@mapequation/infomap 1.9.0 → 2.1.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mapequation/infomap",
-  "version": "1.9.0",
+  "version": "2.1.0",
   "description": "Infomap network clustering algorithm",
   "browser": "index.js",
   "publishConfig": {
@@ -56,15 +56,15 @@
   "homepage": "https://www.mapequation.org/infomap",
   "devDependencies": {
     "arraybuffer-loader": "^1.0.8",
-    "conventional-commits-parser": "^3.1.0",
-    "git-raw-commits": "^2.0.7",
-    "prettier": "^2.3.2",
-    "raw-loader": "^4.0.1",
-    "standard-version": "^8.0.2",
-    "ts-loader": "^9.2.3",
-    "typescript": "^4.3.4",
-    "webpack": "^5.39.1",
-    "webpack-cli": "^4.7.2"
+    "conventional-commits-parser": "^3.2.4",
+    "git-raw-commits": "^2.0.11",
+    "prettier": "^2.5.1",
+    "raw-loader": "^4.0.2",
+    "standard-version": "^9.3.2",
+    "ts-loader": "^9.2.6",
+    "typescript": "^4.5.4",
+    "webpack": "^5.66.0",
+    "webpack-cli": "^4.9.1"
   },
   "standard-version": {
     "bumpFiles": [
@@ -73,6 +73,10 @@
       {
         "filename": "src/io/version.cpp",
         "updater": "utils/update-version-cpp.js"
+      },
+      {
+        "filename": "CITATION.cff",
+        "updater": "utils/update-citation-cff.js"
       }
     ]
   },

package/parser.d.ts

@@ -1,7 +1,11 @@
 import type { NodeBase, CluNode, TreeNode as JsonTreeNode } from "./filetypes";
 import type { Header as JsonHeader, Module } from "./index";
-declare type Header = Omit<JsonHeader, "directed">;
-declare type TreeNode = Omit<JsonTreeNode, "modules" | "modularCentrality">;
+declare type Optional<T, K extends keyof T> = Pick<Partial<T>, K> & Omit<T, K>;
+declare type Header = Optional<JsonHeader, "directed">;
+declare type Path = {
+    path: string | number[];
+};
+declare type TreeNode = Omit<JsonTreeNode, "modules" | "mec" | "path"> & Path;
 export declare type Result<NodeType extends NodeBase> = Header & {
     nodes: NodeType[];
     modules?: Module[];
@@ -9,8 +13,8 @@ export declare type Result<NodeType extends NodeBase> = Header & {
 export declare type Extension = "clu" | "tree";
 export declare function extension(filename: string): string | null;
 export declare function readFile(file: File): Promise<unknown>;
-export declare function parse(file: string | string[], type?: Extension): Result<CluNode<"moduleId">> | Result<TreeNode> | null;
-export declare function parseClu<NodeType extends CluNode>(file: string | string[], nodeHeader?: string[]): Result<NodeType> | null;
-export declare function parseTree<NodeType extends TreeNode>(file: string | string[], nodeHeader?: string[], parseLinks?: boolean): Result<NodeType> | null;
-export declare function parseHeader(file: string | string[]): Header | null;
+export declare function parse(file: string | string[], type?: Extension, parseLinks?: boolean): Result<CluNode<"moduleId">> | Result<TreeNode> | null;
+export declare function parseClu<NodeType extends CluNode>(file: string | string[], nodeHeader?: string[]): Result<NodeType>;
+export declare function parseTree<NodeType extends TreeNode>(file: string | string[], nodeHeader?: string[], parseLinks?: boolean): Result<NodeType>;
+export declare function parseHeader(file: string | string[]): Header;
 export {};

package/parser.js

@@ -1 +1 @@
-!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.infomap=e():t.infomap=e()}(self,(function(){return(()=>{"use strict";var t={};return(()=>{var e=t;Object.defineProperty(e,"__esModule",{value:!0}),e.parseHeader=e.parseTree=e.parseClu=e.parse=e.readFile=e.extension=void 0,e.extension=function(t){var e;return null!==(e=t.split(".").pop())&&void 0!==e?e:null},e.readFile=function(t){return new Promise(((e,n)=>{const i=new FileReader;i.onload=()=>e(i.result),i.onerror=n,i.readAsText(t)}))},e.parse=function(t,e){"string"==typeof t&&(t=t.split("\n"));const n=r(t);if(null===n)return null;if(e&&"clu"===e||n.includes("module")){if("node_id"===n[0])return i(t,n);if("state_id"===n[0])return i(t,n)}else if(e&&"tree"===e||n.includes("path")){if("name"===n[n.length-2])return o(t,n);if("state_id"===n[n.length-2])return o(t,n)}return null};const n={node_id:"id",module:"moduleId",flow:"flow",name:"name",state_id:"stateId",layer_id:"layerId",path:"path"};function i(t,e){var i;"string"==typeof t&&(t=t.split("\n"));const o=l(t);if(!o)return null;if(!e&&0===(e=null!==(i=r(t))&&void 0!==i?i:[]).length)return null;const u=[];for(const[i,o]of s(t)){const t=o.split(" ").map(Number);if(t.length<e.length)continue;const i={};for(let o=0;o<e.length;++o){const s=e[o];i[n[s]]=t[o]}u.push(i)}return Object.assign(Object.assign({},o),{nodes:u})}function o(t,e,i=!1){var o,u;"string"==typeof t&&(t=t.split("\n"));const a=l(t);if(!a)return null;if(!e&&0===(e=null!==(o=r(t))&&void 0!==o?o:[]).length)return null;const c=[];let d=0;for(const[i,o]of s(t)){d=i;const t=o.match(/[^\s"']+|"([^"]*)"/g);if(null===t||t.length<e.length)continue;const s={};for(let i=0;i<e.length;++i){const o=e[i],r=n[o];switch(o){case"path":s.path=t[i].split(":").map(Number);break;case"name":s.name=t[i].slice(1,-1);break;case"node_id":s.id=Number(t[i]);break;case"state_id":case"layer_id":case"flow":s[r]=Number(t[i])}}c.push(s)}if(++d,t.length<=d+1)return Object.assign(Object.assign({},a),{nodes:c});const f=[];let p=null;for(const[e,n]of function*(t,e=0){if(!(t.length<=e)&&t[e].startsWith("*Links"))for(let n=++e;n<t.length;++n){const e=t[n];0!==e.length&&(yield[n,e])}}(t,d)){if(n.startsWith("*Links")){const[t,...e]=n.split(" "),o="root"===t?[0]:t.split(":").map(Number),[s,r,l,u]=e.map(Number);p={path:o,enterFlow:s,exitFlow:r,numEdges:l,numChildren:u,links:i?[]:void 0},f.push(p);continue}if(!i||!p)continue;const[t,e,o]=n.split(" ").map(Number);null===(u=p.links)||void 0===u||u.push({source:t,target:e,flow:o})}return Object.assign(Object.assign({},a),{nodes:c,modules:f})}function*s(t){for(let e=0;e<t.length;++e){const n=t[e];if(!n.startsWith("#")&&0!==n.length){if(n.startsWith("*"))break;yield[e,n]}}}function r(t){const e=["# path","# node_id","# state_id"];"string"==typeof t&&(t=t.split("\n"));for(const n of t){if(!n.startsWith("#"))break;if(e.some((t=>n.startsWith(t))))return n.slice(2).split(" ")}return null}function l(t){var e,n,i,o,s,r,l;const u={};if("string"==typeof t&&(t=t.split("\n")),t.length<8)return null;const a=null===(e=t[0].match(/^# (v\d+\.\d+\.\d+)/))||void 0===e?void 0:e[1];if(!a)return null;u.version=a;const c=null===(n=t[1].match(/^# (.+)/))||void 0===n?void 0:n[1];if(!c)return null;u.args=c;for(let e=2;e<t.length;++e){const n=t[e];if(!n.startsWith("#"))break;const a=null===(i=n.match(/^# started at (.+)/))||void 0===i?void 0:i[1];if(a){u.startedAt=a;continue}const c=null===(o=n.match(/^# completed in (.+) s/))||void 0===o?void 0:o[1];if(c){u.completedIn=Number(c);continue}const d=n.match(/^# partitioned into (\d+) levels with (\d+) top modules/);if(d){u.numLevels=Number(d[1]),u.numTopModules=Number(d[2]);continue}const f=null===(s=n.match(/^# codelength (.+) bits/))||void 0===s?void 0:s[1];if(f){u.codelength=Number(f);continue}const p=null===(r=n.match(/^# relative codelength savings (.+)%/))||void 0===r?void 0:r[1];if(p){u.relativeCodelengthSavings=Number(p)/100;continue}const h=null===(l=n.match(/^# bipartite start id (\d+)/))||void 0===l?void 0:l[1];h&&(u.bipartiteStartId=Number(h))}return u}e.parseClu=i,e.parseTree=o,e.parseHeader=l})(),t})()}));
+!function(e,t){"object"==typeof exports&&"object"==typeof module?module.exports=t():"function"==typeof define&&define.amd?define([],t):"object"==typeof exports?exports.infomap=t():e.infomap=t()}(self,(function(){return(()=>{"use strict";var e={};return(()=>{var t=e;Object.defineProperty(t,"__esModule",{value:!0}),t.parseHeader=t.parseTree=t.parseClu=t.parse=t.readFile=t.extension=void 0,t.extension=function(e){var t;return null!==(t=e.split(".").pop())&&void 0!==t?t:null},t.readFile=function(e){return new Promise(((t,n)=>{const o=new FileReader;o.onload=()=>t(o.result),o.onerror=n,o.readAsText(e)}))},t.parse=function(e,t,n=!1){"string"==typeof e&&(e=e.split("\n"));const r=s(e);if(t&&"clu"===t||r.includes("module")){if("node_id"===r[0])return o(e,r);if("state_id"===r[0])return o(e,r)}else if(t&&"tree"===t||r.includes("path")){if("name"===r[r.length-2])return i(e,r,n);if("state_id"===r[r.length-2]||"layer_id"===r[r.length-1])return i(e,r,n)}return null};const n={node_id:"id",module:"moduleId",flow:"flow",name:"name",state_id:"stateId",layer_id:"layerId",path:"path"};function o(e,t){"string"==typeof e&&(e=e.split("\n"));const o=l(e);t||(t=s(e));const i=[];for(const[o,s]of r(e)){const e=s.split(" ").map(Number);if(e.length<t.length)continue;const r={};for(let o=0;o<t.length;++o){const i=t[o];r[n[i]]=e[o]}if(void 0===r.id||void 0===r.moduleId||void 0===r.flow)throw new Error(`Invalid node at line ${o+1}: ${s}`);i.push(r)}return Object.assign(Object.assign({},o),{nodes:i})}function i(e,t,o=!1){var i;"string"==typeof e&&(e=e.split("\n"));const a=l(e);t||(t=s(e));const d=[];let c=0;for(const[o,i]of r(e)){c=o;const e=i.match(/[^\s"']+|"([^"]*)"/g);if(null===e||e.length<t.length)continue;const r={};for(let o=0;o<t.length;++o){const i=t[o],s=n[i];switch(i){case"path":r.path=e[o];break;case"name":r.name=e[o].slice(1,-1);break;case"node_id":r.id=Number(e[o]);break;case"state_id":case"layer_id":case"flow":r[s]=Number(e[o]);break;default:console.warn(`Unknown field ${i}`)}}if(void 0===r.path||void 0===r.flow||void 0===r.name||void 0===r.id)throw new Error(`Invalid node at line ${o+1}: ${i}`);d.push(r)}if(++c,e.length<=c+1)return Object.assign(Object.assign({},a),{nodes:d});const u=[];let f=null;const p=e[c];let h=!1;if(null==p?void 0:p.startsWith("*Links")){const e=p.trim().split(" ");h=e.length>1&&"directed"===e[1]}for(const[t,n]of function*(e,t=0){if(!(e.length<=t)&&e[t].startsWith("*Links"))for(let n=++t;n<e.length;++n){const t=e[n];0!==t.length&&(yield[n,t])}}(e,c)){if(n.startsWith("*Links")){const[e,t,...i]=n.split(" "),r="root"===t?[0]:t.split(":").map(Number),[s,l,a,d]=i.map(Number);f={path:r,enterFlow:s,exitFlow:l,numEdges:a,numChildren:d,links:o?[]:void 0},u.push(f);continue}if(!o||!f)continue;const[e,t,r]=n.split(" ").map(Number);null===(i=f.links)||void 0===i||i.push({source:e,target:t,flow:r})}return Object.assign(Object.assign({},a),{directed:h,nodes:d,modules:u})}function*r(e){for(let t=0;t<e.length;++t){const n=e[t];if(!n.startsWith("#")&&0!==n.length){if(n.startsWith("*"))break;yield[t,n]}}}function s(e){const t=["# path","# node_id","# state_id"];"string"==typeof e&&(e=e.split("\n"));for(const n of e){if(!n.startsWith("#"))break;if(t.some((e=>n.startsWith(e))))return n.slice(2).split(" ")}throw new Error("Could not parse node header")}function l(e){var t,n,o,i,r,s,l;const a={};if("string"==typeof e&&(e=e.split("\n")),e.length<8)throw new Error("Expected file header to have at least 8 lines");const d=null===(t=e[0].match(/^# (v\d+\.\d+\.\d+)/))||void 0===t?void 0:t[1];if(!d)throw new Error("Could not parse version");a.version=d;const c=null===(n=e[1].match(/^# (.+)/))||void 0===n?void 0:n[1];if(!c)throw new Error("Could not parse args");a.args=c;for(let t=2;t<e.length;++t){const n=e[t];if(!n.startsWith("#"))break;const d=null===(o=n.match(/^# started at (.+)/))||void 0===o?void 0:o[1];if(d){a.startedAt=d;continue}const c=null===(i=n.match(/^# completed in (.+) s/))||void 0===i?void 0:i[1];if(c){a.completedIn=Number(c);continue}const u=n.match(/^# partitioned into (\d+) levels with (\d+) top modules/);if(u){a.numLevels=Number(u[1]),a.numTopModules=Number(u[2]);continue}const f=null===(r=n.match(/^# codelength (.+) bits/))||void 0===r?void 0:r[1];if(f){a.codelength=Number(f);continue}const p=null===(s=n.match(/^# relative codelength savings (.+)%/))||void 0===s?void 0:s[1];if(p){a.relativeCodelengthSavings=Number(p)/100;continue}const h=null===(l=n.match(/^# bipartite start id (\d+)/))||void 0===l?void 0:l[1];h&&(a.bipartiteStartId=Number(h))}if(!(a.startedAt&&a.completedIn&&a.numLevels&&a.numTopModules&&a.codelength&&a.relativeCodelengthSavings))throw new Error("Could not parse file header");return a}t.parseClu=o,t.parseTree=i,t.parseHeader=l})(),e})()}));