From be7f2df2f6d6ad625c0e7c54c7b59c5b16fe9fab Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Fri, 17 Apr 2026 19:28:24 +0200
Subject: [PATCH 01/11] ci: replace documentationjs with typedoc workflow

---
 .github/workflows/documentationjs.yml | 21 ---------------------
 .github/workflows/typedoc.yml         | 15 +++++++++++++++
 2 files changed, 15 insertions(+), 21 deletions(-)
 delete mode 100644 .github/workflows/documentationjs.yml
 create mode 100644 .github/workflows/typedoc.yml

diff --git a/.github/workflows/documentationjs.yml b/.github/workflows/documentationjs.yml
deleted file mode 100644
index 0ae90e1..0000000
--- a/.github/workflows/documentationjs.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-name: Deploy documentation.js on GitHub pages
-
-on:
-  workflow_dispatch:
-  release:
-    types: [published]
-
-jobs:
-  deploy:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - name: Build documentation
-        uses: zakodium/documentationjs-action@v1
-      - name: Deploy to GitHub pages
-        uses: JamesIves/github-pages-deploy-action@releases/v4
-        with:
-          token: ${{ secrets.BOT_TOKEN }}
-          branch: gh-pages
-          folder: docs
-          clean: true
diff --git a/.github/workflows/typedoc.yml b/.github/workflows/typedoc.yml
new file mode 100644
index 0000000..81c1ff6
--- /dev/null
+++ b/.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 }}

From 4bcfb996ab3fa757fdb566d0c209ffd1be1e6327 Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Fri, 17 Apr 2026 19:28:27 +0200
Subject: [PATCH 02/11] chore: ignore .claude and drop stale gitignore entries

---
 .gitignore | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index e4a63b2..3faf0bf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -29,8 +29,8 @@ node_modules
 # webstorm generated files
 .idea
 
-conrec.js
-lib-esm
 lib
 
 .DS_Store
+
+.claude

From a99b011070c364cec374c301a295d48764c99b3f Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Fri, 17 Apr 2026 19:28:30 +0200
Subject: [PATCH 03/11] chore: add .DS_Store to src/.npmignore

---
 src/.npmignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/.npmignore b/src/.npmignore
index d7a3323..76cf446 100644
--- a/src/.npmignore
+++ b/src/.npmignore
@@ -1,2 +1,3 @@
 __tests__
+.DS_Store
 .npmignore

From 361ba7c5d50cc2168d36974f122b2609cca3b17a Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Fri, 17 Apr 2026 19:28:33 +0200
Subject: [PATCH 04/11] chore: migrate ESLint to flat config (v9)

---
 .eslintignore    | 1 -
 .eslintrc.yml    | 6 ------
 eslint.config.js | 4 ++++
 3 files changed, 4 insertions(+), 7 deletions(-)
 delete mode 100644 .eslintignore
 delete mode 100644 .eslintrc.yml
 create mode 100644 eslint.config.js

diff --git a/.eslintignore b/.eslintignore
deleted file mode 100644
index b80e164..0000000
--- a/.eslintignore
+++ /dev/null
@@ -1 +0,0 @@
-src/Conrec.js
diff --git a/.eslintrc.yml b/.eslintrc.yml
deleted file mode 100644
index cf10b61..0000000
--- a/.eslintrc.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-extends: cheminfo-typescript
-parserOptions:
-  sourceType: module
-env:
-  jest: true
-  node: true
diff --git a/eslint.config.js b/eslint.config.js
new file mode 100644
index 0000000..00cc43d
--- /dev/null
+++ b/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);

From 1b6496847c13db9cc675c9e1a567d05c10db4e75 Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Fri, 17 Apr 2026 19:28:40 +0200
Subject: [PATCH 05/11] chore: remove babel configuration

---
 .babelrc.json   | 3 ---
 babel.config.js | 4 ----
 2 files changed, 7 deletions(-)
 delete mode 100644 .babelrc.json
 delete mode 100644 babel.config.js

diff --git a/.babelrc.json b/.babelrc.json
deleted file mode 100644
index 34bc6d2..0000000
--- a/.babelrc.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "plugins": ["@babel/plugin-transform-modules-commonjs"]
-}
diff --git a/babel.config.js b/babel.config.js
deleted file mode 100644
index f5f790b..0000000
--- a/babel.config.js
+++ /dev/null
@@ -1,4 +0,0 @@
-module.exports = {
-  presets: ['@babel/preset-typescript'],
-  plugins: ['@babel/plugin-transform-modules-commonjs'],
-};

From a379f1bfa96ed73ae3e30c957d98d6c51a110f23 Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Fri, 17 Apr 2026 19:28:43 +0200
Subject: [PATCH 06/11] chore: use @zakodium/tsconfig with single build config

---
 tsconfig.build.json |  5 +++++
 tsconfig.cjs.json   |  9 ---------
 tsconfig.esm.json   |  7 -------
 tsconfig.json       | 11 ++++-------
 4 files changed, 9 insertions(+), 23 deletions(-)
 create mode 100644 tsconfig.build.json
 delete mode 100644 tsconfig.cjs.json
 delete mode 100644 tsconfig.esm.json

diff --git a/tsconfig.build.json b/tsconfig.build.json
new file mode 100644
index 0000000..1fec47c
--- /dev/null
+++ b/tsconfig.build.json
@@ -0,0 +1,5 @@
+{
+  "extends": "./tsconfig.json",
+  "include": ["src"],
+  "exclude": ["**/__tests__", "**/*.test.ts"]
+}
diff --git a/tsconfig.cjs.json b/tsconfig.cjs.json
deleted file mode 100644
index 3b9e100..0000000
--- a/tsconfig.cjs.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
-  "extends": "./tsconfig.json",
-  "compilerOptions": {
-    "module": "commonjs",
-    "declaration": true,
-    "declarationMap": true
-  },
-  "exclude": ["./src/**/__tests__"]
-}
diff --git a/tsconfig.esm.json b/tsconfig.esm.json
deleted file mode 100644
index 050b45d..0000000
--- a/tsconfig.esm.json
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-  "extends": "./tsconfig.cjs.json",
-  "compilerOptions": {
-    "module": "es2020",
-    "outDir": "lib-esm"
-  }
-}
diff --git a/tsconfig.json b/tsconfig.json
index 321f97e..119b52a 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -1,12 +1,9 @@
 {
+  "extends": "@zakodium/tsconfig",
   "compilerOptions": {
-    "esModuleInterop": true,
-    "moduleResolution": "node",
+    "noUncheckedIndexedAccess": false,
     "outDir": "lib",
-    "skipLibCheck": true,
-    "sourceMap": true,
-    "strict": true,
-    "target": "es2020"
+    "types": ["node"]
   },
-  "include": ["./src/**/*"]
+  "include": ["src", "benchmark", "vitest.config.ts"]
 }

From 5ec501e2290bab00e3ea9c431ecdbd2c0dea7b78 Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Fri, 17 Apr 2026 19:28:46 +0200
Subject: [PATCH 07/11] test: add vitest config with full snapshot output

---
 vitest.config.ts | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 vitest.config.ts

diff --git a/vitest.config.ts b/vitest.config.ts
new file mode 100644
index 0000000..7ed5e86
--- /dev/null
+++ b/vitest.config.ts
@@ -0,0 +1,9 @@
+import { defineConfig } from 'vitest/config';
+
+export default defineConfig({
+  test: {
+    snapshotFormat: {
+      maxOutputLength: Number.MAX_SAFE_INTEGER,
+    },
+  },
+});

From ac5082a675950e48ecd42de38be8e810d3d898db Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Sat, 18 Apr 2026 06:25:01 +0200
Subject: [PATCH 08/11] feat!: migrate package to ESM
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Convert to a pure ESM package: `"type": "module"`, `"exports"` field,
single `lib/` output, `.ts` extensions on local imports, and split
`type` imports. The `lib-esm` entry point is removed; use `lib` via
the `exports` field.

BREAKING CHANGE: package is now ESM-only; consumers using
require() must migrate to import, or run Node.js ≥ 20.19
(or ≥ 22.12 / any 24.x), which supports require() of ESM.
---
 package.json              | 47 ++++++++++++++++++---------------------
 src/BasicContourDrawer.ts |  2 +-
 src/ContourBuilder.ts     | 12 +++++-----
 src/ShapeContourDrawer.ts |  9 ++++----
 src/calculateContour.ts   | 27 ++++++++++++----------
 src/index.ts              |  8 +++----
 6 files changed, 53 insertions(+), 52 deletions(-)

diff --git a/package.json b/package.json
index 345d710..b9864d0 100644
--- a/package.json
+++ b/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"
   }
 }
diff --git a/src/BasicContourDrawer.ts b/src/BasicContourDrawer.ts
index 905de11..c6f4576 100644
--- a/src/BasicContourDrawer.ts
+++ b/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({
diff --git a/src/ContourBuilder.ts b/src/ContourBuilder.ts
index f02c0ae..5bce3f2 100644
--- a/src/ContourBuilder.ts
+++ b/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.
  *
diff --git a/src/ShapeContourDrawer.ts b/src/ShapeContourDrawer.ts
index 85a5a12..fe3d4e7 100644
--- a/src/ShapeContourDrawer.ts
+++ b/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;
diff --git a/src/calculateContour.ts b/src/calculateContour.ts
index d43d7b8..69be7c8 100644
--- a/src/calculateContour.ts
+++ b/src/calculateContour.ts
@@ -1,7 +1,7 @@
 // https://github.com/jasondavies/conrec.js
-import { NumberArray, NumberMatrix } from 'cheminfo-types';
+import type { NumberArray, NumberMatrix } from 'cheminfo-types';
 
-import { ContourDrawer } from '.';
+import type { ContourDrawer } from './index.ts';
 
 // Changes have been done by MLJS team
 
@@ -21,12 +21,12 @@ import { ContourDrawer } from '.';
  *
  * 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.
  *
@@ -95,7 +95,6 @@ interface CalculateContourOptions {
  *
  * Any number of contour levels may be specified but they must be in order of
  * increasing value.
- *
  * @private
  * @param matrix - matrix of data to contour
  *
@@ -104,9 +103,10 @@ interface CalculateContourOptions {
  * @param x  - data matrix column coordinates
  * @param y  - data matrix row coordinates
  * @param z  - contour levels in increasing order.
- * @param contourDrawer object that implements contourDraw for drawing contour.  Defaults to a
+ * @param contourDrawer - object that implements contourDraw for drawing contour.  Defaults to a
  *                               custom "contour builder", which populates the
  *                               contours property.
+ * @param options - additional calculation options (timeout and index bounds).
  * @returns Whether contour generation had to stop early because it reached the timeout
  */
 export function calculateContour(
@@ -135,7 +135,6 @@ export function calculateContour(
 
   const start = Date.now();
 
-  /** private */
   function xsect(p1: number, p2: number) {
     return (h[p2] * xh[p1] - h[p1] * xh[p2]) / (h[p2] - h[p1]);
   }
@@ -147,10 +146,10 @@ export function calculateContour(
   let m1;
   let m2;
   let m3;
-  let x1 = 0.0;
-  let x2 = 0.0;
-  let y1 = 0.0;
-  let y2 = 0.0;
+  let x1 = 0;
+  let x2 = 0;
+  let y1 = 0;
+  let y2 = 0;
 
   // The indexing of im and jm should be noted as it has to start from zero
   // unlike the fortran counter part
@@ -208,6 +207,10 @@ export function calculateContour(
       const dmin = Math.min(min1, min2);
       const dmax = Math.max(max1, max2);
       // Ternary operator is now much slower: https://jsbench.me/d5l0dh502g
+
+      //const dmin = (min1 + min2 - Math.abs(min1 - min2)) / 2;
+      //const dmax = (max1 + max2 + Math.abs(max1 - max2)) / 2;
+
       //let dmin = min1 > min2 ? min2 : min1;
       //let dmax = max1 > max2 ? max1 : max2;
       if (dmax >= z0 && dmin <= znc1) {
diff --git a/src/index.ts b/src/index.ts
index 9fc3a25..0500f47 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -1,8 +1,8 @@
-import { NumberArray, NumberMatrix } from 'cheminfo-types';
+import type { NumberArray, NumberMatrix } from 'cheminfo-types';
 
-import { BasicContourDrawer } from './BasicContourDrawer';
-import { ShapeContourDrawer } from './ShapeContourDrawer';
-import { calculateContour } from './calculateContour';
+import { BasicContourDrawer } from './BasicContourDrawer.ts';
+import { ShapeContourDrawer } from './ShapeContourDrawer.ts';
+import { calculateContour } from './calculateContour.ts';
 
 interface ConrecOptions {
   xs?: Readonly<NumberArray>;

From 2f54aff9b88a110be7e9f266d85560193d71bce4 Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Fri, 17 Apr 2026 19:29:46 +0200
Subject: [PATCH 09/11] test: migrate to flat vitest structure with node:
 imports

---
 .../__snapshots__/conrec.test.ts.snap         |   4 +-
 src/__tests__/conrec.test.ts                  | 169 +++++++++---------
 src/__tests__/shape.test.ts                   | 140 ++++++++-------
 3 files changed, 162 insertions(+), 151 deletions(-)

diff --git a/src/__tests__/__snapshots__/conrec.test.ts.snap b/src/__tests__/__snapshots__/conrec.test.ts.snap
index 62b98a5..098caa8 100644
--- a/src/__tests__/__snapshots__/conrec.test.ts.snap
+++ b/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,
diff --git a/src/__tests__/conrec.test.ts b/src/__tests__/conrec.test.ts
index 80d33d5..445accc 100644
--- a/src/__tests__/conrec.test.ts
+++ b/src/__tests__/conrec.test.ts
@@ -1,101 +1,108 @@
-import fs from 'fs';
+import { readFileSync } from 'node:fs';
+import { join } from 'node:path';
 
-import { NumberMatrix } from 'cheminfo-types';
+import type { NumberMatrix } from 'cheminfo-types';
 import { convert } from 'jcampconverter';
-import { describe, it, expect } from 'vitest';
+import { expect, test } from 'vitest';
 
-import { Conrec } from '..';
+import { Conrec } from '../index.ts';
 
-const data = fs.readFileSync(`${__dirname}/data/zhmbc_0.jdx`, 'utf8');
+const data = readFileSync(
+  join(import.meta.dirname, 'data/zhmbc_0.jdx'),
+  'utf8',
+);
 const parsed = convert(data, { noContour: true }).flatten[0];
 const matrix: NumberMatrix = parsed.minMax?.z || [];
-describe('conrec basic test', () => {
-  it('no result because level too far', () => {
-    const conrec = new Conrec(matrix);
-    const { contours, timeout } = conrec.drawContour({
-      contourDrawer: 'basic',
-      levels: [-1000000000, 1000000000],
-      timeout: 10000,
-    });
-    expect(timeout).toBeFalsy();
-    expect(contours).toStrictEqual([
-      { lines: [], zValue: -1000000000 },
-      { lines: [], zValue: 1000000000 },
-    ]);
+
+test('no result because level too far', () => {
+  const conrec = new Conrec(matrix);
+  const { contours, timeout } = conrec.drawContour({
+    contourDrawer: 'basic',
+    levels: [-1000000000, 1000000000],
+    timeout: 10000,
   });
 
-  it('2 specified levels', () => {
-    const conrec = new Conrec(matrix);
-    const { contours, timeout } = conrec.drawContour({
-      contourDrawer: 'basic',
-      levels: [-100000, 100000],
-      timeout: 10000,
-    });
-    expect(timeout).toBeFalsy();
-    expect(contours).toHaveLength(2);
-    expect(contours[0].lines).toHaveLength(36864);
-    expect(contours[1].lines).toHaveLength(119720);
+  expect(timeout).toBe(false);
+  expect(contours).toStrictEqual([
+    { lines: [], zValue: -1000000000 },
+    { lines: [], zValue: 1000000000 },
+  ]);
+});
+
+test('2 specified levels', () => {
+  const conrec = new Conrec(matrix);
+  const { contours, timeout } = conrec.drawContour({
+    contourDrawer: 'basic',
+    levels: [-100000, 100000],
+    timeout: 10000,
   });
 
-  it('no levels', () => {
-    const conrec = new Conrec(matrix);
-    const start = Date.now();
-    const { contours, timeout } = conrec.drawContour({
-      contourDrawer: 'basic',
-      levels: [],
-      timeout: 10000,
-    });
-    expect(Date.now() - start).toBeLessThan(25);
-    expect(timeout).toBeFalsy();
-    expect(contours).toHaveLength(0);
+  expect(timeout).toBe(false);
+  expect(contours).toHaveLength(2);
+  expect(contours[0].lines).toHaveLength(36864);
+  expect(contours[1].lines).toHaveLength(119720);
+});
+
+test('no levels', () => {
+  const conrec = new Conrec(matrix);
+  const start = Date.now();
+  const { contours, timeout } = conrec.drawContour({
+    contourDrawer: 'basic',
+    levels: [],
+    timeout: 10000,
   });
 
-  it('auto select levels', () => {
-    const conrec = new Conrec(matrix);
-    const { contours, timeout } = conrec.drawContour({
-      contourDrawer: 'basic',
-      nbLevels: 10,
-      timeout: 10000,
-    });
+  expect(Date.now() - start).toBeLessThan(25);
+  expect(timeout).toBe(false);
+  expect(contours).toHaveLength(0);
+});
 
-    expect(timeout).toBeFalsy();
-    expect(contours).toHaveLength(10);
-    expect(contours[0].lines).toHaveLength(0);
-    expect(contours[1].lines).toHaveLength(4984);
-    expect(contours[8].lines).toHaveLength(32);
-    expect(contours[8].lines).toMatchSnapshot();
-    expect(contours[9].lines).toHaveLength(0);
+test('auto select levels', () => {
+  const conrec = new Conrec(matrix);
+  const { contours, timeout } = conrec.drawContour({
+    contourDrawer: 'basic',
+    nbLevels: 10,
+    timeout: 10000,
   });
 
-  it('auto select levels with swapAxes', () => {
-    const conrec = new Conrec(matrix, { swapAxes: true });
-    const { contours, timeout } = conrec.drawContour({
-      contourDrawer: 'basic',
-      nbLevels: 10,
-      timeout: 10000,
-    });
+  expect(timeout).toBe(false);
+  expect(contours).toHaveLength(10);
+  expect(contours[0].lines).toHaveLength(0);
+  expect(contours[1].lines).toHaveLength(4984);
+  expect(contours[8].lines).toHaveLength(32);
+  expect(contours[8].lines).toMatchSnapshot();
+  expect(contours[9].lines).toHaveLength(0);
+});
 
-    expect(timeout).toBeFalsy();
-    expect(contours).toHaveLength(10);
-    expect(contours[0].lines).toHaveLength(0);
-    expect(contours[1].lines).toHaveLength(4984);
-    expect(contours[8].lines).toHaveLength(32);
-    expect(contours[8].lines).toMatchSnapshot();
-    expect(contours[9].lines).toHaveLength(0);
+test('auto select levels with swapAxes', () => {
+  const conrec = new Conrec(matrix, { swapAxes: true });
+  const { contours, timeout } = conrec.drawContour({
+    contourDrawer: 'basic',
+    nbLevels: 10,
+    timeout: 10000,
   });
 
-  it('return available contours within 100ms', () => {
-    const conrec = new Conrec(matrix);
-    const { contours, timeout } = conrec.drawContour({
-      contourDrawer: 'basic',
-      nbLevels: 10,
-      timeout: 10,
-    });
-    expect(timeout).toBeTruthy();
-    expect(contours).toHaveLength(10);
-    expect(contours[0].lines).toHaveLength(0);
-    expect(contours[1].lines.length).toBeLessThan(2000);
-    expect(contours[8].lines).toHaveLength(0);
-    expect(contours[9].lines).toHaveLength(0);
+  expect(timeout).toBe(false);
+  expect(contours).toHaveLength(10);
+  expect(contours[0].lines).toHaveLength(0);
+  expect(contours[1].lines).toHaveLength(4984);
+  expect(contours[8].lines).toHaveLength(32);
+  expect(contours[8].lines).toMatchSnapshot();
+  expect(contours[9].lines).toHaveLength(0);
+});
+
+test('return available contours within 100ms', () => {
+  const conrec = new Conrec(matrix);
+  const { contours, timeout } = conrec.drawContour({
+    contourDrawer: 'basic',
+    nbLevels: 10,
+    timeout: 10,
   });
+
+  expect(timeout).toBe(true);
+  expect(contours).toHaveLength(10);
+  expect(contours[0].lines).toHaveLength(0);
+  expect(contours[1].lines.length).toBeLessThan(2000);
+  expect(contours[8].lines).toHaveLength(0);
+  expect(contours[9].lines).toHaveLength(0);
 });
diff --git a/src/__tests__/shape.test.ts b/src/__tests__/shape.test.ts
index b7946c2..4aa9e3d 100644
--- a/src/__tests__/shape.test.ts
+++ b/src/__tests__/shape.test.ts
@@ -1,93 +1,97 @@
-import { describe, it, expect } from 'vitest';
+import { expect, test } from 'vitest';
 
-import { Conrec } from '..';
+import { Conrec } from '../index.ts';
 
-describe('shape', () => {
-  it('square', () => {
-    const matrix = parse(`
-      00000
-      01110
-      01110
-      01110
-      00000
-    `);
+test('square', () => {
+  const matrix = parse(`
+    00000
+    01110
+    01110
+    01110
+    00000
+  `);
 
-    const conrec = new Conrec(matrix);
-    const { contours, timeout } = conrec.drawContour({
-      contourDrawer: 'shape',
-      levels: [0.5],
-    });
-    expect(timeout).toBeFalsy();
-    expect(contours[0].lines).toHaveLength(25);
+  const conrec = new Conrec(matrix);
+  const { contours, timeout } = conrec.drawContour({
+    contourDrawer: 'shape',
+    levels: [0.5],
   });
 
-  it('2 squares', () => {
-    const matrix = parse(`
-      000000000
-      011101110
-      011101110
-      011101110
-      000000000
-    `);
+  expect(timeout).toBe(false);
+  expect(contours[0].lines).toHaveLength(25);
+});
 
-    const conrec = new Conrec(matrix);
-    const { contours, timeout } = conrec.drawContour({
-      contourDrawer: 'shape',
-      levels: [0.5],
-    });
+test('2 squares', () => {
+  const matrix = parse(`
+    000000000
+    011101110
+    011101110
+    011101110
+    000000000
+  `);
 
-    expect(timeout).toBeFalsy();
-    expect(contours[0].lines).toHaveLength(25);
+  const conrec = new Conrec(matrix);
+  const { contours, timeout } = conrec.drawContour({
+    contourDrawer: 'shape',
+    levels: [0.5],
   });
 
-  it('2 diagonal squares', () => {
-    const matrix = parse(`
-      000000000
-      011100000
-      011100000
-      011100000
-      000011100
-      000011100
-      000011100
-      000000000
-    `);
+  expect(timeout).toBe(false);
+  expect(contours[0].lines).toHaveLength(25);
+});
+
+test('2 diagonal squares', () => {
+  const matrix = parse(`
+    000000000
+    011100000
+    011100000
+    011100000
+    000011100
+    000011100
+    000011100
+    000000000
+  `);
 
-    const conrec = new Conrec(matrix);
-    const { contours, timeout } = conrec.drawContour({
-      contourDrawer: 'shape',
-      levels: [0.5],
-    });
-    expect(timeout).toBeFalsy();
-    expect(contours[0].lines).toHaveLength(49);
+  const conrec = new Conrec(matrix);
+  const { contours, timeout } = conrec.drawContour({
+    contourDrawer: 'shape',
+    levels: [0.5],
   });
-  it('square float matrix', () => {
-    const matrix: Float64Array[] = [
-      Float64Array.from([0, 0, 0.1, 0, 0]),
-      Float64Array.from([0, 0.9, 1, 1, 0]),
-      Float64Array.from([0, 1, 1, 1, 0]),
-      Float64Array.from([0, 1, 1, 0.8, 0]),
-      Float64Array.from([0, 0, 0, 0, 0.1]),
-    ];
 
-    const conrec = new Conrec(matrix);
-    const { contours, timeout } = conrec.drawContour({
-      contourDrawer: 'shape',
-      levels: [0.5],
-    });
-    expect(timeout).toBeFalsy();
-    expect(contours[0].lines).toHaveLength(29);
+  expect(timeout).toBe(false);
+  expect(contours[0].lines).toHaveLength(49);
+});
+
+test('square float matrix', () => {
+  const matrix: Float64Array[] = [
+    Float64Array.from([0, 0, 0.1, 0, 0]),
+    Float64Array.from([0, 0.9, 1, 1, 0]),
+    Float64Array.from([0, 1, 1, 1, 0]),
+    Float64Array.from([0, 1, 1, 0.8, 0]),
+    Float64Array.from([0, 0, 0, 0, 0.1]),
+  ];
+
+  const conrec = new Conrec(matrix);
+  const { contours, timeout } = conrec.drawContour({
+    contourDrawer: 'shape',
+    levels: [0.5],
   });
+
+  expect(timeout).toBe(false);
+  expect(contours[0].lines).toHaveLength(29);
 });
 
 function parse(string: string) {
   const lines = string
     .split(/\r?\n/)
     .map((line) => line.trim())
-    .filter((line) => line);
+    .filter(Boolean);
 
   const matrix: number[][] = [];
   for (const line of lines) {
-    matrix.push(line.split('').map((value: string) => parseInt(value, 10)));
+    matrix.push(
+      line.split('').map((value: string) => Number.parseInt(value, 10)),
+    );
   }
   return matrix;
 }

From 16a44caed341377de364a52ac42891e69cec9e5e Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Fri, 17 Apr 2026 19:29:48 +0200
Subject: [PATCH 10/11] chore: migrate benchmark script to TypeScript

---
 benchmark/contour.mjs | 58 -------------------------------------------
 benchmark/contour.ts  | 54 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 54 insertions(+), 58 deletions(-)
 delete mode 100644 benchmark/contour.mjs
 create mode 100644 benchmark/contour.ts

diff --git a/benchmark/contour.mjs b/benchmark/contour.mjs
deleted file mode 100644
index fd07504..0000000
--- a/benchmark/contour.mjs
+++ /dev/null
@@ -1,58 +0,0 @@
-// node --cpu-prof benchmark/contour.mjs
-
-import { readFileSync } from 'fs';
-import { join } from 'path'
-
-import { convert } from 'jcampconverter';
-
-import { Conrec } from '../lib/index.js';
-
-const __dirname = new URL('.', import.meta.url).pathname;
-
-const data = readFileSync(join(__dirname, '../src/__tests__/data/zhmbc_0.jdx'), 'utf8');
-const parsed = convert(data, { noContour: true }).flatten[0];
-
-for (let i = 0; i < parsed.minMax.z.length; i++) {
-  parsed.minMax.z[i] = Float64Array.from(parsed.minMax.z[i])
-}
-
-console.log('Size: ', parsed.minMax.z[0].length, 'x', parsed.minMax.z.length);
-
-const conrec = new Conrec(parsed.minMax.z);
-
-let levels = [];
-for (let level = -1e4; level <= 1e4; level += 2e2) {
-  levels.push(level);
-}
-
-console.log(`We calculate ${levels.length} levels close to zero to be close to noise`);
-
-let result;
-
-if (true) {
-  console.time('basic');
-
-  result = (conrec.drawContour({
-    contourDrawer: 'basic',
-    levels,
-    timeout: 100000,
-  }));
-  console.log(result.contours.length)
-  console.timeEnd('basic');
-  const totalNumberContours = result.contours.reduce((acc, contour) => acc + contour.lines.length, 0);
-  console.log({ totalNumberContours })
-} else {
-  console.time('shape');
-  result = conrec.drawContour({
-    contourDrawer: 'shape',
-    levels,
-    timeout: 1000000,
-  });
-  console.timeEnd('shape');
-  // console.log(result)
-  console.log(result.contours.length)
-  const totalNumberContours = result.contours.reduce((acc, contour) => acc + contour.lines.length, 0);
-  console.log({ totalNumberContours })
-
-}
-
diff --git a/benchmark/contour.ts b/benchmark/contour.ts
new file mode 100644
index 0000000..3023ae2
--- /dev/null
+++ b/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 });

From 9ebce1b5572364f6388dc2c72afcf09d153a93ba Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Tue, 21 Apr 2026 10:20:23 +0200
Subject: [PATCH 11/11] chore: remove outdated comment

---
 src/calculateContour.ts | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/src/calculateContour.ts b/src/calculateContour.ts
index 69be7c8..a8f07b1 100644
--- a/src/calculateContour.ts
+++ b/src/calculateContour.ts
@@ -206,13 +206,7 @@ export function calculateContour(
       }
       const dmin = Math.min(min1, min2);
       const dmax = Math.max(max1, max2);
-      // Ternary operator is now much slower: https://jsbench.me/d5l0dh502g
 
-      //const dmin = (min1 + min2 - Math.abs(min1 - min2)) / 2;
-      //const dmax = (max1 + max2 + Math.abs(max1 - max2)) / 2;
-
-      //let dmin = min1 > min2 ? min2 : min1;
-      //let dmax = max1 > max2 ? max1 : max2;
       if (dmax >= z0 && dmin <= znc1) {
         for (let k = 0; k < nc; k++) {
           if (z[k] >= dmin && z[k] <= dmax) {