@jbrowse/cli 3.5.1 → 3.6.0

package/package.json

@@ -1,11 +1,10 @@
 {
   "name": "@jbrowse/cli",
-  "version": "3.5.1",
+  "version": "3.6.0",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
-    "jbrowse2",
-    "oclif"
+    "jbrowse2"
   ],
   "license": "Apache-2.0",
   "homepage": "https://jbrowse.org",
@@ -16,39 +15,27 @@
     "directory": "products/jbrowse-cli"
   },
   "author": "JBrowse Team",
-  "main": "lib/index.js",
-  "types": "lib/index.d.ts",
+  "main": "dist/index.js",
   "bin": {
     "jbrowse": "./bin/run"
   },
   "files": [
     "/bin",
-    "/lib",
-    "/npm-shrinkwrap.json",
-    "/oclif.manifest.json"
+    "/bundle",
+    "/dist"
   ],
   "engines": {
-    "node": ">=16"
+    "node": ">=18.3.0"
   },
   "scripts": {
     "prebuild": "npm run clean",
-    "build": "tsc --build",
-    "postpack": "rimraf oclif.manifest.json",
-    "clean": "rimraf lib",
-    "prepack": "npm run clean  && npm run build && npm run manifest && npm run docs",
-    "manifest": "oclif manifest",
-    "version": "npm run docs && npm run docs:version:add",
+    "build": "tsc --build && webpack",
+    "clean": "rimraf dist bundle",
+    "prepack": "npm run clean  && npm run docs",
     "predocs": "npm run build",
-    "docs": "npm run docs:create && npm run docs:format",
-    "docs:create": "oclif readme",
-    "docs:format": "prettier --write README.md",
-    "docs:version:add": "git add README.md"
+    "docs": "./generate_readme.sh > README.md"
   },
   "dependencies": {
-    "@oclif/core": "^4.0.19",
-    "@oclif/plugin-help": "^6.0.15",
-    "boxen": "^4.2.0",
-    "chalk": "^4.1.0",
     "cli-progress": "^3.9.0",
     "command-exists": "^1.2.9",
     "cors": "^2.8.5",
@@ -56,22 +43,10 @@
     "express": "^4.17.1",
     "ixixx": "^2.0.1",
     "json-parse-better-errors": "^1.0.2",
-    "node-fetch-native": "^1.6.4",
-    "tslib": "^2.3.1"
-  },
-  "devDependencies": {
-    "typescript": "^5.1.3"
-  },
-  "oclif": {
-    "commands": "./lib/commands",
-    "bin": "jbrowse",
-    "plugins": [
-      "@oclif/plugin-help"
-    ],
-    "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/products/jbrowse-cli/<%- commandPath %>"
+    "node-fetch-native": "^1.6.4"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "cb8859da9d838ad2594964777c5c54f385d98f5e"
+  "gitHead": "133a68815ab348d156c18d83cffc997356c3cfbb"
 }

package/bin/dev

@@ -1,17 +0,0 @@
-#!/usr/bin/env node
-
-const oclif = require('@oclif/core')
-
-const path = require('path')
-const project = path.join(__dirname, '..', 'tsconfig.json')
-
-// In dev mode -> use ts-node and dev plugins
-process.env.NODE_ENV = 'development'
-
-require('ts-node').register({ project })
-
-// In dev mode, always show stack traces
-oclif.settings.debug = true
-
-// Start the CLI
-oclif.run().then(oclif.flush).catch(oclif.Errors.handle)

package/bin/dev.cmd

@@ -1,3 +0,0 @@
-@echo off
-
-node "%~dp0\dev" %*

package/bin/run.cmd

@@ -1,3 +0,0 @@
-@echo off
-
-node "%~dp0\run" %*

package/lib/base.js

@@ -1,157 +0,0 @@
-"use strict";
-/**
- * By convention, exit codes in this base class are below 100
- */
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const fs_1 = require("fs");
-const path_1 = __importDefault(require("path"));
-const core_1 = require("@oclif/core");
-const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
-const fetchWithProxy_1 = __importDefault(require("./fetchWithProxy"));
-class JBrowseCommand extends core_1.Command {
-    async init() { }
-    async readFile(location) {
-        return fs_1.promises.readFile(location, { encoding: 'utf8' });
-    }
-    async readJsonFile(location) {
-        let contents;
-        try {
-            contents = await fs_1.promises.readFile(location, { encoding: 'utf8' });
-        }
-        catch (error) {
-            this.error(error instanceof Error ? error : `${error}`, {
-                suggestions: [
-                    `Make sure the file "${location}" exists or use --out to point to a directory with a config.json`,
-                    'Run `jbrowse add-assembly` to create a config file',
-                ],
-                exit: 40,
-            });
-        }
-        let result;
-        try {
-            result = (0, json_parse_better_errors_1.default)(contents);
-        }
-        catch (error) {
-            this.error(error instanceof Error ? error : `${error}`, {
-                suggestions: [`Make sure "${location}" is a valid JSON file`],
-                exit: 50,
-            });
-        }
-        return result;
-    }
-    async writeJsonFile(location, contents) {
-        this.debug(`Writing JSON file to ${process.cwd()} ${location}`);
-        return fs_1.promises.writeFile(location, JSON.stringify(contents, null, 2));
-    }
-    async resolveFileLocation(location, check = true, inPlace = false) {
-        let locationUrl;
-        try {
-            locationUrl = new URL(location);
-        }
-        catch (error) {
-            // ignore
-        }
-        if (locationUrl) {
-            if (check) {
-                // @ts-expect-error
-                const response = await (0, fetchWithProxy_1.default)(locationUrl, { method: 'HEAD' });
-                if (!response.ok) {
-                    throw new Error(`${locationUrl} result ${response.statusText}`);
-                }
-            }
-            return locationUrl.href;
-        }
-        let locationPath;
-        try {
-            locationPath = check ? await fs_1.promises.realpath(location) : location;
-        }
-        catch (e) {
-            // ignore
-        }
-        if (locationPath) {
-            const filePath = path_1.default.relative(process.cwd(), locationPath);
-            if (inPlace && filePath.startsWith('..')) {
-                this.warn(`Location ${filePath} is not in the JBrowse directory. Make sure it is still in your server directory.`);
-            }
-            return inPlace ? location : filePath;
-        }
-        return this.error(`Could not resolve to a file or a URL: "${location}"`, {
-            exit: 40,
-        });
-    }
-    async readInlineOrFileJson(inlineOrFileName) {
-        let result;
-        // see if it's inline JSON
-        try {
-            result = (0, json_parse_better_errors_1.default)(inlineOrFileName);
-        }
-        catch (error) {
-            this.debug(`Not valid inline JSON, attempting to parse as filename: '${inlineOrFileName}'`);
-            // not inline JSON, must be location of a JSON file
-            result = await this.readJsonFile(inlineOrFileName);
-        }
-        return result;
-    }
-    async fetchGithubVersions() {
-        let versions = [];
-        for await (const iter of this.fetchVersions()) {
-            versions = [...versions, ...iter];
-        }
-        return versions;
-    }
-    async getLatest() {
-        for await (const versions of this.fetchVersions()) {
-            // if a release was just uploaded, or an erroneous build was made then it
-            // might have no build asset
-            const nonprereleases = versions
-                .filter(release => !release.prerelease)
-                .filter(release => release.assets?.length);
-            if (nonprereleases.length > 0) {
-                // @ts-expect-error
-                const file = nonprereleases[0].assets.find(f => f.name.includes('jbrowse-web'))?.browser_download_url;
-                if (!file) {
-                    throw new Error('no jbrowse-web download found');
-                }
-                return file;
-            }
-        }
-        throw new Error('no version tags found');
-    }
-    async *fetchVersions() {
-        let page = 1;
-        let result;
-        do {
-            const url = `https://api.github.com/repos/GMOD/jbrowse-components/releases?page=${page}`;
-            const response = await (0, fetchWithProxy_1.default)(url);
-            if (response.ok) {
-                result = (await response.json());
-                yield result.filter(release => release.tag_name.startsWith('v'));
-                page++;
-            }
-            else {
-                throw new Error(`HTTP ${response.status} fetching ${url}`);
-            }
-        } while (result.length);
-    }
-    async getTag(tag) {
-        const response = await (0, fetchWithProxy_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases/tags/${tag}`);
-        if (response.ok) {
-            const result = (await response.json());
-            const file = result.assets?.find(f => f.name.includes('jbrowse-web'))?.browser_download_url;
-            if (!file) {
-                this.error('Could not find version specified. Use --listVersions to see all available versions', { exit: 90 });
-            }
-            return file;
-        }
-        return this.error(`Could not find version: ${response.statusText}`, {
-            exit: 90,
-        });
-    }
-    async getBranch(branch) {
-        return `https://s3.amazonaws.com/jbrowse.org/code/jb2/${branch}/jbrowse-web-${branch}.zip`;
-    }
-}
-exports.default = JBrowseCommand;