1 files changed, 51 insertions, 28 deletions
diff --git a/pkgs/development/python-modules/mdtraj/default.nix b/pkgs/development/python-modules/mdtraj/default.nix
index 971688348a1d5..0d2cb8f5125c9 100644
--- a/pkgs/development/python-modules/mdtraj/default.nix
+++ b/pkgs/development/python-modules/mdtraj/default.nix
@@ -1,24 +1,26 @@
-{ lib
-, stdenv
-, buildPythonPackage
-, fetchFromGitHub
-, fetchpatch
-, llvmPackages
-, zlib
-, cython_0
-, oldest-supported-numpy
-, setuptools
-, wheel
-, astunparse
-, numpy
-, pyparsing
-, scipy
-, gsd
-, networkx
-, pandas
-, pytest-xdist
-, pytestCheckHook
-, tables
+{
+  lib,
+  stdenv,
+  buildPythonPackage,
+  fetchFromGitHub,
+  fetchpatch,
+  llvmPackages,
+  zlib,
+  cython_0,
+  oldest-supported-numpy,
+  setuptools,
+  wheel,
+  astunparse,
+  numpy,
+  packaging,
+  pyparsing,
+  scipy,
+  gsd,
+  networkx,
+  pandas,
+  pytest-xdist,
+  pytestCheckHook,
+  tables,
 }:
 
 buildPythonPackage rec {
@@ -39,24 +41,43 @@ buildPythonPackage rec {
       url = "https://github.com/mdtraj/mdtraj/commit/81209d00817ab07cfc4668bf5ec88088d16904c0.patch";
       hash = "sha256-ttNmij7csxF0Z5wPPwhGumRX055W2IgFjRAe6nI6GNY=";
     })
+    # remove pkg_resources usage
+    # https://github.com/mdtraj/mdtraj/pull/1837
+    (fetchpatch {
+      name = "fix-runtime-error.patch";
+      url = "https://github.com/mdtraj/mdtraj/commit/02d44d4db7039fceb199c85b4f993244804f470d.patch";
+      hash = "sha256-nhbi3iOrDSM87DyIp1KVt383Vvb6aYOgkjuYzviqiq8=";
+    })
+    # remove distutils usage
+    # https://github.com/mdtraj/mdtraj/pull/1834
+    (fetchpatch {
+      name = "python312-compatibility.patch";
+      url = "https://github.com/mdtraj/mdtraj/commit/95d79747deef42c976ca362a57806b61933409f3.patch";
+      hash = "sha256-Cq7/d745q6ZgAyWGM4ULnSsWezsbnu1CjSz5eqYSb+g=";
+    })
+    # disable intrinsics when SIMD is not available
+    # TODO: enable SIMD with python3.12
+    # https://github.com/mdtraj/mdtraj/pull/1884
+    (fetchpatch {
+      name = "fix-intrinsics-flag.patch";
+      url = "https://github.com/mdtraj/mdtraj/commit/d6041c645d51898e2a09030633210213eec7d4c5.patch";
+      hash = "sha256-kcnlHMoA/exJzV8iQltH+LWXrvSk7gsUV+yWK6xn0jg=";
+    })
   ];
 
-  nativeBuildInputs = [
+  build-system = [
     cython_0
     oldest-supported-numpy
     setuptools
     wheel
   ];
 
-  buildInputs = [
-    zlib
-  ] ++ lib.optionals stdenv.cc.isClang [
-    llvmPackages.openmp
-  ];
+  buildInputs = [ zlib ] ++ lib.optionals stdenv.cc.isClang [ llvmPackages.openmp ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     astunparse
     numpy
+    packaging
     pyparsing
     scipy
   ];
@@ -87,7 +108,9 @@ buildPythonPackage rec {
     "test_read_atomindices_2"
 
     # flaky test
+    "test_compare_rdf_t_master"
     "test_distances_t"
+    "test_precentered_2"
   ];
 
   pythonImportsCheck = [ "mdtraj" ];