dress-graph 0.7.0 → 0.8.0

package/dress.d.ts

@@ -18,8 +18,8 @@ export interface DressOptions {
     targets: Int32Array | number[];
     /** Optional edge weights (same length as sources) */
     weights?: Float64Array | number[] | null;
-    /** Optional node weights (length numVertices) */
-    nodeWeights?: Float64Array | number[] | null;
+    /** Optional vertex weights (length numVertices) */
+    vertexWeights?: Float64Array | number[] | null;
     /** Graph variant (default: Variant.UNDIRECTED) */
     variant?: number;
     /** Maximum fitting iterations (default: 100) */
@@ -39,8 +39,8 @@ export interface DressResult {
     edgeWeight: Float64Array;
     /** Per-edge dress similarity values */
     edgeDress: Float64Array;
-    /** Per-node aggregated dress similarity */
-    nodeDress: Float64Array;
+    /** Per-vertex aggregated dress similarity */
+    vertexDress: Float64Array;
     /** Number of iterations performed */
     iterations: number;
     /** Final maximum per-edge change */
@@ -61,8 +61,8 @@ export interface DRESSOptions {
     targets: Int32Array | number[];
     /** Optional edge weights (same length as sources) */
     weights?: Float64Array | number[] | null;
-    /** Optional node weights (length numVertices) */
-    nodeWeights?: Float64Array | number[] | null;
+    /** Optional vertex weights (length numVertices) */
+    vertexWeights?: Float64Array | number[] | null;
     /** Graph variant (default: Variant.UNDIRECTED) */
     variant?: number;
     /** Pre-compute neighbourhood intercepts (default: false) */
@@ -90,8 +90,8 @@ export interface DeltaDressOptions {
     targets: Int32Array | number[];
     /** Optional edge weights (same length as sources) */
     weights?: Float64Array | number[] | null;
-    /** Optional node weights (length numVertices) */
-    nodeWeights?: Float64Array | number[] | null;
+    /** Optional vertex weights (length numVertices) */
+    vertexWeights?: Float64Array | number[] | null;
     /** Vertices to remove per subset (default: 0 = original graph) */
     k?: number;
     /** Graph variant (default: Variant.UNDIRECTED) */
@@ -141,8 +141,8 @@ export interface NablaDressOptions {
     targets: Int32Array | number[];
     /** Optional edge weights (same length as sources) */
     weights?: Float64Array | number[] | null;
-    /** Optional node weights (length numVertices) */
-    nodeWeights?: Float64Array | number[] | null;
+    /** Optional vertex weights (length numVertices) */
+    vertexWeights?: Float64Array | number[] | null;
     /** Vertices to remove per tuple (default: 0 = original graph) */
     k?: number;
     /** Graph variant (default: Variant.UNDIRECTED) */

package/dress.js

@@ -75,7 +75,7 @@ export const Variant = Object.freeze({
  * @property {Int32Array}    targets     - Edge target vertices
  * @property {Float64Array}  edgeWeight  - Per-edge variant weights
  * @property {Float64Array}  edgeDress   - Per-edge dress similarity
- * @property {Float64Array}  nodeDress   - Per-node aggregated similarity
+ * @property {Float64Array}  vertexDress   - Per-vertex aggregated similarity
  * @property {number}        iterations  - Iterations performed
  * @property {number}        delta       - Final max per-edge change
  */
@@ -128,15 +128,15 @@ export async function fit(opts) {
         }
     }
 
-    // Node weights (nullable)
+    // vertex weights (nullable)
     let nwPtr = 0; // NULL
-    if (opts.nodeWeights) {
-        if (opts.nodeWeights.length !== N) {
-            throw new Error(`nodeWeights (${opts.nodeWeights.length}) must equal vertex count (${N})`);
+    if (opts.vertexWeights) {
+        if (opts.vertexWeights.length !== N) {
+            throw new Error(`vertexWeights (${opts.vertexWeights.length}) must equal vertex count (${N})`);
         }
         nwPtr = M._malloc(N * 8);
         const heapF64 = M.HEAPF64;
-        const nw = opts.nodeWeights;
+        const nw = opts.vertexWeights;
         for (let i = 0; i < N; i++) {
             heapF64[(nwPtr >> 3) + i] = nw[i];
         }
@@ -173,16 +173,16 @@ export async function fit(opts) {
     //   offset 40: *edge_weight   (ptr32)
     //   offset 44: *edge_dress    (ptr32)
     //   offset 48: *edge_dress_next (ptr32)
-    //   offset 52: *node_dress    (ptr32)
+    //   offset 52: *vertex_dress    (ptr32)
     //   offset 56: *NW            (ptr32)
     const ewPtr = M.getValue(g + 40, 'i32');  // edge_weight pointer
     const edPtr = M.getValue(g + 44, 'i32');  // edge_dress pointer
-    const ndPtr = M.getValue(g + 52, 'i32');  // node_dress pointer
+    const ndPtr = M.getValue(g + 52, 'i32');  // vertex_dress pointer
 
     // Copy results into JS-owned typed arrays
     const edgeWeight = new Float64Array(E);
     const edgeDress  = new Float64Array(E);
-    const nodeDress  = new Float64Array(N);
+    const vertexDress  = new Float64Array(N);
 
     const heapF64 = M.HEAPF64;
     for (let i = 0; i < E; i++) {
@@ -190,7 +190,7 @@ export async function fit(opts) {
         edgeDress[i]  = heapF64[(edPtr >> 3) + i];
     }
     for (let i = 0; i < N; i++) {
-        nodeDress[i] = heapF64[(ndPtr >> 3) + i];
+        vertexDress[i] = heapF64[(ndPtr >> 3) + i];
     }
 
     // Copy sources/targets before free
@@ -211,7 +211,7 @@ export async function fit(opts) {
         targets:    targetsOut,
         edgeWeight: edgeWeight,
         edgeDress:  edgeDress,
-        nodeDress:  nodeDress,
+        vertexDress:  vertexDress,
         iterations: iterations,
         delta:      delta,
     };
@@ -286,10 +286,10 @@ export class DRESS {
         }
 
         let nwPtr = 0;
-        if (opts.nodeWeights && opts.nodeWeights.length === N) {
+        if (opts.vertexWeights && opts.vertexWeights.length === N) {
             nwPtr = M._malloc(N * 8);
             for (let i = 0; i < N; i++) {
-                M.HEAPF64[(nwPtr >> 3) + i] = opts.nodeWeights[i];
+                M.HEAPF64[(nwPtr >> 3) + i] = opts.vertexWeights[i];
             }
         }
 
@@ -346,14 +346,14 @@ export class DRESS {
 
         const edgeWeight = new Float64Array(E);
         const edgeDress  = new Float64Array(E);
-        const nodeDress  = new Float64Array(N);
+        const vertexDress  = new Float64Array(N);
 
         for (let i = 0; i < E; i++) {
             edgeWeight[i] = M.HEAPF64[(ewPtr >> 3) + i];
             edgeDress[i]  = M.HEAPF64[(edPtr >> 3) + i];
         }
         for (let i = 0; i < N; i++) {
-            nodeDress[i] = M.HEAPF64[(ndPtr >> 3) + i];
+            vertexDress[i] = M.HEAPF64[(ndPtr >> 3) + i];
         }
 
         return {
@@ -361,7 +361,7 @@ export class DRESS {
             targets:    new Int32Array(this._targets),
             edgeWeight,
             edgeDress,
-            nodeDress,
+            vertexDress,
             iterations: 0,
             delta:      0,
         };
@@ -606,11 +606,11 @@ export async function deltaFit(opts) {
     }
 
     let nwPtr = 0;
-    if (opts.nodeWeights && opts.nodeWeights.length === N) {
+    if (opts.vertexWeights && opts.vertexWeights.length === N) {
         nwPtr = M._malloc(N * 8);
         const heapF64 = M.HEAPF64;
         for (let i = 0; i < N; i++) {
-            heapF64[(nwPtr >> 3) + i] = opts.nodeWeights[i];
+            heapF64[(nwPtr >> 3) + i] = opts.vertexWeights[i];
         }
     }
 
@@ -739,11 +739,11 @@ export async function nablaFit(opts) {
     }
 
     let nwPtr = 0;
-    if (opts.nodeWeights && opts.nodeWeights.length === N) {
+    if (opts.vertexWeights && opts.vertexWeights.length === N) {
         nwPtr = M._malloc(N * 8);
         const heapF64 = M.HEAPF64;
         for (let i = 0; i < N; i++) {
-            heapF64[(nwPtr >> 3) + i] = opts.nodeWeights[i];
+            heapF64[(nwPtr >> 3) + i] = opts.vertexWeights[i];
         }
     }
 

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "dress-graph",
-    "version": "0.7.0",
+    "version": "0.8.0",
     "description": "DRESS is a deterministic, parameter-free framework that iteratively refines the structural similarity of edges in a graph to produce a canonical fingerprint: a real-valued edge vector, obtained by converging a non-linear dynamical system to its unique fixed point. The fingerprint is self-contained, isomorphism-invariant by construction, numerically stable (no overflow, no error amplification, no undefined behavior), fast and embarrassingly parallel to compute: DRESS total runtime is O(I * m * d_max) for I iterations to convergence, and convergence is guaranteed by Birkhoff contraction.",
     "type": "module",
     "main": "dress.js",

package/dress_wasm.cjs

@@ -1,2 +0,0 @@
-var createDressModule=(()=>{var _scriptName=globalThis.document?.currentScript?.src;return async function(moduleArg={}){var moduleRtn;var Module=moduleArg;var ENVIRONMENT_IS_WEB=!!globalThis.window;var ENVIRONMENT_IS_WORKER=!!globalThis.WorkerGlobalScope;var ENVIRONMENT_IS_NODE=globalThis.process?.versions?.node&&globalThis.process?.type!="renderer";var arguments_=[];var thisProgram="./this.program";var quit_=(status,toThrow)=>{throw toThrow};if(typeof __filename!="undefined"){_scriptName=__filename}else{}var scriptDirectory="";function locateFile(path){if(Module["locateFile"]){return Module["locateFile"](path,scriptDirectory)}return scriptDirectory+path}var readAsync,readBinary;if(ENVIRONMENT_IS_NODE){var fs=require("node:fs");scriptDirectory=__dirname+"/";readBinary=filename=>{filename=isFileURI(filename)?new URL(filename):filename;var ret=fs.readFileSync(filename);return ret};readAsync=async(filename,binary=true)=>{filename=isFileURI(filename)?new URL(filename):filename;var ret=fs.readFileSync(filename,binary?undefined:"utf8");return ret};if(process.argv.length>1){thisProgram=process.argv[1].replace(/\\/g,"/")}arguments_=process.argv.slice(2);quit_=(status,toThrow)=>{process.exitCode=status;throw toThrow}}else if(ENVIRONMENT_IS_WEB||ENVIRONMENT_IS_WORKER){try{scriptDirectory=new URL(".",_scriptName).href}catch{}{readAsync=async url=>{var response=await fetch(url,{credentials:"same-origin"});if(response.ok){return response.arrayBuffer()}throw new Error(response.status+" : "+response.url)}}}else{}var out=console.log.bind(console);var err=console.error.bind(console);var wasmBinary;var ABORT=false;var isFileURI=filename=>filename.startsWith("file://");var readyPromiseResolve,readyPromiseReject;var HEAP8,HEAPU8,HEAP16,HEAPU16,HEAP32,HEAPU32,HEAPF32,HEAPF64;var HEAP64,HEAPU64;var runtimeInitialized=false;function updateMemoryViews(){var b=wasmMemory.buffer;HEAP8=new Int8Array(b);HEAP16=new Int16Array(b);HEAPU8=new Uint8Array(b);HEAPU16=new Uint16Array(b);Module["HEAP32"]=HEAP32=new Int32Array(b);Module["HEAPU32"]=HEAPU32=new Uint32Array(b);HEAPF32=new Float32Array(b);Module["HEAPF64"]=HEAPF64=new Float64Array(b);HEAP64=new BigInt64Array(b);HEAPU64=new BigUint64Array(b)}function preRun(){if(Module["preRun"]){if(typeof Module["preRun"]=="function")Module["preRun"]=[Module["preRun"]];while(Module["preRun"].length){addOnPreRun(Module["preRun"].shift())}}callRuntimeCallbacks(onPreRuns)}function initRuntime(){runtimeInitialized=true;wasmExports["c"]()}function postRun(){if(Module["postRun"]){if(typeof Module["postRun"]=="function")Module["postRun"]=[Module["postRun"]];while(Module["postRun"].length){addOnPostRun(Module["postRun"].shift())}}callRuntimeCallbacks(onPostRuns)}function abort(what){Module["onAbort"]?.(what);what="Aborted("+what+")";err(what);ABORT=true;what+=". Build with -sASSERTIONS for more info.";var e=new WebAssembly.RuntimeError(what);readyPromiseReject?.(e);throw e}var wasmBinaryFile;function findWasmBinary(){return locateFile("dress_wasm.wasm")}function getBinarySync(file){if(file==wasmBinaryFile&&wasmBinary){return new Uint8Array(wasmBinary)}if(readBinary){return readBinary(file)}throw"both async and sync fetching of the wasm failed"}async function getWasmBinary(binaryFile){if(!wasmBinary){try{var response=await readAsync(binaryFile);return new Uint8Array(response)}catch{}}return getBinarySync(binaryFile)}async function instantiateArrayBuffer(binaryFile,imports){try{var binary=await getWasmBinary(binaryFile);var instance=await WebAssembly.instantiate(binary,imports);return instance}catch(reason){err(`failed to asynchronously prepare wasm: ${reason}`);abort(reason)}}async function instantiateAsync(binary,binaryFile,imports){if(!binary&&!ENVIRONMENT_IS_NODE){try{var response=fetch(binaryFile,{credentials:"same-origin"});var instantiationResult=await WebAssembly.instantiateStreaming(response,imports);return instantiationResult}catch(reason){err(`wasm streaming compile failed: ${reason}`);err("falling back to ArrayBuffer instantiation")}}return instantiateArrayBuffer(binaryFile,imports)}function getWasmImports(){var imports={a:wasmImports};return imports}async function createWasm(){function receiveInstance(instance,module){wasmExports=instance.exports;assignWasmExports(wasmExports);updateMemoryViews();return wasmExports}function receiveInstantiationResult(result){return receiveInstance(result["instance"])}var info=getWasmImports();if(Module["instantiateWasm"]){return new Promise((resolve,reject)=>{Module["instantiateWasm"](info,(inst,mod)=>{resolve(receiveInstance(inst,mod))})})}wasmBinaryFile??=findWasmBinary();var result=await instantiateAsync(wasmBinary,wasmBinaryFile,info);var exports=receiveInstantiationResult(result);return exports}class ExitStatus{name="ExitStatus";constructor(status){this.message=`Program terminated with exit(${status})`;this.status=status}}var callRuntimeCallbacks=callbacks=>{while(callbacks.length>0){callbacks.shift()(Module)}};var onPostRuns=[];var addOnPostRun=cb=>onPostRuns.push(cb);var onPreRuns=[];var addOnPreRun=cb=>onPreRuns.push(cb);function getValue(ptr,type="i8"){if(type.endsWith("*"))type="*";switch(type){case"i1":return HEAP8[ptr];case"i8":return HEAP8[ptr];case"i16":return HEAP16[ptr>>1];case"i32":return HEAP32[ptr>>2];case"i64":return HEAP64[ptr>>3];case"float":return HEAPF32[ptr>>2];case"double":return HEAPF64[ptr>>3];case"*":return HEAPU32[ptr>>2];default:abort(`invalid type for getValue: ${type}`)}}var noExitRuntime=true;function setValue(ptr,value,type="i8"){if(type.endsWith("*"))type="*";switch(type){case"i1":HEAP8[ptr]=value;break;case"i8":HEAP8[ptr]=value;break;case"i16":HEAP16[ptr>>1]=value;break;case"i32":HEAP32[ptr>>2]=value;break;case"i64":HEAP64[ptr>>3]=BigInt(value);break;case"float":HEAPF32[ptr>>2]=value;break;case"double":HEAPF64[ptr>>3]=value;break;case"*":HEAPU32[ptr>>2]=value;break;default:abort(`invalid type for setValue: ${type}`)}}var stackRestore=val=>__emscripten_stack_restore(val);var stackSave=()=>_emscripten_stack_get_current();var getHeapMax=()=>2147483648;var alignMemory=(size,alignment)=>Math.ceil(size/alignment)*alignment;var growMemory=size=>{var oldHeapSize=wasmMemory.buffer.byteLength;var pages=(size-oldHeapSize+65535)/65536|0;try{wasmMemory.grow(pages);updateMemoryViews();return 1}catch(e){}};var _emscripten_resize_heap=requestedSize=>{var oldSize=HEAPU8.length;requestedSize>>>=0;var maxHeapSize=getHeapMax();if(requestedSize>maxHeapSize){return false}for(var cutDown=1;cutDown<=4;cutDown*=2){var overGrownHeapSize=oldSize*(1+.2/cutDown);overGrownHeapSize=Math.min(overGrownHeapSize,requestedSize+100663296);var newSize=Math.min(maxHeapSize,alignMemory(Math.max(requestedSize,overGrownHeapSize),65536));var replacement=growMemory(newSize);if(replacement){return true}}return false};var getCFunc=ident=>{var func=Module["_"+ident];return func};var writeArrayToMemory=(array,buffer)=>{HEAP8.set(array,buffer)};var lengthBytesUTF8=str=>{var len=0;for(var i=0;i<str.length;++i){var c=str.charCodeAt(i);if(c<=127){len++}else if(c<=2047){len+=2}else if(c>=55296&&c<=57343){len+=4;++i}else{len+=3}}return len};var stringToUTF8Array=(str,heap,outIdx,maxBytesToWrite)=>{if(!(maxBytesToWrite>0))return 0;var startIdx=outIdx;var endIdx=outIdx+maxBytesToWrite-1;for(var i=0;i<str.length;++i){var u=str.codePointAt(i);if(u<=127){if(outIdx>=endIdx)break;heap[outIdx++]=u}else if(u<=2047){if(outIdx+1>=endIdx)break;heap[outIdx++]=192|u>>6;heap[outIdx++]=128|u&63}else if(u<=65535){if(outIdx+2>=endIdx)break;heap[outIdx++]=224|u>>12;heap[outIdx++]=128|u>>6&63;heap[outIdx++]=128|u&63}else{if(outIdx+3>=endIdx)break;heap[outIdx++]=240|u>>18;heap[outIdx++]=128|u>>12&63;heap[outIdx++]=128|u>>6&63;heap[outIdx++]=128|u&63;i++}}heap[outIdx]=0;return outIdx-startIdx};var stringToUTF8=(str,outPtr,maxBytesToWrite)=>stringToUTF8Array(str,HEAPU8,outPtr,maxBytesToWrite);var stackAlloc=sz=>__emscripten_stack_alloc(sz);var stringToUTF8OnStack=str=>{var size=lengthBytesUTF8(str)+1;var ret=stackAlloc(size);stringToUTF8(str,ret,size);return ret};var UTF8Decoder=globalThis.TextDecoder&&new TextDecoder;var findStringEnd=(heapOrArray,idx,maxBytesToRead,ignoreNul)=>{var maxIdx=idx+maxBytesToRead;if(ignoreNul)return maxIdx;while(heapOrArray[idx]&&!(idx>=maxIdx))++idx;return idx};var UTF8ArrayToString=(heapOrArray,idx=0,maxBytesToRead,ignoreNul)=>{var endPtr=findStringEnd(heapOrArray,idx,maxBytesToRead,ignoreNul);if(endPtr-idx>16&&heapOrArray.buffer&&UTF8Decoder){return UTF8Decoder.decode(heapOrArray.subarray(idx,endPtr))}var str="";while(idx<endPtr){var u0=heapOrArray[idx++];if(!(u0&128)){str+=String.fromCharCode(u0);continue}var u1=heapOrArray[idx++]&63;if((u0&224)==192){str+=String.fromCharCode((u0&31)<<6|u1);continue}var u2=heapOrArray[idx++]&63;if((u0&240)==224){u0=(u0&15)<<12|u1<<6|u2}else{u0=(u0&7)<<18|u1<<12|u2<<6|heapOrArray[idx++]&63}if(u0<65536){str+=String.fromCharCode(u0)}else{var ch=u0-65536;str+=String.fromCharCode(55296|ch>>10,56320|ch&1023)}}return str};var UTF8ToString=(ptr,maxBytesToRead,ignoreNul)=>ptr?UTF8ArrayToString(HEAPU8,ptr,maxBytesToRead,ignoreNul):"";var ccall=(ident,returnType,argTypes,args,opts)=>{var toC={string:str=>{var ret=0;if(str!==null&&str!==undefined&&str!==0){ret=stringToUTF8OnStack(str)}return ret},array:arr=>{var ret=stackAlloc(arr.length);writeArrayToMemory(arr,ret);return ret}};function convertReturnValue(ret){if(returnType==="string"){return UTF8ToString(ret)}if(returnType==="boolean")return Boolean(ret);return ret}var func=getCFunc(ident);var cArgs=[];var stack=0;if(args){for(var i=0;i<args.length;i++){var converter=toC[argTypes[i]];if(converter){if(stack===0)stack=stackSave();cArgs[i]=converter(args[i])}else{cArgs[i]=args[i]}}}var ret=func(...cArgs);function onDone(ret){if(stack!==0)stackRestore(stack);return convertReturnValue(ret)}ret=onDone(ret);return ret};var cwrap=(ident,returnType,argTypes,opts)=>{var numericArgs=!argTypes||argTypes.every(type=>type==="number"||type==="boolean");var numericRet=returnType!=="string";if(numericRet&&numericArgs&&!opts){return getCFunc(ident)}return(...args)=>ccall(ident,returnType,argTypes,args,opts)};{if(Module["noExitRuntime"])noExitRuntime=Module["noExitRuntime"];if(Module["print"])out=Module["print"];if(Module["printErr"])err=Module["printErr"];if(Module["wasmBinary"])wasmBinary=Module["wasmBinary"];if(Module["arguments"])arguments_=Module["arguments"];if(Module["thisProgram"])thisProgram=Module["thisProgram"];if(Module["preInit"]){if(typeof Module["preInit"]=="function")Module["preInit"]=[Module["preInit"]];while(Module["preInit"].length>0){Module["preInit"].shift()()}}}Module["ccall"]=ccall;Module["cwrap"]=cwrap;Module["setValue"]=setValue;Module["getValue"]=getValue;var _dress_init_graph,_malloc,_free,_dress_fit,_dress_free_graph,_dress_get,_dress_delta_fit,_dress_delta_fit_strided,_dress_nabla_fit,__emscripten_stack_restore,__emscripten_stack_alloc,_emscripten_stack_get_current,memory,__indirect_function_table,wasmMemory;function assignWasmExports(wasmExports){_dress_init_graph=Module["_dress_init_graph"]=wasmExports["d"];_malloc=Module["_malloc"]=wasmExports["e"];_free=Module["_free"]=wasmExports["f"];_dress_fit=Module["_dress_fit"]=wasmExports["g"];_dress_free_graph=Module["_dress_free_graph"]=wasmExports["h"];_dress_get=Module["_dress_get"]=wasmExports["i"];_dress_delta_fit=Module["_dress_delta_fit"]=wasmExports["j"];_dress_delta_fit_strided=Module["_dress_delta_fit_strided"]=wasmExports["k"];_dress_nabla_fit=Module["_dress_nabla_fit"]=wasmExports["l"];__emscripten_stack_restore=wasmExports["m"];__emscripten_stack_alloc=wasmExports["n"];_emscripten_stack_get_current=wasmExports["o"];memory=wasmMemory=wasmExports["b"];__indirect_function_table=wasmExports["__indirect_function_table"]}var wasmImports={a:_emscripten_resize_heap};function run(){preRun();function doRun(){Module["calledRun"]=true;if(ABORT)return;initRuntime();readyPromiseResolve?.(Module);Module["onRuntimeInitialized"]?.();postRun()}if(Module["setStatus"]){Module["setStatus"]("Running...");setTimeout(()=>{setTimeout(()=>Module["setStatus"](""),1);doRun()},1)}else{doRun()}}var wasmExports;wasmExports=await (createWasm());run();if(runtimeInitialized){moduleRtn=Module}else{moduleRtn=new Promise((resolve,reject)=>{readyPromiseResolve=resolve;readyPromiseReject=reject})}
-;return moduleRtn}})();if(typeof exports==="object"&&typeof module==="object"){module.exports=createDressModule;module.exports.default=createDressModule}else if(typeof define==="function"&&define["amd"])define([],()=>createDressModule);