From 99271ca28ef55a79b305722737a71054ca43f263 Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Fri, 24 Oct 2025 14:04:55 +0000
Subject: [PATCH 1/2] python3Packages.scikit-bio: cleanup

---
 .../python-modules/scikit-bio/default.nix     | 37 +++++++++++--------
 1 file changed, 22 insertions(+), 15 deletions(-)

diff --git a/pkgs/development/python-modules/scikit-bio/default.nix b/pkgs/development/python-modules/scikit-bio/default.nix
index ef4e4ed9719b..10e635b53b65 100644
--- a/pkgs/development/python-modules/scikit-bio/default.nix
+++ b/pkgs/development/python-modules/scikit-bio/default.nix
@@ -3,24 +3,27 @@
   buildPythonPackage,
   fetchFromGitHub,
 
+  # build-system
   setuptools,
   cython,
   oldest-supported-numpy,
 
-  requests,
+  # dependencies
+  array-api-compat,
+  biom-format,
   decorator,
+  h5py,
   natsort,
   numpy,
   pandas,
-  scipy,
-  h5py,
-  biom-format,
-  statsmodels,
   patsy,
-  array-api-compat,
+  requests,
+  scipy,
+  statsmodels,
 
-  python,
+  # tests
   pytestCheckHook,
+  python,
 }:
 
 buildPythonPackage rec {
@@ -42,20 +45,22 @@ buildPythonPackage rec {
   ];
 
   dependencies = [
-    requests
+    array-api-compat
+    biom-format
     decorator
+    h5py
     natsort
     numpy
     pandas
-    scipy
-    h5py
-    biom-format
-    statsmodels
     patsy
-    array-api-compat
+    requests
+    scipy
+    statsmodels
   ];
 
-  nativeCheckInputs = [ pytestCheckHook ];
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
 
   # only the $out dir contains the built cython extensions, so we run the tests inside there
   enabledTestPaths = [ "${placeholder "out"}/${python.sitePackages}/skbio" ];
@@ -63,8 +68,10 @@ buildPythonPackage rec {
   pythonImportsCheck = [ "skbio" ];
 
   meta = {
-    homepage = "http://scikit-bio.org/";
     description = "Data structures, algorithms and educational resources for bioinformatics";
+    homepage = "http://scikit-bio.org/";
+    downloadPage = "https://github.com/scikit-bio/scikit-bio";
+    changelog = "https://github.com/scikit-bio/scikit-bio/blob/${version}/CHANGELOG.md";
     license = lib.licenses.bsd3;
     maintainers = with lib.maintainers; [ tomasajt ];
   };

From 0d8c133ee49b412cf73cab7cda8124af49896729 Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Fri, 24 Oct 2025 14:29:59 +0000
Subject: [PATCH 2/2] python3Packages.scikit-bio: disable tests on darwin

---
 pkgs/development/python-modules/scikit-bio/default.nix | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/pkgs/development/python-modules/scikit-bio/default.nix b/pkgs/development/python-modules/scikit-bio/default.nix
index 10e635b53b65..151ae1f21f42 100644
--- a/pkgs/development/python-modules/scikit-bio/default.nix
+++ b/pkgs/development/python-modules/scikit-bio/default.nix
@@ -1,5 +1,6 @@
 {
   lib,
+  stdenv,
   buildPythonPackage,
   fetchFromGitHub,
 
@@ -65,6 +66,10 @@ buildPythonPackage rec {
   # only the $out dir contains the built cython extensions, so we run the tests inside there
   enabledTestPaths = [ "${placeholder "out"}/${python.sitePackages}/skbio" ];
 
+  # The trick above makes test collection fail on darwin:
+  # PermissionError: [Errno 1] Operation not permitted: '/nix/.Trashes'
+  doCheck = !stdenv.hostPlatform.isDarwin;
+
   pythonImportsCheck = [ "skbio" ];
 
   meta = {