graphbox 1.0.8 → 1.2.0

package/dist/cli.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 import * as a from "node:process";
-const i = "1.0.7", r = {
+const i = "1.1.0", r = {
   version: {
     name: "version",
     description: "Show version information",

package/dist/experiments/evaluation/fixtures/benchmark-datasets.d.ts

@@ -22,6 +22,12 @@ export interface BenchmarkDatasetMeta {
     delimiter: string | RegExp;
     /** Source/citation for the dataset */
     source: string;
+    /**
+     * Remote URL for downloading the dataset.
+     * Used for browser environments or when local files aren't available.
+     * Should point to a raw text file in edge list format.
+     */
+    remoteUrl?: string;
 }
 /**
  * A loaded benchmark dataset with graph and metadata.
@@ -120,6 +126,99 @@ export declare const loadBenchmarkById: (id: string, benchmarksRoot?: string) =>
  * @returns Map of dataset ID to loaded benchmark
  */
 export declare const loadAllBenchmarks: (benchmarksRoot?: string) => Promise<Map<string, LoadedBenchmark>>;
+/**
+ * Load a benchmark dataset from a URL.
+ *
+ * This function works in both browser and Node.js environments.
+ * Automatically handles gzip-compressed files (.gz extension).
+ *
+ * @param url - URL to the edge list file (can be .txt or .txt.gz)
+ * @param meta - Dataset metadata (for parsing configuration)
+ * @returns Loaded benchmark with graph and metadata
+ * @throws Error if fetch fails or parsing fails
+ *
+ * @example
+ * ```typescript
+ * // Plain text file
+ * const benchmark = await loadBenchmarkFromUrl(
+ *   'https://raw.githubusercontent.com/user/repo/main/data/karate.edges',
+ *   KARATE
+ * );
+ *
+ * // Gzip-compressed file (automatically decompressed)
+ * const compressed = await loadBenchmarkFromUrl(
+ *   'https://snap.stanford.edu/data/facebook_combined.txt.gz',
+ *   FACEBOOK
+ * );
+ * ```
+ */
+export declare const loadBenchmarkFromUrl: (url: string, meta: BenchmarkDatasetMeta) => Promise<LoadedBenchmark>;
+/**
+ * Load a benchmark dataset by ID from a URL.
+ *
+ * If the dataset has a remoteUrl configured, uses that. Otherwise, you must provide a URL.
+ * Works in both browser and Node.js environments.
+ *
+ * @param id - Dataset identifier (e.g., 'cora', 'karate')
+ * @param url - Optional URL override (required if dataset has no remoteUrl)
+ * @returns Loaded benchmark with graph and metadata
+ * @throws Error if dataset ID not found or no URL available
+ *
+ * @example
+ * ```typescript
+ * // Using custom URL
+ * const karate = await loadBenchmarkByIdFromUrl('karate',
+ *   'https://example.com/datasets/karate.edges'
+ * );
+ * ```
+ */
+export declare const loadBenchmarkByIdFromUrl: (id: string, url?: string) => Promise<LoadedBenchmark>;
+/**
+ * Load a benchmark from edge list content string.
+ *
+ * This is the most flexible loader - works with any string content.
+ * Useful when you've already fetched the data or have it embedded.
+ *
+ * @param content - Edge list content as string
+ * @param meta - Dataset metadata (for parsing configuration)
+ * @returns Loaded benchmark with graph and metadata
+ *
+ * @example
+ * ```typescript
+ * const content = "1 2\n2 3\n3 1";
+ * const benchmark = loadBenchmarkFromContent(content, {
+ *   ...KARATE,
+ *   expectedNodes: 3,
+ *   expectedEdges: 3
+ * });
+ * ```
+ */
+export declare const loadBenchmarkFromContent: (content: string, meta: BenchmarkDatasetMeta) => LoadedBenchmark;
+/**
+ * Create a custom benchmark metadata for ad-hoc datasets.
+ *
+ * Helper function to create metadata for datasets not in the standard list.
+ *
+ * @param options - Partial metadata (id and name are required)
+ * @returns Complete benchmark metadata
+ *
+ * @example
+ * ```typescript
+ * const myDataset = createBenchmarkMeta({
+ *   id: 'my-graph',
+ *   name: 'My Custom Graph',
+ *   expectedNodes: 100,
+ *   expectedEdges: 500,
+ *   directed: false
+ * });
+ *
+ * const benchmark = await loadBenchmarkFromUrl(
+ *   'https://example.com/my-graph.edges',
+ *   myDataset
+ * );
+ * ```
+ */
+export declare const createBenchmarkMeta: (options: Pick<BenchmarkDatasetMeta, "id" | "name"> & Partial<Omit<BenchmarkDatasetMeta, "id" | "name">>) => BenchmarkDatasetMeta;
 /**
  * Get summary statistics for a loaded benchmark.
  *

package/dist/experiments/evaluation/fixtures/benchmark-datasets.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"benchmark-datasets.d.ts","sourceRoot":"","sources":["../../../../src/experiments/evaluation/fixtures/benchmark-datasets.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAMH,OAAO,EAAE,KAAK,EAAE,MAAM,iCAAiC,CAAC;AACxD,OAAO,EAA2B,KAAK,UAAU,EAAe,KAAK,UAAU,EAAE,MAAM,kBAAkB,CAAC;AAM1G;;GAEG;AACH,MAAM,WAAW,oBAAoB;IACpC,0BAA0B;IAC1B,IAAI,EAAE,MAAM,CAAC;IAEb,uCAAuC;IACvC,EAAE,EAAE,MAAM,CAAC;IAEX,wBAAwB;IACxB,WAAW,EAAE,MAAM,CAAC;IAEpB,iCAAiC;IACjC,QAAQ,EAAE,OAAO,CAAC;IAElB,wDAAwD;IACxD,aAAa,EAAE,MAAM,CAAC;IAEtB,wDAAwD;IACxD,aAAa,EAAE,MAAM,CAAC;IAEtB,6CAA6C;IAC7C,YAAY,EAAE,MAAM,CAAC;IAErB,8CAA8C;IAC9C,SAAS,EAAE,MAAM,GAAG,MAAM,CAAC;IAE3B,sCAAsC;IACtC,MAAM,EAAE,MAAM,CAAC;IAEf;;;;OAIG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;CACnB;AAED;;GAEG;AACH,MAAM,WAAW,eAAe;IAC/B,uBAAuB;IACvB,KAAK,EAAE,KAAK,CAAC,UAAU,EAAE,UAAU,CAAC,CAAC;IAErC,uBAAuB;IACvB,IAAI,EAAE,oBAAoB,CAAC;IAE3B,sCAAsC;IACtC,SAAS,EAAE,MAAM,CAAC;IAElB,sCAAsC;IACtC,SAAS,EAAE,MAAM,CAAC;CAClB;AAMD;;;;;GAKG;AACH,eAAO,MAAM,IAAI,EAAE,oBAUlB,CAAC;AAEF;;;;;GAKG;AACH,eAAO,MAAM,QAAQ,EAAE,oBAUtB,CAAC;AAEF;;;;;GAKG;AACH,eAAO,MAAM,QAAQ,EAAE,oBAUtB,CAAC;AAEF;;;;;GAKG;AACH,eAAO,MAAM,MAAM,EAAE,oBAUpB,CAAC;AAEF;;;;;GAKG;AACH,eAAO,MAAM,MAAM,EAAE,oBAUpB,CAAC;AAEF;;;;;;GAMG;AACH,eAAO,MAAM,IAAI,EAAE,oBAUlB,CAAC;AAEF;;GAEG;AACH,eAAO,MAAM,kBAAkB,EAAE,oBAAoB,EAAqD,CAAC;AAE3G;;GAEG;AACH,eAAO,MAAM,cAAc,EAAE,GAAG,CAAC,MAAM,EAAE,oBAAoB,CAE5D,CAAC;AAMF;;;;;;GAMG;AACH,eAAO,MAAM,oBAAoB,GAAI,MAAM,oBAAoB,EAAE,iBAAiB,MAAM,KAAG,MAU1F,CAAC;AAEF;;;;;;;GAOG;AACH,eAAO,MAAM,aAAa,GAAU,MAAM,oBAAoB,EAAE,iBAAiB,MAAM,KAAG,OAAO,CAAC,eAAe,CAkBhH,CAAC;AAEF;;;;;;;GAOG;AACH,eAAO,MAAM,iBAAiB,GAAU,IAAI,MAAM,EAAE,iBAAiB,MAAM,KAAG,OAAO,CAAC,eAAe,CAOpG,CAAC;AAEF;;;;;GAKG;AACH,eAAO,MAAM,iBAAiB,GAAU,iBAAiB,MAAM,KAAG,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,eAAe,CAAC,CAarG,CAAC;AAMF;;;;;;;;;;;;;;;;;;;;;;;;;GAyBG;AACH,eAAO,MAAM,oBAAoB,GAAU,KAAK,MAAM,EAAE,MAAM,oBAAoB,KAAG,OAAO,CAAC,eAAe,CAkB3G,CAAC;AAEF;;;;;;;;;;;;;;;;;;GAkBG;AACH,eAAO,MAAM,wBAAwB,GAAU,IAAI,MAAM,EAAE,MAAM,MAAM,KAAG,OAAO,CAAC,eAAe,CAehG,CAAC;AAEF;;;;;;;;;;;;;;;;;;;GAmBG;AACH,eAAO,MAAM,wBAAwB,GAAI,SAAS,MAAM,EAAE,MAAM,oBAAoB,KAAG,eAetF,CAAC;AAEF;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AACH,eAAO,MAAM,mBAAmB,GAC/B,SAAS,IAAI,CAAC,oBAAoB,EAAE,IAAI,GAAG,MAAM,CAAC,GACjD,OAAO,CAAC,IAAI,CAAC,oBAAoB,EAAE,IAAI,GAAG,MAAM,CAAC,CAAC,KACjD,oBAUD,CAAC;AAMH;;;;;GAKG;AACH,eAAO,MAAM,mBAAmB,GAAI,WAAW,eAAe,KAAG,MAIhE,CAAC;AAEF;;;;;;GAMG;AACH,eAAO,MAAM,iBAAiB,GAAI,WAAW,eAAe,EAAE,kBAAgB,KAAG;IAAE,KAAK,EAAE,OAAO,CAAC;IAAC,QAAQ,EAAE,MAAM,EAAE,CAAA;CAuBpH,CAAC"}

package/dist/experiments/evaluation/fixtures/index.d.ts

@@ -3,5 +3,5 @@
  *
  * Provides benchmark datasets and test fixtures for evaluation experiments.
  */
-export { BENCHMARK_DATASETS, type BenchmarkDatasetMeta, CITESEER, CORA, DATASETS_BY_ID, DBLP, FACEBOOK, getBenchmarkSummary, KARATE, LESMIS, loadAllBenchmarks, loadBenchmark, loadBenchmarkById, type LoadedBenchmark, resolveBenchmarkPath, validateBenchmark, } from './benchmark-datasets';
+export { BENCHMARK_DATASETS, type BenchmarkDatasetMeta, CITESEER, CORA, createBenchmarkMeta, DATASETS_BY_ID, DBLP, FACEBOOK, getBenchmarkSummary, KARATE, LESMIS, loadAllBenchmarks, loadBenchmark, loadBenchmarkById, loadBenchmarkByIdFromUrl, loadBenchmarkFromContent, loadBenchmarkFromUrl, type LoadedBenchmark, resolveBenchmarkPath, validateBenchmark, } from './benchmark-datasets';
 //# sourceMappingURL=index.d.ts.map

package/dist/experiments/evaluation/fixtures/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/experiments/evaluation/fixtures/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EACN,kBAAkB,EAElB,KAAK,oBAAoB,EACzB,QAAQ,EAER,IAAI,EACJ,cAAc,EACd,IAAI,EACJ,QAAQ,EAER,mBAAmB,EACnB,MAAM,EACN,MAAM,EACN,iBAAiB,EAEjB,aAAa,EACb,iBAAiB,EACjB,KAAK,eAAe,EACpB,oBAAoB,EACpB,iBAAiB,GACjB,MAAM,sBAAsB,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/experiments/evaluation/fixtures/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EACN,kBAAkB,EAElB,KAAK,oBAAoB,EACzB,QAAQ,EAER,IAAI,EAEJ,mBAAmB,EACnB,cAAc,EACd,IAAI,EACJ,QAAQ,EAER,mBAAmB,EACnB,MAAM,EACN,MAAM,EACN,iBAAiB,EAEjB,aAAa,EACb,iBAAiB,EAEjB,wBAAwB,EACxB,wBAAwB,EACxB,oBAAoB,EACpB,KAAK,eAAe,EACpB,oBAAoB,EACpB,iBAAiB,GACjB,MAAM,sBAAsB,CAAC"}

package/dist/experiments/evaluation/index.d.ts

@@ -12,8 +12,8 @@ export { addNoisePaths, type CitationPathConfig, type CitationPathType, type Het
 export { benjaminiHochberg, bonferroniCorrection, bootstrapCI, bootstrapDifferenceTest, cliffsDelta, cohensD, glassDelta, holmBonferroni, pairedTTest, rankBiserialCorrelation, storeyQValues, wilcoxonSignedRank, } from './statistics';
 export type { ExperimentConfig, FullExperimentConfig, GraphSpec, MethodConfig, MetricType, PathRanker, StatisticalTestType, } from './runner';
 export { generateHTMLReport, generateJSONSummary, generateLatexTable, generateMarkdownReport, runCrossValidation, runExperiment, } from './runner';
-export { type EdgeListConfig, type LoadedEdge, loadEdgeList, type LoadedNode, loadGraph, loadGraphFromUrl, type LoadResult, loadTriples, type TripleConfig, } from './loaders';
+export { decompressGzip, type EdgeListConfig, fetchAndDecompressGzip, fetchWithAutoDecompress, isGzipUrl, type LoadedEdge, loadEdgeList, type LoadedNode, loadGraph, loadGraphFromUrl, type LoadResult, loadTriples, type TripleConfig, } from './loaders';
 export { type BetweenGraphOptions, type BetweenGraphResult, computeAllGroundTruths, computeEgoNetwork, computeGroundTruth, createAttributeImportance, enumerateBetweenGraph, enumerateMultiSeedBetweenGraph, type GroundTruthConfig, type GroundTruthPath, type GroundTruthType, type PrecomputedImportance, precomputeImportance, } from './ground-truth';
 export { aggregateRepresentativenessResults, compareDegreeDistributions, computeCommunityCoverage, computeDegreeDistribution, computeDegreeHistogram, computeHubCoverage, computePathDiversityMetrics, computeSetOverlap, computeStructuralRepresentativeness, degreeDistributionFromMap, type DegreeDistributionMetrics, degreeToRanking, earthMoversDistance, identifyHubNodes, jaccardDistance, jsDivergence, klDivergence, meanPairwiseEdgeJaccardDistance, meanPairwiseJaccardDistance, type PathDiversityMetrics, pathToNodeSet, spearmanRankCorrelation, type StructuralRepresentativenessResult, } from './metrics';
-export { BENCHMARK_DATASETS, type BenchmarkDatasetMeta, CITESEER, CORA, DATASETS_BY_ID, DBLP, FACEBOOK, getBenchmarkSummary, KARATE, LESMIS, loadAllBenchmarks, loadBenchmark, loadBenchmarkById, type LoadedBenchmark, resolveBenchmarkPath, validateBenchmark, } from './fixtures';
+export { BENCHMARK_DATASETS, type BenchmarkDatasetMeta, CITESEER, CORA, createBenchmarkMeta, DATASETS_BY_ID, DBLP, FACEBOOK, getBenchmarkSummary, KARATE, LESMIS, loadAllBenchmarks, loadBenchmark, loadBenchmarkById, loadBenchmarkByIdFromUrl, loadBenchmarkFromContent, loadBenchmarkFromUrl, type LoadedBenchmark, resolveBenchmarkPath, validateBenchmark, } from './fixtures';
 //# sourceMappingURL=index.d.ts.map

package/dist/experiments/evaluation/index.d.ts.map

@@ -1 +1 @@
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package/dist/experiments/evaluation/loaders/decompress.d.ts

@@ -0,0 +1,67 @@
+/**
+ * Universal decompression utilities for browser and Node.js environments.
+ *
+ * Supports gzip decompression using:
+ * - Node.js: Built-in `zlib` module (works in all Node versions)
+ * - Browser: Native `DecompressionStream` API (Chrome 80+, Firefox 113+, Safari 16.4+)
+ *
+ * No external dependencies required.
+ */
+/**
+ * Decompress gzip-compressed data to a string.
+ *
+ * Automatically uses the best available method for the current environment:
+ * - Node.js: Uses built-in zlib module
+ * - Browser: Uses native DecompressionStream API
+ *
+ * @param data - Gzip-compressed data as Uint8Array
+ * @returns Promise resolving to decompressed UTF-8 string
+ * @throws Error if decompression fails or no decompression method is available
+ *
+ * @example
+ * ```typescript
+ * const response = await fetch('https://example.com/data.gz');
+ * const compressed = new Uint8Array(await response.arrayBuffer());
+ * const text = await decompressGzip(compressed);
+ * ```
+ */
+export declare const decompressGzip: (data: Uint8Array) => Promise<string>;
+/**
+ * Fetch and decompress gzip content from a URL.
+ *
+ * @param url - URL to fetch gzip-compressed content from
+ * @returns Promise resolving to decompressed UTF-8 string
+ * @throws Error if fetch fails or decompression fails
+ *
+ * @example
+ * ```typescript
+ * const text = await fetchAndDecompressGzip('https://snap.stanford.edu/data/facebook_combined.txt.gz');
+ * ```
+ */
+export declare const fetchAndDecompressGzip: (url: string) => Promise<string>;
+/**
+ * Detect if a URL points to a gzip-compressed file based on extension.
+ *
+ * @param url - URL to check
+ * @returns True if URL ends with .gz or .gzip
+ */
+export declare const isGzipUrl: (url: string) => boolean;
+/**
+ * Fetch content from URL, automatically decompressing if gzip.
+ *
+ * Detects compression based on:
+ * 1. URL extension (.gz, .gzip)
+ * 2. Content-Encoding header
+ *
+ * @param url - URL to fetch content from
+ * @returns Promise resolving to text content (decompressed if needed)
+ *
+ * @example
+ * ```typescript
+ * // Automatically handles both compressed and uncompressed URLs
+ * const text1 = await fetchWithAutoDecompress('https://example.com/data.txt');
+ * const text2 = await fetchWithAutoDecompress('https://example.com/data.txt.gz');
+ * ```
+ */
+export declare const fetchWithAutoDecompress: (url: string) => Promise<string>;
+//# sourceMappingURL=decompress.d.ts.map

package/dist/experiments/evaluation/loaders/decompress.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"decompress.d.ts","sourceRoot":"","sources":["../../../../src/experiments/evaluation/loaders/decompress.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAgDH;;;;;;;;;;;;;;;;;GAiBG;AACH,eAAO,MAAM,cAAc,GAAU,MAAM,UAAU,KAAG,OAAO,CAAC,MAAM,CAcrE,CAAC;AAEF;;;;;;;;;;;GAWG;AACH,eAAO,MAAM,sBAAsB,GAAU,KAAK,MAAM,KAAG,OAAO,CAAC,MAAM,CAWxE,CAAC;AAEF;;;;;GAKG;AACH,eAAO,MAAM,SAAS,GAAI,KAAK,MAAM,KAAG,OAGvC,CAAC;AAEF;;;;;;;;;;;;;;;;GAgBG;AACH,eAAO,MAAM,uBAAuB,GAAU,KAAK,MAAM,KAAG,OAAO,CAAC,MAAM,CAczE,CAAC"}

package/dist/experiments/evaluation/loaders/decompress.unit.test.d.ts

@@ -0,0 +1,5 @@
+/**
+ * Unit tests for decompression utilities
+ */
+export {};
+//# sourceMappingURL=decompress.unit.test.d.ts.map

package/dist/experiments/evaluation/loaders/decompress.unit.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"decompress.unit.test.d.ts","sourceRoot":"","sources":["../../../../src/experiments/evaluation/loaders/decompress.unit.test.ts"],"names":[],"mappings":"AAAA;;GAEG"}

package/dist/experiments/evaluation/loaders/index.d.ts

@@ -3,5 +3,6 @@
  *
  * Support for loading benchmark datasets in various formats.
  */
+export { decompressGzip, fetchAndDecompressGzip, fetchWithAutoDecompress, isGzipUrl, } from './decompress';
 export { type EdgeListConfig, type LoadedEdge, loadEdgeList, type LoadedNode, loadGraph, loadGraphFromUrl, type LoadResult, loadTriples, type TripleConfig, } from './edge-list-loader';
 //# sourceMappingURL=index.d.ts.map

package/dist/experiments/evaluation/loaders/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/experiments/evaluation/loaders/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EACN,cAAc,EACd,sBAAsB,EACtB,uBAAuB,EACvB,SAAS,GACT,MAAM,cAAc,CAAC;AACtB,OAAO,EACN,KAAK,cAAc,EACnB,KAAK,UAAU,EACf,YAAY,EACZ,KAAK,UAAU,EACf,SAAS,EACT,gBAAgB,EAChB,KAAK,UAAU,EACf,WAAW,EACX,KAAK,YAAY,GACjB,MAAM,oBAAoB,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "graphbox",
-  "version": "1.0.8",
+  "version": "1.2.0",
   "description": "Graph Sandbox + Graph Toolbox: Abstract and experimental graph algorithms for academic research",
   "packageManager": "pnpm@10.27.0",
   "type": "module",