Merge origin/main

GMOD · May 18, 2023 · 25c6eea · 25c6eea
2 parents 81f5410 + 001f2cc
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diff --git a/.eslintrc.json b/.eslintrc.json
@@ -154,7 +154,8 @@
         "test": true
       },
       "rules": {
-        "import/no-extraneous-dependencies": "off"
+        "import/no-extraneous-dependencies": "off",
+        "@typescript-eslint/no-non-null-assertion": "off"
       }
     },
     {

diff --git a/.ignore b/.ignore
@@ -14,7 +14,7 @@ plugins/wiggle/src/util.ts
 plugins/protein/src/ProteinReferenceSequenceRenderer/aminoAcids.js
 plugins/spreadsheet-view/src/SpreadsheetView/test_data/starfusion_example.fusion_predictions.tsv
 products/jbrowse-aws-lambda-functions/
-products/jbrowse-desktop/src/JBrowse.test.tsx
+products/jbrowse-desktop/src/components/JBrowse.test.tsx
 test_data/volvox/names/
 products/jbrowse-web/src/sessionSharing.ts
 website/docs/models/

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,131 @@
+## 2.5.0 (2023-05-04)
+
+<details><summary>Packages in this release</summary>
+<p>
+
+| Package                                 | Download                                                          |
+| --------------------------------------- | ----------------------------------------------------------------- |
+| @jbrowse/core                           | https://www.npmjs.com/package/@jbrowse/core                       |
+| @jbrowse/plugin-alignments              | https://www.npmjs.com/package/@jbrowse/plugin-alignments          |
+| @jbrowse/plugin-arc                     |                                                                   |
+| @jbrowse/plugin-circular-view           | https://www.npmjs.com/package/@jbrowse/plugin-circular-view       |
+| @jbrowse/plugin-config                  | https://www.npmjs.com/package/@jbrowse/plugin-config              |
+| @jbrowse/plugin-data-management         | https://www.npmjs.com/package/@jbrowse/plugin-data-management     |
+| @jbrowse/plugin-dotplot-view            |                                                                   |
+| @jbrowse/plugin-grid-bookmark           | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark       |
+| @jbrowse/plugin-gtf                     | https://www.npmjs.com/package/@jbrowse/plugin-gtf                 |
+| @jbrowse/plugin-hic                     |                                                                   |
+| @jbrowse/plugin-legacy-jbrowse          | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse      |
+| @jbrowse/plugin-linear-comparative-view |                                                                   |
+| @jbrowse/plugin-linear-genome-view      | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view  |
+| @jbrowse/plugin-lollipop                |                                                                   |
+| @jbrowse/plugin-rdf                     |                                                                   |
+| @jbrowse/plugin-sequence                | https://www.npmjs.com/package/@jbrowse/plugin-sequence            |
+| @jbrowse/plugin-spreadsheet-view        |                                                                   |
+| @jbrowse/plugin-trix                    | https://www.npmjs.com/package/@jbrowse/plugin-trix                |
+| @jbrowse/plugin-variants                | https://www.npmjs.com/package/@jbrowse/plugin-variants            |
+| @jbrowse/plugin-wiggle                  | https://www.npmjs.com/package/@jbrowse/plugin-wiggle              |
+| @jbrowse/cli                            | https://www.npmjs.com/package/@jbrowse/cli                        |
+| @jbrowse/desktop                        |                                                                   |
+| @jbrowse/img                            | https://www.npmjs.com/package/@jbrowse/img                        |
+| @jbrowse/react-circular-genome-view     | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
+| @jbrowse/react-linear-genome-view       | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view   |
+| @jbrowse/web                            |                                                                   |
+
+</p>
+</details>
+
+#### :rocket: Enhancement
+
+- Other
+  - [#3675](https://github.com/GMOD/jbrowse-components/pull/3675) Use
+    react-popper for tooltips in DotplotView
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3637](https://github.com/GMOD/jbrowse-components/pull/3637) Fix
+    renderDelay not being applied to dynamicBlocks
+    ([@cmdcolin](https://github.com/cmdcolin))
+- `core`
+  - [#3677](https://github.com/GMOD/jbrowse-components/pull/3677) Adjust
+    RefNameAutocomplete width calculation to avoid ellipses
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3660](https://github.com/GMOD/jbrowse-components/pull/3660) Bump
+    x-data-grid dependency, refactors for BaseFeatureDetails, add GridToolbar
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3626](https://github.com/GMOD/jbrowse-components/pull/3626) Update to mui
+    x-data-grid 6 ([@cmdcolin](https://github.com/cmdcolin))
+
+#### :bug: Bug Fix
+
+- `core`
+  - [#3681](https://github.com/GMOD/jbrowse-components/pull/3681) Guard against
+    undefined in CoreGetFeatureDetails
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3662](https://github.com/GMOD/jbrowse-components/pull/3662) Fix empty
+    feature sequence on top-level gene feature
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3666](https://github.com/GMOD/jbrowse-components/pull/3666) Fix text boxes
+    being too small in Dialog boxes ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3642](https://github.com/GMOD/jbrowse-components/pull/3642) Fix error
+    handling of feature detail formatter jexl callbacks
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3621](https://github.com/GMOD/jbrowse-components/pull/3621) Update plugin
+    rollup polyfill package
+    ([@garrettjstevens](https://github.com/garrettjstevens))
+  - [#3620](https://github.com/GMOD/jbrowse-components/pull/3620) Fix potential
+    crashes where alignment SEQ field may be empty, simplify some display model
+    code ([@cmdcolin](https://github.com/cmdcolin))
+- Other
+  - [#3670](https://github.com/GMOD/jbrowse-components/pull/3670) Only
+    double-click zoom if not clicking on feature
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3652](https://github.com/GMOD/jbrowse-components/pull/3652) Fix text being
+    invisible on overview scalebar when cytobands shown
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3632](https://github.com/GMOD/jbrowse-components/pull/3632) Fix mouse
+    click-and-drag behavior in the alternative "cursor mode" for the dotplot
+    view ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3625](https://github.com/GMOD/jbrowse-components/pull/3625) Fix UCSC
+    trackhub assembly aliases matching
+    ([@andrzejgrzelak](https://github.com/andrzejgrzelak))
+- `__mocks__`, `core`
+  - [#3630](https://github.com/GMOD/jbrowse-components/pull/3630) Fix flakiness
+    of connection test ([@cmdcolin](https://github.com/cmdcolin))
+
+#### :memo: Documentation
+
+- Other
+  - [#3676](https://github.com/GMOD/jbrowse-components/pull/3676) Refactor
+    circular genome view storybook ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3671](https://github.com/GMOD/jbrowse-components/pull/3671) Fix website
+    documentation sidebar on browsers with prefers-reduced-motion
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3654](https://github.com/GMOD/jbrowse-components/pull/3654) Add some docs
+    for configuring defaultSession ([@cmdcolin](https://github.com/cmdcolin))
+- `core`
+  - [#3646](https://github.com/GMOD/jbrowse-components/pull/3646) Refactor
+    linear genome view storybook ([@cmdcolin](https://github.com/cmdcolin))
+
+#### :house: Internal
+
+- `core`
+  - [#3647](https://github.com/GMOD/jbrowse-components/pull/3647) Refactoring
+    navToMultiple, navToLocString, and related
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3629](https://github.com/GMOD/jbrowse-components/pull/3629) Typescript
+    checking for config slot names ([@rbuels](https://github.com/rbuels))
+  - [#3618](https://github.com/GMOD/jbrowse-components/pull/3618) Rename APIs
+    for feature density stats and quantitative stats
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#3615](https://github.com/GMOD/jbrowse-components/pull/3615) Add check for
+    default export to plugin loader ([@rbuels](https://github.com/rbuels))
+
+#### Committers: 4
+
+- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin))
+- Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens))
+- Robert Buels ([@rbuels](https://github.com/rbuels))
+- [@andrzejgrzelak](https://github.com/andrzejgrzelak)
+
 ## 2.4.2 (2023-03-27)
 
 <details><summary>Packages in this release</summary>

diff --git a/component_tests/cgv/package.json b/component_tests/cgv/package.json
@@ -41,6 +41,8 @@
     "@jbrowse/plugin-trix": "file:./packed/jbrowse-plugin-trix.tgz",
     "@jbrowse/plugin-variants": "file:./packed/jbrowse-plugin-variants.tgz",
     "@jbrowse/plugin-wiggle": "file:./packed/jbrowse-plugin-wiggle.tgz",
+    "@jbrowse/product-core": "file:./packed/jbrowse-product-core.tgz",
+    "@jbrowse/embedded-core": "file:./packed/jbrowse-embedded-core.tgz",
     "@jbrowse/react-linear-genome-view": "file:./packed/jbrowse-react-linear-genome-view.tgz",
     "@jbrowse/react-circular-genome-view": "file:./packed/jbrowse-react-circular-genome-view.tgz"
   },

diff --git a/component_tests/lgv/package.json b/component_tests/lgv/package.json
@@ -40,6 +40,8 @@
     "@jbrowse/plugin-trix": "file:./packed/jbrowse-plugin-trix.tgz",
     "@jbrowse/plugin-variants": "file:./packed/jbrowse-plugin-variants.tgz",
     "@jbrowse/plugin-wiggle": "file:./packed/jbrowse-plugin-wiggle.tgz",
+    "@jbrowse/product-core": "file:./packed/jbrowse-product-core.tgz",
+    "@jbrowse/embedded-core": "file:./packed/jbrowse-embedded-core.tgz",
     "@jbrowse/react-linear-genome-view": "file:./packed/jbrowse-react-linear-genome-view.tgz"
   },
   "scripts": {

diff --git a/config/jest/resizeObserver.js b/config/jest/resizeObserver.js
diff --git a/docs/README.md b/docs/README.md
@@ -1,5 +1,5 @@
-All documentation is in the website folder `website`, so it can be published
-nicely on jbrowse.org. 😄
+All documentation is in the website folder `website`, which powers
+https://jbrowse.org/jb2/docs/
 
 ## For devs
 

diff --git a/docs/generateConfigDocs.ts b/docs/generateConfigDocs.ts
@@ -21,6 +21,7 @@ interface Id {
 interface Conf {
   name: string
   docs: string
+  category?: string
   id: string
 }
 interface Slot {
@@ -53,17 +54,43 @@ function generateConfigDocs(files: string[]) {
     }
     const current = contents[fn]
     const name = rm(obj.comment, '#' + obj.type) || obj.name
-    const docs = filter(obj.comment, '#' + obj.type)
+    const docs = filter(filter(obj.comment, '#' + obj.type), '#category')
     const code = removeComments(obj.node)
     const id = slugify(name, { lower: true })
+
+    // category currently unused, but can organize sidebar
+    let category = rm(obj.comment, '#category')
+
+    if (!category) {
+      if (name.endsWith('Adapter')) {
+        category = 'adapter'
+      } else if (name.endsWith('Display')) {
+        category = 'display'
+      } else if (name.endsWith('View')) {
+        category = 'view'
+      } else if (name.endsWith('Renderer')) {
+        category = 'renderer'
+      } else if (name.includes('Root')) {
+        category = 'root'
+      } else if (name.endsWith('Track')) {
+        category = 'track'
+      } else if (name.endsWith('InternetAccount')) {
+        category = 'internetAccount'
+      } else if (name.endsWith('Connection')) {
+        category = 'connection'
+      } else if (name.endsWith('RpcDriver')) {
+        category = 'rpcDriver'
+      }
+    }
+
     if (obj.type === 'baseConfiguration') {
       current.derives = { ...obj, name, docs, code }
     } else if (obj.type === 'identifier') {
       current.id = { ...obj, name, docs, code }
     } else if (obj.type === 'slot') {
       current.slots.push({ ...obj, name, docs, code })
     } else if (obj.type === 'config') {
-      current.config = { ...obj, name, docs, id }
+      current.config = { ...obj, name, docs, id, category }
     }
   })
   return contents
@@ -82,7 +109,7 @@ function generateConfigDocs(files: string[]) {
 #### slot: ${id.name}`
           : ''
         const derivesstr = derives
-          ? `## ${config.name} - Derives from
+          ? `### ${config.name} - Derives from
 
 
 ${derives.docs}
@@ -108,32 +135,30 @@ ${code}
             })
             .join('\n')
 
+        const dir = `website/docs/config`
+        try {
+          fs.mkdirSync(dir)
+        } catch (e) {}
         fs.writeFileSync(
-          `website/docs/config/${config.name}.md`,
+          `${dir}/${config.name}.md`,
           `---
 id: ${config.id}
 title: ${config.name}
-toplevel: true
 ---
 Note: this document is automatically generated from configuration objects in
 our source code. See [Config guide](/docs/config_guide) for more info
 
-## Source file
+### Source file
 
 [${filename}](https://github.com/GMOD/jbrowse-components/blob/main/${filename})
 
-## Docs
-
 ${config.docs}
 
 ${idstr}
 
-
-
 ${slotstr}
 
 ${derivesstr}
-
 `,
         )
       }