diff --git a/pkgs/development/python-modules/jupytext/default.nix b/pkgs/development/python-modules/jupytext/default.nix
index 368cc19fdd94..b554ce129fb1 100644
--- a/pkgs/development/python-modules/jupytext/default.nix
+++ b/pkgs/development/python-modules/jupytext/default.nix
@@ -2,6 +2,7 @@
 , buildPythonPackage
 , fetchFromGitHub
 , GitPython
+, isort
 , jupyter-client
 , jupyter-packaging
 , jupyterlab
@@ -44,6 +45,7 @@ buildPythonPackage rec {
 
   checkInputs = [
     GitPython
+    isort
     jupyter-client
     notebook
     pytestCheckHook
@@ -65,6 +67,10 @@ buildPythonPackage rec {
     "--ignore-glob='tests/test_pre_commit_*.py'"
   ];
 
+  disabledTests = [
+    "test_apply_black_through_jupytext" # we can't do anything about ill-formatted notebooks
+  ];
+
   pythonImportsCheck = [
     "jupytext"
     "jupytext.cli"