Merge origin/master

.github/workflows/push.yml

@@ -4,14 +4,14 @@ on: push
 
 jobs:
   test:
-    name: Lint, build, and test on node 14.x and ubuntu-latest
+    name: Lint, build, and test on node 20.x and ubuntu-latest
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Use Node.js 14.x
-        uses: actions/setup-node@v1
+      - uses: actions/checkout@v4
+      - name: Use Node.js 20.x
+        uses: actions/setup-node@v4
         with:
-          node-version: 14.x
+          node-version: 20.x
       - name: Install deps (with cache)
         uses: bahmutov/npm-install@v1
       - name: Lint codebase

CHANGELOG.md

@@ -1,19 +1,13 @@
 ## [5.0.10](https://github.com/GMOD/vcf-js/compare/v5.0.9...v5.0.10) (2022-12-17)
 
-
-
 - Use es2015 for nodejs build
 
 ## [5.0.9](https://github.com/GMOD/vcf-js/compare/v5.0.8...v5.0.9) (2022-11-23)
 
-
-
 - Fix erroneous parsing of symbolic alleles as breakends
 
 ## [5.0.8](https://github.com/GMOD/vcf-js/compare/v5.0.7...v5.0.8) (2022-11-20)
 
-
-
 - Parse single breakends and large insertion shorthand notation (#95)
 
 <a name="5.0.7"></a>

eslint.config.mjs

@@ -0,0 +1,46 @@
+import eslint from '@eslint/js'
+import tseslint from 'typescript-eslint'
+
+export default tseslint.config(
+  {
+    ignores: ['esm/**/*', 'dist/**/*', '*.js', '*.mjs', 'example/*'],
+  },
+  {
+    languageOptions: {
+      parserOptions: {
+        project: ['./tsconfig.lint.json'],
+        tsconfigRootDir: import.meta.dirname,
+      },
+    },
+  },
+  eslint.configs.recommended,
+  ...tseslint.configs.recommended,
+  ...tseslint.configs.stylisticTypeChecked,
+  ...tseslint.configs.strictTypeChecked,
+  {
+    rules: {
+      curly: 'error',
+
+      '@typescript-eslint/no-unused-vars': [
+        'warn',
+        {
+          argsIgnorePattern: '^_',
+          caughtErrors: 'none',
+          ignoreRestSiblings: true,
+        },
+      ],
+
+      '@typescript-eslint/ban-ts-comment': 'off',
+      '@typescript-eslint/no-this-alias': 'off',
+      '@typescript-eslint/no-unsafe-member-access': 'off',
+      '@typescript-eslint/no-unsafe-argument': 'off',
+      '@typescript-eslint/no-explicit-any': 'off',
+      '@typescript-eslint/no-unsafe-assignment': 'off',
+      '@typescript-eslint/no-unsafe-call': 'off',
+      '@typescript-eslint/no-unsafe-return': 'off',
+      '@typescript-eslint/no-non-null-assertion': 'off',
+      '@typescript-eslint/restrict-template-expressions': 'off',
+      '@typescript-eslint/no-base-to-string': 'off',
+    },
+  },
+)

jest.config.js

@@ -2,4 +2,4 @@
 module.exports = {
   preset: 'ts-jest',
   testEnvironment: 'node',
-};
+}

package.json

@@ -24,35 +24,40 @@
     "node": ">=6"
   },
   "scripts": {
-    "test": "jest",
-    "coverage": "npm test -- --coverage",
-    "lint": "eslint . --ext .ts,.js",
+    "test": "vitest",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "docs": "documentation readme src/parse.ts --section=API  --shallow",
     "postdocs": "prettier --write README.md",
     "clean": "rimraf dist esm",
     "build:esm": "tsc --module esnext --outDir esm",
     "build:es5": "tsc --module commonjs --outDir dist",
     "build": "npm run build:esm && npm run build:es5",
     "prebuild": "npm run clean && npm run lint",
-    "preversion": "npm run lint && npm test && npm run build",
+    "preversion": "npm run lint && npm test --run && npm run build",
     "version": "standard-changelog && git add CHANGELOG.md",
     "postversion": "git push --follow-tags"
   },
   "devDependencies": {
-    "@babel/core": "^7.21.3",
-    "@types/jest": "^29.5.0",
-    "@typescript-eslint/eslint-plugin": "^5.55.0",
-    "@typescript-eslint/parser": "^5.55.0",
+    "@babel/core": "^7.20.5",
+    "@eslint/eslintrc": "^3.1.0",
+    "@eslint/js": "^9.7.0",
+    "@types/jest": "^29.2.4",
+    "@typescript-eslint/eslint-plugin": "^8.8.1",
+    "@typescript-eslint/parser": "^8.8.1",
+    "@vitest/coverage-v8": "^2.1.3",
     "documentation": "^14.0.1",
-    "eslint": "^8.36.0",
-    "eslint-config-prettier": "^8.7.0",
-    "eslint-plugin-prettier": "^4.0.0",
-    "jest": "^29.5.0",
-    "prettier": "^2.8.4",
-    "rimraf": "^4.4.0",
-    "standard-changelog": "^2.0.27",
-    "ts-jest": "^29.0.5",
-    "typescript": "^5.0.2"
+    "eslint": "^9.7.0",
+    "eslint-config-prettier": "^9.1.0",
+    "eslint-plugin-prettier": "^5.1.3",
+    "eslint-plugin-unicorn": "^56.0.0",
+    "jest": "^29.3.1",
+    "prettier": "^3.2.4",
+    "rimraf": "^6.0.1",
+    "standard-changelog": "^6.0.0",
+    "ts-jest": "^29.1.2",
+    "typescript": "^5.3.3",
+    "typescript-eslint": "^8.8.1",
+    "vitest": "^2.1.3"
   },
   "keywords": [
     "vcf",

src/index.ts

@@ -15,8 +15,7 @@ export function parseBreakend(breakendString: string): Breakend | undefined {
     let Join
     let Replacement
     let MatePosition
-    for (let i = 0; i < tokens.length; i += 1) {
-      const tok = tokens[i]
+    for (const tok of tokens) {
       if (tok) {
         if (tok.includes(':')) {
           // this is the remote location
@@ -45,32 +44,32 @@ export function parseBreakend(breakendString: string): Breakend | undefined {
         SingleBreakend: true,
         Replacement: breakendString.slice(0, breakendString.length - 1),
       }
-    } else if (breakendString[0] === '<') {
-      const res = breakendString.match('<(.*)>(.*)')
+    } else if (breakendString.startsWith('<')) {
+      const res = /<(.*)>(.*)/.exec(breakendString)
       if (!res) {
         throw new Error(`failed to parse ${breakendString}`)
       }
-      const Replacement = res?.[2]
+      const Replacement = res[2]
       return Replacement
         ? {
             Join: 'left',
             Replacement,
             MateDirection: 'right',
-            MatePosition: `<${res?.[1]}>:1`,
+            MatePosition: `<${res[1]!}>:1`,
           }
         : undefined
     } else if (breakendString.includes('<')) {
-      const res = breakendString.match('(.*)<(.*)>')
+      const res = /(.*)<(.*)>/.exec(breakendString)
       if (!res) {
         throw new Error(`failed to parse ${breakendString}`)
       }
-      const Replacement = res?.[1]
+      const Replacement = res[1]
       return Replacement
         ? {
             Join: 'right',
             Replacement,
             MateDirection: 'right',
-            MatePosition: `<${res?.[2]}>:1`,
+            MatePosition: `<${res[2]!}>:1`,
           }
         : undefined
     }