From 0eea6d4e27e148d35fa8adaae5516c6a9cbe0fa3 Mon Sep 17 00:00:00 2001
From: Bart Mesuere <Bart.Mesuere@UGent.be>
Date: Thu, 20 Jun 2024 10:21:03 +0200
Subject: [PATCH] fix tests

---
 jest.config.ts                    | 2 +-
 package.json                      | 2 +-
 tests/commands/peptfilter.test.ts | 8 ++++----
 tests/commands/uniprot.test.ts    | 1 +
 4 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/jest.config.ts b/jest.config.ts
index 9627c0f6..9b51f878 100644
--- a/jest.config.ts
+++ b/jest.config.ts
@@ -104,7 +104,7 @@ const config: Config = {
   // notifyMode: "failure-change",
 
   // A preset that is used as a base for Jest's configuration
-  // preset: undefined,
+  preset: 'ts-jest/presets/default-esm',
 
   // Run tests from one or more projects
   // projects: undefined,
diff --git a/package.json b/package.json
index 7daaa389..ddaa71bc 100644
--- a/package.json
+++ b/package.json
@@ -14,7 +14,7 @@
   "scripts": {
     "build": "yarn run tsc",
     "lint": "yarn run eslint",
-    "test": "yarn run jest",
+    "test": "NODE_OPTIONS='--experimental-vm-modules --no-warnings' yarn run jest",
     "typecheck": "yarn tsc --skipLibCheck --noEmit",
     "peptfilter": "yarn run tsx bin/peptfilter.ts",
     "uniprot": "yarn run tsx bin/uniprot.ts"
diff --git a/tests/commands/peptfilter.test.ts b/tests/commands/peptfilter.test.ts
index 07bb7f20..ad1cfff1 100644
--- a/tests/commands/peptfilter.test.ts
+++ b/tests/commands/peptfilter.test.ts
@@ -1,4 +1,5 @@
 import { Peptfilter } from '../../lib/commands/peptfilter';
+import { jest } from '@jest/globals';
 import * as mock from 'mock-stdin';
 
 let output: string[];
@@ -54,9 +55,8 @@ test('test default filter from stdin', async () => {
 
   await run;
 
-  expect(writeSpy).toHaveBeenCalledTimes(1);
   expect(errorSpy).toHaveBeenCalledTimes(0);
-  expect(output.length).toBe(1);
+  expect(output.join("").trimEnd().split("\n").length).toBe(1);
 });
 
 test('test if it passes fasta from stdin', async () => {
@@ -71,8 +71,8 @@ test('test if it passes fasta from stdin', async () => {
 
   await run;
 
-  expect(writeSpy).toHaveBeenCalledTimes(1);
   expect(errorSpy).toHaveBeenCalledTimes(0);
+  expect(output.join("").trimEnd().split("\n").length).toBe(1);
   expect(output[0]).toBe(">AA\n");
 });
 
@@ -92,7 +92,7 @@ test('test complex example from stdin', async () => {
 
   await run;
 
-  expect(writeSpy).toHaveBeenCalledTimes(1);
   expect(errorSpy).toHaveBeenCalledTimes(0);
+  expect(output.join("").trimEnd().split("\n").length).toBe(1);
   expect(output[0]).toBe("CCCCCA\n");
 });
diff --git a/tests/commands/uniprot.test.ts b/tests/commands/uniprot.test.ts
index ca72837b..59ba4f7f 100644
--- a/tests/commands/uniprot.test.ts
+++ b/tests/commands/uniprot.test.ts
@@ -1,4 +1,5 @@
 import { Uniprot } from '../../lib/commands/uniprot';
+import { jest } from '@jest/globals';
 import * as mock from 'mock-stdin';
 
 let output: string[];