@jbrowse/img 3.6.5 → 4.0.0

package/package.json

@@ -1,44 +1,50 @@
 {
   "name": "@jbrowse/img",
-  "version": "3.6.5",
+  "version": "4.0.0",
   "main": "dist/index.js",
-  "module": "esm/index.js",
+  "types": "dist/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./esm/index.js",
+      "require": "./dist/index.js"
+    }
+  },
   "author": "JBrowse Team",
   "license": "Apache-2.0",
   "engines": {
-    "node": ">=14"
+    "node": ">=20"
   },
   "bin": {
     "jb2export": "./dist/bin.js"
   },
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "clean": "rm -rf dist esm *.tsbuildinfo",
-    "prebuild": "yarn clean",
-    "build": "npm-run-all build:*",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "preversion": "npm run build"
-  },
+  "sideEffects": false,
   "dependencies": {
-    "@babel/runtime": "^7.17.9",
-    "@emotion/cache": "^11.7.1",
-    "@emotion/react": "^11.9.0",
-    "@jbrowse/react-linear-genome-view2": "^3.6.5",
-    "canvas": "^3.0.0",
-    "jsdom": "^26.0.0",
-    "mobx": "^6.6.0",
-    "node-fetch": "^2.6.7",
-    "react": "^19.0.0",
-    "react-dom": "^19.0.0",
-    "tmp": "^0.2.1",
-    "yargs": "^17.3.0"
+    "@emotion/cache": "^11.14.0",
+    "@emotion/react": "^11.14.0",
+    "canvas": "^3.2.0",
+    "@types/jsdom": "^21.1.7",
+    "@types/yargs": "^17.0.33",
+    "jsdom": "27.0.0",
+    "node-fetch": "^2.7.0",
+    "react": "^19.2.3",
+    "react-dom": "^19.2.3",
+    "tmp": "^0.2.5",
+    "yargs": "^18.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^4.0.0",
+    "@jbrowse/react-linear-genome-view2": "^4.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
-}
+  "scripts": {
+    "clean": "rm -rf esm *.tsbuildinfo",
+    "prebuild": "pnpm clean",
+    "build": "pnpm run /^build:/",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "preversion": "pnpm build"
+  }
+}

package/dist/bin.d.ts

@@ -1,2 +0,0 @@
-#!/usr/bin/env node
-export {};

package/dist/bin.js

@@ -1,11 +0,0 @@
-#!/usr/bin/env node
-"use strict";
-const Module = require('module');
-const originalRequire = Module.prototype.require;
-Module.prototype.require = function (path) {
-    if (path.endsWith('.css')) {
-        return {};
-    }
-    return Reflect.apply(originalRequire, this, arguments);
-};
-require('./index.js');

package/dist/index.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/index.js

@@ -1,146 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const fs_1 = __importDefault(require("fs"));
-const yargs_1 = __importDefault(require("yargs"));
-const parseArgv_1 = require("./parseArgv");
-const renderRegion_1 = require("./renderRegion");
-const setupEnv_1 = __importDefault(require("./setupEnv"));
-const util_1 = require("./util");
-(0, setupEnv_1.default)();
-const err = console.error;
-console.error = (...p) => {
-    if (!/useLayoutEffect/.exec(`${p[0]}`)) {
-        err(p);
-    }
-};
-const warn = console.warn;
-console.warn = (...p) => {
-    if (!/estimation reached timeout/.exec(`${p[0]}`)) {
-        warn(p);
-    }
-};
-yargs_1.default
-    .command('jb2export', 'Creates a jbrowse 2 image snapshot')
-    .option('config', {
-    description: 'Path to config file',
-    type: 'string',
-})
-    .option('session', {
-    description: 'Path to session file',
-    type: 'string',
-})
-    .option('assembly', {
-    description: 'Path to an assembly configuration, or a name of an assembly in the configFile',
-    type: 'string',
-})
-    .option('tracks', {
-    description: 'Path to tracks portion of a session',
-    type: 'string',
-})
-    .option('loc', {
-    description: 'A locstring to navigate to, or --loc all to view the whole genome',
-    type: 'string',
-})
-    .option('fasta', {
-    description: 'Supply a fasta for the assembly',
-    type: 'string',
-})
-    .option('aliases', {
-    description: 'Supply aliases for the assembly, e.g. mapping of 1 to chr1. Tab separated file where column 1 matches the names from the FASTA',
-    type: 'string',
-})
-    .option('width', {
-    description: 'Set the width of the window that jbrowse renders to, default: 1500px',
-    type: 'number',
-})
-    .option('pngwidth', {
-    description: 'Set the width of the png canvas if using png output, default 2048px',
-    type: 'number',
-    default: 2048,
-})
-    .option('configtracks', {
-    description: 'A list of track labels from a config file',
-    type: 'array',
-})
-    .option('bam', {
-    description: 'A bam file, flag --bam can be used multiple times to specify multiple bam files',
-    type: 'array',
-})
-    .option('bigwig', {
-    description: 'A bigwig file, the --bigwig flag can be used multiple times to specify multiple bigwig files',
-    type: 'array',
-})
-    .option('cram', {
-    description: 'A cram file, the --cram flag can be used multiple times to specify multiple cram files',
-    type: 'array',
-})
-    .option('vcfgz', {
-    description: 'A tabixed VCF, the --vcfgz flag can be used multiple times to specify multiple vcfgz files',
-    type: 'array',
-})
-    .option('gffgz', {
-    description: 'A tabixed GFF, the --gffgz can be used multiple times to specify multiple gffgz files',
-    type: 'array',
-})
-    .option('hic', {
-    description: 'A .hic file, the --hic can be used multiple times to specify multiple hic files',
-    type: 'array',
-})
-    .option('bigbed', {
-    description: 'A .bigBed file, the --bigbed can be used multiple times to specify multiple bigbed files',
-    type: 'array',
-})
-    .option('bedgz', {
-    description: 'A bed tabix file, the --bedgz can be used multiple times to specify multiple bedtabix files',
-    type: 'array',
-})
-    .option('out', {
-    description: 'File to output to. Default: out.svg. If a filename with extension .png is supplied the program will try to automatically execute rsvg-convert to convert it to png',
-    type: 'string',
-    default: 'out.svg',
-})
-    .option('noRasterize', {
-    description: 'Use full SVG rendering with no rasterized layers, this can substantially increase filesize',
-    type: 'boolean',
-})
-    .option('defaultSession', {
-    description: 'Use the defaultSession from config.json',
-    type: 'boolean',
-})
-    .help()
-    .alias('help', 'h')
-    .alias('width', 'w').argv;
-const args = (0, parseArgv_1.standardizeArgv)((0, parseArgv_1.parseArgv)(process.argv.slice(2)), [
-    'bam',
-    'cram',
-    'vcfgz',
-    'hic',
-    'bigwig',
-    'bigbed',
-    'bedgz',
-    'gffgz',
-    'configtracks',
-]);
-(async () => {
-    try {
-        const result = await (0, renderRegion_1.renderRegion)(args);
-        const { out = 'out.svg', pngwidth = '2048' } = args;
-        if (out.endsWith('.png')) {
-            (0, util_1.convert)(result, { out, pngwidth });
-        }
-        else if (out.endsWith('.pdf')) {
-            (0, util_1.convert)(result, { out, pngwidth }, ['-f', 'pdf']);
-        }
-        else {
-            fs_1.default.writeFileSync(out, result);
-        }
-        process.exit(0);
-    }
-    catch (e) {
-        console.error(e);
-        process.exit(1);
-    }
-})();

package/dist/parseArgv.d.ts

@@ -1,8 +0,0 @@
-export type Entry = [string, string[]];
-export declare function parseArgv(argv: string[]): Entry[];
-export declare function standardizeArgv(args: Entry[], trackTypes: string[]): {
-    [key: string]: unknown;
-    trackList: Entry[];
-    out?: string;
-    pngwidth?: string;
-};

package/dist/parseArgv.js

@@ -1,33 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseArgv = parseArgv;
-exports.standardizeArgv = standardizeArgv;
-function parseArgv(argv) {
-    const map = [];
-    while (argv.length) {
-        const val = argv[0].slice(2);
-        argv = argv.slice(1);
-        const next = argv.findIndex(arg => arg.startsWith('-'));
-        if (next !== -1) {
-            map.push([val, argv.slice(0, next)]);
-            argv = argv.slice(next);
-        }
-        else {
-            map.push([val, argv]);
-            break;
-        }
-    }
-    return map;
-}
-function standardizeArgv(args, trackTypes) {
-    const result = { trackList: [] };
-    for (const arg of args) {
-        if (trackTypes.includes(arg[0])) {
-            result.trackList.push(arg);
-        }
-        else {
-            result[arg[0]] = arg[1][0] || true;
-        }
-    }
-    return result;
-}

package/dist/renderRegion.d.ts

@@ -1,34 +0,0 @@
-import type { Entry } from './parseArgv';
-export interface Opts {
-    noRasterize?: boolean;
-    loc?: string;
-    width?: number;
-    session?: string;
-    assembly?: string;
-    config?: string;
-    fasta?: string;
-    aliases?: string;
-    cytobands?: string;
-    defaultSession?: string;
-    trackList?: Entry[];
-    tracks?: string;
-}
-interface Assembly {
-    name: string;
-    sequence: Record<string, unknown>;
-    refNameAliases?: Record<string, unknown>;
-    cytobands?: Record<string, unknown>;
-}
-interface Track {
-    trackId: string;
-    [key: string]: unknown;
-}
-interface Config {
-    assemblies: Assembly[];
-    assembly: Assembly;
-    tracks: Track[];
-    [key: string]: unknown;
-}
-export declare function readData({ assembly: asm, config, session, fasta, aliases, cytobands, defaultSession, tracks, trackList, }: Opts): Config;
-export declare function renderRegion(opts: Opts): Promise<string>;
-export {};