Bump deps

Author: cmdcolin

.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

README.md

@@ -2,7 +2,7 @@
 [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/bgzf-filehandle/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/bgzf-filehandle/branch/master)
 [![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/bgzf-filehandle/push.yml?branch=master)](https://github.com/GMOD/bgzf-filehandle/actions)
 
-Transparently read [indexed block-gzipped (BGZF)](http://www.htslib.org/doc/bgzip.html) files, such as those created by bgzip, using coordinates from the uncompressed file. The module is used in @gmod/indexedfasta to read bgzip-indexed fasta files (with gzi index, fai index, and fa). 
+Transparently read [indexed block-gzipped (BGZF)](http://www.htslib.org/doc/bgzip.html) files, such as those created by bgzip, using coordinates from the uncompressed file. The module is used in @gmod/indexedfasta to read bgzip-indexed fasta files (with gzi index, fai index, and fa).
 
 Users can also use the `unzip` function to unzip bgzip files whole (which pako has trouble with natively)
 

eslint.config.mjs

@@ -0,0 +1,56 @@
+import prettier from 'eslint-plugin-prettier'
+import typescriptEslint from '@typescript-eslint/eslint-plugin'
+import tsParser from '@typescript-eslint/parser'
+import path from 'node:path'
+import { fileURLToPath } from 'node:url'
+import js from '@eslint/js'
+import { FlatCompat } from '@eslint/eslintrc'
+
+const __filename = fileURLToPath(import.meta.url)
+const __dirname = path.dirname(__filename)
+const compat = new FlatCompat({
+  baseDirectory: __dirname,
+  recommendedConfig: js.configs.recommended,
+  allConfig: js.configs.all,
+})
+
+export default [
+  ...compat.extends(
+    'plugin:@typescript-eslint/recommended',
+    'plugin:@typescript-eslint/recommended-type-checked',
+    'plugin:@typescript-eslint/stylistic-type-checked',
+    'plugin:prettier/recommended',
+    'plugin:unicorn/recommended',
+  ),
+  {
+    plugins: {
+      prettier,
+      '@typescript-eslint': typescriptEslint,
+    },
+
+    languageOptions: {
+      parser: tsParser,
+      ecmaVersion: 5,
+      sourceType: 'script',
+
+      parserOptions: {
+        project: './tsconfig.lint.json',
+      },
+    },
+
+    rules: {
+      'no-underscore-dangle': 0,
+      curly: 'error',
+      'unicorn/prefer-node-protocol': 0,
+      'unicorn/numeric-separators-style': 0,
+      'unicorn/prevent-abbreviations': 0,
+      'unicorn/no-new-array': 0,
+      'unicorn/filename-case': 0,
+      '@typescript-eslint/restrict-template-expressions': 0,
+      '@typescript-eslint/no-explicit-any': 0,
+      '@typescript-eslint/explicit-module-boundary-types': 0,
+      '@typescript-eslint/ban-ts-comment': 0,
+      semi: ['error', 'never'],
+    },
+  },
+]

jest.config.js

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

package.json

@@ -21,7 +21,7 @@
   ],
   "scripts": {
     "test": "jest",
-    "lint": "eslint src test",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src test",
     "clean": "rimraf dist esm",
     "prebuild": "npm run clean",
     "build:esm": "tsc --target es2018 --outDir esm",
@@ -44,17 +44,18 @@
     "@types/es6-promisify": "^6.0.0",
     "@types/jest": "^29.5.2",
     "@types/long": "^4.0.1",
-    "@types/node": "^18.11.16",
+    "@types/node": "^20.14.11",
     "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^5.59.9",
-    "@typescript-eslint/parser": "^5.59.9",
-    "eslint": "^8.42.0",
-    "eslint-config-prettier": "^8.8.0",
+    "@typescript-eslint/eslint-plugin": "^7.7.1",
+    "@typescript-eslint/parser": "^7.7.1",
+    "eslint": "^9.7.0",
+    "eslint-config-prettier": "^9.1.0",
     "eslint-plugin-import": "^2.27.5",
-    "eslint-plugin-prettier": "^4.2.1",
+    "eslint-plugin-prettier": "^5.1.3",
+    "eslint-plugin-unicorn": "^54.0.0",
     "jest": "^29.5.0",
-    "prettier": "^2.8.8",
-    "rimraf": "^5.0.1",
+    "prettier": "^3.2.5",
+    "rimraf": "^6.0.1",
     "ts-jest": "^29.1.0",
     "typescript": "^5.1.3"
   },

src/bgzFilehandle.ts

@@ -50,7 +50,11 @@ export default class BgzFilehandle {
   async getUncompressedFileSize() {
     // read the last block's ISIZE (see gzip RFC),
     // and add it to its uncompressedPosition
-    const [, uncompressedPosition] = await this.gzi.getLastBlock()
+    const ret = await this.gzi.getLastBlock()
+    if (!ret) {
+      throw new Error('no blocks')
+    }
+    const [, uncompressedPosition] = ret
 
     const { size } = await this.filehandle.stat()
 
@@ -72,7 +76,8 @@ export default class BgzFilehandle {
   ) {
     let next = nextCompressedPosition
     if (!next) {
-      next = (await this.filehandle.stat()).size
+      const stat = await this.filehandle.stat()
+      next = stat.size
     }
 
     // read the compressed data into the block buffer
@@ -90,7 +95,7 @@ export default class BgzFilehandle {
       blockBuffer.slice(0, blockCompressedLength),
     )
 
-    return unzippedBuffer as Buffer
+    return unzippedBuffer
   }
 
   async read(buf: Buffer, offset: number, length: number, position: number) {
@@ -108,7 +113,6 @@ export default class BgzFilehandle {
       blockNum < blockPositions.length - 1;
       blockNum += 1
     ) {
-      // eslint-disable-next-line no-await-in-loop
       const uncompressedBuffer = await this._readAndUncompressBlock(
         blockBuffer,
         blockPositions[blockNum],

src/gziIndex.ts

@@ -8,7 +8,7 @@ const UNCOMPRESSED_POSITION = 1
 export default class GziIndex {
   filehandle: GenericFilehandle
 
-  index?: any
+  index?: Promise<[number, number][]>
 
   constructor({
     filehandle,
@@ -46,15 +46,15 @@ export default class GziIndex {
     return this.index
   }
 
-  async _readIndex() {
+  async _readIndex(): Promise<[number, number][]> {
     let buf = Buffer.allocUnsafe(8)
     await this.filehandle.read(buf, 0, 8, 0)
     const numEntries = this._readLongWithOverflow(buf, 0, true)
     if (!numEntries) {
       return [[0, 0]]
     }
 
-    const entries = new Array(numEntries + 1)
+    const entries = new Array(numEntries + 1) as [number, number][]
     entries[0] = [0, 0]
 
     // TODO rewrite this to make an index-index that stays in memory
@@ -81,10 +81,7 @@ export default class GziIndex {
 
   async getLastBlock() {
     const entries = await this._getIndex()
-    if (!entries.length) {
-      return undefined
-    }
-    return entries[entries.length - 1]
+    return entries.at(-1)!
   }
 
   async getRelevantBlocksForRead(length: number, position: number) {
@@ -93,11 +90,11 @@ export default class GziIndex {
       return []
     }
     const entries = await this._getIndex()
-    const relevant = []
+    const relevant = [] as [number, number][]
 
     // binary search to find the block that the
     // read starts in and extend forward from that
-    const compare = (entry: any, nextEntry: any) => {
+    const compare = (entry: number[], nextEntry: number[]) => {
       const uncompressedPosition = entry[UNCOMPRESSED_POSITION]
       const nextUncompressedPosition = nextEntry
         ? nextEntry[UNCOMPRESSED_POSITION]
@@ -144,9 +141,9 @@ export default class GziIndex {
         break
       }
     }
-    if (relevant[relevant.length - 1][UNCOMPRESSED_POSITION] < endPosition) {
-      relevant.push([])
-    }
+    // if (relevant.at(-1)![UNCOMPRESSED_POSITION] < endPosition) {
+    //   relevant.push([])
+    // }
     return relevant
   }
 }

src/index.ts

@@ -1,4 +1,2 @@
-import BgzfFilehandle from './bgzFilehandle'
-import { unzip, unzipChunk, unzipChunkSlice } from './unzip'
-
-export { BgzfFilehandle, unzip, unzipChunk, unzipChunkSlice }
+export { default as BgzfFilehandle } from './bgzFilehandle'
+export { unzip, unzipChunkSlice, unzipChunk } from './unzip'

src/unzip-pako.ts

@@ -12,9 +12,12 @@ interface Chunk {
 }
 
 // browserify-zlib, which is the zlib shim used by default in webpacked code,
-// does not properly uncompress bgzf chunks that contain more than
-// one bgzf block, so export an unzip function that uses pako directly
-// if we are running in a browser.
+// does not properly uncompress bgzf chunks that contain more than one bgzf
+// block, so export an unzip function that uses pako directly if we are running
+// in a browser.
+//
+//
+// eslint-disable-next-line @typescript-eslint/require-await
 async function unzip(inputData: Buffer) {
   try {
     let strm
@@ -28,15 +31,18 @@ async function unzip(inputData: Buffer) {
       inflator = new Inflate()
       //@ts-ignore
       ;({ strm } = inflator)
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-argument
       inflator.push(remainingInput, Z_SYNC_FLUSH)
       if (inflator.err) {
         throw new Error(inflator.msg)
       }
 
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
       pos += strm.next_in
       chunks[i] = inflator.result as Uint8Array
       totalSize += chunks[i].length
       i += 1
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
     } while (strm.avail_in)
 
     const result = new Uint8Array(totalSize)
@@ -45,20 +51,21 @@ async function unzip(inputData: Buffer) {
       offset += chunks[i].length
     }
     return Buffer.from(result)
-  } catch (e) {
+  } catch (error) {
     //cleanup error message
-    if (`${e}`.match(/incorrect header check/)) {
+    if (/incorrect header check/.test(`${error}`)) {
       throw new Error(
         'problem decompressing block: incorrect gzip header check',
       )
     }
-    throw e
+    throw error
   }
 }
 
-// similar to pakounzip, except it does extra counting
-// to return the positions of compressed and decompressed
-// data offsets
+// similar to pakounzip, except it does extra counting to return the positions
+// of compressed and decompressed data offsets
+//
+// eslint-disable-next-line @typescript-eslint/require-await
 async function unzipChunk(inputData: Buffer) {
   try {
     let strm
@@ -72,6 +79,7 @@ async function unzipChunk(inputData: Buffer) {
       const inflator = new Inflate()
       // @ts-ignore
       ;({ strm } = inflator)
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-argument
       inflator.push(remainingInput, Z_SYNC_FLUSH)
       if (inflator.err) {
         throw new Error(inflator.msg)
@@ -83,25 +91,29 @@ async function unzipChunk(inputData: Buffer) {
       cpositions.push(cpos)
       dpositions.push(dpos)
 
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
       cpos += strm.next_in
       dpos += buffer.length
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
     } while (strm.avail_in)
 
     const buffer = Buffer.concat(blocks)
     return { buffer, cpositions, dpositions }
-  } catch (e) {
+  } catch (error) {
     //cleanup error message
-    if (`${e}`.match(/incorrect header check/)) {
+    if (/incorrect header check/.test(`${error}`)) {
       throw new Error(
         'problem decompressing block: incorrect gzip header check',
       )
     }
-    throw e
+    throw error
   }
 }
 
 // similar to unzipChunk above but slices (0,minv.dataPosition) and
 // (maxv.dataPosition,end) off
+//
+// eslint-disable-next-line @typescript-eslint/require-await
 async function unzipChunkSlice(inputData: Buffer, chunk: Chunk) {
   try {
     let strm
@@ -119,6 +131,7 @@ async function unzipChunkSlice(inputData: Buffer, chunk: Chunk) {
       const inflator = new Inflate()
       // @ts-ignore
       ;({ strm } = inflator)
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-argument
       inflator.push(remainingInput, Z_SYNC_FLUSH)
       if (inflator.err) {
         throw new Error(inflator.msg)
@@ -136,6 +149,7 @@ async function unzipChunkSlice(inputData: Buffer, chunk: Chunk) {
         len = chunks[0].length
       }
       const origCpos = cpos
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
       cpos += strm.next_in
       dpos += len
 
@@ -158,6 +172,7 @@ async function unzipChunkSlice(inputData: Buffer, chunk: Chunk) {
       }
       totalSize += chunks[i].length
       i++
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
     } while (strm.avail_in)
 
     const result = new Uint8Array(totalSize)
@@ -168,14 +183,14 @@ async function unzipChunkSlice(inputData: Buffer, chunk: Chunk) {
     const buffer = Buffer.from(result)
 
     return { buffer, cpositions, dpositions }
-  } catch (e) {
+  } catch (error) {
     //cleanup error message
-    if (`${e}`.match(/incorrect header check/)) {
+    if (/incorrect header check/.test(`${error}`)) {
       throw new Error(
         'problem decompressing block: incorrect gzip header check',
       )
     }
-    throw e
+    throw error
   }
 }