Merge pull request #280 from unipept/chore-migrate-to-vitest-10559607753500242316

Migrate to Vitest

Author: bmesuere

jest.config.ts

@@ -16,7 +16,7 @@
   "scripts": {
     "build": "yarn run tsc",
     "lint": "yarn run eslint",
-    "test": "NODE_OPTIONS='--experimental-vm-modules --no-warnings' yarn run jest",
+    "test": "vitest run",
     "typecheck": "yarn tsc --skipLibCheck --noEmit",
     "peptfilter": "yarn run tsx bin/peptfilter.ts",
     "prot2pept": "yarn run tsx bin/prot2pept.ts",
@@ -32,19 +32,17 @@
   },
   "devDependencies": {
     "@eslint/js": "^9.5.0",
-    "@types/jest": "^29.5.12",
     "@types/node": "^24.0.8",
     "@typescript-eslint/eslint-plugin": "^7.13.1",
     "@typescript-eslint/parser": "^7.13.1",
     "eslint": "9.x",
     "globals": "^16.0.0",
-    "jest": "^29.7.0",
     "mock-stdin": "^1.0.0",
     "np": "^10.0.7",
-    "ts-jest": "^29.1.5",
     "ts-node": "^10.9.2",
     "tsx": "^4.15.6",
     "typescript": "^5.4.5",
-    "typescript-eslint": "^8.16.0"
+    "typescript-eslint": "^8.16.0",
+    "vitest": "^4.0.16"
   }
 }

package.json

@@ -1,14 +1,14 @@
 import { Peptfilter } from '../../lib/commands/peptfilter';
-import { jest } from '@jest/globals';
+import { vi } from 'vitest';
 import * as mock from 'mock-stdin';
 
 let output: string[];
 let error: string[];
 // eslint-disable-next-line @typescript-eslint/no-unused-vars
-const writeSpy = jest
+const writeSpy = vi
   .spyOn(process.stdout, "write")
   .mockImplementation((data: unknown) => { output.push(data as string); return true; });
-const errorSpy = jest
+const errorSpy = vi
   .spyOn(process.stderr, "write")
   .mockImplementation((data: unknown) => { error.push(data as string); return true; });
 

tests/commands/peptfilter.test.ts

@@ -1,14 +1,14 @@
 import { Prot2pept } from '../../lib/commands/prot2pept';
-import { jest } from '@jest/globals';
+import { vi } from 'vitest';
 import * as mock from 'mock-stdin';
 
 let output: string[];
 let error: string[];
 // eslint-disable-next-line @typescript-eslint/no-unused-vars
-const writeSpy = jest
+const writeSpy = vi
   .spyOn(process.stdout, "write")
   .mockImplementation((data: unknown) => { output.push(data as string); return true; });
-const errorSpy = jest
+const errorSpy = vi
   .spyOn(process.stderr, "write")
   .mockImplementation((data: unknown) => { error.push(data as string); return true; });
 

tests/commands/prot2pept.test.ts

@@ -1,9 +1,9 @@
-import { jest } from '@jest/globals';
+import { vi } from 'vitest';
 import { Pept2ec } from "../../../lib/commands/unipept/pept2ec";
 import { setupMockFetch } from '../../mocks/mockFetch';
 
 let output: string[];
-jest
+vi
   .spyOn(process.stdout, "write")
   .mockImplementation((data: unknown) => { output.push(data as string); return true; });
 

tests/commands/unipept/pept2ec.test.ts

@@ -1,9 +1,9 @@
-import { jest } from '@jest/globals';
+import { vi } from 'vitest';
 import { Pept2funct } from "../../../lib/commands/unipept/pept2funct";
 import { setupMockFetch } from '../../mocks/mockFetch';
 
 let output: string[];
-jest
+vi
   .spyOn(process.stdout, "write")
   .mockImplementation((data: unknown) => { output.push(data as string); return true; });
 

tests/commands/unipept/pept2funct.test.ts

@@ -1,9 +1,9 @@
-import { jest } from '@jest/globals';
+import { vi } from 'vitest';
 import { Pept2go } from "../../../lib/commands/unipept/pept2go";
 import { setupMockFetch } from '../../mocks/mockFetch';
 
 let output: string[];
-jest
+vi
   .spyOn(process.stdout, "write")
   .mockImplementation((data: unknown) => { output.push(data as string); return true; });
 

tests/commands/unipept/pept2go.test.ts

@@ -1,9 +1,9 @@
-import { jest } from '@jest/globals';
+import { vi } from 'vitest';
 import { Pept2interpro } from "../../../lib/commands/unipept/pept2interpro";
 import { setupMockFetch } from '../../mocks/mockFetch';
 
 let output: string[];
-jest
+vi
   .spyOn(process.stdout, "write")
   .mockImplementation((data: unknown) => { output.push(data as string); return true; });
 

tests/commands/unipept/pept2interpro.test.ts

@@ -1,9 +1,9 @@
-import { jest } from '@jest/globals';
+import { vi } from 'vitest';
 import { Pept2lca } from "../../../lib/commands/unipept/pept2lca";
 import { setupMockFetch } from '../../mocks/mockFetch';
 
 let output: string[];
-jest
+vi
   .spyOn(process.stdout, "write")
   .mockImplementation((data: unknown) => { output.push(data as string); return true; });
 

tests/commands/unipept/pept2lca.test.ts

@@ -1,9 +1,9 @@
-import { jest } from '@jest/globals';
+import { vi } from 'vitest';
 import { Pept2prot } from "../../../lib/commands/unipept/pept2prot";
 import { setupMockFetch } from '../../mocks/mockFetch';
 
 let output: string[];
-jest
+vi
   .spyOn(process.stdout, "write")
   .mockImplementation((data: unknown) => { output.push(data as string); return true; });