Update to our last standards

.github/workflows/typedoc.yml

@@ -0,0 +1,15 @@
+name: TypeDoc
+
+on:
+  workflow_dispatch:
+  release:
+    types: [published]
+
+jobs:
+  typedoc:
+    # Documentation: https://github.com/zakodium/workflows#typedoc
+    uses: zakodium/workflows/.github/workflows/typedoc.yml@typedoc-v1
+    with:
+      entry: 'src/index.ts'
+    secrets:
+      github-token: ${{ secrets.BOT_TOKEN }}

.gitignore

@@ -29,8 +29,8 @@ node_modules
 # webstorm generated files
 .idea
 
-conrec.js
-lib-esm
 lib
 
 .DS_Store
+
+.claude

benchmark/contour.ts

@@ -0,0 +1,54 @@
+// node --cpu-prof benchmark/contour.ts
+
+import { readFileSync } from 'node:fs';
+import { join } from 'node:path';
+
+import type { NumberMatrix } from 'cheminfo-types';
+import { convert } from 'jcampconverter';
+
+import { Conrec } from '../src/index.ts';
+
+const data = readFileSync(
+  join(import.meta.dirname, '../src/__tests__/data/zhmbc_0.jdx'),
+  'utf8',
+);
+const parsed = convert(data, { noContour: true }).flatten[0];
+
+const rawMatrix = parsed.minMax?.z;
+if (!rawMatrix) {
+  throw new Error('Failed to parse matrix from JCAMP file');
+}
+
+const matrix: NumberMatrix = rawMatrix.map((row) => Float64Array.from(row));
+
+// eslint-disable-next-line no-console
+console.log('Size: ', matrix[0].length, 'x', matrix.length);
+
+const conrec = new Conrec(matrix);
+
+const levels: number[] = [];
+for (let level = -1e4; level <= 1e4; level += 2e2) {
+  levels.push(level);
+}
+
+// eslint-disable-next-line no-console
+console.log(
+  `We calculate ${levels.length} levels close to zero to be close to noise`,
+);
+
+console.time('basic');
+
+const result = conrec.drawContour({
+  contourDrawer: 'basic',
+  levels,
+  timeout: 100000,
+});
+// eslint-disable-next-line no-console
+console.log(result.contours.length);
+console.timeEnd('basic');
+const totalNumberContours = result.contours.reduce(
+  (acc, contour) => acc + contour.lines.length,
+  0,
+);
+// eslint-disable-next-line no-console
+console.log({ totalNumberContours });

eslint.config.js

@@ -0,0 +1,4 @@
+import { defineConfig, globalIgnores } from 'eslint/config';
+import cheminfo from 'eslint-config-cheminfo-typescript';
+
+export default defineConfig(globalIgnores(['coverage', 'lib']), cheminfo);

package.json

@@ -2,31 +2,30 @@
   "name": "ml-conrec",
   "version": "5.0.3",
   "description": "JavaScript implementation of the CONREC contouring algorithm",
-  "main": "./lib/index.js",
-  "module": "./lib-esm/index.js",
-  "types": "./lib/index.d.ts",
+  "type": "module",
+  "exports": {
+    ".": "./lib/index.js"
+  },
   "files": [
-    "src",
     "lib",
-    "lib-esm"
+    "src"
   ],
   "scripts": {
     "check-types": "tsc --noEmit",
-    "clean": "rimraf lib lib-esm",
+    "clean": "rimraf lib",
     "eslint": "eslint src",
     "eslint-fix": "npm run eslint -- --fix",
     "prepack": "npm run tsc",
     "prettier": "prettier --check src",
     "prettier-write": "prettier --write src",
-    "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types",
+    "test": "npm run test-only && npm run check-types && npm run eslint && npm run prettier",
     "test-only": "vitest run --coverage",
-    "tsc": "npm run clean && npm run tsc-cjs && npm run tsc-esm",
-    "tsc-cjs": "tsc --project tsconfig.cjs.json",
-    "tsc-esm": "tsc --project tsconfig.esm.json"
+    "tsc": "npm run clean && npm run tsc-build",
+    "tsc-build": "tsc --project tsconfig.build.json"
   },
   "repository": {
     "type": "git",
-    "url": "https://github.com/mljs/conrec.git"
+    "url": "git+https://github.com/mljs/conrec.git"
   },
   "keywords": [
     "algorithm",
@@ -46,21 +45,19 @@
     "url": "https://github.com/mljs/conrec/issues"
   },
   "homepage": "https://github.com/mljs/conrec#readme",
+  "dependencies": {
+    "cheminfo-types": "^1.10.0"
+  },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.24.8",
-    "@babel/preset-typescript": "^7.24.7",
-    "@types/node": "^22.5.4",
-    "@vitest/coverage-v8": "^2.1.0",
-    "eslint": "^8.38.0",
-    "eslint-config-cheminfo-typescript": "^11.3.1",
-    "esm": "^3.2.25",
+    "@types/node": "^25.3.0",
+    "@vitest/coverage-v8": "^4.0.18",
+    "@zakodium/tsconfig": "^1.0.2",
+    "eslint": "^9.39.2",
+    "eslint-config-cheminfo-typescript": "^21.1.0",
     "jcampconverter": "^9.6.4",
-    "prettier": "^3.3.3",
-    "rimraf": "^6.0.1",
-    "typescript": "^5.6.2",
-    "vitest": "^2.1.0"
-  },
-  "dependencies": {
-    "cheminfo-types": "^1.8.0"
+    "prettier": "^3.8.1",
+    "rimraf": "^6.1.3",
+    "typescript": "^5.9.3",
+    "vitest": "^4.0.18"
   }
 }

src/.npmignore

@@ -1,2 +1,3 @@
 __tests__
+.DS_Store
 .npmignore

src/BasicContourDrawer.ts

@@ -7,7 +7,7 @@ export class BasicContourDrawer {
   private contour: BasicContour[];
   private swapAxes: boolean;
 
-  constructor(levels: Readonly<number[]>, swapAxes: boolean) {
+  constructor(levels: readonly number[], swapAxes: boolean) {
     this.contour = [];
     for (const level of levels) {
       this.contour.push({

src/ContourBuilder.ts

@@ -15,12 +15,12 @@
  *
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *     * Redistributions of source code must retain the above copyright
+ *     Redistributions of source code must retain the above copyright
  *       notice, this list of conditions and the following disclaimer.
- *     * Redistributions in binary form must reproduce the above copyright
+ *     Redistributions in binary form must reproduce the above copyright
  *       notice, this list of conditions and the following disclaimer in the
  *       documentation and/or other materials provided with the distribution.
- *     * Neither the name of the <organization> nor the
+ *     Neither the name of the <organization> nor the
  *       names of its contributors may be used to endorse or promote products
  *       derived from this software without specific prior written permission.
  *
@@ -80,12 +80,12 @@
  *
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *     * Redistributions of source code must retain the above copyright
+ *     Redistributions of source code must retain the above copyright
  *       notice, this list of conditions and the following disclaimer.
- *     * Redistributions in binary form must reproduce the above copyright
+ *     Redistributions in binary form must reproduce the above copyright
  *       notice, this list of conditions and the following disclaimer in the
  *       documentation and/or other materials provided with the distribution.
- *     * Neither the name of the <organization> nor the
+ *     Neither the name of the <organization> nor the
  *       names of its contributors may be used to endorse or promote products
  *       derived from this software without specific prior written permission.
  *

src/ShapeContourDrawer.ts

@@ -16,12 +16,12 @@
  *
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *     * Redistributions of source code must retain the above copyright
+ *     Redistributions of source code must retain the above copyright
  *       notice, this list of conditions and the following disclaimer.
- *     * Redistributions in binary form must reproduce the above copyright
+ *     Redistributions in binary form must reproduce the above copyright
  *       notice, this list of conditions and the following disclaimer in the
  *       documentation and/or other materials provided with the distribution.
- *     * Neither the name of the <organization> nor the
+ *     Neither the name of the <organization> nor the
  *       names of its contributors may be used to endorse or promote products
  *       derived from this software without specific prior written permission.
  *
@@ -66,7 +66,8 @@
  * MODIFICATIONS.
  */
 
-import { ContourBuilder, Point, SequenceNode } from './ContourBuilder';
+import type { Point, SequenceNode } from './ContourBuilder.ts';
+import { ContourBuilder } from './ContourBuilder.ts';
 
 export interface ShapeContour {
   level: number;

src/__tests__/__snapshots__/conrec.test.ts.snap

@@ -1,6 +1,6 @@
 // Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
-exports[`conrec basic test > auto select levels 1`] = `
+exports[`auto select levels 1`] = `
 [
   167.3376920421198,
   182.66230795788022,
@@ -37,7 +37,7 @@ exports[`conrec basic test > auto select levels 1`] = `
 ]
 `;
 
-exports[`conrec basic test > auto select levels with swapAxes 1`] = `
+exports[`auto select levels with swapAxes 1`] = `
 [
   182.66230795788022,
   167.3376920421198,