python3Packages.parsnip: fix Numpy 2.5 error (#540990)

pkgs/development/python-modules/parsnip/default.nix

@@ -2,11 +2,19 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+  fetchpatch,
+
+  # build-system
   setuptools,
+
+  # dependencies
   more-itertools,
   numpy,
+
+  # tests
   ase,
   gemmi,
+  gsd,
   pycifrw,
   pytest-doctestplus,
   pytestCheckHook,
@@ -15,7 +23,7 @@
 
 buildPythonPackage (finalAttrs: {
   pname = "parsnip";
-  version = "0.6.0";
+  version = "1.0.0";
   pyproject = true;
 
   __structuredAttrs = true;
@@ -24,9 +32,21 @@ buildPythonPackage (finalAttrs: {
     owner = "glotzerlab";
     repo = "parsnip";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-A1YoTBRN3ukcueUso5P2zPZ/pxu25k9h6aI7+AQvr1Q=";
+    hash = "sha256-27FEp+Z+Q4a2RR01YVmN7eUClpto8uUysp5mZWeKz7M=";
   };
 
+  patches = [
+    # Numpy 2.5 compatibility, see: https://github.com/glotzerlab/parsnip/pull/245
+    (fetchpatch {
+      url = "https://github.com/glotzerlab/parsnip/commit/41a6bd6e42ea212203d5ce5864c687927b834586.patch";
+      includes = [
+        # Other files are changelog & credits
+        "parsnip/parsnip.py"
+      ];
+      hash = "sha256-Y91fITsPkmcct2tDsaHtNB8ct41IMtw1A+QnRwChc7k=";
+    })
+  ];
+
   build-system = [
     setuptools
   ];
@@ -39,6 +59,7 @@ buildPythonPackage (finalAttrs: {
   nativeCheckInputs = [
     ase
     gemmi
+    gsd
     pycifrw
     pytest-doctestplus
     pytestCheckHook