From 5f1daf04129bac9d6a86a32c1d08574fd0ec3ec4 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sun, 5 May 2024 02:07:56 +0900
Subject: [PATCH 1/4] python311Packages.mdtraj: fix runtime error

---
 pkgs/development/python-modules/mdtraj/default.nix | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/pkgs/development/python-modules/mdtraj/default.nix b/pkgs/development/python-modules/mdtraj/default.nix
index 971688348a1d..74378da65e6c 100644
--- a/pkgs/development/python-modules/mdtraj/default.nix
+++ b/pkgs/development/python-modules/mdtraj/default.nix
@@ -39,6 +39,13 @@ 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=";
+    })
   ];
 
   nativeBuildInputs = [

From c88f9d5c9e3d9d90a81f08e7ce1a6bd798ac98de Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sun, 5 May 2024 02:08:51 +0900
Subject: [PATCH 2/4] python312Packages.mdtraj: enable python312 support

---
 .../python-modules/mdtraj/default.nix           | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/pkgs/development/python-modules/mdtraj/default.nix b/pkgs/development/python-modules/mdtraj/default.nix
index 74378da65e6c..7d1f0521cdbd 100644
--- a/pkgs/development/python-modules/mdtraj/default.nix
+++ b/pkgs/development/python-modules/mdtraj/default.nix
@@ -11,6 +11,7 @@
 , wheel
 , astunparse
 , numpy
+, packaging
 , pyparsing
 , scipy
 , gsd
@@ -46,6 +47,21 @@ buildPythonPackage rec {
       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 = [
@@ -64,6 +80,7 @@ buildPythonPackage rec {
   propagatedBuildInputs = [
     astunparse
     numpy
+    packaging
     pyparsing
     scipy
   ];

From 34399938c658031b3f6350358318794d435e487b Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sun, 5 May 2024 02:09:16 +0900
Subject: [PATCH 3/4] python311Packages.mdtraj: adopt new parameter

---
 pkgs/development/python-modules/mdtraj/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/mdtraj/default.nix b/pkgs/development/python-modules/mdtraj/default.nix
index 7d1f0521cdbd..73ee09929cfc 100644
--- a/pkgs/development/python-modules/mdtraj/default.nix
+++ b/pkgs/development/python-modules/mdtraj/default.nix
@@ -64,7 +64,7 @@ buildPythonPackage rec {
      })
   ];
 
-  nativeBuildInputs = [
+  build-system = [
     cython_0
     oldest-supported-numpy
     setuptools
@@ -77,7 +77,7 @@ buildPythonPackage rec {
     llvmPackages.openmp
   ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     astunparse
     numpy
     packaging

From 958181e1603bc03b69061aff91d4b01ef86c03d6 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sun, 12 May 2024 08:59:37 +0900
Subject: [PATCH 4/4] python311Packages.mdtraj: disable flaky tests

---
 pkgs/development/python-modules/mdtraj/default.nix | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pkgs/development/python-modules/mdtraj/default.nix b/pkgs/development/python-modules/mdtraj/default.nix
index 73ee09929cfc..a99b36c78765 100644
--- a/pkgs/development/python-modules/mdtraj/default.nix
+++ b/pkgs/development/python-modules/mdtraj/default.nix
@@ -111,7 +111,9 @@ buildPythonPackage rec {
     "test_read_atomindices_2"
 
     # flaky test
+    "test_compare_rdf_t_master"
     "test_distances_t"
+    "test_precentered_2"
   ];
 
   pythonImportsCheck = [ "mdtraj" ];