@mapequation/infomap 2.0.2 → 2.3.0

package/network.d.ts

@@ -1,12 +1,12 @@
-interface Node {
+export interface Node {
     id: number;
     name?: string;
     weight?: number;
 }
-interface StateNode extends Omit<Node, "weight"> {
+export interface StateNode extends Omit<Node, "weight"> {
     stateId: number;
 }
-interface Link {
+export interface Link {
     source: number;
     target: number;
     weight?: number;
@@ -22,14 +22,14 @@ export interface StateNetwork extends Required<Network> {
     states: StateNode[];
 }
 export declare type BipartiteStateNetwork = Required<BipartiteNetwork> & StateNetwork;
-interface MultilayerLink extends Link {
+export interface MultilayerLink extends Link {
     sourceLayer: number;
     targetLayer: number;
 }
-interface IntraLink extends Link {
+export interface IntraLink extends Link {
     layerId: number;
 }
-interface InterLink extends Omit<MultilayerLink, "source" | "target"> {
+export interface InterLink extends Omit<MultilayerLink, "source" | "target"> {
     id: number;
 }
 export declare type MultilayerNetwork = Network<MultilayerLink>;
@@ -39,4 +39,3 @@ export interface MultilayerIntraInterNetwork extends Omit<Network, "links"> {
 }
 export declare type NetworkTypes = Network | BipartiteNetwork | StateNetwork | BipartiteStateNetwork | MultilayerNetwork | MultilayerIntraInterNetwork;
 export default function toString(network: NetworkTypes): string | undefined;
-export {};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mapequation/infomap",
-  "version": "2.0.2",
+  "version": "2.3.0",
   "description": "Infomap network clustering algorithm",
   "browser": "index.js",
   "publishConfig": {

package/parser.d.ts

@@ -1,17 +1,21 @@
-import type { NodeBase, CluNode, TreeNode as JsonTreeNode } from "./filetypes";
+import type { CluNode, NodeBase, TreeNode as JsonTreeNode } from "./filetypes";
 import type { Header as JsonHeader, Module } from "./index";
 declare type Optional<T, K extends keyof T> = Pick<Partial<T>, K> & Omit<T, K>;
 declare type Header = Optional<JsonHeader, "directed">;
-declare type TreeNode = Omit<JsonTreeNode, "modules" | "mec">;
+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[];
 };
 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, parseLinks?: boolean): 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 lines(file: string): string[];
+export declare function readFile(file: File): Promise<string>;
+export declare function parse(file: string | string[], type?: Extension, parseLinks?: boolean, strictHeader?: boolean): Result<CluNode<"moduleId">> | Result<TreeNode>;
+export declare function parseClu<NodeType extends CluNode>(file: string | string[], nodeHeader?: string[], strictHeader?: boolean): Result<NodeType>;
+export declare function parseTree<NodeType extends TreeNode>(file: string | string[], nodeHeader?: string[], parseLinks?: boolean, strictHeader?: boolean): Result<NodeType>;
+export declare function parseHeader(file: string | string[], strict?: boolean): Header;
 export {};

package/parser.js

@@ -1 +1 @@
-!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 s=r(e);if(null===s)return null;if(t&&"clu"===t||s.includes("module")){if("node_id"===s[0])return o(e,s);if("state_id"===s[0])return o(e,s)}else if(t&&"tree"===t||s.includes("path")){if("name"===s[s.length-2])return i(e,s,n);if("state_id"===s[s.length-2]||"layer_id"===s[s.length-1])return i(e,s,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){var o;"string"==typeof e&&(e=e.split("\n"));const i=l(e);if(!i)return console.warn("No header"),null;if(!t&&0===(t=null!==(o=r(e))&&void 0!==o?o:[]).length)return console.warn("No node header"),null;const a=[];for(const[o,i]of s(e)){const e=i.split(" ").map(Number);if(e.length<t.length)continue;const o={};for(let i=0;i<t.length;++i){const s=t[i];o[n[s]]=e[i]}a.push(o)}return Object.assign(Object.assign({},i),{nodes:a})}function i(e,t,o=!1){var i,a;"string"==typeof e&&(e=e.split("\n"));const u=l(e);if(!u)return console.warn("No header"),null;if(!t&&0===(t=null!==(i=r(e))&&void 0!==i?i:[]).length)return console.warn("No node header"),null;const c=[];let d=0;for(const[o,i]of s(e)){d=o;const e=i.match(/[^\s"']+|"([^"]*)"/g);if(null===e||e.length<t.length)continue;const s={};for(let o=0;o<t.length;++o){const i=t[o],r=n[i];switch(i){case"path":s.path=e[o].split(":").map(Number);break;case"name":s.name=e[o].slice(1,-1);break;case"node_id":s.id=Number(e[o]);break;case"state_id":case"layer_id":case"flow":s[r]=Number(e[o]);break;default:console.warn(`Unknown field ${i}`)}}c.push(s)}if(++d,e.length<=d+1)return Object.assign(Object.assign({},u),{nodes:c});const f=[];let p=null;const h=e[d];let m=!1;if(null==h?void 0:h.startsWith("*Links")){const e=h.trim().split(" ");m=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,d)){if(n.startsWith("*Links")){const[e,t,...i]=n.split(" "),s="root"===t?[0]:t.split(":").map(Number),[r,l,a,u]=i.map(Number);p={path:s,enterFlow:r,exitFlow:l,numEdges:a,numChildren:u,links:o?[]:void 0},f.push(p);continue}if(!o||!p)continue;const[e,t,i]=n.split(" ").map(Number);null===(a=p.links)||void 0===a||a.push({source:e,target:t,flow:i})}return Object.assign(Object.assign({},u),{directed:m,nodes:c,modules:f})}function*s(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 r(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(" ")}return null}function l(e){var t,n,o,i,s,r,l;const a={};if("string"==typeof e&&(e=e.split("\n")),e.length<8)return null;const u=null===(t=e[0].match(/^# (v\d+\.\d+\.\d+)/))||void 0===t?void 0:t[1];if(!u)return null;a.version=u;const c=null===(n=e[1].match(/^# (.+)/))||void 0===n?void 0:n[1];if(!c)return null;a.args=c;for(let t=2;t<e.length;++t){const n=e[t];if(!n.startsWith("#"))break;const u=null===(o=n.match(/^# started at (.+)/))||void 0===o?void 0:o[1];if(u){a.startedAt=u;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 d=n.match(/^# partitioned into (\d+) levels with (\d+) top modules/);if(d){a.numLevels=Number(d[1]),a.numTopModules=Number(d[2]);continue}const f=null===(s=n.match(/^# codelength (.+) bits/))||void 0===s?void 0:s[1];if(f){a.codelength=Number(f);continue}const p=null===(r=n.match(/^# relative codelength savings (.+)%/))||void 0===r?void 0:r[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))}return a}t.parseClu=o,t.parseTree=i,t.parseHeader=l})(),e})()}));
+!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;function n(e){return e.split(/\r?\n/)}Object.defineProperty(t,"__esModule",{value:!0}),t.parseHeader=t.parseTree=t.parseClu=t.parse=t.readFile=t.lines=t.extension=void 0,t.extension=function(e){var t;return null!==(t=e.split(".").pop())&&void 0!==t?t:null},t.lines=n,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,o=!1,s=!0){"string"==typeof e&&(e=n(e));const d=l(e);if(t&&"clu"===t||d.includes("module")){if("node_id"===d[0])return i(e,d,s);if("state_id"===d[0])return i(e,d,s)}else if(t&&"tree"===t||d.includes("path")){if("name"===d[d.length-2])return r(e,d,o,s);if("state_id"===d[d.length-2]||"layer_id"===d[d.length-1])return r(e,d,o,s)}throw new Error("File must be either a tree or a clu file")};const o={node_id:"id",module:"moduleId",flow:"flow",name:"name",state_id:"stateId",layer_id:"layerId",path:"path"};function i(e,t,i=!0){"string"==typeof e&&(e=n(e));const r=d(e,i);t||(t=l(e));const a=[];for(const[n,i]of s(e)){const e=i.split(" ").map(Number);if(e.length<t.length)continue;const r={};for(let n=0;n<t.length;++n){const i=t[n];r[o[i]]=e[n]}if(void 0===r.id||void 0===r.moduleId||void 0===r.flow)throw new Error(`Invalid node at line ${n+1}: ${i}`);a.push(r)}return Object.assign(Object.assign({},r),{nodes:a})}function r(e,t,i=!1,r=!0){var a;"string"==typeof e&&(e=n(e));const c=d(e,r);t||(t=l(e));const u=[];let f=0;for(const[n,i]of s(e)){f=n;const e=i.match(/[^\s"']+|"([^"]*)"/g);if(null===e||e.length<t.length)continue;const r={};for(let n=0;n<t.length;++n){const i=t[n],s=o[i];switch(i){case"path":r.path=e[n];break;case"name":r.name=e[n].slice(1,-1);break;case"node_id":r.id=Number(e[n]);break;case"state_id":case"layer_id":case"flow":r[s]=Number(e[n]);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 ${n+1}: ${i}`);u.push(r)}if(++f,e.length<=f+1)return Object.assign(Object.assign({},c),{nodes:u});const h=[];let p=null;const m=e[f];let v=!1;if(null==m?void 0:m.startsWith("*Links")){const e=m.trim().split(" ");v=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,f)){if(n.startsWith("*Links")){const[e,t,...o]=n.split(" "),r="root"===t?[0]:t.split(":").map(Number),[s,l,d,a]=o.map(Number);p={path:r,enterFlow:s,exitFlow:l,numEdges:d,numChildren:a,links:i?[]:void 0},h.push(p);continue}if(!i||!p)continue;const[e,t,o]=n.split(" ").map(Number);null===(a=p.links)||void 0===a||a.push({source:e,target:t,flow:o})}return Object.assign(Object.assign({},c),{directed:v,nodes:u,modules:h})}function*s(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 l(e){const t=/^#\s*(path|node_id|state_id)/;"string"==typeof e&&(e=n(e));for(const n of e){if(!n.startsWith("#"))break;if(t.test(n))return n.slice(1).trim().split(" ")}function o(e){return e.every((e=>!isNaN(Number(e))))}function i(e){throw new Error(`Invalid node line: ${e}`)}for(const t of e)if(!t.startsWith("#")){if(t.includes('"')){const e=t.match(/[^\s"']+|"([^"]*)"/g);e||i(t);const n=0,r=2,s=e.slice();s.splice(r,1),s.splice(n,1);const l=e[n].split(":");switch(o(s)&&o(l)||i(t),e.length){case 4:return["path","flow","name","node_id"];case 5:return["path","flow","name","state_id","node_id"];case 6:return["path","flow","name","state_id","node_id","layer_id"];default:i(t)}}else{const e=t.split(" ");switch(o(e)||i(t),e.length){case 4:return["node_id","module","flow"];case 5:return["state_id","module","flow","node_id"];case 6:return["state_id","module","flow","node_id","layer_id"];default:i(t)}}break}throw new Error("Could not parse node header")}function d(e,t=!0){var o,i,r,s,l,d,a,c,u,f;const h={};if("string"==typeof e&&(e=n(e)),e.length<8&&t)throw new Error("Expected file header to have at least 8 lines");const p=e[0]&&(null===(o=e[0].match(/^# (v\d+\.\d+\.\d+)/))||void 0===o?void 0:o[1]);if(p)h.version=p;else if(t)throw new Error("Could not parse version");const m=e[1]&&(null===(i=e[1].match(/^# (.+)/))||void 0===i?void 0:i[1]);if(m)h.args=m;else if(t)throw new Error("Could not parse args");for(let t=2;t<e.length;++t){const n=e[t];if(!n.startsWith("#"))break;const o=null===(r=n.match(/^# started at (.+)/))||void 0===r?void 0:r[1];if(o){h.startedAt=o;continue}const i=null===(s=n.match(/^# completed in (.+) s/))||void 0===s?void 0:s[1];if(i){h.completedIn=Number(i);continue}const p=n.match(/^# partitioned into (\d+) levels with (\d+) top modules/);if(p){h.numLevels=Number(p[1]),h.numTopModules=Number(p[2]);continue}const m=null===(l=n.match(/^# codelength (.+) bits/))||void 0===l?void 0:l[1];if(m){h.codelength=Number(m);continue}const v=null===(d=n.match(/^# relative codelength savings (.+)%/))||void 0===d?void 0:d[1];if(v){h.relativeCodelengthSavings=Number(v)/100;continue}const g=null===(a=n.match(/^# flow model (.+)/))||void 0===a?void 0:a[1];if(g){h.flowModel=g;continue}(null===(c=n.match(/^# higher order/))||void 0===c?void 0:c[1])&&(h.higherOrder=!0);const w=null===(u=n.match(/^# (state|physical) level/))||void 0===u?void 0:u[1];w&&(h.stateLevel="state"===w);const b=null===(f=n.match(/^# bipartite start id (\d+)/))||void 0===f?void 0:f[1];b&&(h.bipartiteStartId=Number(b))}if(h.higherOrder||(h.higherOrder=!1),t&&!(h.startedAt&&h.completedIn&&h.numLevels&&h.numTopModules&&h.codelength&&h.relativeCodelengthSavings))throw new Error("Could not parse file header");return h}t.parseClu=i,t.parseTree=r,t.parseHeader=d})(),e})()}));