python3Packages.anndata: init at 0.11.4 (#418562)

{

  array-api-compat,

  awkward,

  boltons,

  buildPythonPackage,

  dask,

  distributed,

  fetchFromGitHub,

  filelock,

  h5py,

  hatch-vcs,

  hatchling,

  joblib,

  lib,

  natsort,

  numba,

  numpy,

  openpyxl,

  packaging,

  pandas,

  pyarrow,

  pytest-mock,

  pytest-xdist,

  pytestCheckHook,

  pythonOlder,

  scikit-learn,

  scipy,

  stdenv,

  typing-extensions,

  zarr,

}:

buildPythonPackage rec {

  pname = "anndata";

  version = "0.11.4";

  pyproject = true;

  src = fetchFromGitHub {

    owner = "scverse";

    repo = "anndata";

    tag = version;

    hash = "sha256-9RDR0veZ8n2sq0kUbAkS2nP57u47cQxmubzuWWYBKBY=";

  };

  build-system = [

    hatch-vcs

    hatchling

  ];

  dependencies = [

    array-api-compat

    h5py

    natsort

    numpy

    pandas

    scipy

  ];

  nativeCheckInputs = [

    awkward

    boltons

    dask

    distributed

    filelock

    joblib

    numba

    openpyxl

    pyarrow

    pytest-mock

    pytest-xdist

    pytestCheckHook

    scikit-learn

    zarr

  ];

  # Optionally disable pytest-xdist to make it easier to debug the test suite.

  # Test suite takes ~5 minutes without pytest-xdist. Note that some tests will

  # fail when running without pytest-xdist ("worker_id not found").

  # pytestFlagsArray = [ "-o" "addopts=" ];

  disabledTestPaths = [

    # Tests that require scanpy, creating a circular dependency chain

    "src/anndata/_core/anndata.py"

    "src/anndata/_core/merge.py"

    "src/anndata/_core/sparse_dataset.py"

    "src/anndata/_io/specs/registry.py"

    "src/anndata/_io/utils.py"

    "src/anndata/_warnings.py"

    "src/anndata/experimental/merge.py"

    "src/anndata/experimental/multi_files/_anncollection.py"

    "src/anndata/utils.py"

  ];

  disabledTests =

    [

      # doctests that require scanpy, creating a circular dependency chain. These

      # do not work in disabledTestPaths for some reason.

      "anndata._core.anndata.AnnData.concatenate"

      "anndata._core.anndata.AnnData.obs_names_make_unique"

      "anndata._core.anndata.AnnData.var_names_make_unique"

      "anndata._core.merge.concat"

      "anndata._core.merge.gen_reindexer"

      "anndata._core.sparse_dataset.sparse_dataset"

      "anndata._io.specs.registry.read_elem_as_dask"

      "anndata._io.utils.report_read_key_on_error"

      "anndata._io.utils.report_write_key_on_error"

      "anndata._warnings.ImplicitModificationWarning"

      "anndata.experimental.merge.concat_on_disk"

      "anndata.experimental.multi_files._anncollection.AnnCollection"

      "anndata.utils.make_index_unique"

      "ci.scripts.min-deps.min_dep"

      "concatenation.rst"

      # Tests that require cupy and GPU access. Introducing cupy as a dependency

      # would make this package unfree and GPU access is not possible within the

      # nix build environment anyhow.

      "test_adata_raw_gpu"

      "test_as_cupy_dask"

      "test_as_dask_functions"

      "test_concat_different_types_dask"

      "test_concat_on_var_outer_join"

      "test_concatenate_layers_misaligned"

      "test_concatenate_layers_outer"

      "test_concatenate_layers"

      "test_concatenate_roundtrip"

      "test_dask_to_memory_unbacked"

      "test_ellipsis_index"

      "test_error_on_mixed_device"

      "test_gpu"

      "test_io_spec_cupy"

      "test_modify_view_component"

      "test_nan_merge"

      "test_pairwise_concat"

      "test_raw_gpu"

      "test_set_scalar_subset_X"

      "test_transposed_concat"

      "test_view_different_type_indices"

      "test_view_of_view"

      # Tests that are seemingly broken. See https://github.com/scverse/anndata/issues/2017.

      "test_concat_dask_sparse_matches_memory"

    ]

    ++ lib.optionals (stdenv.isAarch64 && stdenv.isDarwin) [

      # RuntimeError: Cluster failed to start: [Errno 1] Operation not permitted

      "test_dask_distributed_write"

      "test_read_lazy_h5_cluster"

    ];

  pythonImportsCheck = [ "anndata" ];

  meta = {

    changelog = "https://github.com/scverse/anndata/blob/main/docs/release-notes/${version}.md";

    description = "Python package for handling annotated data matrices in memory and on disk";

    homepage = "https://anndata.readthedocs.io/";

    license = lib.licenses.bsd3;

    maintainers = with lib.maintainers; [ samuela ];

  };

}

  anitopy = callPackage ../development/python-modules/anitopy { };

  anndata = callPackage ../development/python-modules/anndata { };

  annexremote = callPackage ../development/python-modules/annexremote { };

  annotated-types = callPackage ../development/python-modules/annotated-types { };