Add support for single file hubs

.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@v3
+      - name: Use Node.js 20.x
+        uses: actions/setup-node@v3
         with:
-          node-version: 14.x
+          node-version: 20.x
       - name: Install deps (with cache)
         uses: bahmutov/npm-install@v1
       - name: Lint codebase

README.md

@@ -12,7 +12,7 @@ read and write UCSC track and assembly hub files in node or the browser
 
 Read about hub.txt, genomes.txt, and trackDb.txt files here: <https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html>
 
-Files are essentially JavaScript `Map`s. A hub.txt file is a map with th keys as the first word in each line and the value as the rest of the line, like this:
+Files are essentially JavaScript `Map`s. A hub.txt file is a map with keys as the first word in each line and the value as the rest of the line, like this:
 
     Map {
       "hub" => "UCSCHub",
@@ -66,7 +66,7 @@ values of the first line of each section and the value is a `Map` of the lines i
       },
     }
 
-Example usage:
+Example usage for a "standard" multi-file hub:
 
 ```javascript
 const fs = require('fs')
@@ -85,6 +85,24 @@ console.log(trackDbFile.get('dnaseSignal').get('shortLabel'))
 // ↳ DNAse Signal
 ```
 
+Example usage for a single-file hub:
+
+```javascript
+const fs = require('fs')
+const { SingleFileHub } = require('@gmod/ucsc-hub')
+
+const hubFile = new HubFile(fs.readFileSync('hub.txt', 'utf8'))
+console.log(hubFile.get('genomesFile'))
+// ↳ genomes.txt
+
+const genomesFile = new GenomesFile(fs.readFileSync('genomes.txt', 'utf8'))
+console.log(genomesFile.get('hg19').get('trackDb'))
+// ↳ hg19/trackDb.txt
+
+const trackDbFile = new TrackDbFile(fs.readFileSync('hg19/trackDb.txt', 'utf8'))
+console.log(trackDbFile.get('dnaseSignal').get('shortLabel'))
+```
+
 ## API
 
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
@@ -117,10 +135,14 @@ console.log(trackDbFile.get('dnaseSignal').get('shortLabel'))
         *   [Parameters](#parameters-9)
     *   [clear](#clear-1)
     *   [toString](#tostring-1)
-*   [TrackDbFile](#trackdbfile)
+*   [SingleFileHub](#singlefilehub)
     *   [Parameters](#parameters-10)
+    *   [genome](#genome)
+    *   [trackDbs](#trackdbs)
+*   [TrackDbFile](#trackdbfile)
+    *   [Parameters](#parameters-11)
     *   [settings](#settings)
-        *   [Parameters](#parameters-11)
+        *   [Parameters](#parameters-12)
 
 ### GenomesFile
 
@@ -170,7 +192,7 @@ as it performs more validity checks than using `set()`.
 *   `raFile` **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String) | [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)** An ra file, either as a single
     string or an array of strings with one stanza per entry. Supports both LF
     and CRLF line terminators. (optional, default `[]`)
-*   `options` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**  (optional, default `{checkIndent:true}`)
+*   `options` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**&#x20;
 
     *   `options.checkIndent` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** \[true] - Check if a the stanzas within
         the file are indented consistently and keep track of the indentation
@@ -246,7 +268,7 @@ than using `set()`.
 *   `stanza` **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String) | [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)** An ra file stanza, either as a
     string or a array of strings with one line per entry. Supports both LF and
     CRLF line terminators. (optional, default `[]`)
-*   `options` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**  (optional, default `{checkIndent:true}`)
+*   `options` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**&#x20;
 
     *   `options.checkIndent` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** \[true] - Check if a stanza is indented
         consistently and keep track of the indentation
@@ -314,6 +336,34 @@ as a single line and all comments will have the same indentations as the
 rest of the stanza. Comments between joined lines will move before that
 line.
 
+### SingleFileHub
+
+**Extends RaFile**
+
+Class representing a "single-file" hub.txt file that contains all the sections
+of a hub in a single file.
+
+#### Parameters
+
+*   `hubText` **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String) | [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)** A hub.txt file as a string (optional, default `[]`)
+
+<!---->
+
+*   Throws **[Error](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Error)** Throws if the first line of the hub.txt file doesn't start
+    with "genome \<genome\_name>" or if it has invalid entries
+
+#### genome
+
+a GenomesFile object for the hub's genome section
+
+Type: [GenomesFile](#genomesfile)
+
+#### trackDbs
+
+an array of TrackDbFile objects for the hub's trackDb sections
+
+Type: [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[TrackDbFile](#trackdbfile)>
+
 ### TrackDbFile
 
 **Extends RaFile**
@@ -323,6 +373,7 @@ Class representing a genomes.txt file.
 #### Parameters
 
 *   `trackDbFile` **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String) | [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)** A trackDb.txt file as a string (optional, default `[]`)
+*   `options` **any?**&#x20;
 
 <!---->
 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/ucsc-hub",
-  "version": "0.1.7",
+  "version": "0.2.0",
   "description": "Read and write UCSC track and assembly hub files in node or the browser",
   "license": "MIT",
   "repository": "github:GMOD/ucsc-hub-js",
@@ -18,15 +18,13 @@
   ],
   "scripts": {
     "test": "jest --rootDir=./src",
-    "coverage": "npm test -- --coverage",
-    "postcoverage": "opn coverage/lcov-report/index.html",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts src",
     "docs": "documentation readme src --section=API",
     "postdocs": "git add README.md",
     "clean": "rimraf dist esm",
     "prebuild": "npm run docs && npm run clean",
     "build:esm": "tsc --target es2018 --outDir esm",
-    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
+    "build:es5": "tsc --target es2018 --module commonjs --outDir dist",
     "build": "npm run build:esm && npm run build:es5",
     "preversion": "npm run lint && npm test && npm run build",
     "postversion": "git push --follow-tags",
@@ -40,22 +38,22 @@
   ],
   "devDependencies": {
     "@types/jest": "^29.2.4",
-    "@types/node": "^18.11.16",
-    "@typescript-eslint/eslint-plugin": "^5.46.1",
-    "@typescript-eslint/parser": "^5.46.1",
+    "@types/node": "^20.7.2",
+    "@typescript-eslint/eslint-plugin": "^6.7.3",
+    "@typescript-eslint/parser": "^6.7.3",
     "documentation": "^14.0.1",
     "eslint": "^8.30.0",
     "eslint-config-airbnb-typescript": "^17.0.0",
-    "eslint-config-prettier": "^8.5.0",
+    "eslint-config-prettier": "^9.0.0",
     "eslint-plugin-import": "^2.26.0",
-    "eslint-plugin-prettier": "^4.2.1",
+    "eslint-plugin-prettier": "^5.0.0",
+    "eslint-plugin-unicorn": "^49.0.0",
     "husky": "^8.0.2",
     "jest": "^29.3.1",
-    "opn-cli": "^5.0.0",
-    "prettier": "^2.8.1",
-    "rimraf": "^3.0.2",
+    "prettier": "^3.0.3",
+    "rimraf": "^5.0.5",
     "ts-jest": "^29.0.1",
-    "typescript": "^4.9.4"
+    "typescript": "^5.2.2"
   },
   "publishConfig": {
     "access": "public"

src/__snapshots__/raFile.test.ts.snap

@@ -72,6 +72,11 @@ Map {
     "key2" => "valH",
     "key3" => "valI",
   },
+  "Foot" => Map {
+    "key1" => "Foot",
+    "key2" => "Ankle",
+    "key3" => "Knee",
+  },
 }
 `;