python3Packages.scanpy: 1.12.1 -> 1.12.2 (#536694)

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

@@ -26,6 +26,7 @@
   pynndescent,
   scikit-learn,
   scipy,
+  scverse-misc,
   seaborn,
   session-info2,
   statsmodels,
@@ -63,14 +64,15 @@
 
 buildPythonPackage (finalAttrs: {
   pname = "scanpy";
-  version = "1.12.1";
+  version = "1.12.2";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "scverse";
     repo = "scanpy";
     tag = finalAttrs.version;
-    hash = "sha256-r8kicjCFyEKLxQtFYuZg0NKK7gRBoaLSSFGWqcQtBqM=";
+    hash = "sha256-0CtFaj0+mCNDLG5h728vJkvYGcsa48SbDd3/Y8TXtQo=";
   };
 
   # Otherwise, several tests fail to be collected:
@@ -105,6 +107,7 @@ buildPythonPackage (finalAttrs: {
     pynndescent
     scikit-learn
     scipy
+    scverse-misc
     seaborn
     session-info2
     statsmodels
@@ -206,6 +209,7 @@ buildPythonPackage (finalAttrs: {
     "test_burczynski06"
     "test_clip"
     "test_doc_shape"
+    "test_download_atomic"
     "test_download_failure"
     "test_ebi_expression_atlas"
     "test_mean_var"

pkgs/development/python-modules/scverse-misc/default.nix

@@ -0,0 +1,87 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+
+  # build-system
+  hatch-vcs,
+  hatchling,
+
+  # dependencies
+  session-info2,
+  typing-extensions,
+
+  # optional-dependencies
+  # datasets:
+  anndata,
+  pooch,
+  pyyaml,
+  tqdm,
+  # settings:
+  pydantic-settings,
+  python-dotenv,
+  # sphinx:
+  sphinx,
+
+  # tests
+  pytestCheckHook,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "scverse-misc";
+  version = "0.1.1";
+  pyproject = true;
+  __structuredAttrs = true;
+
+  src = fetchFromGitHub {
+    owner = "scverse";
+    repo = "scverse-misc";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-PkvOaxGbZ1i10xgghdvGLCKiXcwg/eZzYvQ7Gp3K+JE=";
+  };
+
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
+
+  dependencies = [
+    session-info2
+    typing-extensions
+  ];
+
+  optional-dependencies = {
+    datasets = [
+      anndata
+      pooch
+      pyyaml
+      tqdm
+    ];
+    settings = [
+      pydantic-settings
+      python-dotenv
+    ];
+    spatialdata = [
+      # spatialdata (unpackaged)
+    ];
+    sphinx = [
+      # pydocstring-rs (unpackaged)
+      sphinx
+    ];
+  };
+
+  pythonImportsCheck = [ "scverse_misc" ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+    pyyaml
+  ];
+
+  meta = {
+    description = "Miscellaneous utility code used by scverse packages";
+    homepage = "https://github.com/scverse/scverse-misc";
+    changelog = "https://github.com/scverse/scverse-misc/blob/${finalAttrs.src.tag}/CHANGELOG.md";
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+})

pkgs/top-level/python-packages.nix

@@ -17932,6 +17932,8 @@ self: super: with self; {
 
   scspell = callPackage ../development/python-modules/scspell { };
 
+  scverse-misc = callPackage ../development/python-modules/scverse-misc { };
+
   sdbus = callPackage ../development/python-modules/sdbus { };
 
   sdbus-networkmanager = callPackage ../development/python-modules/sdbus-networkmanager { };