python3Packages.scanpy: 1.11.5 -> 1.12.0

Diff: https://github.com/scverse/scanpy/compare/1.11.5...1.12.0

Changelog: https://github.com/scverse/scanpy/releases/tag/1.12.0

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

@@ -2,9 +2,14 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   hatch-vcs,
   hatchling,
+
+  # dependencies
   anndata,
+  fast-array-utils,
   h5py,
   joblib,
   legacy-api-wrap,
@@ -25,35 +30,54 @@
   tqdm,
   typing-extensions,
   umap-learn,
-  dask,
-  dask-ml,
 
+  # optional-attrs
+  # dask
+  dask,
+  # dask-ml
+  dask-ml,
+  # leiden
   igraph,
   leidenalg,
+  # scrublet
   scikit-image,
+  # skmisc
   scikit-misc,
-  zarr,
-  pytestCheckHook,
+
+  # tests
+  jinja2,
   pytest-cov-stub,
   pytest-mock,
   pytest-randomly,
   pytest-rerunfailures,
   pytest-xdist,
+  pytestCheckHook,
   tuna,
+  writableTmpDirAsHomeHook,
+  zarr,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "scanpy";
-  version = "1.11.5";
+  version = "1.12.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "scverse";
     repo = "scanpy";
-    tag = version;
-    hash = "sha256-GnZ1qJ4SaTLDzfLAH6IHrYeuMBo8PglKUlj4f3ljeR0=";
+    tag = finalAttrs.version;
+    hash = "sha256-jpi3SyTaG5mxCqUNSM564MMIrNdz4LBYo9+dn5nYmeY=";
   };
 
+  # Otherwise, several tests fail to be collected:
+  # AssertionError: scanpy is already imported, this will mess up test coverage
+  postPatch = ''
+    substituteInPlace src/testing/scanpy/_pytest/__init__.py \
+      --replace-fail \
+        'assert "scanpy" not in sys.modules,' \
+        'assert True,'
+  '';
+
   build-system = [
     hatch-vcs
     hatchling
@@ -61,6 +85,7 @@ buildPythonPackage rec {
 
   dependencies = [
     anndata
+    fast-array-utils
     h5py
     joblib
     legacy-api-wrap
@@ -81,7 +106,9 @@ buildPythonPackage rec {
     tqdm
     typing-extensions
     umap-learn
-  ];
+  ]
+  ++ fast-array-utils.optional-dependencies.accel
+  ++ fast-array-utils.optional-dependencies.sparse;
 
   optional-dependencies = {
     # commented attributes are due to some dependencies not being in Nixpkgs
@@ -129,13 +156,15 @@ buildPythonPackage rec {
   };
 
   nativeCheckInputs = [
-    pytestCheckHook
+    jinja2
     pytest-cov-stub
     pytest-mock
     pytest-randomly
     pytest-rerunfailures
     pytest-xdist
+    pytestCheckHook
     tuna
+    writableTmpDirAsHomeHook
     zarr
   ];
 
@@ -151,35 +180,57 @@ buildPythonPackage rec {
     "tests/test_pca.py"
     "tests/test_plotting.py"
     "tests/test_plotting_embedded/"
+
+    # fixture 'backed_adata' not found
+    "tests/test_backed.py"
   ];
 
   disabledTests = [
     # try to download data:
     "scanpy.get._aggregated.aggregate"
     "scanpy.plotting._tools.scatterplots.spatial"
+    "test_burczynski06"
     "test_clip"
+    "test_doc_shape"
     "test_download_failure"
+    "test_ebi_expression_atlas"
     "test_mean_var"
+    "test_paul15"
+    "test_pbmc3k"
+    "test_pbmc3k_processed"
     "test_regress_out_int"
     "test_score_with_reference"
+    "test_visium_datasets"
+    "test_visium_datasets_dir_change"
+    "test_visium_datasets_images"
 
     # fails to find the trivial test script for some reason:
     "test_external"
 
+    # fixture 'original_settings' not found
+    "test_defaults"
+
     # AssertionError: Not equal to tolerance rtol=1e-07, atol=0
     "test_connectivities_euclidean"
+
+    # assert sc.settings.autoshow
+    # AssertionError: assert False
+    "test_resets"
+
+    # FileNotFoundError: [Errno 2] Unable to synchronously create file (unable to open file: name =
+    # 'write/test.h5ad', errno = 2, error message = 'No such file or directory', flags = 13, o_flags
+    # = 242)
+    "test_write"
   ];
 
-  pythonImportsCheck = [
-    "scanpy"
-  ];
+  pythonImportsCheck = [ "scanpy" ];
 
   meta = {
     description = "Single-cell analysis in Python which scales to >100M cells";
     homepage = "https://scanpy.readthedocs.io";
-    changelog = "https://github.com/scverse/scanpy/releases/tag/${src.tag}";
+    changelog = "https://github.com/scverse/scanpy/releases/tag/${finalAttrs.src.tag}";
     license = lib.licenses.bsd3;
     maintainers = with lib.maintainers; [ bcdarwin ];
     mainProgram = "scanpy";
   };
-}
+})