From 39510dfd3f4428c2566e0d6014dab772dacdf26e Mon Sep 17 00:00:00 2001
From: Doron Behar <doron.behar@gmail.com>
Date: Mon, 13 Jul 2026 10:57:44 +0300
Subject: [PATCH 1/3] python3Packages.parsnip: categorize inputs

---
 pkgs/development/python-modules/parsnip/default.nix | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/pkgs/development/python-modules/parsnip/default.nix b/pkgs/development/python-modules/parsnip/default.nix
index 01cc2248d975..e5b7af805993 100644
--- a/pkgs/development/python-modules/parsnip/default.nix
+++ b/pkgs/development/python-modules/parsnip/default.nix
@@ -2,9 +2,15 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   setuptools,
+
+  # dependencies
   more-itertools,
   numpy,
+
+  # tests
   ase,
   gemmi,
   pycifrw,

From a77e5341c588b4b1b237d152ace787a3ef107554 Mon Sep 17 00:00:00 2001
From: Doron Behar <doron.behar@gmail.com>
Date: Sun, 12 Jul 2026 12:07:23 +0300
Subject: [PATCH 2/3] python3Packages.parsnip: fix Numpy 2.5 error

---
 pkgs/development/python-modules/parsnip/default.nix | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/pkgs/development/python-modules/parsnip/default.nix b/pkgs/development/python-modules/parsnip/default.nix
index e5b7af805993..d71458cca8bf 100644
--- a/pkgs/development/python-modules/parsnip/default.nix
+++ b/pkgs/development/python-modules/parsnip/default.nix
@@ -2,6 +2,7 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+  fetchpatch,
 
   # build-system
   setuptools,
@@ -33,6 +34,18 @@ buildPythonPackage (finalAttrs: {
     hash = "sha256-A1YoTBRN3ukcueUso5P2zPZ/pxu25k9h6aI7+AQvr1Q=";
   };
 
+  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
   ];

From 8a8445ec5e05530d1fa3910c778156297d7196c5 Mon Sep 17 00:00:00 2001
From: Doron Behar <doron.behar@gmail.com>
Date: Sun, 12 Jul 2026 11:51:11 +0300
Subject: [PATCH 3/3] python3Packages.parsnip: 0.6.0 -> 1.0.0

Diff: https://github.com/glotzerlab/parsnip/compare/v0.6.0...v1.0.0

Changelog: https://github.com/glotzerlab/parsnip/blob/v1.0.0/changelog.rst
---
 pkgs/development/python-modules/parsnip/default.nix | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/parsnip/default.nix b/pkgs/development/python-modules/parsnip/default.nix
index d71458cca8bf..ecba18084e7b 100644
--- a/pkgs/development/python-modules/parsnip/default.nix
+++ b/pkgs/development/python-modules/parsnip/default.nix
@@ -14,6 +14,7 @@
   # tests
   ase,
   gemmi,
+  gsd,
   pycifrw,
   pytest-doctestplus,
   pytestCheckHook,
@@ -22,7 +23,7 @@
 
 buildPythonPackage (finalAttrs: {
   pname = "parsnip";
-  version = "0.6.0";
+  version = "1.0.0";
   pyproject = true;
 
   __structuredAttrs = true;
@@ -31,7 +32,7 @@ buildPythonPackage (finalAttrs: {
     owner = "glotzerlab";
     repo = "parsnip";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-A1YoTBRN3ukcueUso5P2zPZ/pxu25k9h6aI7+AQvr1Q=";
+    hash = "sha256-27FEp+Z+Q4a2RR01YVmN7eUClpto8uUysp5mZWeKz7M=";
   };
 
   patches = [
@@ -58,6 +59,7 @@ buildPythonPackage (finalAttrs: {
   nativeCheckInputs = [
     ase
     gemmi
+    gsd
     pycifrw
     pytest-doctestplus
     pytestCheckHook