Fix website documentation sidebar on browsers with prefers-reduced-motion

plugins/data-management/src/PluginStoreWidget/components/PluginStoreWidget.tsx

@@ -154,16 +154,13 @@ function PluginStoreWidget({ model }: { model: PluginStoreModel }) {
         ) : pluginArray ? (
           pluginArray
             .filter(plugin => {
-              // If pugin only has cjsUrl, don't display outside desktop
-              if (
-                !isElectron &&
-                !(plugin.esmUrl || plugin.url || plugin.umdUrl)
-              ) {
-                return false
-              }
-              return plugin.name
-                .toLowerCase()
-                .includes(model.filterText.toLowerCase())
+              // If plugin only has cjsUrl, don't display outside desktop
+              return (
+                !(isElectron && plugin.cjsUrl) &&
+                plugin.name
+                  .toLowerCase()
+                  .includes(model.filterText.toLowerCase())
+              )
             })
             .map(plugin => (
               <PluginCard

products/jbrowse-desktop/src/jbrowseConfig.ts

@@ -64,13 +64,15 @@ export default function JBrowseConfigF(
     /**
      * #slot
      * defines plugins of the format
-     * \{ umdUrl: string, name:string \} |
-     * \{ url: string, name: string \} |
-     * \{ esmUrl: string \} |
-     * \{ cjsUrl: string \} |
-     * \{ umdLoc: \{ uri: string \} \} |
-     * \{ esmLoc: \{ uri: string \} \} |
-     * \{ cjsLoc: \{ uri: string \} \}
+     * ```typescript
+     * type PluginDefinition=
+     *    { umdUrl: string, name:string } |
+     *    { url: string, name: string } |
+     *    { esmUrl: string } |
+     *    { cjsUrl: string } |
+     *    { umdLoc: { uri: string } } |
+     *    { esmLoc: { uri: string } } |
+     * ```
      */
     plugins: types.array(types.frozen<PluginDefinition>()),
     /**

products/jbrowse-web/src/jbrowseConfig.ts

@@ -119,13 +119,15 @@ export default function JBrowseConfigF(
     /**
      * #slot
      * defines plugins of the format
-     * \{ umdUrl: string, name:string \} |
-     * \{ url: string, name: string \} |
-     * \{ esmUrl: string \} |
-     * \{ cjsUrl: string \} |
-     * \{ umdLoc: \{ uri: string \} \} |
-     * \{ esmLoc: \{ uri: string \} \} |
-     * \{ cjsLoc: \{ uri: string \} \}
+     * ```typescript
+     * type PluginDefinition=
+     *    { umdUrl: string, name:string } |
+     *    { url: string, name: string } |
+     *    { esmUrl: string } |
+     *    { cjsUrl: string } |
+     *    { umdLoc: { uri: string } } |
+     *    { esmLoc: { uri: string } } |
+     * ```
      */
     plugins: types.array(types.frozen<PluginDefinition>()),
     /**

website/blog/2021-11-04-v1.5.1-release.md

@@ -15,10 +15,6 @@ configs on JBrowse Desktop
 
 ![](/img/cytobands.png)
 
-<!--
-http://localhost:3000/?config=test_data%2Fconfig_demo.json&session=share-TSa1mZhU4h&password=37iWg
--->
-
 This can also appear in SVG exports
 
 ![](/img/cytobands_svg.png)

website/docs/config/JBrowseDesktopConfiguration.md

@@ -67,10 +67,17 @@ logoPath: {
 
 #### slot: plugins
 
-defines plugins of the format \{ umdUrl: string, name:string \} | \{ url:
-string, name: string \} | \{ esmUrl: string \} | \{ cjsUrl: string \} | \{
-umdLoc: \{ uri: string \} \} | \{ esmLoc: \{ uri: string \} \} | \{ cjsLoc: \{
-uri: string \} \}
+defines plugins of the format
+
+```typescript
+type PluginDefinition=
+   { umdUrl: string, name:string } |
+   { url: string, name: string } |
+   { esmUrl: string } |
+   { cjsUrl: string } |
+   { umdLoc: { uri: string } } |
+   { esmLoc: { uri: string } } |
+```
 
 ```js
 plugins: types.array(types.frozen<PluginDefinition>())

website/docs/config/JBrowseWebConfiguration.md

@@ -131,10 +131,17 @@ logoPath: {
 
 #### slot: plugins
 
-defines plugins of the format \{ umdUrl: string, name:string \} | \{ url:
-string, name: string \} | \{ esmUrl: string \} | \{ cjsUrl: string \} | \{
-umdLoc: \{ uri: string \} \} | \{ esmLoc: \{ uri: string \} \} | \{ cjsLoc: \{
-uri: string \} \}
+defines plugins of the format
+
+```typescript
+type PluginDefinition=
+   { umdUrl: string, name:string } |
+   { url: string, name: string } |
+   { esmUrl: string } |
+   { cjsUrl: string } |
+   { umdLoc: { uri: string } } |
+   { esmLoc: { uri: string } } |
+```
 
 ```js
 plugins: types.array(types.frozen<PluginDefinition>())

website/docs/models/LinearGenomeView.md

@@ -234,13 +234,6 @@ any
 boolean
 ```
 
-#### getter: isSearchDialogDisplayed
-
-```js
-// type
-boolean
-```
-
 #### getter: scaleBarHeight
 
 ```js
@@ -379,7 +372,7 @@ BlockSet
 #### getter: dynamicBlocks
 
 dynamic blocks represent the exact coordinates of the currently visible genome
-regions on the screen. they are similar to static blocks, but statcic blocks can
+regions on the screen. they are similar to static blocks, but static blocks can
 go offscreen while dynamic blocks represent exactly what is on screen
 
 ```js
@@ -621,7 +614,9 @@ zoomTo: (bpPerPx: number, offset?: number, centerAtOffset?: boolean) => number
 
 #### action: setOffsets
 
-sets offsets used in the get sequence dialog
+sets offsets of rubberband, used in the get sequence dialog can call
+view.getSelectedRegions(view.leftOffset,view.rightOffset) to compute the
+selected regions from the offsets
 
 ```js
 // type signature
@@ -632,14 +627,7 @@ setOffsets: (left?: BpOffset, right?: BpOffset) => void
 
 ```js
 // type signature
-setSearchResults: (results?: BaseResult[], query?: string) => void
-```
-
-#### action: setGetSequenceDialogOpen
-
-```js
-// type signature
-setGetSequenceDialogOpen: (open: boolean) => void
+setSearchResults: (searchResults: BaseResult[], searchQuery: string, assemblyName?: string) => void
 ```
 
 #### action: setNewView
@@ -699,7 +687,7 @@ toggleTrack: (trackId: string) => void
 
 ```js
 // type signature
-setTrackLabels: (setting: "hidden" | "offset" | "overlapping") => void
+setTrackLabels: (setting: "offset" | "hidden" | "overlapping") => void
 ```
 
 #### action: toggleCenterLine
@@ -820,18 +808,29 @@ moveTo: (start?: BpOffset, end?: BpOffset) => void
 
 #### action: navToLocString
 
-navigate to the given locstring
+Navigate to the given locstring, will change displayed regions if needed, and
+wait for assemblies to be initialized
 
 ```js
 // type signature
-navToLocString: (locString: string, optAssemblyName?: string) => Promise<void>
+navToLocString: (input: string, optAssemblyName?: string) => Promise<any>
+```
+
+#### action: navToLocations
+
+Similar to `navToLocString`, but accepts parsed location objects instead of
+strings. Will try to perform `setDisplayedRegions` if changing regions
+
+```js
+// type signature
+navToLocations: (parsedLocStrings: ParsedLocString[], assemblyName?: string) => Promise<void>
 ```
 
 #### action: navTo
 
 Navigate to a location based on its refName and optionally start, end, and
-assemblyName. Can handle if there are multiple displayedRegions from same
-refName. Only navigates to a location if it is entirely within a
+assemblyName. Will not try to change displayed regions, use `navToLocations`
+instead. Only navigates to a location if it is entirely within a
 displayedRegion. Navigates to the first matching location encountered.
 
 Throws an error if navigation was unsuccessful
@@ -843,6 +842,13 @@ navTo: (query: NavLocation) => void
 
 #### action: navToMultiple
 
+Navigate to a location based on its refName and optionally start, end, and
+assemblyName. Will not try to change displayed regions, use navToLocations
+instead. Only navigates to a location if it is entirely within a
+displayedRegion. Navigates to the first matching location encountered.
+
+Throws an error if navigation was unsuccessful
+
 ```js
 // type signature
 navToMultiple: (locations: NavLocation[]) => void

website/docs/models/LinearWiggleDisplay.md

@@ -324,7 +324,7 @@ boolean
 
 ```js
 // type
-;1 | 0 | 2
+;0 | 1 | 2
 ```
 
 ### LinearWiggleDisplay - Methods

website/package.json

@@ -19,11 +19,11 @@
   },
   "dependencies": {
     "@cmfcmf/docusaurus-search-local": "^1.1.0",
-    "@docusaurus/core": "2.4.0",
-    "@docusaurus/preset-classic": "2.4.0",
+    "@docusaurus/core": "0.0.0-5562",
+    "@docusaurus/preset-classic": "0.0.0-5562",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
-    "@mdx-js/react": "^1.0.0",
+    "@mdx-js/react": "^2.3.0",
     "@mui/icons-material": "^5.11.16",
     "@mui/material": "^5.12.0",
     "acorn": "^8.8.2",
@@ -36,7 +36,7 @@
     "react-player": "^2.12.0"
   },
   "devDependencies": {
-    "@docusaurus/module-type-aliases": "2.4.0",
+    "@docusaurus/module-type-aliases": "0.0.0-5562",
     "@tsconfig/docusaurus": "^1.0.7",
     "typescript": "^5.0.4"
   },