diff --git a/pkgs/development/python-modules/onnx/default.nix b/pkgs/development/python-modules/onnx/default.nix
index d5db23bc2b0b..a266fb4e6b44 100644
--- a/pkgs/development/python-modules/onnx/default.nix
+++ b/pkgs/development/python-modules/onnx/default.nix
@@ -11,6 +11,8 @@
 , six
 , tabulate
 , typing-extensions
+, pythonRelaxDepsHook
+, pytest-runner
 }:
 
 buildPythonPackage rec {
@@ -27,8 +29,11 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [
     cmake
+    pythonRelaxDepsHook
   ];
 
+  pythonRelaxDeps = [ "protobuf" ];
+
   propagatedBuildInputs = [
     protobuf
     numpy
@@ -39,6 +44,7 @@ buildPythonPackage rec {
   checkInputs = [
     nbval
     pytestCheckHook
+    pytest-runner
     tabulate
   ];
 
@@ -47,8 +53,6 @@ buildPythonPackage rec {
     patchShebangs tools/protoc-gen-mypy.py
     substituteInPlace tools/protoc-gen-mypy.sh.in \
       --replace "/bin/bash" "${bash}/bin/bash"
-
-    sed -i '/pytest-runner/d' setup.py
   '';
 
   preBuild = ''