Merge branch 'main' of https://github.com/GMOD/Apollo3 into gff-conve…

…rsion-test

.eslintrc.js

@@ -5,12 +5,11 @@ module.exports = {
     'eslint:recommended',
     'plugin:unicorn/recommended',
     'plugin:cypress/recommended',
-    'plugin:import/recommended',
     'plugin:import/typescript',
     'plugin:@typescript-eslint/strict-type-checked',
     'plugin:@typescript-eslint/stylistic-type-checked',
   ],
-  plugins: ['tsdoc', 'sort-destructure-keys'],
+  plugins: ['import', 'tsdoc', 'sort-destructure-keys'],
   parser: '@typescript-eslint/parser',
   parserOptions: {
     project: true,
@@ -71,8 +70,11 @@ module.exports = {
       { allowNumber: true },
     ],
     '@typescript-eslint/return-await': 'error',
-    // eslint-plugin-import rules (override recommended)
+    // eslint-plugin-import rules
+    'import/export': 'error',
+    'import/no-duplicates': 'warn',
     'import/no-extraneous-dependencies': 'error',
+    'import/no-named-as-default': 'warn',
     // eslint-plugin-sort-destructure-keys rules
     'sort-destructure-keys/sort-destructure-keys': 'warn',
     // eslint-plugin-tsdoc rules

.github/workflows/website.yml

@@ -0,0 +1,34 @@
+name: Deploy Docusaurus to website
+
+on:
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  reload:
+    name: Deploy Docusaurus to website
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+      - name: Use Node.js 18.x
+        uses: actions/setup-node@v4
+        with:
+          node-version: 18
+          cache: yarn
+      - name: Install
+        run: yarn --immutable
+      - name: Build website
+        working-directory: packages/website
+        run: yarn build
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+      - name: Upload
+        working-directory: packages/website
+        run: |
+          aws s3 sync --delete build/ s3://apollo.jbrowse.org/
+          aws cloudfront create-invalidation --distribution-id EL84YTOVCGNJZ --paths '/*'

.husky/pre-commit.js

@@ -29,13 +29,30 @@ function main() {
     spawn.sync(
       'yarn',
       ['workspace', '@apollo-annotation/cli', 'oclif', 'readme'],
-      {
-        stdio: 'inherit',
-      },
+      { stdio: 'inherit' },
+    )
+    spawn.sync(
+      'yarn',
+      [
+        'workspace',
+        '@apollo-annotation/cli',
+        'oclif',
+        'readme',
+        '--multi',
+        '--dir',
+        '../website/docs/cli/',
+      ],
+      { stdio: 'inherit' },
+    )
+    spawn.sync(
+      'git',
+      [
+        'add',
+        'packages/apollo-cli/README.md',
+        'packages/website/docs/cli/*.md',
+      ],
+      { stdio: 'inherit' },
     )
-    spawn.sync('git', ['add', 'packages/apollo-cli/README.md'], {
-      stdio: 'inherit',
-    })
   }
 }
 

packages/apollo-cli/README.md

@@ -5,6 +5,7 @@
 - [Table of contents](#table-of-contents)
 - [Usage](#usage)
 - [Commands](#commands)
+- [Command Topics](#command-topics)
 <!-- tocstop -->
 
 # Usage
@@ -29,27 +30,22 @@ USAGE
 
 <!-- commands -->
 
-- [`apollo help [COMMANDS]`](#apollo-help-commands)
-
-## `apollo help [COMMANDS]`
-
-Display help for apollo.
-
-```
-USAGE
-  $ apollo help [COMMANDS] [-n]
-
-ARGUMENTS
-  COMMANDS  Command to show help for.
-
-FLAGS
-  -n, --nested-commands  Include all nested commands in the output.
-
-DESCRIPTION
-  Display help for apollo.
-```
-
-_See code:
-[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.8/src/commands/help.ts)_
+# Command Topics
+
+- [`apollo assembly`](../website/docs/cli//assembly.md) - Commands to handle
+  assemblies
+- [`apollo change`](../website/docs/cli//change.md) - Commands to handle the log
+  of changes made to the database
+- [`apollo config`](../website/docs/cli//config.md) - Get or set apollo
+  configuration options
+- [`apollo feature`](../website/docs/cli//feature.md) - Commands to handle
+  features
+- [`apollo help`](../website/docs/cli//help.md) - Display help for apollo.
+- [`apollo login`](../website/docs/cli//login.md) - Login to Apollo
+- [`apollo logout`](../website/docs/cli//logout.md) - Logout of Apollo
+- [`apollo refseq`](../website/docs/cli//refseq.md) - Commands to handle
+  reference sequences
+- [`apollo status`](../website/docs/cli//status.md) - View authentication status
+- [`apollo user`](../website/docs/cli//user.md) - Commands to handle users
 
 <!-- commandsstop -->

packages/apollo-cli/package.json

@@ -29,7 +29,7 @@
     "test": "mocha --require src/test/fixtures.ts 'src/**/*.test.ts'",
     "posttest": "yarn lint",
     "test:ci": "nyc mocha 'src/**/*.test.ts'",
-    "version": "oclif readme && git add README.md"
+    "version": "oclif readme --multi --dir ../website/docs/cli/ && oclif readme && git add README.md"
   },
   "oclif": {
     "bin": "apollo",

packages/apollo-collaboration-server/package.json

@@ -105,7 +105,7 @@
     "@types/passport-jwt": "^3.0.6",
     "@types/passport-local": "^1.0.34",
     "@types/passport-microsoft": "^0.0.0",
-    "@types/react": "^17.0.34",
+    "@types/react": "^18.3.4",
     "@types/supertest": "^2.0.11",
     "jest": "^29.6.2",
     "mongodb": "^4.7.0",

packages/jbrowse-plugin-apollo/package.json

@@ -82,7 +82,7 @@
     "@types/file-saver": "^2",
     "@types/node": "^18.14.2",
     "@types/prop-types": "^15",
-    "@types/react": "^17.0.34",
+    "@types/react": "^18.3.4",
     "@types/react-dom": "^18",
     "cypress": "12.17.3",
     "cypress-mongodb": "^6.2.0",

packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts

@@ -1,6 +1,5 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-/* eslint-disable import/no-named-as-default-member */
 // jsonpath triggers this rule for some reason. import { query } from 'jsonpath' does not work
 
 import { checkAbortSignal } from '@jbrowse/core/util'

packages/website/.gitignore

@@ -0,0 +1,6 @@
+# Production
+/build
+
+# Generated files
+.docusaurus
+.cache-loader

packages/website/README.md

@@ -0,0 +1,45 @@
+# Website
+
+This website is built using [Docusaurus](https://docusaurus.io/), a modern
+static website generator.
+
+### Installation
+
+```
+$ yarn
+```
+
+### Local Development
+
+```
+$ yarn start
+```
+
+This command starts a local development server and opens up a browser window.
+Most changes are reflected live without having to restart the server.
+
+### Build
+
+```
+$ yarn build
+```
+
+This command generates static content into the `build` directory and can be
+served using any static contents hosting service.
+
+### Deployment
+
+Using SSH:
+
+```
+$ USE_SSH=true yarn deploy
+```
+
+Not using SSH:
+
+```
+$ GIT_USER=<Your GitHub username> yarn deploy
+```
+
+If you are using GitHub pages for hosting, this command is a convenient way to
+build the website and push to the `gh-pages` branch.

packages/website/babel.config.js

@@ -0,0 +1,4 @@
+/* eslint-disable no-undef */
+module.exports = {
+  presets: [require.resolve('@docusaurus/core/lib/babel/preset')],
+}

packages/website/docs/cli/_category_.json

@@ -0,0 +1,8 @@
+{
+  "label": "CLI",
+  "position": 3,
+  "link": {
+    "type": "generated-index",
+    "description": "Apollo 3 Command Line Interface (CLI)"
+  }
+}