Merge branch 'main' into bookmark-highlights

CHANGELOG.md

@@ -1,3 +1,55 @@
+yarn run v1.22.19 $ lerna-changelog --silent --next-version 2.8.0
+
+## 2.8.0 (2023-11-09)
+
+#### :rocket: Enhancement
+
+- Other
+  - [#4045](https://github.com/GMOD/jbrowse-components/pull/4045) Create
+    multi-region arc display type for variant tracks
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4050](https://github.com/GMOD/jbrowse-components/pull/4050) Allow
+    specifying alternative config.json path via global variable
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4046](https://github.com/GMOD/jbrowse-components/pull/4046) Show last
+    autosave on jbrowse-web start screen
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4044](https://github.com/GMOD/jbrowse-components/pull/4044) Speed up
+    "multi-region" navigation in search box
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4032](https://github.com/GMOD/jbrowse-components/pull/4032) Add
+    `jbrowse sort-gff` subcommand ([@cmdcolin](https://github.com/cmdcolin))
+- `product-core`
+  - [#4040](https://github.com/GMOD/jbrowse-components/pull/4040) Strip baseUri
+    in 'About track' copy config ([@cmdcolin](https://github.com/cmdcolin))
+- `core`
+  - [#4035](https://github.com/GMOD/jbrowse-components/pull/4035) Prompt to
+    horizontally flip view when launching linear synteny view on inverted
+    feature ([@cmdcolin](https://github.com/cmdcolin))
+- `app-core`
+  - [#4024](https://github.com/GMOD/jbrowse-components/pull/4024) Add
+    right-handed arrow to view title to emphasize the focused view
+    ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr))
+
+#### :bug: Bug Fix
+
+- [#4052](https://github.com/GMOD/jbrowse-components/pull/4052) Fix browser back
+  button behavior in jbrowse-web ([@cmdcolin](https://github.com/cmdcolin))
+- [#4043](https://github.com/GMOD/jbrowse-components/pull/4043) Fix crash in
+  "Open session" widget for sessions that have 'track-less views'
+  ([@cmdcolin](https://github.com/cmdcolin))
+
+#### :memo: Documentation
+
+- [#4027](https://github.com/GMOD/jbrowse-components/pull/4027) Add office hours
+  and community meetings ([@cmdcolin](https://github.com/cmdcolin))
+
+#### Committers: 2
+
+- Caroline Bridge
+  ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr))
+- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 2.23s.
+
 yarn run v1.22.19 $ lerna-changelog --silent --next-version 2.7.2
 
 ## 2.7.2 (2023-10-27)

README.md

@@ -17,8 +17,8 @@ new community meeting that anyone can join via a public Google Meet link.
 Details below:
 
 - [Schedule 1-on-1 appointment](https://calendar.app.google/E9i5fyZN4UcZawuNA)
-- [Community call - Monthly on the third Thursday, 10am EST (North America, Europe friendly)](https://meet.google.com/rnq-exdt-tuz)
-- [Community call - Monthly on the last Tuesday, 8pm EST (Asia Pacific friendly)](https://meet.google.com/uti-xsjf-xbu)
+- [Community call - Monthly on the third Thursday, 10am EST (North America, Europe friendly)](https://meet.google.com/uti-xsjf-xbu)
+- [Community call - Monthly on the last Tuesday, 8pm EST (Asia Pacific friendly)](https://meet.google.com/rnq-exdt-tuz)
 - [Add both events to your Google calendar](https://calendar.google.com/calendar/u/2?cid=ZDgxZmE0Yjk3YjdiZTAxYThjMDAzYzNkOThkMjUyOGQ1ZWM4YzNkMzRjNjgwMmQ3YjZhOWEwYmU4NDYxZDBiM0Bncm91cC5jYWxlbmRhci5nb29nbGUuY29t)
 
 ## Pre-requisites

lerna.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.7.2",
+  "version": "2.8.0",
   "npmClient": "yarn",
   "$schema": "node_modules/lerna/schemas/lerna-schema.json"
 }

package.json

@@ -78,11 +78,10 @@
     "@types/node-fetch": "^2.5.7",
     "@types/offscreencanvas": "^2019.6.4",
     "@types/pako": "^2.0.0",
-    "@types/pluralize": "^0.0.30",
+    "@types/pluralize": "^0.0.33",
     "@types/range-parser": "^1.2.3",
     "@types/rbush": "^3.0.0",
     "@types/react": "^18.0.26",
-    "@types/react-color": "^3.0.4",
     "@types/react-dom": "^18.0.0",
     "@types/react-virtualized-auto-sizer": "^1.0.0",
     "@types/set-value": "^4.0.1",
@@ -106,7 +105,7 @@
     "dependency-graph": "^0.11.0",
     "dotenv": "^16.3.1",
     "dotenv-expand": "^10.0.0",
-    "electron": "27.0.2",
+    "electron": "27.0.4",
     "electron-builder": "^24.8.0",
     "electron-mock-ipc": "^0.3.8",
     "eslint": "^8.0.0",
@@ -116,7 +115,7 @@
     "eslint-plugin-react-hooks": "^4.3.0",
     "eslint-plugin-react-refresh": "^0.4.3",
     "eslint-plugin-tsdoc": "^0.2.4",
-    "eslint-plugin-unicorn": "^48.0.0",
+    "eslint-plugin-unicorn": "^49.0.0",
     "express": "^4.18.2",
     "express-basic-auth": "^1.2.1",
     "file-loader": "^6.2.0",
@@ -153,7 +152,6 @@
     "storybook": "^7.0.0",
     "style-loader": "^3.3.1",
     "terser-webpack-plugin": "^5.2.5",
-    "ts-loader": "^9.5.0",
     "ts-node": "^10.4.0",
     "tslib": "^2.0.1",
     "tss-react": "^4.0.0",

packages/app-core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/app-core",
-  "version": "2.7.2",
+  "version": "2.8.0",
   "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop",
   "keywords": [
     "jbrowse",
@@ -42,7 +42,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/product-core": "^2.7.2",
+    "@jbrowse/product-core": "^2.8.0",
     "@mui/icons-material": "^5.0.0",
     "@mui/material": "^5.10.17",
     "clsx": "^2.0.0",

packages/core/BaseFeatureWidget/BaseFeatureDetail/util.ts

@@ -39,6 +39,6 @@ export function accessNested(arr: string[], obj: Record<string, unknown> = {}) {
   return typeof obj2 === 'string'
     ? obj2
     : isObject(obj2) && typeof obj2?.Description === 'string'
-    ? obj2.Description
-    : undefined
+      ? obj2.Description
+      : undefined
 }

packages/core/PluginLoader.ts

@@ -194,8 +194,8 @@ export default class PluginLoader {
       'url' in def
         ? new URL(def.url, baseUri)
         : 'umdUrl' in def
-        ? new URL(def.umdUrl, baseUri)
-        : new URL(def.umdLoc.uri, def.umdLoc.baseUri)
+          ? new URL(def.umdUrl, baseUri)
+          : new URL(def.umdLoc.uri, def.umdLoc.baseUri)
 
     if (parsedUrl.protocol !== 'http:' && parsedUrl.protocol !== 'https:') {
       throw new Error(

packages/core/configuration/types.ts

@@ -23,13 +23,13 @@ export type GetOptions<SCHEMA> = SCHEMA extends ConfigurationSchemaType<
 export type GetBase<SCHEMA> = SCHEMA extends undefined
   ? never
   : GetOptions<SCHEMA> extends ConfigurationSchemaOptions<undefined, any>
-  ? undefined
-  : GetOptions<SCHEMA> extends ConfigurationSchemaOptions<
-      infer BASE extends AnyConfigurationSchemaType,
-      any
-    >
-  ? BASE
-  : never
+    ? undefined
+    : GetOptions<SCHEMA> extends ConfigurationSchemaOptions<
+          infer BASE extends AnyConfigurationSchemaType,
+          any
+        >
+      ? BASE
+      : never
 
 export type GetExplicitIdentifier<SCHEMA> =
   GetOptions<SCHEMA> extends ConfigurationSchemaOptions<
@@ -48,13 +48,13 @@ export type ConfigurationSchemaForModel<MODEL> = MODEL extends IStateTreeNode<
 export type ConfigurationSlotName<SCHEMA> = SCHEMA extends undefined
   ? never
   : SCHEMA extends ConfigurationSchemaType<infer D, any>
-  ?
-      | (keyof D & string)
-      | GetExplicitIdentifier<SCHEMA>
-      | (GetBase<SCHEMA> extends ConfigurationSchemaType<any, any>
-          ? ConfigurationSlotName<GetBase<SCHEMA>>
-          : never)
-  : never
+    ?
+        | (keyof D & string)
+        | GetExplicitIdentifier<SCHEMA>
+        | (GetBase<SCHEMA> extends ConfigurationSchemaType<any, any>
+            ? ConfigurationSlotName<GetBase<SCHEMA>>
+            : never)
+    : never
 
 export type AnyConfigurationSchemaType = ConfigurationSchemaType<any, any>
 export type AnyConfigurationModel = Instance<AnyConfigurationSchemaType>

packages/core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.7.2",
+  "version": "2.8.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",

packages/core/ui/CascadingMenu.tsx

@@ -7,6 +7,7 @@ import {
   Menu,
   MenuItem,
   PopoverOrigin,
+  SvgIconProps,
 } from '@mui/material'
 import { MenuItem as JBMenuItem, MenuItemEndDecoration } from './Menu'
 import {
@@ -49,15 +50,18 @@ function CascadingMenuItem({
 
 function CascadingSubmenu({
   title,
+  Icon,
   inset,
   popupId,
   ...props
 }: {
   children: React.ReactNode
   title: string
   onMenuItemClick: Function
-  menuItems: JBMenuItem[]
+  Icon: React.ComponentType<SvgIconProps> | undefined
+
   inset: boolean
+  menuItems: JBMenuItem[]
   popupId: string
 }) {
   const { parentPopupState } = React.useContext(CascadingContext)
@@ -69,6 +73,11 @@ function CascadingSubmenu({
   return (
     <>
       <MenuItem {...bindHover(popupState)} {...bindFocus(popupState)}>
+        {Icon ? (
+          <ListItemIcon>
+            <Icon />
+          </ListItemIcon>
+        ) : null}
         <ListItemText primary={title} inset={inset} />
         <ChevronRight />
       </MenuItem>
@@ -167,9 +176,7 @@ function CascadingMenuList({
     }
   }
 
-  const hasIcon = menuItems.some(
-    menuItem => 'icon' in menuItem && menuItem.icon,
-  )
+  const hasIcon = menuItems.some(m => 'icon' in m && m.icon)
   return (
     <>
       {menuItems.map((item, idx) => {
@@ -178,7 +185,8 @@ function CascadingMenuList({
             key={`subMenu-${item.label}-${idx}`}
             popupId={`subMenu-${item.label}`}
             title={item.label}
-            inset={hasIcon}
+            Icon={item.icon}
+            inset={hasIcon && !item.icon}
             onMenuItemClick={onMenuItemClick}
             menuItems={item.subMenu}
           >

packages/core/ui/react-colorful.js

@@ -247,8 +247,8 @@ const i = (e, r = 0, t = 1) => (e > t ? t : e < r ? r : e),
         ? a === e
           ? (r - t) / l
           : a === r
-          ? 2 + (t - e) / l
-          : 4 + (e - r) / l
+            ? 2 + (t - e) / l
+            : 4 + (e - r) / l
         : 0
     return {
       h: b(60 * (n < 0 ? n + 6 : n)),

packages/core/util/simpleFeature.ts

@@ -156,8 +156,8 @@ export default class SimpleFeature implements Feature {
     return name === 'subfeatures'
       ? this.subfeatures
       : name === 'parent'
-      ? this.parent()
-      : this.data[name]
+        ? this.parent()
+        : this.data[name]
   }
 
   /**

packages/embedded-core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/embedded-core",
-  "version": "2.7.2",
+  "version": "2.8.0",
   "description": "JBrowse 2 code shared between embedded products",
   "keywords": [
     "jbrowse",
@@ -42,7 +42,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/product-core": "^2.7.2",
+    "@jbrowse/product-core": "^2.8.0",
     "@mui/icons-material": "^5.0.0",
     "@mui/material": "^5.10.17",
     "copy-to-clipboard": "^3.3.1",

packages/product-core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/product-core",
-  "version": "2.7.2",
+  "version": "2.8.0",
   "sideEffects": false,
   "description": "JBrowse 2 code shared between products but not used by plugins",
   "keywords": [
@@ -43,7 +43,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/core": "^2.7.2",
+    "@jbrowse/core": "^2.8.0",
     "@mui/icons-material": "^5.0.0",
     "@mui/material": "^5.10.17",
     "copy-to-clipboard": "^3.3.1",

packages/text-indexing/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/text-indexing",
-  "version": "2.7.2",
+  "version": "2.8.0",
   "description": "JBrowse 2 text indexing for desktop",
   "keywords": [
     "jbrowse",

packages/web-core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/web-core",
-  "version": "2.7.2",
+  "version": "2.8.0",
   "description": "JBrowse 2 code shared between web-app type products",
   "keywords": [
     "jbrowse",
@@ -42,8 +42,8 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/app-core": "^2.7.2",
-    "@jbrowse/product-core": "^2.7.2",
+    "@jbrowse/app-core": "^2.8.0",
+    "@jbrowse/product-core": "^2.8.0",
     "@mui/icons-material": "^5.0.0",
     "@mui/material": "^5.10.17",
     "clone": "^2.0.0",

plugins/alignments/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.7.2",
+  "version": "2.8.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",

plugins/arc/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-arc",
-  "version": "2.7.2",
+  "version": "2.8.0",
   "description": "JBrowse 2 arc adapters, tracks, etc.",
   "keywords": [
     "jbrowse",