Enable verbatimModuleSyntax in tsconfig (#759)

* Enbale verbatimModuleSyntax

This includes enabling the
`@typescript-eslint/no-import-type-side-effects` rule and running the
auto-fix to move all possible type imports to the top level, so that
verbatimModuleSyntax can work as intended.

* Remove unused packageExtensions

* Increase MongoDB version for CI testing

* Use different version specifier in MongoDB action

Author: garrettjstevens

.github/workflows/cypress_debug.yml

@@ -23,9 +23,9 @@ jobs:
         working-directory: packages/jbrowse-plugin-apollo
 
       - name: Start MongoDB
-        uses: supercharge/mongodb-github-action@1.10.0
+        uses: supercharge/mongodb-github-action@1.12.1
         with:
-          mongodb-version: 7
+          mongodb-version: 8
           mongodb-replica-set: test-rs
 
       - name: Start local file server

.github/workflows/pull_request.yml

@@ -45,9 +45,9 @@ jobs:
         run: yarn run jbrowse create --nightly .jbrowse
         working-directory: packages/jbrowse-plugin-apollo
       - name: Start MongoDB
-        uses: supercharge/mongodb-github-action@1.10.0
+        uses: supercharge/mongodb-github-action@1.12.1
         with:
-          mongodb-version: 7
+          mongodb-version: 8
           mongodb-replica-set: test-rs
       - name: Start local file server
         run:

.yarnrc.yml

@@ -5,9 +5,6 @@ enableGlobalCache: false
 npmMinimalAgeGate: 2880
 
 packageExtensions:
-  "@jbrowse/cli@*":
-    dependencies:
-      tmp: ^0.2.1
   "@jbrowse/core@*":
     peerDependencies:
       "@emotion/react": "*"
@@ -30,10 +27,6 @@ packageExtensions:
   mobx-react@*:
     peerDependencies:
       react-dom: "*"
-  mocha@*:
-    dependencies:
-      source-map-support: "*"
-      ts-node: "*"
   mongoose-id-validator@*:
     peerDependencies:
       mongoose: "*"

eslint.config.mjs

@@ -67,13 +67,14 @@ export default [
       radix: 'error',
       // @typescript-eslint/eslint-plugin rules (override recommended)
       '@typescript-eslint/consistent-type-imports': [
-        'warn',
+        'error',
         { fixStyle: 'inline-type-imports' },
       ],
       '@typescript-eslint/no-extraneous-class': [
         'error',
         { allowWithDecorator: true },
       ],
+      '@typescript-eslint/no-import-type-side-effects': 'error',
       '@typescript-eslint/no-unused-vars': [
         'warn',
         { argsIgnorePattern: '^_', ignoreRestSiblings: true },
@@ -84,7 +85,6 @@ export default [
       ],
       '@typescript-eslint/return-await': 'error',
       // eslint-plugin-import rules
-      'import/consistent-type-specifier-style': ['warn', 'prefer-inline'],
       'import/export': 'error',
       'import/no-duplicates': ['warn', { 'prefer-inline': true }],
       'import/no-extraneous-dependencies': 'error',

packages/apollo-cli/src/commands/assembly/add-from-fasta.ts

@@ -2,13 +2,13 @@
 import * as fs from 'node:fs'
 import path from 'node:path'
 
-import {
-  type SerializedAddAssemblyFromExternalChange,
-  type SerializedAddAssemblyFromFileChange,
+import type {
+  SerializedAddAssemblyFromExternalChange,
+  SerializedAddAssemblyFromFileChange,
 } from '@apollo-annotation/shared'
 import { Args, Flags } from '@oclif/core'
 import { ObjectId } from 'bson'
-import { type Response } from 'undici'
+import type { Response } from 'undici'
 
 import { FileCommand } from '../../fileCommand.js'
 import { queryApollo, submitAssembly } from '../../utils.js'

packages/apollo-cli/src/commands/assembly/add-from-gff.ts

@@ -1,10 +1,10 @@
 import * as fs from 'node:fs'
 import path from 'node:path'
 
-import {
-  type SerializedAddAssemblyAndFeaturesFromFileChange,
-  type SerializedAddAssemblyFromExternalChange,
-  type SerializedAddAssemblyFromFileChange,
+import type {
+  SerializedAddAssemblyAndFeaturesFromFileChange,
+  SerializedAddAssemblyFromExternalChange,
+  SerializedAddAssemblyFromFileChange,
 } from '@apollo-annotation/shared'
 import { Args, Flags } from '@oclif/core'
 import { ObjectId } from 'bson'

packages/apollo-cli/src/commands/assembly/get.ts

@@ -1,5 +1,5 @@
 import { Flags } from '@oclif/core'
-import { type Response } from 'undici'
+import type { Response } from 'undici'
 
 import { BaseCommand } from '../../baseCommand.js'
 import { convertAssemblyNameToId, idReader, queryApollo } from '../../utils.js'

packages/apollo-cli/src/commands/assembly/sequence.ts

@@ -1,6 +1,6 @@
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 
-import { type ApolloRefSeqSnapshot } from '@apollo-annotation/mst'
+import type { ApolloRefSeqSnapshot } from '@apollo-annotation/mst'
 import { Flags } from '@oclif/core'
 import { Agent, type RequestInit, type Response, fetch } from 'undici'
 

packages/apollo-cli/src/commands/change/get.ts

@@ -1,5 +1,5 @@
 import { Flags } from '@oclif/core'
-import { type Response } from 'undici'
+import type { Response } from 'undici'
 
 import { BaseCommand } from '../../baseCommand.js'
 import { convertAssemblyNameToId, idReader, queryApollo } from '../../utils.js'

packages/apollo-cli/src/commands/feature/add-child.ts

@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import { type SerializedAddFeatureChange } from '@apollo-annotation/shared'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { SerializedAddFeatureChange } from '@apollo-annotation/shared'
 import { Flags } from '@oclif/core'
 import { ObjectId } from 'bson'
 import { type Response, fetch } from 'undici'