Use vitest

eslint.config.mjs

@@ -6,7 +6,13 @@ import tseslint from "typescript-eslint";
 
 export default tseslint.config(
   {
-    ignores: ["**/build/**/*", "**/dist/**/*", "**/esm/**/*", "**/public/**/*"],
+    ignores: [
+      "**/build/**/*",
+      "**/dist/**/*",
+      "**/esm/**/*",
+      "**/public/**/*",
+      "eslint.config.mjs",
+    ],
   },
   {
     languageOptions: {
@@ -42,6 +48,11 @@ export default tseslint.config(
   },
   {
     rules: {
+      "@typescript-eslint/ban-ts-comment": "off",
+      "@typescript-eslint/no-base-to-string": "off",
+      "@typescript-eslint/restrict-template-expressions": "off",
+      "@typescript-eslint/no-non-null-assertion": "off",
+      "react/react-in-jsx-scope": "off",
       "no-console": [
         "warn",
         {

lib/src/accessFasta.ts

@@ -24,8 +24,8 @@ export async function accessFasta(
   const downstream = await t.getSequence(refseq, end, downstreamend);
 
   return {
-    seq: seq || "",
-    upstream: upstream || "",
-    downstream: downstream || "",
+    seq: seq ?? "",
+    upstream: upstream ?? "",
+    downstream: downstream ?? "",
   };
 }

lib/src/components/GenericGeneSeqPanel.tsx

@@ -1,4 +1,3 @@
-
 import { useState, useEffect } from "react";
 import GenericSeqPanel from "./GenericSeqPanel";
 import transcriptList from "../fetchTranscripts";
@@ -19,7 +18,7 @@ export default function GenericGeneSeqPanel(props: {
   const [result, setResult] = useState<Feature[]>();
   const [error, setError] = useState<unknown>();
   const [transcript, setTranscript] = useState<Feature>();
-  const feature = transcript || result?.[0];
+  const feature = transcript ?? result?.[0];
   const [model] = useState(SequenceFeatureDetailsF().create({}));
 
   useEffect(() => {
@@ -51,9 +50,9 @@ export default function GenericGeneSeqPanel(props: {
         <p>
           Transcript:
           <select
-            onChange={e =>
-              { setTranscript(result.find(r => r.id() === e.target.value)); }
-            }
+            onChange={e => {
+              setTranscript(result.find(r => r.id() === e.target.value));
+            }}
           >
             {result.map(r => (
               <option key={r.id()} value={r.id()}>
@@ -62,7 +61,11 @@ export default function GenericGeneSeqPanel(props: {
             ))}
           </select>
           &nbsp; Mode:
-          <select onChange={e => { model.setMode(e.target.value); }}>
+          <select
+            onChange={e => {
+              model.setMode(e.target.value);
+            }}
+          >
             <option value="gene">gene</option>
             <option value="cds">CDS</option>
             <option value="cdna">cDNA</option>

lib/src/components/GenericSeqPanel.tsx

@@ -1,4 +1,3 @@
-
 import { useState, useEffect, useRef } from "react";
 import SequencePanel from "@jbrowse/core/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel";
 import { assembleBundle } from "../assembleBundle";
@@ -38,6 +37,7 @@ export default function GenericSeqPanel({
   const [tooltipOpen, setTooltipOpen] = useState(false);
 
   useEffect(() => {
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
     (async () => {
       try {
         const res = await assembleBundle({
@@ -80,9 +80,11 @@ export default function GenericSeqPanel({
             onClick={() => {
               const ref = seqPanelRef.current;
               if (ref) {
-                copy(ref.textContent || "", { format: "text/plain" });
+                copy(ref.textContent ?? "", { format: "text/plain" });
                 setCopied(true);
-                setTimeout(() => { setCopied(false); }, 1000);
+                setTimeout(() => {
+                  setCopied(false);
+                }, 1000);
               }
             }}
           >
@@ -101,7 +103,9 @@ export default function GenericSeqPanel({
               }
               copy(ref.innerHTML, { format: "text/html" });
               setCopiedHtml(true);
-              setTimeout(() => { setCopiedHtml(false); }, 1000);
+              setTimeout(() => {
+                setCopiedHtml(false);
+              }, 1000);
             }}
           >
             {copiedHtml ? "Copied to clipboard!" : "Copy highlighted fasta"}

lib/src/fetchTranscripts.ts

@@ -45,8 +45,9 @@ export default async function fetchTranscripts({
     start: start,
     end: end,
   })) {
-    if (feature.get("name") === gene) {
-      return feature.get("subfeatures");
+    const f = feature as Feature;
+    if (f.get("name") === gene) {
+      return f.get("subfeatures") ?? [];
     }
   }
   return [];

lib/src/index.test.tsx

@@ -1,11 +1,10 @@
-
-import React from "react";
+/**
+ * @vitest-environment jsdom
+ */
+
+import { test } from "vitest";
 import { render } from "@testing-library/react";
 import GenericGeneSeqPanel from "./components/GenericGeneSeqPanel";
-import fetch from "node-fetch";
-
-// @ts-expect-error
-globalThis.fetch = fetch;
 
 test("expect protein rendering", async () => {
   const { findByText } = render(

package.json

@@ -6,15 +6,13 @@
     "app"
   ],
   "scripts": {
-    "test": "jest",
-    "lint": "eslint lib app"
+    "test": "vitest",
+    "lint": "eslint"
   },
   "devDependencies": {
     "@testing-library/dom": "^10.4.0",
-    "@testing-library/jest-dom": "^6.6.3",
     "@testing-library/react": "^16.1.0",
     "@testing-library/user-event": "^14.4.3",
-    "@types/jest": "^29.5.14",
     "@types/node": "^20.14.2",
     "@types/node-fetch": "^2.6.12",
     "@typescript-eslint/eslint-plugin": "^7.13.0",
@@ -24,13 +22,12 @@
     "eslint-plugin-react-hooks": "^5.1.0",
     "eslint-plugin-react-refresh": "^0.4.16",
     "eslint-plugin-unicorn": "^56.0.1",
-    "jest": "^29.5.0",
-    "jest-environment-jsdom": "^29.5.0",
+    "jsdom": "^25.0.1",
     "node-fetch": "^2.0.0",
     "prettier": "^3.4.2",
     "rimraf": "^6.0.1",
-    "ts-jest": "^29.2.5",
     "typescript": "^5.7.2",
-    "typescript-eslint": "^8.18.0"
+    "typescript-eslint": "^8.18.0",
+    "vitest": "^2.1.8"
   }
 }