linter-rules.d.ts

@@ -290,7 +290,7 @@ export declare const LintingRules: {
             readonly certainty: import("./linter-format").LintingRuleCertainty.BestEffort;
             readonly tags: readonly [import("./linter-tags").LintingRuleTag.Smell, import("./linter-tags").LintingRuleTag.Readability];
             readonly defaultConfig: {
-                readonly loopyFunctions: Set<"builtin:default" | "builtin:eval" | "builtin:apply" | "builtin:expression-list" | "builtin:source" | "builtin:access" | "builtin:if-then-else" | "builtin:get" | "builtin:rm" | "builtin:library" | "builtin:assignment" | "builtin:special-bin-op" | "builtin:pipe" | "builtin:function-definition" | "builtin:quote" | "builtin:for-loop" | "builtin:repeat-loop" | "builtin:while-loop" | "builtin:replacement" | "builtin:list" | "builtin:vector">;
+                readonly loopyFunctions: Set<"builtin:access" | "builtin:apply" | "builtin:assignment" | "builtin:assignment-like" | "builtin:default" | "builtin:eval" | "builtin:expression-list" | "builtin:for-loop" | "builtin:function-definition" | "builtin:get" | "builtin:if-then-else" | "builtin:library" | "builtin:list" | "builtin:pipe" | "builtin:quote" | "builtin:register-hook" | "builtin:repeat-loop" | "builtin:replacement" | "builtin:rm" | "builtin:source" | "builtin:special-bin-op" | "builtin:stopifnot" | "builtin:try" | "builtin:vector" | "builtin:while-loop">;
             };
         };
     };

package/linter/rules/seeded-randomness.js

@@ -55,22 +55,24 @@ exports.SEEDED_RANDOMNESS = {
                 // filter by calls that aren't preceded by a randomness producer
                 .flatMap(element => {
                 const dfgElement = dataflow.graph.getVertex(element.searchElement.node.info.id);
-                const cds = dfgElement ? new Set(dfgElement.cds) : new Set();
+                const cds = dfgElement ? new Set(dfgElement.controlDependencies) : new Set();
                 const producers = (0, search_enrichers_1.enrichmentContent)(element.searchElement, search_enrichers_1.Enrichment.LastCall).linkedIds
                     .map(e => dataflow.graph.getVertex(e.node.info.id));
                 const { assignment, func } = Object.groupBy(producers, f => assignmentArgIndexes.has(f.name) ? 'assignment' : 'func');
                 let nonConstant = false;
-                let otherBranch = false;
+                const cdsOfProduces = new Set();
                 // function calls are already taken care of through the LastCall enrichment itself
                 for (const f of func ?? []) {
                     if (isConstantArgument(dataflow.graph, f, 0, analyzer.inspectContext())) {
-                        const fCds = new Set(f.cds).difference(cds);
+                        const fCds = new Set(f.controlDependencies).difference(cds);
+                        metadata.callsWithFunctionProducers++;
                         if (fCds.size <= 0 || (0, info_1.happensInEveryBranchSet)(fCds)) {
-                            metadata.callsWithFunctionProducers++;
                             return [];
                         }
                         else {
-                            otherBranch = true;
+                            for (const f of fCds) {
+                                cdsOfProduces.add(f);
+                            }
                         }
                     }
                     else {
@@ -84,28 +86,31 @@ exports.SEEDED_RANDOMNESS = {
                     if (dest !== undefined && assignmentProducers.has((0, node_id_1.recoverName)(dest, dataflow.graph.idMap))) {
                         // we either have arg index 0 or 1 for the assignmentProducers destination, so we select the assignment value as 1-argIdx here
                         if (isConstantArgument(dataflow.graph, a, 1 - argIdx, analyzer.inspectContext())) {
-                            const aCds = new Set(a.cds).difference(cds);
+                            const aCds = new Set(a.controlDependencies).difference(cds);
                             if (aCds.size <= 0 || (0, info_1.happensInEveryBranchSet)(aCds)) {
                                 metadata.callsWithAssignmentProducers++;
                                 return [];
                             }
                             else {
-                                otherBranch = true;
+                                for (const f of aCds) {
+                                    cdsOfProduces.add(f);
+                                }
                             }
                         }
-                        else {
-                            nonConstant = true;
-                        }
                     }
                 }
+                if ((0, info_1.happensInEveryBranchSet)(cdsOfProduces)) {
+                    // all producers happen in every branch, so we are good
+                    return [];
+                }
                 if (nonConstant) {
                     metadata.callsWithNonConstantProducers++;
                 }
-                if (otherBranch) {
+                if (cdsOfProduces.size > 0) {
                     metadata.callsWithOtherBranchProducers++;
                 }
                 return [{
-                        certainty: otherBranch ? linter_format_1.LintingResultCertainty.Uncertain : linter_format_1.LintingResultCertainty.Certain,
+                        certainty: cdsOfProduces.size > 0 ? linter_format_1.LintingResultCertainty.Uncertain : linter_format_1.LintingResultCertainty.Certain,
                         function: element.target,
                         range: element.range
                     }];

package/linter/rules/useless-loop.d.ts

@@ -41,7 +41,7 @@ export declare const USELESS_LOOP: {
         readonly certainty: LintingRuleCertainty.BestEffort;
         readonly tags: readonly [LintingRuleTag.Smell, LintingRuleTag.Readability];
         readonly defaultConfig: {
-            readonly loopyFunctions: Set<"builtin:default" | "builtin:eval" | "builtin:apply" | "builtin:expression-list" | "builtin:source" | "builtin:access" | "builtin:if-then-else" | "builtin:get" | "builtin:rm" | "builtin:library" | "builtin:assignment" | "builtin:special-bin-op" | "builtin:pipe" | "builtin:function-definition" | "builtin:quote" | "builtin:for-loop" | "builtin:repeat-loop" | "builtin:while-loop" | "builtin:replacement" | "builtin:list" | "builtin:vector">;
+            readonly loopyFunctions: Set<"builtin:access" | "builtin:apply" | "builtin:assignment" | "builtin:assignment-like" | "builtin:default" | "builtin:eval" | "builtin:expression-list" | "builtin:for-loop" | "builtin:function-definition" | "builtin:get" | "builtin:if-then-else" | "builtin:library" | "builtin:list" | "builtin:pipe" | "builtin:quote" | "builtin:register-hook" | "builtin:repeat-loop" | "builtin:replacement" | "builtin:rm" | "builtin:source" | "builtin:special-bin-op" | "builtin:stopifnot" | "builtin:try" | "builtin:vector" | "builtin:while-loop">;
         };
     };
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@eagleoutice/flowr",
-  "version": "2.7.6",
+  "version": "2.8.0",
   "description": "Static Dataflow Analyzer and Program Slicer for the R Programming Language",
   "types": "dist/src/index.d.ts",
   "repository": {
@@ -15,7 +15,8 @@
     "setup:dev": "git lfs fetch && npm ci && git config --local core.hooksPath .githooks/ && git push --dry-run",
     "main": "npm run build:bundle-flowr && node dist/src/cli/flowr.min.js",
     "flowr": "npm run main --",
-    "main-dev": "ts-node-dev src/cli/flowr.ts",
+    "flowr:dev": "npm run main-dev --",
+    "main-dev": "node -r ts-node/register --watch src/cli/flowr.ts",
     "publish-library": "cp .npmignore package.json README.md LICENSE dist/src/ && cd dist/src && npm publish --access public",
     "release": "npx release-it --ci",
     "stats": "ts-node src/cli/statistics-app.ts",
@@ -27,14 +28,14 @@
     "export-quads": "ts-node src/cli/export-quads-app.ts",
     "capabilities-markdown": "ts-node src/documentation/doc-capabilities.ts",
     "wiki": "ts-node src/cli/wiki.ts",
-    "wiki:watch": "ts-node-dev src/cli/wiki.ts -- --keep-alive",
+    "wiki:watch": "node -r ts-node/register --watch src/cli/wiki.ts --keep-alive",
     "build": "tsc --project .",
     "build-dev": "npm run build && npm run build:copy-wasm",
     "build:bundle-flowr": "npm run build && esbuild --bundle dist/src/cli/flowr.js --platform=node --tree-shaking=true --bundle --minify --external:clipboardy --target=node22 --outfile=dist/src/cli/flowr.min.js && npm run build:copy-wasm",
     "build:copy-wasm": "mkdir -p dist/node_modules/@eagleoutice/tree-sitter-r/ && mkdir -p dist/node_modules/web-tree-sitter && cp node_modules/@eagleoutice/tree-sitter-r/tree-sitter-r.wasm dist/node_modules/@eagleoutice/tree-sitter-r/  && cp node_modules/web-tree-sitter/tree-sitter.wasm dist/node_modules/web-tree-sitter/",
     "lint-local": "npx eslint --version && npx eslint src/ test/ --rule \"no-warning-comments: off\"",
     "lint": "npm run license-compat -- --summary && npx eslint --version && npx eslint src/ test/",
-    "license-compat": "license-checker --onlyAllow 'MIT;MIT OR X11;GPLv2;LGPL;GNUGPL;ISC;Apache-2.0;FreeBSD;BSD-2-Clause;clearbsd;ModifiedBSD;BSD-3-Clause;Python-2.0;Unlicense;WTFPL;BlueOak-1.0.0;CC-BY-4.0;CC-BY-3.0;CC0-1.0;0BSD'",
+    "license-compat": "license-checker-rseidelsohn --onlyAllow 'MIT;MIT OR X11;GPLv2;LGPL;GNUGPL;ISC;Apache-2.0;FreeBSD;BSD-2-Clause;clearbsd;ModifiedBSD;BSD-3-Clause;Python-2.0;Unlicense;WTFPL;BlueOak-1.0.0;CC-BY-4.0;CC-BY-3.0;CC0-1.0;0BSD'",
     "doc": "typedoc",
     "test": "vitest --exclude \"test/system-tests/**\" --config test/vitest.config.mts",
     "test:system": "vitest --dir test/system-tests --config test/system-tests/vitest.config.mts",
@@ -182,17 +183,16 @@
     "@types/ws": "^8.18.1",
     "@typescript-eslint/eslint-plugin": "^8.40.0",
     "@vitest/coverage-v8": "^3.2.4",
-    "esbuild": "^0.25.9",
+    "esbuild": "^0.27.2",
     "eslint": "^9.34.0",
-    "license-checker": "^25.0.1",
+    "license-checker-rseidelsohn": "^4.4.2",
     "npm-run-all": "^4.1.5",
-    "release-it": "^19.0.2",
+    "release-it": "^19.2.2",
     "ts-node": "^10.9.2",
-    "ts-node-dev": "^2.0.0",
     "typedoc": "^0.27.7",
     "typedoc-plugin-missing-exports": "^3.1.0",
     "typedoc-theme-hierarchy": "^5.0.4",
-    "typedoc-umlclass": "^0.10.1",
+    "typedoc-umlclass": "^0.10.2",
     "typescript": "^5.7.3",
     "vitest": "^3.2.4"
   },

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

@@ -9,6 +9,7 @@ import type { CfgSimplificationPassName } from '../../control-flow/cfg-simplific
 import type { ControlFlowInformation } from '../../control-flow/control-flow-graph';
 import type { CfgKind } from '../cfg-kind';
 import type { FlowrAnalyzerContext } from '../context/flowr-analyzer-context';
+import type { CallGraph } from '../../dataflow/graph/call-graph';
 interface FlowrAnalyzerCacheOptions<Parser extends KnownParser> {
     parser: Parser;
     context: FlowrAnalyzerContext;
@@ -23,6 +24,7 @@ export declare class FlowrAnalyzerCache<Parser extends KnownParser> extends Flow
     private args;
     private pipeline;
     private controlFlowCache;
+    private callGraphCache;
     protected constructor(args: FlowrAnalyzerCacheOptions<Parser>);
     private initCacheProviders;
     static create<Parser extends KnownParser>(data: FlowrAnalyzerCacheOptions<Parser>): FlowrAnalyzerCache<Parser>;
@@ -80,5 +82,14 @@ export declare class FlowrAnalyzerCache<Parser extends KnownParser> extends Flow
      * @see {@link FlowrAnalyzerCache#controlflow} - to get the control flow graph, computing if necessary.
      */
     peekControlflow(kind: CfgKind, simplifications: readonly CfgSimplificationPassName[] | undefined): ControlFlowInformation | undefined;
+    /**
+     * Get the call graph for the request, computing if necessary.
+     * @param force - Do not use the cache, instead force new analyses.
+     */
+    callGraph(force?: boolean): Promise<CallGraph>;
+    /**
+     * Get the call graph for the request if already available, otherwise return `undefined`.
+     */
+    peekCallGraph(): CallGraph | undefined;
 }
 export {};

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

@@ -5,6 +5,7 @@ const flowr_cache_1 = require("./flowr-cache");
 const default_pipelines_1 = require("../../core/steps/pipeline/default-pipelines");
 const assert_1 = require("../../util/assert");
 const flowr_analyzer_controlflow_cache_1 = require("./flowr-analyzer-controlflow-cache");
+const call_graph_1 = require("../../dataflow/graph/call-graph");
 /**
  * This provides the full analyzer caching layer, please avoid using this directly
  * and prefer the {@link FlowrAnalyzer}.
@@ -13,6 +14,7 @@ class FlowrAnalyzerCache extends flowr_cache_1.FlowrCache {
     args;
     pipeline = undefined;
     controlFlowCache = undefined;
+    callGraphCache = undefined;
     constructor(args) {
         super();
         this.args = args;
@@ -24,6 +26,7 @@ class FlowrAnalyzerCache extends flowr_cache_1.FlowrCache {
             getId: this.args.getId
         });
         this.controlFlowCache = new flowr_analyzer_controlflow_cache_1.FlowrAnalyzerControlFlowCache();
+        this.callGraphCache = undefined;
     }
     static create(data) {
         return new FlowrAnalyzerCache(data);
@@ -132,6 +135,22 @@ class FlowrAnalyzerCache extends flowr_cache_1.FlowrCache {
     peekControlflow(kind, simplifications) {
         return this.controlFlowCache.peek(kind, simplifications);
     }
+    /**
+     * Get the call graph for the request, computing if necessary.
+     * @param force - Do not use the cache, instead force new analyses.
+     */
+    async callGraph(force) {
+        if (!this.callGraphCache || force) {
+            this.callGraphCache = (0, call_graph_1.computeCallGraph)((await this.dataflow(force)).graph);
+        }
+        return this.callGraphCache;
+    }
+    /**
+     * Get the call graph for the request if already available, otherwise return `undefined`.
+     */
+    peekCallGraph() {
+        return this.callGraphCache;
+    }
 }
 exports.FlowrAnalyzerCache = FlowrAnalyzerCache;
 //# sourceMappingURL=flowr-analyzer-cache.js.map

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

@@ -23,7 +23,11 @@ export interface ReadOnlyFlowrAnalyzerDependenciesContext {
      * @param name - The name of the dependency to get.
      * @returns The dependency with the given name, or undefined if it does not exist.
      */
-    getDependency(name: string): Package | undefined;
+    getDependency(name: string): Readonly<Package> | undefined;
+    /**
+     * Get all dependencies known to this context.
+     */
+    getDependencies(): readonly Readonly<Package>[];
 }
 /**
  * This context is responsible for managing the dependencies of the project, including their versions and interplays with {@link FlowrAnalyzerPackageVersionsPlugin}s.
@@ -40,4 +44,5 @@ export declare class FlowrAnalyzerDependenciesContext extends AbstractFlowrAnaly
     resolveStaticDependencies(): void;
     addDependency(pkg: Package): void;
     getDependency(name: string): Package | undefined;
+    getDependencies(): Package[];
 }

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

@@ -40,6 +40,12 @@ class FlowrAnalyzerDependenciesContext extends abstract_flowr_analyzer_context_1
         }
         return this.dependencies.get(name);
     }
+    getDependencies() {
+        if (!this.staticsLoaded) {
+            this.resolveStaticDependencies();
+        }
+        return Array.from(this.dependencies.values());
+    }
 }
 exports.FlowrAnalyzerDependenciesContext = FlowrAnalyzerDependenciesContext;
 //# sourceMappingURL=flowr-analyzer-dependencies-context.js.map

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

@@ -6,6 +6,7 @@ import { FlowrAnalyzerFilePlugin } from '../plugins/file-plugins/flowr-analyzer-
 import { FlowrFile, type FlowrFileProvider, FileRole } from './flowr-file';
 import type { FlowrDescriptionFile } from '../plugins/file-plugins/files/flowr-description-file';
 import type { FlowrNewsFile } from '../plugins/file-plugins/files/flowr-news-file';
+import type { FlowrNamespaceFile } from '../plugins/file-plugins/files/flowr-namespace-file';
 /**
  * This is a request to process a folder as a project, which will be expanded by the registered {@link FlowrAnalyzerProjectDiscoveryPlugin}s.
  */
@@ -20,7 +21,9 @@ export type RAnalysisRequest = RParseRequest | RProjectAnalysisRequest;
 export type RoleBasedFiles = {
     [FileRole.Description]: FlowrDescriptionFile[];
     [FileRole.News]: FlowrNewsFile[];
-    [FileRole.Namespace]: FlowrFileProvider[];
+    [FileRole.Namespace]: FlowrNamespaceFile[];
+    [FileRole.Vignette]: FlowrFileProvider[];
+    [FileRole.Test]: FlowrFileProvider[];
     [FileRole.Source]: FlowrFileProvider[];
     [FileRole.Data]: FlowrFileProvider[];
     [FileRole.Other]: FlowrFileProvider[];
@@ -123,7 +126,7 @@ export declare class FlowrAnalyzerFilesContext extends AbstractFlowrAnalyzerCont
      * Add a file to the context. If the file has a special role, it will be added to the corresponding list of special files.
      * This method also applies any registered {@link FlowrAnalyzerFilePlugin}s to the file before adding it to the context.
      */
-    addFile(file: string | FlowrFileProvider | RParseRequestFromFile, role?: FileRole): FlowrFileProvider<{
+    addFile(file: string | FlowrFileProvider | RParseRequestFromFile, roles?: readonly FileRole[]): FlowrFileProvider<{
         toString(): string;
     }>;
     hasFile(path: string): boolean;

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

@@ -14,9 +14,9 @@ const log_1 = require("../../util/log");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const fileLog = log_1.log.getSubLogger({ name: 'flowr-analyzer-files-context' });
-function wrapFile(file, role) {
+function wrapFile(file, roles) {
     if (typeof file === 'string') {
-        return new flowr_file_1.FlowrTextFile(file, role);
+        return new flowr_file_1.FlowrTextFile(file, roles);
     }
     else if ('request' in file) {
         return flowr_file_1.FlowrFile.fromRequest(file);
@@ -40,14 +40,7 @@ class FlowrAnalyzerFilesContext extends abstract_flowr_analyzer_context_1.Abstra
     /** these are all the paths of files that have been considered by the dataflow graph (even if not added) */
     consideredFiles = [];
     /* files that are part of the analysis, e.g. source files */
-    byRole = {
-        [flowr_file_1.FileRole.Description]: [],
-        [flowr_file_1.FileRole.News]: [],
-        [flowr_file_1.FileRole.Namespace]: [],
-        [flowr_file_1.FileRole.Source]: [],
-        [flowr_file_1.FileRole.Data]: [],
-        [flowr_file_1.FileRole.Other]: []
-    };
+    byRole = Object.fromEntries(Object.values(flowr_file_1.FileRole).map(k => [k, []]));
     constructor(loadingOrder, plugins, fileLoaders) {
         super(loadingOrder.getAttachedContext(), flowr_analyzer_project_discovery_plugin_1.FlowrAnalyzerProjectDiscoveryPlugin.defaultPlugin(), plugins);
         this.fileLoaders = [...fileLoaders, flowr_analyzer_file_plugin_1.FlowrAnalyzerFilePlugin.defaultPlugin()];
@@ -56,6 +49,9 @@ class FlowrAnalyzerFilesContext extends abstract_flowr_analyzer_context_1.Abstra
     reset() {
         this.loadingOrder.reset();
         this.files = new Map();
+        this.consideredFiles.length = 0;
+        this.inlineFiles.length = 0;
+        this.byRole = Object.fromEntries(Object.values(flowr_file_1.FileRole).map(k => [k, []]));
     }
     /**
      * Record that a file has been considered during dataflow analysis.
@@ -91,7 +87,7 @@ class FlowrAnalyzerFilesContext extends abstract_flowr_analyzer_context_1.Abstra
                 this.addRequest(req);
             }
             else {
-                this.addFile(req, req.role);
+                this.addFile(req, req.roles);
             }
         }
     }
@@ -107,8 +103,8 @@ class FlowrAnalyzerFilesContext extends abstract_flowr_analyzer_context_1.Abstra
      * Add a file to the context. If the file has a special role, it will be added to the corresponding list of special files.
      * This method also applies any registered {@link FlowrAnalyzerFilePlugin}s to the file before adding it to the context.
      */
-    addFile(file, role) {
-        const f = this.fileLoadPlugins(wrapFile(file, role));
+    addFile(file, roles) {
+        const f = this.fileLoadPlugins(wrapFile(file, roles));
         if (f.path() === flowr_file_1.FlowrFile.INLINE_PATH) {
             this.inlineFiles.push(f);
         }
@@ -117,8 +113,10 @@ class FlowrAnalyzerFilesContext extends abstract_flowr_analyzer_context_1.Abstra
             (0, assert_1.guard)(exist === undefined || exist === f, `File ${f.path()} already added to the context.`);
             this.files.set(f.path(), f);
         }
-        if (f.role) {
-            this.byRole[f.role].push(f);
+        if (f.roles) {
+            for (const r of f.roles) {
+                this.byRole[r].push(f);
+            }
         }
         return f;
     }
@@ -157,8 +155,17 @@ class FlowrAnalyzerFilesContext extends abstract_flowr_analyzer_context_1.Abstra
         for (const loader of this.fileLoaders) {
             if (loader.applies(f.path())) {
                 fileLog.debug(`Applying file loader ${loader.name} to file ${f.path()}`);
-                fFinal = loader.processor(this.ctx, f);
-                break;
+                const res = loader.processor(this.ctx, fFinal);
+                if (Array.isArray(res)) {
+                    fFinal = res[0];
+                    if (!res[1]) {
+                        break;
+                    }
+                }
+                else {
+                    fFinal = res;
+                    break;
+                }
             }
         }
         return fFinal;

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

@@ -17,6 +17,10 @@ export declare enum FileRole {
     Namespace = "namespace",
     /** The `NEWS` file in R packages */
     News = "news",
+    /** Vignette files, e.g., R Markdown files in the `vignettes/` folder */
+    Vignette = "vignette",
+    /** Test source files, e.g., files in the `tests/` folder */
+    Test = "test",
     /** Data files, e.g., `R/sysdata.rda`, currently not specially supported. */
     Data = "data",
     /**
@@ -49,11 +53,11 @@ export interface FlowrFileProvider<Content extends {
     toString(): string;
 }> {
     /**
-     * The role of this file, if any, in general your file should _not_ decide for itself what role it has in the project context,
+     * The role(s) of this file, if any, in general your file should _not_ decide for itself what role it has in the project context,
      * this is for the loaders plugins to decide (cf. {@link PluginType}) as they can, e.g., respect ignore files, updated mappings, etc.
      * However, they will 1) set this role as soon as they decide on it (using {@link assignRole}) and 2) try to respect an already assigned role (however, user configurations may override this).
      */
-    role?: FileRole;
+    roles?: readonly FileRole[];
     /**
      * The path to the file, this is used for identification and logging purposes.
      * If the file does not exist on disk, this can be a virtual path (e.g. for inline files).
@@ -80,9 +84,10 @@ export interface FlowrFileProvider<Content extends {
 export declare abstract class FlowrFile<Content extends StringableContent = StringableContent> implements FlowrFileProvider<Content> {
     private contentCache;
     protected filePath: PathLike;
-    readonly role?: FileRole;
+    private _roles?;
     static readonly INLINE_PATH = "@inline";
-    constructor(filePath: PathLike, role?: FileRole);
+    constructor(filePath: PathLike, roles?: readonly FileRole[]);
+    get roles(): readonly FileRole[] | undefined;
     path(): string;
     content(): Content;
     protected abstract loadContent(): Content;

package/project/context/flowr-file.js

@@ -5,7 +5,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FlowrInlineTextFile = exports.FlowrTextFile = exports.FlowrFile = exports.FileRole = void 0;
 const fs_1 = __importDefault(require("fs"));
-const assert_1 = require("../../util/assert");
 /**
  * Some files have a special meaning in R projects, e.g., the `DESCRIPTION` file in R packages.
  * This list may be extended in the future and reflects files that the {@link FlowrAnalyzer} can do something interesting with.
@@ -19,6 +18,10 @@ var FileRole;
     FileRole["Namespace"] = "namespace";
     /** The `NEWS` file in R packages */
     FileRole["News"] = "news";
+    /** Vignette files, e.g., R Markdown files in the `vignettes/` folder */
+    FileRole["Vignette"] = "vignette";
+    /** Test source files, e.g., files in the `tests/` folder */
+    FileRole["Test"] = "test";
     /** Data files, e.g., `R/sysdata.rda`, currently not specially supported. */
     FileRole["Data"] = "data";
     /**
@@ -39,11 +42,14 @@ var FileRole;
 class FlowrFile {
     contentCache;
     filePath;
-    role;
+    _roles;
     static INLINE_PATH = '@inline';
-    constructor(filePath, role) {
+    constructor(filePath, roles) {
         this.filePath = filePath;
-        this.role = role;
+        this._roles = roles ? Array.from(roles) : undefined;
+    }
+    get roles() {
+        return this._roles;
     }
     path() {
         return this.filePath.toString();
@@ -55,8 +61,16 @@ class FlowrFile {
         return this.contentCache;
     }
     assignRole(role) {
-        (0, assert_1.guard)(this.role === undefined || this.role === role, `File ${this.filePath.toString()} already has a role assigned: ${this.role}`);
-        this.role = role;
+        if (this._roles === undefined) {
+            this._roles = [role];
+        }
+        else if (this._roles.includes(role)) {
+            // already assigned
+            return;
+        }
+        else {
+            this._roles.push(role);
+        }
     }
     /**
      * Creates a {@link FlowrFile} from a given {@link RParseRequest}.

package/project/flowr-analyzer.d.ts

@@ -15,6 +15,7 @@ import type { RAnalysisRequest } from './context/flowr-analyzer-files-context';
 import type { RParseRequestFromFile } from '../r-bridge/retriever';
 import { fileProtocol } from '../r-bridge/retriever';
 import type { FlowrFileProvider } from './context/flowr-file';
+import type { CallGraph } from '../dataflow/graph/call-graph';
 /**
  * Extends the {@link ReadonlyFlowrAnalysisProvider} with methods that allow modifying the analyzer state.
  */
@@ -102,6 +103,14 @@ export interface ReadonlyFlowrAnalysisProvider<Parser extends KnownParser = Know
      * Peek at the control flow graph (CFG) for the request, if it was already computed.
      */
     peekControlflow(simplifications?: readonly CfgSimplificationPassName[], kind?: CfgKind): ControlFlowInformation | undefined;
+    /**
+     * Calculate the call graph for the request.
+     */
+    callGraph(force?: boolean): Promise<CallGraph>;
+    /**
+     * Peek at the call graph for the request, if it was already computed.
+     */
+    peekCallGraph(): CallGraph | undefined;
     /**
      * Access the query API for the request.
      * @param query - The list of queries.
@@ -167,6 +176,8 @@ export declare class FlowrAnalyzer<Parser extends KnownParser = KnownParser> imp
     runFull(force?: boolean): Promise<void>;
     controlflow(simplifications?: readonly CfgSimplificationPassName[], kind?: CfgKind, force?: boolean): Promise<ControlFlowInformation>;
     peekControlflow(simplifications?: readonly CfgSimplificationPassName[], kind?: CfgKind): ControlFlowInformation | undefined;
+    callGraph(force?: boolean): Promise<CallGraph>;
+    peekCallGraph(): CallGraph | undefined;
     query<Types extends SupportedQueryTypes = SupportedQueryTypes>(query: Queries<Types>): Promise<QueryResults<Types>>;
     runSearch<Search extends FlowrSearchLike>(search: Search): Promise<GetSearchElements<SearchOutput<Search>>>;
     /**