From ac6d25fba797345cbf64c0a4d31436210055921a Mon Sep 17 00:00:00 2001
From: Peder Bergebakken Sundt <pbsds@hotmail.com>
Date: Mon, 22 Jul 2024 03:34:33 +0200
Subject: [PATCH 1/3] python312Packages.monty: disable flaky test

fixes https://hydra.nixos.org/build/266533294
---
 pkgs/development/python-modules/monty/default.nix | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pkgs/development/python-modules/monty/default.nix b/pkgs/development/python-modules/monty/default.nix
index 520f266f3c96..cb38fda0ce22 100644
--- a/pkgs/development/python-modules/monty/default.nix
+++ b/pkgs/development/python-modules/monty/default.nix
@@ -63,6 +63,8 @@ buildPythonPackage rec {
     "test_Path_objects"
     "test_zopen"
     "test_zpath"
+    # flaky, precision/rounding error
+    "TestJson.test_datetime"
   ];
 
   meta = with lib; {

From ffdf12ece06b8707c5aac6c6ecc32fe9d42d50f2 Mon Sep 17 00:00:00 2001
From: Peder Bergebakken Sundt <pbsds@hotmail.com>
Date: Mon, 22 Jul 2024 04:44:49 +0200
Subject: [PATCH 2/3] python312Packages.spglib: 2.4.0 -> 2.5.0

Changelog: https://github.com/spglib/spglib/raw/v2.5.0/ChangeLog
---
 pkgs/development/python-modules/spglib/default.nix | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/spglib/default.nix b/pkgs/development/python-modules/spglib/default.nix
index 300402b93107..bebf413b2b58 100644
--- a/pkgs/development/python-modules/spglib/default.nix
+++ b/pkgs/development/python-modules/spglib/default.nix
@@ -21,12 +21,12 @@
 
 buildPythonPackage rec {
   pname = "spglib";
-  version = "2.4.0";
+  version = "2.5.0";
   format = "pyproject";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-bmP57mG3DxU6ItO1ULGD2lMfiQR1kX/OIDutRZeqwkM=";
+    hash = "sha256-+LtjiJe+kbnb1MCF2f3h9pBI9ZSeIPODLLlDjldBjUs=";
   };
 
   nativeBuildInputs = [
@@ -40,6 +40,12 @@ buildPythonPackage rec {
 
   dontUseCmakeConfigure = true;
 
+  postPatch = ''
+    # relax v2 constrain in [build-system] intended for binary backward compat
+    substituteInPlace pyproject.toml \
+      --replace-fail "numpy~=2.0" "numpy"
+  '';
+
   propagatedBuildInputs = [ numpy ];
 
   nativeCheckInputs = [

From 5ce14f81665d6787a0b23c61f6e4e31de5705a64 Mon Sep 17 00:00:00 2001
From: Peder Bergebakken Sundt <pbsds@hotmail.com>
Date: Mon, 22 Jul 2024 05:05:44 +0200
Subject: [PATCH 3/3] python312Packages.pymatgen: 2024.6.10 -> 2024.7.18

---
 pkgs/development/python-modules/pymatgen/default.nix | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/pkgs/development/python-modules/pymatgen/default.nix b/pkgs/development/python-modules/pymatgen/default.nix
index a56164dee5b9..f11bd03ba1b1 100644
--- a/pkgs/development/python-modules/pymatgen/default.nix
+++ b/pkgs/development/python-modules/pymatgen/default.nix
@@ -32,7 +32,7 @@
 
 buildPythonPackage rec {
   pname = "pymatgen";
-  version = "2024.6.10";
+  version = "2024.7.18";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -41,7 +41,7 @@ buildPythonPackage rec {
     owner = "materialsproject";
     repo = "pymatgen";
     rev = "refs/tags/v${version}";
-    hash = "sha256-BV3zwb74ZnwTWUgKt5K6lZLASdO6/UQ8Ke3gBsLhy2M=";
+    hash = "sha256-LL3cZO3LkmBuGGcO7dhO2Wtgqx9nxLureFpC8EqvS3M";
   };
 
   build-system = [ setuptools ];
@@ -82,8 +82,6 @@ buildPythonPackage rec {
   ] ++ lib.flatten (builtins.attrValues passthru.optional-dependencies);
 
   preCheck = ''
-    # hide from tests
-    mv pymatgen _pymatgen
     # ensure tests can find these
     export PMG_TEST_FILES_DIR="$(realpath ./tests/files)"
     # some tests cover the command-line scripts