python3Packages.scanpy: 1.11.5 -> 1.12.0 (#483219)

2026-01-24 09:41:30 +00:00
parent a5755ca3c2 ddcb01a922
commit 03e1994e21
2 changed files with 146 additions and 21 deletions
@@ -1,22 +1,48 @@
 {
+  lib,
  buildPythonPackage,
-  dask,
  fetchFromGitHub,
+
+  # build-system
  hatch-docstring-description,
  hatch-fancy-pypi-readme,
  hatch-min-requirements,
  hatch-vcs,
  hatchling,
-  lib,
-  numba,
+
+  # dependencies
  numpy,
+
+  # optional-dependencies
+  # accel
+  numba,
+  # dask
+  dask,
+  # doc
+  furo,
+  pytest,
+  sphinx,
+  sphinx-autodoc-typehints,
+  # full
+  h5py,
+  zarr,
+  # test
+  anndata,
+  numcodecs,
+  # test-min
+  coverage,
  pytest-codspeed,
  pytest-doctestplus,
+  pytest-xdist,
+  # testing
+  packaging,
+
+  # tests
  pytestCheckHook,
  scipy,
 }:

-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
  pname = "fast-array-utils";
  version = "1.3.1";
  pyproject = true;
@@ -24,7 +50,7 @@ buildPythonPackage rec {
  src = fetchFromGitHub {
    owner = "scverse";
    repo = "fast-array-utils";
-    tag = "v${version}";
+    tag = "v${finalAttrs.version}";
    hash = "sha256-FUzCdDFDqP+izlSWruWzslfPayzRN7MFx1LOikyMDss=";
  };

@@ -43,6 +69,53 @@ buildPythonPackage rec {
    numpy
  ];

+  optional-dependencies = lib.fix (self: {
+    accel = [
+      numba
+    ];
+    dask = [
+      dask
+    ];
+    doc = [
+      furo
+      pytest
+      # scanpydoc
+      sphinx
+      sphinx-autodoc-typehints
+      # sphinx-autofixture
+    ];
+    full = [
+      h5py
+      zarr
+    ]
+    ++ self.accel
+    ++ self.dask
+    ++ self.sparse;
+    sparse = [
+      scipy
+    ];
+    test = [
+      anndata
+      numcodecs
+      zarr
+    ]
+    ++ self.accel
+    ++ self.test-min;
+    test-min = [
+      coverage
+      pytest
+      pytest-codspeed
+      pytest-doctestplus
+      pytest-xdist
+    ]
+    ++ coverage.optional-dependencies.toml
+    ++ self.sparse
+    ++ self.testing;
+    testing = [
+      packaging
+    ];
+  });
+
  nativeCheckInputs = [
    dask
    numba
@@ -62,9 +135,10 @@ buildPythonPackage rec {
  meta = {
    description = "Fast array utilities";
    homepage = "https://icb-fast-array-utils.readthedocs-hosted.com";
+    changelog = "https://github.com/scverse/fast-array-utils/releases/tag/${finalAttrs.src.tag}";
    license = lib.licenses.mpl20;
    maintainers = with lib.maintainers; [
      samuela
    ];
  };
-}
+})
@@ -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";
  };
-}
+})