@eagleoutice/flowr 2.7.5 → 2.8.0

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>>>;
     /**

package/project/flowr-analyzer.js

@@ -115,6 +115,12 @@ class FlowrAnalyzer {
     peekControlflow(simplifications, kind) {
         return this.cache.peekControlflow(kind ?? cfg_kind_1.CfgKind.NoDataflow, simplifications);
     }
+    async callGraph(force) {
+        return this.cache.callGraph(force);
+    }
+    peekCallGraph() {
+        return this.cache.peekCallGraph();
+    }
     async query(query) {
         return (0, query_1.executeQueries)({ analyzer: this }, query);
     }

package/project/plugins/file-plugins/files/flowr-description-file.d.ts

@@ -1,7 +1,8 @@
 import { type FlowrFileProvider, type FileRole, FlowrFile } from '../../../context/flowr-file';
-import type { Info } from 'spdx-expression-parse';
 import type { RAuthorInfo } from '../../../../util/r-author';
 import type { DeepReadonly } from 'ts-essentials';
+import type { RLicenseElementInfo } from '../../../../util/r-license';
+import { Package, type PackageType } from '../../package-version-plugins/package';
 export type DCF = Map<string, string[]>;
 /**
  * This decorates a text file and provides access to its content as a DCF (Debian Control File)-like structure.
@@ -25,15 +26,22 @@ export declare class FlowrDescriptionFile extends FlowrFile<DeepReadonly<DCF>> {
     /**
      * Returns the parsed license information from the 'License' field in the DESCRIPTION file.
      */
-    license(): Info[] | undefined;
+    license(): RLicenseElementInfo[] | undefined;
     /**
      * Returns the parsed authors from the `Authors@R` field in the DESCRIPTION file.
      */
     authors(): RAuthorInfo[] | undefined;
+    suggests(): Package[] | undefined;
 }
 /**
  * Parses the 'License' field from an R DESCRIPTION file into SPDX license expressions.
  * @param licenseField - The 'License' field from the DESCRIPTION file as an array of strings.
  * @returns An array of SPDX license information objects if parsing was successful.
  */
-export declare function parseRLicenseField(...licenseField: string[]): Info[];
+export declare function parseRLicenseField(...licenseField: string[]): RLicenseElementInfo[];
+/**
+ * Parses package strings with optional version constraints into Package objects.
+ * @param packageStrings - The package strings to parse
+ * @param type           - The type of the packages (e.g., 'r' or 'package')
+ */
+export declare function parsePackagesWithVersions(packageStrings: readonly string[], type?: PackageType): Package[];

package/project/plugins/file-plugins/files/flowr-description-file.js

@@ -1,15 +1,13 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FlowrDescriptionFile = void 0;
 exports.parseRLicenseField = parseRLicenseField;
+exports.parsePackagesWithVersions = parsePackagesWithVersions;
 const flowr_file_1 = require("../../../context/flowr-file");
-const spdx_expression_parse_1 = __importDefault(require("spdx-expression-parse"));
-const log_1 = require("../../../../util/log");
 const r_author_1 = require("../../../../util/r-author");
 const args_1 = require("../../../../util/text/args");
+const r_license_1 = require("../../../../util/r-license");
+const package_1 = require("../../package-version-plugins/package");
 /**
  * This decorates a text file and provides access to its content as a DCF (Debian Control File)-like structure.
  */
@@ -20,7 +18,7 @@ class FlowrDescriptionFile extends flowr_file_1.FlowrFile {
      * and handle role assignments.
      */
     constructor(file) {
-        super(file.path(), file.role);
+        super(file.path(), file.roles);
         this.wrapped = file;
     }
     /**
@@ -53,37 +51,27 @@ class FlowrDescriptionFile extends flowr_file_1.FlowrFile {
      * Returns the parsed authors from the `Authors@R` field in the DESCRIPTION file.
      */
     authors() {
-        const authors = this.content().get('Authors@R');
-        return authors ? authors.flatMap(r_author_1.parseRAuthorString) : undefined;
+        let authors = this.content().get('Authors@R');
+        if (authors) {
+            return authors.flatMap(r_author_1.parseRAuthorString);
+        }
+        authors = this.content().get('Author');
+        const parsedAuthors = authors?.flatMap(a => (0, r_author_1.parseTextualAuthorString)(a, [r_author_1.AuthorRole.Author])) ?? [];
+        return parsedAuthors.concat(this.content().get('Maintainer')?.flatMap(m => (0, r_author_1.parseTextualAuthorString)(m, [r_author_1.AuthorRole.Creator])) ?? []);
+    }
+    suggests() {
+        const suggests = this.content().get('Suggests');
+        return suggests ? parsePackagesWithVersions(suggests, 'package') : undefined;
     }
 }
 exports.FlowrDescriptionFile = FlowrDescriptionFile;
-function cleanUpDescLicense(licenseStr) {
-    // we have to replace '\s[|+&]\s' with ' OR ' or ' AND ' respectively
-    return licenseStr
-        .replaceAll(/\s*\|\s*/g, ' OR ')
-        .replaceAll(/\s*[&+,]\s*/g, ' AND ')
-        // we have to replace any variant of 'file LICENSE' with just LicenseRef-FILE
-        .replaceAll(/file(\s+|-)LICENSE/gi, 'LicenseRef-FILE');
-}
 /**
  * Parses the 'License' field from an R DESCRIPTION file into SPDX license expressions.
  * @param licenseField - The 'License' field from the DESCRIPTION file as an array of strings.
  * @returns An array of SPDX license information objects if parsing was successful.
  */
 function parseRLicenseField(...licenseField) {
-    const licenses = [];
-    for (const licenseEntry of licenseField) {
-        const cleanedLicense = cleanUpDescLicense(licenseEntry);
-        try {
-            const parsed = (0, spdx_expression_parse_1.default)(cleanedLicense);
-            licenses.push(parsed);
-        }
-        catch (e) {
-            log_1.log.warn(`Failed to parse license expression '${cleanedLicense}': ${e.message}`);
-        }
-    }
-    return licenses;
+    return licenseField.map(r_license_1.parseRLicense);
 }
 function emplaceDCF(key, val, result) {
     if (!key) {
@@ -129,4 +117,26 @@ function cleanValues(values) {
         .map(s => s.trim())
         .filter(s => s.length > 0);
 }
+const VersionRegex = /^([a-zA-Z0-9.]+)(?:\s*\(([><=~!]+)\s*([^)]+)\))?$/;
+/**
+ * Parses package strings with optional version constraints into Package objects.
+ * @param packageStrings - The package strings to parse
+ * @param type           - The type of the packages (e.g., 'r' or 'package')
+ */
+function parsePackagesWithVersions(packageStrings, type) {
+    const packages = [];
+    for (const entry of packageStrings) {
+        const match = VersionRegex.exec(entry);
+        if (match) {
+            const [, name, operator, version] = match;
+            const range = package_1.Package.parsePackageVersionRange(operator, version);
+            packages.push(new package_1.Package({
+                name: name,
+                type: type,
+                versionConstraints: range ? [range] : undefined
+            }));
+        }
+    }
+    return packages;
+}
 //# sourceMappingURL=flowr-description-file.js.map

package/project/plugins/file-plugins/files/flowr-jupyter-file.js

@@ -13,7 +13,7 @@ class FlowrJupyterFile extends flowr_file_1.FlowrFile {
      * @param file - the file to load as R Markdown
      */
     constructor(file) {
-        super(file.path(), flowr_file_1.FileRole.Source);
+        super(file.path(), file.roles ? [...file.roles, flowr_file_1.FileRole.Source] : [flowr_file_1.FileRole.Source]);
         this.wrapped = file;
     }
     /**

package/project/plugins/file-plugins/files/flowr-namespace-file.js

@@ -12,7 +12,7 @@ class FlowrNamespaceFile extends flowr_file_1.FlowrFile {
      * and handle role assignments.
      */
     constructor(file) {
-        super(file.path(), file.role);
+        super(file.path(), file.roles);
         this.wrapped = file;
     }
     /**

package/project/plugins/file-plugins/files/flowr-news-file.js

@@ -14,7 +14,7 @@ class FlowrNewsFile extends flowr_file_1.FlowrFile {
      * and handle role assignments.
      */
     constructor(file) {
-        super(file.path(), file.role);
+        super(file.path(), file.roles);
         this.wrapped = file;
     }
     /**

package/project/plugins/file-plugins/files/flowr-rmarkdown-file.js

@@ -24,7 +24,7 @@ class FlowrRMarkdownFile extends flowr_file_1.FlowrFile {
      * @param file - the file to load as R Markdown
      */
     constructor(file) {
-        super(file.path(), flowr_file_1.FileRole.Source);
+        super(file.path(), file.roles ? [...file.roles, flowr_file_1.FileRole.Source] : [flowr_file_1.FileRole.Source]);
         this.wrapped = file;
     }
     get rmd() {

package/project/plugins/file-plugins/flowr-analyzer-description-file-plugin.js

@@ -8,7 +8,7 @@ const flowr_description_file_1 = require("./files/flowr-description-file");
 const flowr_file_1 = require("../../context/flowr-file");
 const built_in_source_1 = require("../../../dataflow/internal/process/functions/call/built-in/built-in-source");
 exports.descriptionFileLog = log_1.log.getSubLogger({ name: 'flowr-analyzer-loading-order-description-file-plugin' });
-const DescriptionFilePattern = /^(DESCRIPTION|DESCRIPTION\.txt)$/i;
+const DescriptionFilePattern = /^DESCRIPTION(\.(txt|in))?$/i;
 /**
  * This plugin provides support for R `DESCRIPTION` files.
  */

package/project/plugins/file-plugins/flowr-analyzer-file-plugin.d.ts

@@ -8,10 +8,13 @@ import type { FlowrFileProvider } from '../../context/flowr-file';
  *
  * It is up to the construction to ensure that no two file plugins {@link applies} to the same file, otherwise, the loading order
  * of these plugins will determine which plugin gets to process the file.
+ * On transforming a file, your plugin can indicate whether other plugins should still get to process the file,
+ * by returning a tuple of `[transformedFile, <boolean>]` where a boolean `true` indicates that other plugins should still get to process the file.
+ * One example of a plugin doing this is the {@link FlowrAnalyzerMetaVignetteFilesPlugin}.
  *
  * See {@link DefaultFlowrAnalyzerFilePlugin} for the no-op default implementation.
  */
-export declare abstract class FlowrAnalyzerFilePlugin extends FlowrAnalyzerPlugin<FlowrFileProvider, FlowrFileProvider> {
+export declare abstract class FlowrAnalyzerFilePlugin extends FlowrAnalyzerPlugin<FlowrFileProvider, FlowrFileProvider | [file: FlowrFileProvider, cont: boolean]> {
     readonly type = PluginType.FileLoad;
     /**
      * Determine whether this plugin applies to the given file.

package/project/plugins/file-plugins/flowr-analyzer-file-plugin.js

@@ -11,6 +11,9 @@ const semver_1 = require("semver");
  *
  * It is up to the construction to ensure that no two file plugins {@link applies} to the same file, otherwise, the loading order
  * of these plugins will determine which plugin gets to process the file.
+ * On transforming a file, your plugin can indicate whether other plugins should still get to process the file,
+ * by returning a tuple of `[transformedFile, <boolean>]` where a boolean `true` indicates that other plugins should still get to process the file.
+ * One example of a plugin doing this is the {@link FlowrAnalyzerMetaVignetteFilesPlugin}.
  *
  * See {@link DefaultFlowrAnalyzerFilePlugin} for the no-op default implementation.
  */

package/project/plugins/file-plugins/{flowr-analyzer-namespace-file-plugin.d.ts → flowr-analyzer-namespace-files-plugin.d.ts}

@@ -7,7 +7,7 @@ import { FlowrNamespaceFile } from './files/flowr-namespace-file';
 /**
  * This plugin provides support for R `NAMESPACE` files.
  */
-export declare class FlowrAnalyzerNamespaceFilePlugin extends FlowrAnalyzerFilePlugin {
+export declare class FlowrAnalyzerNamespaceFilesPlugin extends FlowrAnalyzerFilePlugin {
     readonly name = "flowr-analyzer-namespace-file-plugin";
     readonly description = "This plugin provides support for NAMESPACE files and extracts their content into the NAMESPACEFormat.";
     readonly version: SemVer;

package/project/plugins/file-plugins/{flowr-analyzer-namespace-file-plugin.js → flowr-analyzer-namespace-files-plugin.js}

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.FlowrAnalyzerNamespaceFilePlugin = void 0;
+exports.FlowrAnalyzerNamespaceFilesPlugin = void 0;
 const flowr_analyzer_file_plugin_1 = require("./flowr-analyzer-file-plugin");
 const semver_1 = require("semver");
 const flowr_file_1 = require("../../context/flowr-file");
@@ -10,7 +10,7 @@ const NamespaceFilePattern = /^NAMESPACE(\.txt)?$/i;
 /**
  * This plugin provides support for R `NAMESPACE` files.
  */
-class FlowrAnalyzerNamespaceFilePlugin extends flowr_analyzer_file_plugin_1.FlowrAnalyzerFilePlugin {
+class FlowrAnalyzerNamespaceFilesPlugin extends flowr_analyzer_file_plugin_1.FlowrAnalyzerFilePlugin {
     name = 'flowr-analyzer-namespace-file-plugin';
     description = 'This plugin provides support for NAMESPACE files and extracts their content into the NAMESPACEFormat.';
     version = new semver_1.SemVer('0.1.0');
@@ -30,5 +30,5 @@ class FlowrAnalyzerNamespaceFilePlugin extends flowr_analyzer_file_plugin_1.Flow
         return flowr_namespace_file_1.FlowrNamespaceFile.from(file, flowr_file_1.FileRole.Namespace);
     }
 }
-exports.FlowrAnalyzerNamespaceFilePlugin = FlowrAnalyzerNamespaceFilePlugin;
-//# sourceMappingURL=flowr-analyzer-namespace-file-plugin.js.map
+exports.FlowrAnalyzerNamespaceFilesPlugin = FlowrAnalyzerNamespaceFilesPlugin;
+//# sourceMappingURL=flowr-analyzer-namespace-files-plugin.js.map

package/project/plugins/file-plugins/flowr-analyzer-test-file-plugin.d.ts

@@ -0,0 +1,26 @@
+import { FlowrAnalyzerFilePlugin } from './flowr-analyzer-file-plugin';
+import { SemVer } from 'semver';
+import type { PathLike } from 'fs';
+import type { FlowrAnalyzerContext } from '../../context/flowr-analyzer-context';
+import type { FlowrFileProvider } from '../../context/flowr-file';
+/**
+ * This plugin provides supports for the identification of test files.
+ * If you use multiple plugins, this should be included *before* other plugins.
+ */
+export declare class FlowrAnalyzerMetaTestFilesPlugin extends FlowrAnalyzerFilePlugin {
+    readonly name = "flowr-analyzer-test-files-plugin";
+    readonly description = "This plugin provides support for loading test files.";
+    readonly version: SemVer;
+    private readonly pathPattern;
+    /**
+     * Creates a new instance of the TEST file plugin.
+     * @param pathPattern - The pathPattern to identify TEST files, see {@link TestPathPattern} for the default pathPattern.
+     */
+    constructor(pathPattern?: RegExp);
+    applies(file: PathLike): boolean;
+    /**
+     * Processes the given file, assigning it the {@link FileRole.Test} role.
+     * Given that the file may still need to be processed by other plugins, this method returns the `true` flag for that purpose.
+     */
+    process(_ctx: FlowrAnalyzerContext, file: FlowrFileProvider): [FlowrFileProvider, true];
+}

package/project/plugins/file-plugins/flowr-analyzer-test-file-plugin.js

@@ -0,0 +1,39 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FlowrAnalyzerMetaTestFilesPlugin = void 0;
+const flowr_analyzer_file_plugin_1 = require("./flowr-analyzer-file-plugin");
+const semver_1 = require("semver");
+const flowr_file_1 = require("../../context/flowr-file");
+const built_in_source_1 = require("../../../dataflow/internal/process/functions/call/built-in/built-in-source");
+const TestPathPattern = /tests?/i;
+/**
+ * This plugin provides supports for the identification of test files.
+ * If you use multiple plugins, this should be included *before* other plugins.
+ */
+class FlowrAnalyzerMetaTestFilesPlugin extends flowr_analyzer_file_plugin_1.FlowrAnalyzerFilePlugin {
+    name = 'flowr-analyzer-test-files-plugin';
+    description = 'This plugin provides support for loading test files.';
+    version = new semver_1.SemVer('0.1.0');
+    pathPattern;
+    /**
+     * Creates a new instance of the TEST file plugin.
+     * @param pathPattern - The pathPattern to identify TEST files, see {@link TestPathPattern} for the default pathPattern.
+     */
+    constructor(pathPattern = TestPathPattern) {
+        super();
+        this.pathPattern = pathPattern;
+    }
+    applies(file) {
+        return this.pathPattern.test((0, built_in_source_1.platformDirname)(file.toString()));
+    }
+    /**
+     * Processes the given file, assigning it the {@link FileRole.Test} role.
+     * Given that the file may still need to be processed by other plugins, this method returns the `true` flag for that purpose.
+     */
+    process(_ctx, file) {
+        file.assignRole(flowr_file_1.FileRole.Test);
+        return [file, true];
+    }
+}
+exports.FlowrAnalyzerMetaTestFilesPlugin = FlowrAnalyzerMetaTestFilesPlugin;
+//# sourceMappingURL=flowr-analyzer-test-file-plugin.js.map

package/project/plugins/file-plugins/flowr-analyzer-vignette-file-plugin.d.ts

@@ -0,0 +1,26 @@
+import { FlowrAnalyzerFilePlugin } from './flowr-analyzer-file-plugin';
+import { SemVer } from 'semver';
+import type { PathLike } from 'fs';
+import type { FlowrAnalyzerContext } from '../../context/flowr-analyzer-context';
+import type { FlowrFileProvider } from '../../context/flowr-file';
+/**
+ * This plugin provides supports for the loading of Vignette files.
+ * If you use multiple plugins, this should be included *before* other plugins.
+ */
+export declare class FlowrAnalyzerMetaVignetteFilesPlugin extends FlowrAnalyzerFilePlugin {
+    readonly name = "flowr-analyzer-vignette-files-plugin";
+    readonly description = "This plugin provides support for loading vignette files.";
+    readonly version: SemVer;
+    private readonly pathPattern;
+    /**
+     * Creates a new instance of the VIGNETTE file plugin.
+     * @param pathPattern - The pathPattern to identify VIGNETTE files, see {@link VignettePathPattern} for the default pathPattern.
+     */
+    constructor(pathPattern?: RegExp);
+    applies(file: PathLike): boolean;
+    /**
+     * Processes the given file, assigning it the {@link FileRole.Vignette} role.
+     * Given that the file may still need to be processed by other plugins, this method returns the `true` flag for that purpose.
+     */
+    process(_ctx: FlowrAnalyzerContext, file: FlowrFileProvider): [FlowrFileProvider, true];
+}

package/project/plugins/file-plugins/flowr-analyzer-vignette-file-plugin.js

@@ -0,0 +1,39 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FlowrAnalyzerMetaVignetteFilesPlugin = void 0;
+const flowr_analyzer_file_plugin_1 = require("./flowr-analyzer-file-plugin");
+const semver_1 = require("semver");
+const flowr_file_1 = require("../../context/flowr-file");
+const built_in_source_1 = require("../../../dataflow/internal/process/functions/call/built-in/built-in-source");
+const VignettePathPattern = /vignettes?/i;
+/**
+ * This plugin provides supports for the loading of Vignette files.
+ * If you use multiple plugins, this should be included *before* other plugins.
+ */
+class FlowrAnalyzerMetaVignetteFilesPlugin extends flowr_analyzer_file_plugin_1.FlowrAnalyzerFilePlugin {
+    name = 'flowr-analyzer-vignette-files-plugin';
+    description = 'This plugin provides support for loading vignette files.';
+    version = new semver_1.SemVer('0.1.0');
+    pathPattern;
+    /**
+     * Creates a new instance of the VIGNETTE file plugin.
+     * @param pathPattern - The pathPattern to identify VIGNETTE files, see {@link VignettePathPattern} for the default pathPattern.
+     */
+    constructor(pathPattern = VignettePathPattern) {
+        super();
+        this.pathPattern = pathPattern;
+    }
+    applies(file) {
+        return this.pathPattern.test((0, built_in_source_1.platformDirname)(file.toString()));
+    }
+    /**
+     * Processes the given file, assigning it the {@link FileRole.Vignette} role.
+     * Given that the file may still need to be processed by other plugins, this method returns the `true` flag for that purpose.
+     */
+    process(_ctx, file) {
+        file.assignRole(flowr_file_1.FileRole.Vignette);
+        return [file, true];
+    }
+}
+exports.FlowrAnalyzerMetaVignetteFilesPlugin = FlowrAnalyzerMetaVignetteFilesPlugin;
+//# sourceMappingURL=flowr-analyzer-vignette-file-plugin.js.map

package/project/plugins/flowr-analyzer-plugin-defaults.js

@@ -7,20 +7,24 @@ const flowr_analyzer_loading_order_description_file_plugin_1 = require("./loadin
 const flowr_analyzer_rmd_file_plugin_1 = require("./file-plugins/notebooks/flowr-analyzer-rmd-file-plugin");
 const flowr_analyzer_qmd_file_plugin_1 = require("./file-plugins/notebooks/flowr-analyzer-qmd-file-plugin");
 const flowr_analyzer_jupyter_file_plugin_1 = require("./file-plugins/notebooks/flowr-analyzer-jupyter-file-plugin");
-const flowr_analyzer_namespace_file_plugin_1 = require("./file-plugins/flowr-analyzer-namespace-file-plugin");
+const flowr_analyzer_namespace_files_plugin_1 = require("./file-plugins/flowr-analyzer-namespace-files-plugin");
 const flowr_analyzer_news_file_plugin_1 = require("./file-plugins/flowr-analyzer-news-file-plugin");
+const flowr_analyzer_vignette_file_plugin_1 = require("./file-plugins/flowr-analyzer-vignette-file-plugin");
+const flowr_analyzer_test_file_plugin_1 = require("./file-plugins/flowr-analyzer-test-file-plugin");
 /**
  * Provides the default set of Flowr Analyzer plugins.
  */
 function FlowrAnalyzerPluginDefaults() {
     return [
+        new flowr_analyzer_vignette_file_plugin_1.FlowrAnalyzerMetaVignetteFilesPlugin(),
+        new flowr_analyzer_test_file_plugin_1.FlowrAnalyzerMetaTestFilesPlugin(),
         new flowr_analyzer_description_file_plugin_1.FlowrAnalyzerDescriptionFilePlugin(),
         new flowr_analyzer_package_versions_description_file_plugin_1.FlowrAnalyzerPackageVersionsDescriptionFilePlugin(),
         new flowr_analyzer_loading_order_description_file_plugin_1.FlowrAnalyzerLoadingOrderDescriptionFilePlugin(),
         new flowr_analyzer_rmd_file_plugin_1.FlowrAnalyzerRmdFilePlugin(),
         new flowr_analyzer_qmd_file_plugin_1.FlowrAnalyzerQmdFilePlugin(),
         new flowr_analyzer_jupyter_file_plugin_1.FlowrAnalyzerJupyterFilePlugin(),
-        new flowr_analyzer_namespace_file_plugin_1.FlowrAnalyzerNamespaceFilePlugin(),
+        new flowr_analyzer_namespace_files_plugin_1.FlowrAnalyzerNamespaceFilesPlugin(),
         new flowr_analyzer_news_file_plugin_1.FlowrAnalyzerNewsFilePlugin()
     ];
 }

package/project/plugins/package-version-plugins/flowr-analyzer-package-versions-description-file-plugin.js

@@ -4,9 +4,8 @@ exports.FlowrAnalyzerPackageVersionsDescriptionFilePlugin = void 0;
 const flowr_analyzer_package_versions_plugin_1 = require("./flowr-analyzer-package-versions-plugin");
 const flowr_analyzer_description_file_plugin_1 = require("../file-plugins/flowr-analyzer-description-file-plugin");
 const semver_1 = require("semver");
-const package_1 = require("./package");
 const flowr_file_1 = require("../../context/flowr-file");
-const VersionRegex = /^([a-zA-Z0-9.]+)(?:\s*\(([><=~!]+)\s*([\d.]+)\))?$/;
+const flowr_description_file_1 = require("../file-plugins/files/flowr-description-file");
 /**
  * This plugin extracts package versions from R `DESCRIPTION` files.
  * It looks at the `Depends` and `Imports` fields to find package names and their version constraints.
@@ -30,17 +29,8 @@ class FlowrAnalyzerPackageVersionsDescriptionFilePlugin extends flowr_analyzer_p
         this.retrieveVersionsFromField(ctx, deps, 'Imports', 'package');
     }
     retrieveVersionsFromField(ctx, file, field, type) {
-        for (const entry of file.get(field) ?? []) {
-            const match = VersionRegex.exec(entry);
-            if (match) {
-                const [, name, operator, version] = match;
-                const range = package_1.Package.parsePackageVersionRange(operator, version);
-                ctx.deps.addDependency(new package_1.Package({
-                    name: name,
-                    type: type,
-                    versionConstraints: range ? [range] : undefined
-                }));
-            }
+        for (const pkg of (0, flowr_description_file_1.parsePackagesWithVersions)(file.get(field) ?? [], type)) {
+            ctx.deps.addDependency(pkg);
         }
     }
 }

package/project/plugins/package-version-plugins/package.d.ts

@@ -1,4 +1,4 @@
-import { Range } from 'semver';
+import type { Range } from 'semver';
 import type { NamespaceInfo } from '../file-plugins/files/flowr-namespace-file';
 export type PackageType = 'package' | 'system' | 'r';
 export type PackageOptions = {

package/project/plugins/package-version-plugins/package.js

@@ -1,8 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.Package = void 0;
-const semver_1 = require("semver");
 const assert_1 = require("../../../util/assert");
+const r_version_1 = require("../../../util/r-version");
 class Package {
     name;
     derivedVersion;
@@ -68,12 +68,12 @@ class Package {
     }
     deriveVersion() {
         return this.versionConstraints.length > 0
-            ? new semver_1.Range(this.versionConstraints.map(c => c.raw).join(' '))
+            ? (0, r_version_1.parseRRange)(this.versionConstraints.map(c => c.raw).join(' '))
             : undefined;
     }
     static parsePackageVersionRange(constraint, version) {
         if (version) {
-            return constraint ? new semver_1.Range(constraint + version) : new semver_1.Range(version);
+            return constraint ? (0, r_version_1.parseRRange)(constraint + version) : (0, r_version_1.parseRRange)(version);
         }
         else {
             return undefined;

package/project/plugins/plugin-registry.d.ts

@@ -5,12 +5,14 @@ import { FlowrAnalyzerLoadingOrderDescriptionFilePlugin } from './loading-order-
 import { FlowrAnalyzerRmdFilePlugin } from './file-plugins/notebooks/flowr-analyzer-rmd-file-plugin';
 import { FlowrAnalyzerQmdFilePlugin } from './file-plugins/notebooks/flowr-analyzer-qmd-file-plugin';
 import { FlowrAnalyzerJupyterFilePlugin } from './file-plugins/notebooks/flowr-analyzer-jupyter-file-plugin';
-import { FlowrAnalyzerNamespaceFilePlugin } from './file-plugins/flowr-analyzer-namespace-file-plugin';
+import { FlowrAnalyzerNamespaceFilesPlugin } from './file-plugins/flowr-analyzer-namespace-files-plugin';
 import { FlowrAnalyzerNewsFilePlugin } from './file-plugins/flowr-analyzer-news-file-plugin';
+import { FlowrAnalyzerMetaVignetteFilesPlugin } from './file-plugins/flowr-analyzer-vignette-file-plugin';
+import { FlowrAnalyzerMetaTestFilesPlugin } from './file-plugins/flowr-analyzer-test-file-plugin';
 /**
  * The built-in Flowr Analyzer plugins that are always available.
  */
-export declare const BuiltInPlugins: [["file:description", typeof FlowrAnalyzerDescriptionFilePlugin], ["versions:description", typeof FlowrAnalyzerPackageVersionsDescriptionFilePlugin], ["loading-order:description", typeof FlowrAnalyzerLoadingOrderDescriptionFilePlugin], ["file:rmd", typeof FlowrAnalyzerRmdFilePlugin], ["file:qmd", typeof FlowrAnalyzerQmdFilePlugin], ["file:ipynb", typeof FlowrAnalyzerJupyterFilePlugin], ["file:namespace", typeof FlowrAnalyzerNamespaceFilePlugin], ["file:news", typeof FlowrAnalyzerNewsFilePlugin]];
+export declare const BuiltInPlugins: [["file:description", typeof FlowrAnalyzerDescriptionFilePlugin], ["versions:description", typeof FlowrAnalyzerPackageVersionsDescriptionFilePlugin], ["loading-order:description", typeof FlowrAnalyzerLoadingOrderDescriptionFilePlugin], ["files:vignette", typeof FlowrAnalyzerMetaVignetteFilesPlugin], ["files:test", typeof FlowrAnalyzerMetaTestFilesPlugin], ["file:rmd", typeof FlowrAnalyzerRmdFilePlugin], ["file:qmd", typeof FlowrAnalyzerQmdFilePlugin], ["file:ipynb", typeof FlowrAnalyzerJupyterFilePlugin], ["file:namespace", typeof FlowrAnalyzerNamespaceFilesPlugin], ["file:news", typeof FlowrAnalyzerNewsFilePlugin]];
 export type BuiltInFlowrPluginName = typeof BuiltInPlugins[number][0];
 export type BuiltInFlowrPluginArgs<N extends BuiltInFlowrPluginName> = N extends typeof BuiltInPlugins[number][0] ? ConstructorParameters<Extract<typeof BuiltInPlugins[number], [N, PluginProducer]>[1]> : never;
 type PluginProducer = new (...args: never[]) => FlowrAnalyzerPlugin;

package/project/plugins/plugin-registry.js

@@ -11,8 +11,10 @@ const flowr_analyzer_rmd_file_plugin_1 = require("./file-plugins/notebooks/flowr
 const flowr_analyzer_qmd_file_plugin_1 = require("./file-plugins/notebooks/flowr-analyzer-qmd-file-plugin");
 const assert_1 = require("../../util/assert");
 const flowr_analyzer_jupyter_file_plugin_1 = require("./file-plugins/notebooks/flowr-analyzer-jupyter-file-plugin");
-const flowr_analyzer_namespace_file_plugin_1 = require("./file-plugins/flowr-analyzer-namespace-file-plugin");
+const flowr_analyzer_namespace_files_plugin_1 = require("./file-plugins/flowr-analyzer-namespace-files-plugin");
 const flowr_analyzer_news_file_plugin_1 = require("./file-plugins/flowr-analyzer-news-file-plugin");
+const flowr_analyzer_vignette_file_plugin_1 = require("./file-plugins/flowr-analyzer-vignette-file-plugin");
+const flowr_analyzer_test_file_plugin_1 = require("./file-plugins/flowr-analyzer-test-file-plugin");
 /**
  * The built-in Flowr Analyzer plugins that are always available.
  */
@@ -20,10 +22,12 @@ exports.BuiltInPlugins = [
     ['file:description', flowr_analyzer_description_file_plugin_1.FlowrAnalyzerDescriptionFilePlugin],
     ['versions:description', flowr_analyzer_package_versions_description_file_plugin_1.FlowrAnalyzerPackageVersionsDescriptionFilePlugin],
     ['loading-order:description', flowr_analyzer_loading_order_description_file_plugin_1.FlowrAnalyzerLoadingOrderDescriptionFilePlugin],
+    ['files:vignette', flowr_analyzer_vignette_file_plugin_1.FlowrAnalyzerMetaVignetteFilesPlugin],
+    ['files:test', flowr_analyzer_test_file_plugin_1.FlowrAnalyzerMetaTestFilesPlugin],
     ['file:rmd', flowr_analyzer_rmd_file_plugin_1.FlowrAnalyzerRmdFilePlugin],
     ['file:qmd', flowr_analyzer_qmd_file_plugin_1.FlowrAnalyzerQmdFilePlugin],
     ['file:ipynb', flowr_analyzer_jupyter_file_plugin_1.FlowrAnalyzerJupyterFilePlugin],
-    ['file:namespace', flowr_analyzer_namespace_file_plugin_1.FlowrAnalyzerNamespaceFilePlugin],
+    ['file:namespace', flowr_analyzer_namespace_files_plugin_1.FlowrAnalyzerNamespaceFilesPlugin],
     ['file:news', flowr_analyzer_news_file_plugin_1.FlowrAnalyzerNewsFilePlugin]
 ];
 /**

package/project/plugins/project-discovery/flowr-analyzer-project-discovery-plugin.d.ts

@@ -13,3 +13,14 @@ export declare abstract class FlowrAnalyzerProjectDiscoveryPlugin extends FlowrA
     readonly type = PluginType.ProjectDiscovery;
     static defaultPlugin(): FlowrAnalyzerProjectDiscoveryPlugin;
 }
+/** Configuration options for the {@link DefaultFlowrAnalyzerProjectDiscoveryPlugin}. */
+export interface ProjectDiscoveryConfig {
+    /** the regex to trigger R source file discovery on (and hence analyze them as R files) */
+    triggerOnExtensions?: RegExp;
+    /** the regex to ignore certain paths entirely */
+    ignorePathsRegex?: RegExp;
+    /** the regex to exclude certain paths from being requested as R files (they are still collected as text files) */
+    excludePathsRegex?: RegExp;
+    /** if set, only paths matching this regex are traversed */
+    onlyTraversePaths?: RegExp;
+}

package/project/plugins/project-discovery/flowr-analyzer-project-discovery-plugin.js

@@ -34,17 +34,20 @@ class DefaultFlowrAnalyzerProjectDiscoveryPlugin extends FlowrAnalyzerProjectDis
     supportedExtensions;
     ignorePathsRegex;
     excludePathsRegex = excludeRequestsForPaths;
+    onlyTraversePaths;
     /**
      * Creates a new instance of the default project discovery plugin.
      * @param triggerOnExtensions - the regex to trigger R source file discovery on (and hence analyze them as R files)
      * @param ignorePathsRegex    - the regex to ignore certain paths entirely
      * @param excludePathsRegex   - the regex to exclude certain paths from being requested as R files (they are still collected as text files)
+     * @param onlyTraversePaths   - if set, only paths matching this regex are traversed
      */
-    constructor(triggerOnExtensions = discoverRSourcesRegex, ignorePathsRegex = ignorePathsWith, excludePathsRegex = excludeRequestsForPaths) {
+    constructor({ triggerOnExtensions = discoverRSourcesRegex, ignorePathsRegex = ignorePathsWith, excludePathsRegex = excludeRequestsForPaths, onlyTraversePaths } = {}) {
         super();
         this.supportedExtensions = triggerOnExtensions;
         this.ignorePathsRegex = ignorePathsRegex;
         this.excludePathsRegex = excludePathsRegex;
+        this.onlyTraversePaths = onlyTraversePaths;
     }
     process(_context, args) {
         const requests = [];
@@ -53,7 +56,7 @@ class DefaultFlowrAnalyzerProjectDiscoveryPlugin extends FlowrAnalyzerProjectDis
             if (this.ignorePathsRegex.test(file)) {
                 continue;
             }
-            if (this.supportedExtensions.test(file) && !this.excludePathsRegex.test((0, built_in_source_1.platformDirname)(file))) {
+            if (this.supportedExtensions.test(file) && (!this.onlyTraversePaths || this.onlyTraversePaths.test(file)) && !this.excludePathsRegex.test((0, built_in_source_1.platformDirname)(file))) {
                 requests.push({ content: file, request: 'file' });
             }
             else {