fix: update sdf-parser to v9

eslint.config.js

@@ -16,4 +16,10 @@ export default defineConfig(
       'jsdoc/no-defaults': 'off', // this would remove our default values https://github.com/gajus/eslint-plugin-jsdoc/blob/main/docs/rules/no-defaults.md#readme
     },
   },
+  {
+    files: ['examples/**'],
+    rules: {
+      'no-console': 'off',
+    },
+  },
 );

package.json

@@ -22,11 +22,11 @@
     "build": "npm run tsc && cheminfo-build --entry lib/index.js --root OCLUtils",
     "check-types": "tsc --noEmit",
     "clean": "rimraf coverage lib",
-    "eslint": "eslint src",
-    "eslint-fix": "eslint src --fix",
+    "eslint": "eslint .",
+    "eslint-fix": "eslint . --fix",
     "prepack": "npm run tsc",
-    "prettier": "prettier --check src",
-    "prettier-write": "prettier --write src",
+    "prettier": "prettier --check .",
+    "prettier-write": "prettier --write .",
     "test": "npm run test-only && npm run check-types && npm run eslint && npm run prettier && npm run verify-build",
     "test-only": "vitest run --coverage",
     "tsc": "npm run clean && npm run tsc-build",
@@ -36,31 +36,31 @@
   "dependencies": {
     "atom-sorter": "^2.2.1",
     "ensure-string": "^2.0.0",
-    "get-value": "^4.0.1",
+    "get-value": "^4.1.0",
     "ml-floyd-warshall": "^3.0.1",
-    "ml-matrix": "^6.12.2",
-    "papaparse": "^5.5.3",
-    "sdf-parser": "^8.0.0"
+    "ml-matrix": "^6.13.0",
+    "papaparse": "^5.5.4",
+    "sdf-parser": "^9.0.0"
   },
   "peerDependencies": {
     "openchemlib": ">=9.20.1"
   },
   "devDependencies": {
-    "@types/node": "^25.6.0",
-    "@vitest/coverage-v8": "^4.1.5",
+    "@types/node": "^26.0.1",
+    "@vitest/coverage-istanbul": "^4.1.9",
     "@zakodium/tsconfig": "^1.0.5",
     "cheminfo-build": "^1.3.2",
     "cheminfo-types": "^1.15.0",
     "eslint": "^9.39.2",
-    "eslint-config-cheminfo-typescript": "^22.0.0",
+    "eslint-config-cheminfo-typescript": "^22.1.0",
     "fifo-logger": "^2.0.1",
-    "globals": "^17.6.0",
+    "globals": "^17.7.0",
     "mf-parser": "^3.9.1",
-    "openchemlib": "^9.22.1",
-    "prettier": "^3.8.3",
+    "openchemlib": "^9.23.0",
+    "prettier": "^3.9.1",
     "rimraf": "^6.1.3",
-    "typescript": "^5.9.3",
-    "vitest": "^4.1.5"
+    "typescript": "^6.0.3",
+    "vitest": "^4.1.9"
   },
   "repository": {
     "type": "git",

src/reaction/__tests__/applyReactions.test.js

@@ -1,3 +1,5 @@
+/* eslint-disable unicorn/better-dom-traversing */
+
 import { Molecule } from 'openchemlib';
 import { describe, expect, it } from 'vitest';
 

src/topic/__tests__/TopicMolecule.test.js

@@ -498,7 +498,7 @@ function extratMapNo(molfile) {
   const lines = molfile.split(/\r?\n/).slice(4);
   const atomMapNos = [];
   for (let line of lines) {
-    const atomMapNo = line.split(/\s+/)[14];
+    const atomMapNo = line.split(/\s+/, 15)[14];
     if (atomMapNo) {
       atomMapNos.push(Number(atomMapNo));
     }

src/util/applyFragmentLabels.ts

@@ -14,11 +14,7 @@ export interface ApplyFragmentLabelsOptions {
    * @default 'overlapping'
    */
   algorithm?:
-    | 'firstMatch'
-    | 'separated'
-    | 'overlapping'
-    | 'rigorous'
-    | 'unique';
+    'firstMatch' | 'separated' | 'overlapping' | 'rigorous' | 'unique';
   prefix?: string;
   suffix?: string;
 }

tsconfig.build.json

@@ -1,5 +1,8 @@
 {
   "extends": "./tsconfig.json",
   "include": ["src"],
-  "exclude": ["**/__tests__", "**/*.test.*"]
+  "exclude": ["**/__tests__", "**/*.test.*"],
+  "compilerOptions": {
+    "rootDir": "src"
+  }
 }

tsconfig.json

@@ -4,8 +4,7 @@
     "types": ["node"],
     "allowJs": true,
     "noUncheckedIndexedAccess": false,
-    "rootDir": "src",
     "outDir": "lib"
   },
-  "include": ["src"]
+  "include": ["src", "vite*.ts"]
 }

vitest.config.ts

@@ -3,11 +3,13 @@ import { defineConfig } from 'vitest/config';
 export default defineConfig({
   test: {
     coverage: {
-      include: ['src/**/*.{js,ts}'],
-      provider: 'v8',
+      provider: 'istanbul',
+      exclude: ['**/__tests__/**'],
+      include: ['src/**'],
     },
     snapshotFormat: {
       maxOutputLength: Number.MAX_SAFE_INTEGER,
     },
+    include: ['./src/**/*.test.js', './src/**/*.test.ts'],
   },
 });