Typescriptify docusaurus website code (#3448)

GMOD · Jan 10, 2023 · 16da952 · 16da952
1 parent c790a4b
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Showing 22 changed files with 524 additions and 573 deletions.
diff --git a/...hicalTrackSelectorWidget/components/__snapshots__/HierarchicalTrackSelector.test.tsx.snap b/...hicalTrackSelectorWidget/components/__snapshots__/HierarchicalTrackSelector.test.tsx.snap
@@ -81,7 +81,7 @@ exports[`renders with a couple of categorized tracks 1`] = `
         Filter tracks
       </label>
       <div
-        class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-13s3qt4-MuiInputBase-root-MuiInput-root"
+        class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-1blad95-MuiInputBase-root-MuiInput-root"
       >
         <input
           aria-invalid="false"
@@ -178,7 +178,7 @@ exports[`renders with a couple of uncategorized tracks 1`] = `
         Filter tracks
       </label>
       <div
-        class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-13s3qt4-MuiInputBase-root-MuiInput-root"
+        class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-1blad95-MuiInputBase-root-MuiInput-root"
       >
         <input
           aria-invalid="false"

diff --git a/...management/src/PluginStoreWidget/components/__snapshots__/PluginStoreWidget.test.tsx.snap b/...management/src/PluginStoreWidget/components/__snapshots__/PluginStoreWidget.test.tsx.snap
@@ -16,7 +16,7 @@ exports[`renders with the available plugins 1`] = `
       Filter plugins
     </label>
     <div
-      class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-13s3qt4-MuiInputBase-root-MuiInput-root"
+      class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-1blad95-MuiInputBase-root-MuiInput-root"
     >
       <input
         aria-invalid="false"

diff --git a/products/jbrowse-cli/src/commands/text-index.test.ts b/products/jbrowse-cli/src/commands/text-index.test.ts
@@ -30,9 +30,7 @@ function mockRemote1(exampleSite: Scope) {
 
 function mockRemote2(exampleSite: Scope) {
   return exampleSite
-    .get(
-      '/GMOD/jbrowse-components/cli_trix_indexer_stub/test_data/volvox/volvox.sort.gff3.gz',
-    )
+    .get('/GMOD/jbrowse-components/main/test_data/volvox/volvox.sort.gff3.gz')
     .reply(200, fs.createReadStream(dataDir('volvox.sort.gff3.gz')))
 }
 

diff --git a/products/jbrowse-cli/test/data/config.json b/products/jbrowse-cli/test/data/config.json
@@ -142,12 +142,12 @@
       "adapter": {
         "type": "Gff3TabixAdapter",
         "gffGzLocation": {
-          "uri": "https://github.com/GMOD/jbrowse-components/raw/cli_trix_indexer_stub/test_data/volvox/volvox.sort.gff3.gz",
+          "uri": "https://github.com/GMOD/jbrowse-components/raw/main/test_data/volvox/volvox.sort.gff3.gz",
           "locationType": "UriLocation"
         },
         "index": {
           "location": {
-            "uri": "https://github.com/GMOD/jbrowse-components/raw/cli_trix_indexer_stub/test_data/volvox/volvox.sort.gff3.gz.tbi",
+            "uri": "https://github.com/GMOD/jbrowse-components/raw/main/test_data/volvox/volvox.sort.gff3.gz.tbi",
             "locationType": "UriLocation"
           }
         }

diff --git a/products/jbrowse-cli/test/data/indexing_config.json b/products/jbrowse-cli/test/data/indexing_config.json
@@ -120,12 +120,12 @@
       "adapter": {
         "type": "Gff3TabixAdapter",
         "gffGzLocation": {
-          "uri": "https://github.com/GMOD/jbrowse-components/raw/cli_trix_indexer_stub/test_data/volvox/volvox.sort.gff3.gz",
+          "uri": "https://github.com/GMOD/jbrowse-components/raw/main/test_data/volvox/volvox.sort.gff3.gz",
           "locationType": "UriLocation"
         },
         "index": {
           "location": {
-            "uri": "https://github.com/GMOD/jbrowse-components/raw/cli_trix_indexer_stub/test_data/volvox/volvox.sort.gff3.gz.tbi",
+            "uri": "https://github.com/GMOD/jbrowse-components/raw/main/test_data/volvox/volvox.sort.gff3.gz.tbi",
             "locationType": "UriLocation"
           }
         }

diff --git a/products/jbrowse-cli/test/data/trix/volvox_meta.json b/products/jbrowse-cli/test/data/trix/volvox_meta.json
@@ -44,12 +44,12 @@
       "adapterConf": {
         "type": "Gff3TabixAdapter",
         "gffGzLocation": {
-          "uri": "https://github.com/GMOD/jbrowse-components/raw/cli_trix_indexer_stub/test_data/volvox/volvox.sort.gff3.gz",
+          "uri": "https://github.com/GMOD/jbrowse-components/raw/main/test_data/volvox/volvox.sort.gff3.gz",
           "locationType": "UriLocation"
         },
         "index": {
           "location": {
-            "uri": "https://github.com/GMOD/jbrowse-components/raw/cli_trix_indexer_stub/test_data/volvox/volvox.sort.gff3.gz.tbi",
+            "uri": "https://github.com/GMOD/jbrowse-components/raw/main/test_data/volvox/volvox.sort.gff3.gz.tbi",
             "locationType": "UriLocation"
           }
         }

diff --git a/website/blog/2021-11-04-v1.5.1-release.md b/website/blog/2021-11-04-v1.5.1-release.md
@@ -21,7 +21,7 @@ http://localhost:3000/?config=test_data%2Fconfig_demo.json&session=share-TSa1mZh
 
 This can also appear in SVG exports
 
-![](img/cytobands_svg.png)
+![](/img/cytobands_svg.png)
 
 ## Plugins can integrate with "Add track" workflow better
 

diff --git a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_03_simple_site.md b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_03_simple_site.md
@@ -87,7 +87,7 @@ tools (You can use `F12` or `Ctrl-Shift-I` or right-click the page and select
 `Inspect`) and go to the "Network" tab. If you see something like the below with
 a status of 200 for "jbrowse-linear-view.js", then you are good to go!
 
-![Network tab of developer tools showing that script has loaded correctly](../../../img/bcc2020_network_success.png)
+![Network tab of developer tools showing that script has loaded correctly](/img/bcc2020_network_success.png)
 
 Now we need to actually instantiate a view. The code to do so looks like this:
 

diff --git a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_04_assemblies.md b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_04_assemblies.md
@@ -63,7 +63,7 @@ source ~/.bashrc
 Now if you run the command `jbrowse --help` in the terminal, you should see
 something like this:
 
-![The output of `jbrowse --help` in a terminal](../../../img/bcc2020_jbrowse_help.png)
+![The output of `jbrowse --help` in a terminal](/img/bcc2020_jbrowse_help.png)
 
 :::note
 

diff --git a/website/img b/website/img
diff --git a/website/package.json b/website/package.json
@@ -4,36 +4,45 @@
   "homepage": ".",
   "scripts": {
     "prep": "npm run make cli.md && npm run fetchPlugins",
+    "fetchPlugins": "rimraf plugins.json && wget https://s3.amazonaws.com/jbrowse.org/plugin-store/plugins.json",
+    "prebuild": "npm run prep",
     "prestart": "npm run prep",
     "start": "docusaurus start",
-    "prebuild": "npm run prep",
     "build": "docusaurus build",
-    "fetchPlugins": "rimraf plugins.json && wget https://s3.amazonaws.com/jbrowse.org/plugin-store/plugins.json",
-    "swizzle": "docusaurus swizzle",
+    "clear": "docusaurus clear",
+    "serve": "docusaurus serve",
+    "typecheck": "tsc",
     "predeploy": "npm run build && npm run make",
     "deploy": "aws s3 sync --delete build s3://jbrowse.org/jb2/ && aws s3 cp docs/jbrowse2.pdf s3://jbrowse.org/jb2/",
     "postdeploy": "aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths \"/jb2/*\"",
     "make": "make -C docs"
   },
   "dependencies": {
     "@cmfcmf/docusaurus-search-local": "^0.11.0",
-    "@docusaurus/core": "^2.1.0",
-    "@docusaurus/preset-classic": "^2.1.0",
-    "@emotion/react": "^11.10.4",
-    "@emotion/styled": "^11.10.4",
-    "@mui/icons-material": "^5.10.9",
-    "@mui/material": "^5.10.11",
+    "@docusaurus/core": "2.2.0",
+    "@docusaurus/preset-classic": "2.2.0",
+    "@emotion/react": "^11.10.5",
+    "@emotion/styled": "^11.10.5",
+    "@mdx-js/react": "^1.6.22",
+    "@mui/icons-material": "^5.11.0",
+    "@mui/material": "^5.11.4",
     "acorn": "^8.8.1",
-    "acorn-jsx": "^5.3.1",
-    "clsx": "^1.1.1",
-    "copy-to-clipboard": "^3.3.2",
-    "react": "^18.0.0",
-    "react-dom": "^18.0.0",
+    "acorn-jsx": "^5.3.2",
+    "clsx": "^1.2.1",
+    "copy-to-clipboard": "^3.3.3",
+    "prism-react-renderer": "^1.3.5",
+    "react": "^17.0.2",
+    "react-dom": "^17.0.2",
     "react-player": "^2.11.0"
   },
+  "devDependencies": {
+    "@docusaurus/module-type-aliases": "2.2.0",
+    "@tsconfig/docusaurus": "^1.0.5",
+    "typescript": "^4.7.4"
+  },
   "browserslist": {
     "production": [
-      ">0.2%",
+      ">0.5%",
       "not dead",
       "not op_mini all"
     ],
@@ -43,5 +52,7 @@
       "last 1 safari version"
     ]
   },
-  "private": true
+  "engines": {
+    "node": ">=16.14"
+  }
 }
diff --git a/website/release_announcement_drafts/v2.3.0.md b/website/release_announcement_drafts/v2.3.0.md
diff --git a/website/release_announcement_drafts/v2.3.1.md b/website/release_announcement_drafts/v2.3.1.md
diff --git a/website/release_announcement_drafts/v2.3.2.md b/website/release_announcement_drafts/v2.3.2.md
diff --git a/website/src/components/MiniFeatures/index.js → ...ite/src/components/MiniFeatures/index.tsx b/website/src/components/MiniFeatures/index.js → ...ite/src/components/MiniFeatures/index.tsx
@@ -1,7 +1,8 @@
 import React from 'react'
+import ReactPlayer from 'react-player'
 import clsx from 'clsx'
+
 import styles from './styles.module.css'
-import ReactPlayer from 'react-player'
 
 const FeatureList = [
   {

diff --git a/website/src/components/MiniPlugins/index.js → website/src/components/MiniPlugins/index.tsx b/website/src/components/MiniPlugins/index.js → website/src/components/MiniPlugins/index.tsx
diff --git a/website/src/pages/cancer.js → website/src/pages/cancer.tsx b/website/src/pages/cancer.js → website/src/pages/cancer.tsx
@@ -1,13 +1,14 @@
 import React from 'react'
+import { Alert, AlertTitle } from '@mui/material'
 import clsx from 'clsx'
 import Link from '@docusaurus/Link'
 import useDocusaurusContext from '@docusaurus/useDocusaurusContext'
 import Layout from '@theme/Layout'
 import MiniFeatures from '@site/src/components/MiniFeatures'
-import MiniPlugins from '../components/MiniPlugins'
 
+// locals
+import MiniPlugins from '../components/MiniPlugins'
 import styles from './styles.module.css'
-import { Alert, AlertTitle } from '@mui/material'
 
 function Header() {
   const { siteConfig } = useDocusaurusContext()
@@ -26,7 +27,9 @@ function Header() {
         <div className={styles.buttons}>
           <Link
             className="button button--secondary button--lg"
-            href={`https://jbrowse.org/code/jb2/${siteConfig.customFields.currentVersion}/?config=test_data/config_demo.json&session=share-oTyYRpz9fN&password=fYAbt`}
+            href={`https://jbrowse.org/code/jb2/${
+              /* @ts-ignore */ siteConfig.customFields.currentVersion
+            }/?config=test_data/config_demo.json&session=share-oTyYRpz9fN&password=fYAbt`}
           >
             Browse a cancer annotations demo web instance
           </Link>

diff --git a/website/src/pages/index.js → website/src/pages/index.tsx b/website/src/pages/index.js → website/src/pages/index.tsx
@@ -16,9 +16,11 @@ import OpenInBrowserIcon from '@mui/icons-material/OpenInBrowser'
 function Home() {
   const context = useDocusaurusContext()
   const { siteConfig = {} } = context
+  // @ts-ignore
   const { currentVersion } = siteConfig.customFields
 
   return (
+    // @ts-ignore
     <Layout title={`${siteConfig.title}`}>
       <Box sx={{ margin: { xs: '0.5em', sm: '0.5em', md: '3em' } }}>
         <Box

diff --git a/website/src/pages/plugin_store.js → website/src/pages/plugin_store.tsx b/website/src/pages/plugin_store.js → website/src/pages/plugin_store.tsx
@@ -249,6 +249,8 @@ function PluginStore() {
 
   return (
     <ThemeProvider theme={theme}>
+      {/*
+// @ts-ignore */}
       <Layout title={`${siteConfig.title}`}>
         <div className={pluginStyles.body}>
           <div style={{ flexBasis: '50%' }}>

diff --git a/website/tsconfig.json b/website/tsconfig.json
@@ -0,0 +1,8 @@
+{
+  // This file is not used in compilation. It is here just for a nice editor experience.
+  "extends": "@tsconfig/docusaurus/tsconfig.json",
+  "compilerOptions": {
+    "baseUrl": ".",
+    "resolveJsonModule": true
+  }
+}