diff --git a/pkgs/development/python-modules/pytorch-pfn-extras/default.nix b/pkgs/development/python-modules/pytorch-pfn-extras/default.nix
index 2e3455b677e4..21da795609d9 100644
--- a/pkgs/development/python-modules/pytorch-pfn-extras/default.nix
+++ b/pkgs/development/python-modules/pytorch-pfn-extras/default.nix
@@ -1,15 +1,17 @@
 { buildPythonPackage
 , fetchFromGitHub
+, fetchpatch
 , lib
-, setuptools
 , numpy
 , onnx
 , packaging
 , pytestCheckHook
+, pythonAtLeast
+, setuptools
+, stdenv
 , torch
 , torchvision
 , typing-extensions
-, pythonAtLeast
 }:
 
 buildPythonPackage rec {
@@ -24,18 +26,27 @@ buildPythonPackage rec {
     hash = "sha256-vSon/0GxQfaRtSPsQbYAvE3s/F0HEN59VpzE3w1PnVE=";
   };
 
-  nativeBuildInputs = [
+  patches = [
+    (fetchpatch {
+      name = "relax-setuptools.patch";
+      url = "https://github.com/pfnet/pytorch-pfn-extras/commit/96abe38c4baa6a144d604bdd4744c55627e55440.patch";
+      hash = "sha256-85UDGcgJyQS5gINbgpNM58b3XJGvf+ArtGhwJ5EXdhk=";
+    })
+  ];
+
+  build-system = [
     setuptools
   ];
 
-  propagatedBuildInputs = [ numpy packaging torch typing-extensions ];
+  dependencies = [ numpy packaging torch typing-extensions ];
 
   nativeCheckInputs = [ onnx pytestCheckHook torchvision ];
 
-  # ignore all pytest warnings
-  preCheck = ''
-    rm pytest.ini
-  '';
+  pytestFlagsArray = [
+    # Requires CUDA access which is not possible in the nix environment.
+    "-m 'not gpu and not mpi'"
+    "-Wignore::DeprecationWarning"
+  ];
 
   pythonImportsCheck = [ "pytorch_pfn_extras" ];
 
@@ -45,31 +56,28 @@ buildPythonPackage rec {
 
     # requires onnxruntime which was removed because of poor maintainability
     # See https://github.com/NixOS/nixpkgs/pull/105951 https://github.com/NixOS/nixpkgs/pull/155058
+    "tests/pytorch_pfn_extras_tests/onnx_tests/test_annotate.py"
+    "tests/pytorch_pfn_extras_tests/onnx_tests/test_as_output.py"
     "tests/pytorch_pfn_extras_tests/onnx_tests/test_export.py"
+    "tests/pytorch_pfn_extras_tests/onnx_tests/test_export_testcase.py"
+    "tests/pytorch_pfn_extras_tests/onnx_tests/test_lax.py"
+    "tests/pytorch_pfn_extras_tests/onnx_tests/test_load_model.py"
     "tests/pytorch_pfn_extras_tests/onnx_tests/test_torchvision.py"
     "tests/pytorch_pfn_extras_tests/onnx_tests/utils.py"
-    "tests/pytorch_pfn_extras_tests/onnx_tests/test_lax.py"
 
     # RuntimeError: No Op registered for Gradient with domain_version of 9
     "tests/pytorch_pfn_extras_tests/onnx_tests/test_grad.py"
-
-    # Requires CUDA access which is not possible in the nix environment.
-    "tests/pytorch_pfn_extras_tests/cuda_tests/test_allocator.py"
-    "tests/pytorch_pfn_extras_tests/nn_tests/modules_tests/test_lazy_batchnorm.py"
-    "tests/pytorch_pfn_extras_tests/nn_tests/modules_tests/test_lazy_conv.py"
-    "tests/pytorch_pfn_extras_tests/nn_tests/modules_tests/test_lazy_linear.py"
-    "tests/pytorch_pfn_extras_tests/nn_tests/modules_tests/test_lazy.py"
-    "tests/pytorch_pfn_extras_tests/profiler_tests/test_record.py"
-    "tests/pytorch_pfn_extras_tests/runtime_tests/test_to.py"
-    "tests/pytorch_pfn_extras_tests/handler_tests/test_handler.py"
-    "tests/pytorch_pfn_extras_tests/test_reporter.py"
-    "tests/pytorch_pfn_extras_tests/training_tests/test_trainer.py"
-    "tests/pytorch_pfn_extras_tests/utils_tests/test_checkpoint.py"
-    "tests/pytorch_pfn_extras_tests/utils_tests/test_comparer.py"
-    "tests/pytorch_pfn_extras_tests/utils_tests/test_new_comparer.py"
-  ] ++ lib.optionals (pythonAtLeast "3.11") [
-    # Remove this when https://github.com/NixOS/nixpkgs/pull/259068 is merged
+  ] ++ lib.optionals (pythonAtLeast "3.12") [
+    # RuntimeError: Dynamo is not supported on Python 3.12+
     "tests/pytorch_pfn_extras_tests/dynamo_tests/test_compile.py"
+    "tests/pytorch_pfn_extras_tests/test_ops/test_register.py"
+  ] ++ lib.optionals (stdenv.hostPlatform.isDarwin) [
+    # torch.distributed is not available on darwin
+    "tests/pytorch_pfn_extras_tests/training_tests/extensions_tests/test_sharded_snapshot.py"
+  ] ++ lib.optionals (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64) [
+    # RuntimeError: internal error
+    # convolution (e.g. F.conv3d) causes runtime error
+    "tests/pytorch_pfn_extras_tests/nn_tests/modules_tests/test_lazy_conv.py"
   ];
 
   meta = with lib; {