Merge origin/main

.github/workflows/push.yml

@@ -12,7 +12,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Install website deps (with cache)
         uses: bahmutov/npm-install@v1
         with:
@@ -37,7 +37,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Install deps (with cache)
         uses: bahmutov/npm-install@v1
       - name: Build codebase
@@ -69,7 +69,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Install deps (with cache)
         uses: bahmutov/npm-install@v1
       - name: Build project
@@ -153,7 +153,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Install deps and build (with cache)
         uses: bahmutov/npm-install@v1
       - name: Check codebase format

.github/workflows/release.yml

@@ -23,10 +23,10 @@ jobs:
       - uses: actions/checkout@v4
         with:
           persist-credentials: false
-      - name: Use Node.js 20
+      - name: Use Node.js 22
         uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       - name: Install deps
@@ -53,7 +53,7 @@ jobs:
     name: Build Windows desktop app
     runs-on: ubuntu-latest
     container:
-      image: docker://node:20-bullseye
+      image: docker://node:22-bullseye
     steps:
       - uses: actions/checkout@v4
         with:
@@ -107,10 +107,10 @@ jobs:
         with:
           persist-credentials: false
 
-      - name: Use Node.js 20
+      - name: Use Node.js 22
         uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Install build deps
         run: |
           brew install pkg-config cairo pango libpng jpeg giflib librsvg
@@ -135,10 +135,10 @@ jobs:
         with:
           persist-credentials: false
 
-      - name: Use Node.js 20
+      - name: Use Node.js 22
         uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Install deps (with cache)
         uses: bahmutov/npm-install@v1
       - name: Install build deps

.github/workflows/update-docs.yml

@@ -14,7 +14,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Configure AWS Credentials
         uses: aws-actions/configure-aws-credentials@v4
         with:

CHANGELOG.md

@@ -1,3 +1,138 @@
+yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.1
+
+Done in 0.69s.
+
+yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.0
+
+## 3.0.0 (2025-01-29)
+
+#### :boom: Breaking Change
+
+- `core`
+  - [#4716](https://github.com/GMOD/jbrowse-components/pull/4716) Update to
+    generic-filehandle2 ([@cmdcolin](https://github.com/cmdcolin))
+- `__mocks__`, `app-core`, `core`, `embedded-core`, `product-core`, `sv-core`
+  - [#4702](https://github.com/GMOD/jbrowse-components/pull/4702) Update to
+    react 19 ([@cmdcolin](https://github.com/cmdcolin))
+
+#### :rocket: Enhancement
+
+- Other
+  - [#4789](https://github.com/GMOD/jbrowse-components/pull/4789) Allow user to
+    edit region size as 'Custom zoom' ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4796](https://github.com/GMOD/jbrowse-components/pull/4796) Make any
+    bigType track open as BigBedAdapter in ucsc connections
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4788](https://github.com/GMOD/jbrowse-components/pull/4788) Allow
+    supplying a tsv of sample metadata with VCF for multi-variant views
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4782](https://github.com/GMOD/jbrowse-components/pull/4782) Add track
+    filetype guesser for BedGraph ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4774](https://github.com/GMOD/jbrowse-components/pull/4774) Restore
+    concept of linking synteny views ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4770](https://github.com/GMOD/jbrowse-components/pull/4770) Add turbo-zoom
+    buttons ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4756](https://github.com/GMOD/jbrowse-components/pull/4756) Improved
+    mouseover on alignment squiggles in breakpoint split view
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4736](https://github.com/GMOD/jbrowse-components/pull/4736) Bulk delete
+    session tracks ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4733](https://github.com/GMOD/jbrowse-components/pull/4733) Add option to
+    'Hide small indels (less than 10bp)'
+    ([@cmdcolin](https://github.com/cmdcolin))
+- `core`, `web-core`
+  - [#4799](https://github.com/GMOD/jbrowse-components/pull/4799) Add genotype
+    to multi-variant mouseover ([@cmdcolin](https://github.com/cmdcolin))
+- `core`, `product-core`
+  - [#4798](https://github.com/GMOD/jbrowse-components/pull/4798) Add more track
+    metadata to UCSC assembly hub loading
+    ([@cmdcolin](https://github.com/cmdcolin))
+- `core`
+  - [#4795](https://github.com/GMOD/jbrowse-components/pull/4795) Improved
+    rendering of phased VCF and polyploid VCF in multi-variant view
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4792](https://github.com/GMOD/jbrowse-components/pull/4792) Allow
+    uploading a sampleTsv file with per-sample metadata for VCF files
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4786](https://github.com/GMOD/jbrowse-components/pull/4786) Allow opening
+    "synteny tracks" from the default Add track workflow
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4785](https://github.com/GMOD/jbrowse-components/pull/4785) Allow opening
+    BedGraph et al in the default Add track workflow
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4784](https://github.com/GMOD/jbrowse-components/pull/4784) Improve UI for
+    choosing query and target assemblies in the "New track" workflow for synteny
+    tracks ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4767](https://github.com/GMOD/jbrowse-components/pull/4767) Improve load
+    time when multiple tracks use same data file
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4750](https://github.com/GMOD/jbrowse-components/pull/4750) Add some more
+    lazy loading for smaller bundle size
+    ([@cmdcolin](https://github.com/cmdcolin))
+- `sv-core`
+  - [#4753](https://github.com/GMOD/jbrowse-components/pull/4753) Allow
+    launching a single level breakpoint split view focused on the breakends
+    ([@cmdcolin](https://github.com/cmdcolin))
+- `web-core`
+  - [#4745](https://github.com/GMOD/jbrowse-components/pull/4745) Add ability to
+    load a ?hubURL= from URL bar ([@cmdcolin](https://github.com/cmdcolin))
+- `app-core`, `core`
+  - [#4729](https://github.com/GMOD/jbrowse-components/pull/4729) Update cram-js
+    to avoid requesting file size for more CORS compatibility
+    ([@cmdcolin](https://github.com/cmdcolin))
+
+#### :bug: Bug Fix
+
+- Other
+  - [#4778](https://github.com/GMOD/jbrowse-components/pull/4778) Fix GC content
+    calculation consistency across blocks
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4773](https://github.com/GMOD/jbrowse-components/pull/4773) Fix "Color by
+    CDS" for BED12 features ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4771](https://github.com/GMOD/jbrowse-components/pull/4771) Fix generating
+    categories for composite tracks in UCSC hubs
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4769](https://github.com/GMOD/jbrowse-components/pull/4769) Fix facet
+    filter crash ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4765](https://github.com/GMOD/jbrowse-components/pull/4765) Fix repeat
+    masker track BED interpretation ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4764](https://github.com/GMOD/jbrowse-components/pull/4764) Fix
+    modifications coverage calculations
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4731](https://github.com/GMOD/jbrowse-components/pull/4731) Fix naming of
+    subtracks produced by "group by tag" operation
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4732](https://github.com/GMOD/jbrowse-components/pull/4732) Fix persisting
+    alignments "color by" and "filter by" settings in snapshots/session
+    shares/page reloads ([@cmdcolin](https://github.com/cmdcolin))
+- `core`
+  - [#4776](https://github.com/GMOD/jbrowse-components/pull/4776) Fix maximum
+    recursion error in linear synteny view import form
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4768](https://github.com/GMOD/jbrowse-components/pull/4768) Fix navigation
+    via CIGAR string alignment in synteny view
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4766](https://github.com/GMOD/jbrowse-components/pull/4766) Fix some bed12
+    transcripts displaying as bedMethyl features
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4727](https://github.com/GMOD/jbrowse-components/pull/4727) Fix type
+    confusion where sequence feature details crashes for empty subfeatures
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4725](https://github.com/GMOD/jbrowse-components/pull/4725) Avoid error on
+    closing draggable dialog and a couple more refactors
+    ([@cmdcolin](https://github.com/cmdcolin))
+
+#### :house: Internal
+
+- [#4791](https://github.com/GMOD/jbrowse-components/pull/4791) Fix storybook
+  vcf failing to load in dev server ([@cmdcolin](https://github.com/cmdcolin))
+
+#### Committers: 2
+
+- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin))
+- Kim Rutherford ([@kimrutherford](https://github.com/kimrutherford)) Done in
+  2.19s.
+
 yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.18.0
 
 ## 2.18.0 (2024-12-10)

CONTRIBUTING.md

@@ -213,3 +213,23 @@ particular notes include
    subpaths like '@jbrowse/core/util'
 2. The use of tsconfig.build.json to generate types in the final release
 3. The use of referring to the src directory at development time
+
+## What to do if a release fails
+
+### Option A. It already published to NPM
+
+You should probably run another patch release
+
+Note: You must make miniscule source code change or the changelog code will
+fail, so rename a random variable somewhere, commit, and re-run the release
+
+### Option B. It hasn't published to NPM
+
+You can cancel the release script
+
+If it already pushed the tag, then revert the automated commits it made, and
+then delete the tag and push the tag delete (e.g. git tag -d v1.2.3 && git push
+origin :refs/tags/v1.2.3)
+
+If it already made a release draft, delete it, and then re-run the release
+script

README.md

@@ -30,7 +30,7 @@ On macOS with homebrew:
 
 On Ubuntu, with apt:
 
-    sudo apt install -y python make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev
+    sudo apt install -y python3 make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev
 
 ## Install (Linux/Mac)
 

docs/generateConfigDocs.ts

@@ -8,7 +8,7 @@ import {
   getAllFiles,
   removeComments,
   rm,
-} from './util'
+} from './util.ts'
 
 interface Derives {
   name: string

docs/generateStateModelDocs.ts

@@ -8,7 +8,7 @@ import {
   getAllFiles,
   removeComments,
   rm,
-} from './util'
+} from './util.ts'
 
 interface Action {
   name: string

docs/tsconfig.json

@@ -10,6 +10,8 @@
     "strict": true,
     "declaration": true,
     "module": "commonjs",
+    "noEmit": true,
+    "allowImportingTsExtensions": true,
     "moduleResolution": "node"
   },
   "include": ["generateConfigDocs.ts", "generateStateModelDocs.ts", "util.ts"]

eslint.config.mjs

@@ -18,6 +18,7 @@ export default tseslint.config(
       '**/esm/**/*',
       '**/public/**/*',
       '**/storybook-static/**',
+      'docs/*',
       'website/*',
       'packages/core/util/nanoid.js',
       'products/**/webpack.config.js',

lerna.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.18.0",
+  "version": "3.0.1",
   "npmClient": "yarn",
   "$schema": "node_modules/lerna/schemas/lerna-schema.json"
 }

package.json

@@ -8,7 +8,7 @@
     "plugins/*"
   ],
   "scripts": {
-    "build": "yarn useDist && yarn tsx scripts/build.ts && yarn useSrc",
+    "build": "yarn useDist && node --experimental-strip-types scripts/build.ts && yarn useSrc",
     "changelog": "lerna-changelog --silent",
     "useDist": "lerna run useDist --scope \"@jbrowse/plugin*\" --scope @jbrowse/text-indexing",
     "useSrc": "lerna run useSrc --scope \"@jbrowse/plugin*\" --scope @jbrowse/text-indexing",
@@ -21,8 +21,8 @@
     "built-test-ci": "jest --ci integration.test.js",
     "test": "jest",
     "prepare": "husky",
-    "configdocs": "rm -rf website/docs/config && mkdir website/docs/config && yarn tsx docs/generateConfigDocs.ts",
-    "statedocs": "rm -rf website/docs/models && mkdir website/docs/models && yarn tsx docs/generateStateModelDocs.ts",
+    "configdocs": "rm -rf website/docs/config && mkdir website/docs/config && node --experimental-strip-types docs/generateConfigDocs.ts",
+    "statedocs": "rm -rf website/docs/models && mkdir website/docs/models && node --experimental-strip-types docs/generateStateModelDocs.ts",
     "autogen": "yarn statedocs && yarn configdocs && yarn prettier --write website",
     "releasenotes": "yarn prettier --prose-wrap never website/blog/$(ls -Art website/blog/ | tail -n 1)|sed -e '/## Downloads/,+7d'|tail -n +7",
     "copynotes": "yarn --silent releasenotes | xclip -selection clipboard"
@@ -44,10 +44,10 @@
     "@oclif/test": "^4.0.0",
     "@pmmmwh/react-refresh-webpack-plugin": "^0.5.3",
     "@r2wc/react-to-web-component": "^2.0.3",
-    "@storybook/addon-essentials": "~8.3.0",
+    "@storybook/addon-essentials": "^8.5.2",
     "@storybook/node-logger": "^8.3.0",
     "@storybook/react": "^8.3.0",
-    "@storybook/react-webpack5": "~8.3.0",
+    "@storybook/react-webpack5": "^8.5.2",
     "@testing-library/dom": "^10.0.0",
     "@testing-library/jest-dom": "^6.0.0",
     "@testing-library/react": "^16.0.0",
@@ -100,7 +100,7 @@
     "dependency-graph": "^1.0.0",
     "dotenv": "^16.3.1",
     "dotenv-expand": "^11.0.3",
-    "electron": "34.0.0",
+    "electron": "34.0.1",
     "electron-builder": "^25.1.6",
     "electron-mock-ipc": "^0.3.8",
     "eslint": "^9.17.0",
@@ -139,13 +139,12 @@
     "semver": "^7.3.4",
     "slugify": "^1.6.5",
     "source-map-loader": "^5.0.0",
-    "storybook": "~8.3.0",
+    "storybook": "^8.5.2",
     "style-loader": "^3.3.1",
     "terser-webpack-plugin": "^5.2.5",
     "ts-node": "^10.4.0",
     "tslib": "^2.0.1",
     "tss-react": "^4.0.0",
-    "tsx": "^4.17.0",
     "typescript": "^5.8.0-dev.20241213",
     "typescript-eslint": "^8.0.1",
     "webpack": "^5.64.4",

packages/app-core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/app-core",
-  "version": "2.18.0",
+  "version": "3.0.1",
   "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop",
   "keywords": [
     "jbrowse",
@@ -42,20 +42,20 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/product-core": "^2.18.0",
+    "@jbrowse/product-core": "^3.0.1",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
-    "copy-to-clipboard": "^3.3.1"
-  },
-  "peerDependencies": {
+    "copy-to-clipboard": "^3.3.1",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
-    "react": ">=17.0.0",
-    "react-dom": ">=17.0.0",
     "rxjs": "^7.0.0",
     "tss-react": "^4.0.0"
   },
+  "peerDependencies": {
+    "react": ">=18.0.0",
+    "react-dom": ">=18.0.0"
+  },
   "publishConfig": {
     "access": "public"
   }