python3Packages.scikit-bio: cleanup, disable tests on darwin (#455251)

pkgs/development/python-modules/scikit-bio/default.nix

@@ -1,26 +1,30 @@
 {
   lib,
+  stdenv,
   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 {
@@ -42,29 +46,37 @@ 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" ];
 
+  # The trick above makes test collection fail on darwin:
+  # PermissionError: [Errno 1] Operation not permitted: '/nix/.Trashes'
+  doCheck = !stdenv.hostPlatform.isDarwin;
+
   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 ];
   };