Add NAMESPACE-file-plugin

src/project/plugins/file-plugins/flowr-analyzer-namespace-file-plugin.ts

@@ -0,0 +1,27 @@
+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';
+import { SpecialFileRole } from '../../context/flowr-file';
+import { FlowrNamespaceFile } from './flowr-namespace-file';
+
+/**
+ * This plugin provides support for R `NAMESPACE` files.
+ */
+export class FlowrAnalyzerNamespaceFilePlugin extends FlowrAnalyzerFilePlugin {
+	public readonly name = 'flowr-analyzer-namespace-file-plugin';
+	public readonly description = 'This plugin provides support for NAMESPACE files and extracts their content into the NAMESPACEFormat.';
+	public readonly version = new SemVer('0.1.0');
+
+	public applies(file: PathLike): boolean {
+		return /^(NAMESPACE|NAMESPACE\.txt)$/i.test(file.toString().split(/[/\\]/).pop() ?? '');
+	}
+
+	public process(_ctx: FlowrAnalyzerContext, file: FlowrFileProvider<string>): FlowrNamespaceFile {
+		const f = FlowrNamespaceFile.from(file, SpecialFileRole.Namespace);
+		// already load it here
+		f.content();
+		return f;
+	}
+}

src/project/plugins/file-plugins/flowr-namespace-file.ts

@@ -0,0 +1,50 @@
+import type { FlowrFileProvider, SpecialFileRole } from '../../context/flowr-file';
+import { FlowrFile } from '../../context/flowr-file';
+import { parseNAMESPACE } from '../../../util/files';
+
+export interface NamespaceInfo {
+	exportedSymbols:      string[];
+	exportedFunctions:    string[];
+	exportS3Generics:     Map<string, string[]>;
+	loadsWithSideEffects: boolean;
+}
+
+export interface NAMESPACEFormat {
+	this:                  NamespaceInfo;
+	[packageName: string]: NamespaceInfo;
+}
+
+/**
+ *
+ */
+export class FlowrNamespaceFile extends FlowrFile<NAMESPACEFormat> {
+	private readonly wrapped: FlowrFileProvider<string>;
+
+	/**
+	 *
+	 */
+	constructor(file: FlowrFileProvider<string>) {
+		super(file.path(), file.role);
+		this.wrapped = file;
+	}
+
+	/**
+	 *
+	 *
+	 * @see {@link parseNAMESPACE} for details on the parsing logic.
+	 */
+	protected loadContent(): NAMESPACEFormat {
+		return parseNAMESPACE(this.wrapped);
+	}
+
+
+	/**
+	 * Namespace file lifter, this does not re-create if already a namespace file
+	 */
+	public static from(file: FlowrFileProvider<string> | FlowrNamespaceFile, role?: SpecialFileRole): FlowrNamespaceFile {
+		if(role) {
+			file.assignRole(role);
+		}
+		return file instanceof FlowrNamespaceFile ? file : new FlowrNamespaceFile(file);
+	}
+}

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

@@ -42,7 +42,7 @@ export class FlowrAnalyzerPackageVersionsDescriptionFilePlugin extends FlowrAnal
 				const [, name, operator, version] = match;
 
 				const range = Package.parsePackageVersionRange(operator, version);
-				ctx.deps.addDependency(new Package(name, type, undefined, range));
+				ctx.deps.addDependency(new Package(name, type, undefined, undefined, range));
 			}
 		}
 	}

src/project/plugins/package-version-plugins/flowr-analyzer-package-versions-namespace-file-plugin.ts

@@ -0,0 +1,33 @@
+import { FlowrAnalyzerPackageVersionsPlugin } from './flowr-analyzer-package-versions-plugin';
+import {
+	descriptionFileLog
+} from '../file-plugins/flowr-analyzer-description-file-plugin';
+import { SemVer } from 'semver';
+import { Package } from './package';
+import type { FlowrAnalyzerContext } from '../../context/flowr-analyzer-context';
+import { SpecialFileRole } from '../../context/flowr-file';
+import type { NAMESPACEFormat } from '../file-plugins/flowr-namespace-file';
+
+/**
+ *
+ */
+export class FlowrAnalyzerPackageVersionsNamespaceFilePlugin extends FlowrAnalyzerPackageVersionsPlugin {
+	public readonly name = 'flowr-analyzer-package-version-namespace-file-plugin';
+	public readonly description = 'This plugin does...';
+	public readonly version = new SemVer('0.1.0');
+
+	process(ctx: FlowrAnalyzerContext): void {
+		const nmspcFiles = ctx.files.getFilesByRole(SpecialFileRole.Namespace);
+		if(nmspcFiles.length !== 1) {
+			descriptionFileLog.warn(`Supporting only exactly one NAMESPACE file, found ${nmspcFiles.length}`);
+			return;
+		}
+
+		/** this will do the caching etc. for me */
+		const deps = nmspcFiles[0].content() as NAMESPACEFormat;
+
+		for(const pkg in deps) {
+			ctx.deps.addDependency(new Package(pkg, undefined, undefined, deps[pkg]));
+		}
+	}
+}

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

@@ -1,5 +1,6 @@
 import { Range } from 'semver';
 import { guard, isNotUndefined } from '../../../util/assert';
+import type { NamespaceInfo } from '../file-plugins/flowr-namespace-file';
 
 export type PackageType = 'package' | 'system' | 'r';
 
@@ -8,29 +9,34 @@ export class Package {
 	public derivedVersion?:    Range;
 	public type?:              PackageType;
 	public dependencies?:      Package[];
+	public namespaceInfo?:     NamespaceInfo;
 	public versionConstraints: Range[] = [];
 
-	constructor(name: string, type?: PackageType, dependencies?: Package[], ...versionConstraints: readonly (Range | undefined)[]) {
+	constructor(name: string, type?: PackageType, dependencies?: Package[], namespaceInfo?: NamespaceInfo, ...versionConstraints: readonly (Range | undefined)[]) {
 		this.name = name;
-		this.addInfo(type, dependencies, ...(versionConstraints ?? []).filter(isNotUndefined));
+		this.addInfo(type, dependencies, namespaceInfo, ...(versionConstraints ?? []).filter(isNotUndefined));
 	}
 
 	public mergeInPlace(other: Package): void {
 		guard(this.name === other.name, 'Can only merge packages with the same name');
 		this.addInfo(
 			other.type,
 			other.dependencies,
+			other.namespaceInfo,
 			...other.versionConstraints
 		);
 	}
 
-	public addInfo(type?: PackageType, dependencies?: Package[], ...versionConstraints: readonly Range[]): void {
+	public addInfo(type?: PackageType, dependencies?: Package[], namespaceInfo?: NamespaceInfo, ...versionConstraints: readonly Range[]): void {
 		if(type !== undefined) {
 			this.type = type;
 		}
 		if(dependencies !== undefined) {
 			this.dependencies = dependencies;
 		}
+		if(namespaceInfo !== undefined) {
+			this.namespaceInfo = namespaceInfo;
+		}
 		if(versionConstraints !== undefined) {
 			this.derivedVersion ??= versionConstraints[0];
 

src/queries/catalog/dependencies-query/dependencies-query-executor.ts

@@ -142,7 +142,8 @@ function getResults(queries: readonly DependenciesQuery[], { dataflow, config, n
 					linkedIds:          linked?.length ? linked : undefined,
 					value:              value ?? defaultValue,
 					versionConstraints:	dep?.versionConstraints,
-					derivedVersion:	    dep?.derivedVersion
+					derivedVersion:	    dep?.derivedVersion,
+					namespaceInfo:	     dep?.namespaceInfo,
 				} as DependencyInfo);
 				if(result) {
 					results.push(result);

src/queries/catalog/dependencies-query/dependencies-query-format.ts

@@ -16,6 +16,7 @@ import { RType } from '../../../r-bridge/lang-4.x/ast/model/type';
 import type { CallContextQueryResult } from '../call-context-query/call-context-query-format';
 import type { Range } from 'semver';
 import type { AsyncOrSync } from 'ts-essentials';
+import type { NamespaceInfo } from '../../../project/plugins/file-plugins/flowr-namespace-file';
 
 export const Unknown = 'unknown';
 
@@ -43,7 +44,8 @@ export const DefaultDependencyCategories = {
 							functionName:       (n.info.fullLexeme ?? n.lexeme).includes(':::') ? ':::' : '::',
 							value:              n.namespace,
 							versionConstraints:	dep?.versionConstraints,
-							derivedVersion:	    dep?.derivedVersion
+							derivedVersion:	    dep?.derivedVersion,
+							namespaceInfo:	     dep?.namespaceInfo
 						});
 					}
 				});
@@ -92,7 +94,8 @@ export interface DependencyInfo extends Record<string, unknown>{
     /** The library name, file, source, destination etc. being sourced, read from, or written to. */
     value?:           string
 	versionConstraints?: Range[],
-	derivedVersion?:     Range
+	derivedVersion?:     Range,
+	namespaceInfo?:	     NamespaceInfo,
 }
 
 function printResultSection(title: string, infos: DependencyInfo[], result: string[]): void {

src/util/files.ts

@@ -5,6 +5,7 @@ import { log } from './log';
 import LineByLine from 'n-readlines';
 import type { RParseRequestFromFile } from '../r-bridge/retriever';
 import type { FlowrFileProvider } from '../project/context/flowr-file';
+import type { NAMESPACEFormat } from '../project/plugins/file-plugins/flowr-namespace-file';
 
 /**
  * Represents a table, identified by a header and a list of rows.
@@ -217,7 +218,78 @@ export function parseDCF(file: FlowrFileProvider<string>): Map<string, string[]>
 	return result;
 }
 
+/**
+ * Parses the given NAMESPACE file
+ * @param file - The file to parse
+ * @returns
+ */
+export function parseNAMESPACE(file: FlowrFileProvider<string>): NAMESPACEFormat {
+	const result = {
+		this: {
+			exportedSymbols:      [] as string[],
+			exportedFunctions:    [] as string[],
+			exportS3Generics:     new Map<string, string[]>(),
+			loadsWithSideEffects: false,
+		},
+	} as NAMESPACEFormat;
+	const fileContent = file.content().replaceAll(cleanLineCommentRegex, '').trim()
+		.split(/\r?\n/).filter(Boolean);
+
+	for(const line of fileContent) {
+		const match = line.trim().match(/^(\w+)\(([^)]*)\)$/);
+		if(!match) {
+			continue;
+		}
+		const [, type, args] = match;
+
+		switch(type) {
+			case 'exportClasses':
+			case 'exportMethods':
+				result.this.exportedFunctions.push(args);
+				break;
+			case 'S3method':
+			{
+				const parts = args.split(',').map(s => s.trim());
+				if(parts.length !== 2) {
+					continue;
+				}
+				const [pkg, func] = parts;
+				let arr = result.this.exportS3Generics.get(pkg);
+				if(!arr) {
+					arr = [];
+					result.this.exportS3Generics.set(pkg, arr);
+				}
+				arr.push(func);
+				break; 
+			}
+			case 'export':
+				result.this.exportedSymbols.push(args);
+				break;
+			case 'useDynLib':
+			{
+				const parts = args.split(',').map(s => s.trim());
+				if(parts.length !== 2) {
+					continue;
+				}
+				const [pkg, _func] = parts;
+				if(!result[pkg]) {
+					result[pkg] = {
+						exportedSymbols:      [],
+						exportedFunctions:    [],
+						exportS3Generics:     new Map<string, string[]>(),
+						loadsWithSideEffects: false,
+					};
+				}
+				result[pkg].loadsWithSideEffects = true;
+				break;
+			}
+		}
+	}
+
+	return result;
+}
 
+const cleanLineCommentRegex = /^#.*$/gm;
 const cleanSplitRegex = /[\n,]+/;
 const cleanQuotesRegex = /'/g;
 

test/functionality/project/package.test.ts

@@ -6,10 +6,10 @@ describe('DESCRIPTION-file', function() {
 	describe.sequential('Parsing', function() {
 		test('Library-Versions-Plugin', () => {
 			const p1 = new Package('Test Package');
-			p1.addInfo('package', undefined, new Range('>= 1.3'));
-			p1.addInfo(undefined, undefined, new Range('<= 2.3'));
-			p1.addInfo(undefined, undefined, new Range('>= 1.5'));
-			p1.addInfo(undefined, undefined, new Range('<= 2.2.5'));
+			p1.addInfo('package', undefined, undefined, new Range('>= 1.3'));
+			p1.addInfo(undefined, undefined, undefined, new Range('<= 2.3'));
+			p1.addInfo(undefined, undefined, undefined, new Range('>= 1.5'));
+			p1.addInfo(undefined, undefined, undefined, new Range('<= 2.2.5'));
 
 			assert.isTrue(p1.derivedVersion?.test('1.7.0'));
 		});

test/functionality/project/plugin/namespace-file.test.ts

@@ -0,0 +1,49 @@
+import { assert, describe, test } from 'vitest';
+import path from 'path';
+import { FlowrAnalyzerContext } from '../../../../src/project/context/flowr-analyzer-context';
+
+
+import { arraysGroupBy } from '../../../../src/util/collections/arrays';
+
+
+
+
+import { FlowrInlineTextFile } from '../../../../src/project/context/flowr-file';
+import {
+	FlowrAnalyzerNamespaceFilePlugin
+} from '../../../../src/project/plugins/file-plugins/flowr-analyzer-namespace-file-plugin';
+import {
+	FlowrAnalyzerPackageVersionsNamespaceFilePlugin
+} from '../../../../src/project/plugins/package-version-plugins/flowr-analyzer-package-versions-namespace-file-plugin';
+
+
+describe('NAMESPACE-file', function() {
+	const ctx = new FlowrAnalyzerContext(
+		arraysGroupBy([
+			new FlowrAnalyzerNamespaceFilePlugin(),
+			new FlowrAnalyzerPackageVersionsNamespaceFilePlugin()
+		], p => p.type)
+	);
+
+	ctx.files.addFiles(new FlowrInlineTextFile(path.resolve('NAMESPACE'), `# Generated by roxygen2 (4.0.2): do not edit by hand
+S3method(as.character,expectation)
+S3method(compare,character)
+export(auto_test)
+export(auto_test_package)
+export(colourise)
+export(context)
+exportClasses(ListReporter)
+exportClasses(MinimalReporter)
+importFrom(methods,setRefClass)
+useDynLib(testthat,duplicate_)
+useDynLib(testthat,reassign_function)`));
+	ctx.files.addRequest({ request: 'file', content: 'pete.R' });
+	ctx.resolvePreAnalysis();
+	describe.sequential('Parsing', function() {
+		test('Library-Versions-Plugin', () => {
+			const deps = ctx.deps.getDependency('this');
+			assert.isDefined(deps);
+			assert.isTrue(deps.namespaceInfo?.loadsWithSideEffects === false);
+		});
+	});
+});