python313Packages.scanpy: init at 1.11.4 (#433795)

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

···
 {
+  anndata,
   array-api-compat,
   awkward,
   boltons,
···
   numba,
   numpy,
   openpyxl,
-  packaging,
   pandas,
   pyarrow,
   pytest-mock,
   pytest-xdist,
   pytestCheckHook,
-  pythonOlder,
+  scanpy,
   scikit-learn,
   scipy,
   stdenv,
-  typing-extensions,
   zarr,
 }:
 
···
     numpy
     pandas
     scipy
+    zarr
   ];
 
   nativeCheckInputs = [
···
     pytest-xdist
     pytestCheckHook
     scikit-learn
-    zarr
+    scanpy
   ];
 
   # Optionally disable pytest-xdist to make it easier to debug the test suite.
···
   # fail when running without pytest-xdist ("worker_id not found").
   # pytestFlags = [ "-oaddopts=" ];
 
-  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"
-  ];
+  preCheck = ''
+    export NUMBA_CACHE_DIR=$(mktemp -d);
+  '';
+
+  doCheck = false; # use passthru.tests instead to prevent circularity with `scanpy`
+
+  passthru.tests = anndata.overridePythonAttrs { doCheck = true; };
 
   disabledTests = [
     # requires data from a previous test execution:
     "test_no_diff"
 
-    # 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.extensions.register_anndata_namespac"
-    "anndata._core.merge.concat"
-    "anndata._core.merge.gen_reindexer"
-    "anndata._core.sparse_dataset.sparse_dataset"
-    "anndata._io.specs.registry.read_elem_as_dask"
+    # try to download data:
     "anndata._io.specs.registry.read_elem_lazy"
-    "anndata._io.utils.report_read_key_on_error"
-    "anndata._io.utils.report_write_key_on_error"
-    "anndata._warnings.ImplicitModificationWarning"
-    "anndata.experimental.backed._io.read_lazy"
     "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

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

···
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  hatch-vcs,
+  hatchling,
+  anndata,
+  h5py,
+  joblib,
+  legacy-api-wrap,
+  matplotlib,
+  natsort,
+  networkx,
+  numba,
+  numpy,
+  packaging,
+  pandas,
+  patsy,
+  pynndescent,
+  scikit-learn,
+  scipy,
+  seaborn,
+  session-info2,
+  statsmodels,
+  tqdm,
+  typing-extensions,
+  umap-learn,
+  dask,
+  dask-ml,
+
+  igraph,
+  leidenalg,
+  scikit-image,
+  scikit-misc,
+  zarr,
+  pytestCheckHook,
+  pytest-cov-stub,
+  pytest-mock,
+  pytest-randomly,
+  pytest-rerunfailures,
+  pytest-xdist,
+  tuna,
+}:
+
+buildPythonPackage rec {
+  pname = "scanpy";
+  version = "1.11.4";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "scverse";
+    repo = "scanpy";
+    tag = version;
+    hash = "sha256-EvNelorfLOpYLGGZ1RSq4+jk6emuCWCKBdUop24iLf4=";
+  };
+
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
+
+  dependencies = [
+    anndata
+    h5py
+    joblib
+    legacy-api-wrap
+    matplotlib
+    natsort
+    networkx
+    numba
+    numpy
+    packaging
+    pandas
+    patsy
+    pynndescent
+    scikit-learn
+    scipy
+    seaborn
+    session-info2
+    statsmodels
+    tqdm
+    typing-extensions
+    umap-learn
+  ];
+
+  optional-dependencies = {
+    # commented attributes are due to some dependencies not being in Nixpkgs
+    #bbknn = [
+    #  bbknn
+    #];
+    dask = [
+      anndata
+      dask
+    ];
+    dask-ml = [
+      dask-ml
+    ];
+    #harmony = [
+    #  harmonypy
+    #];
+    leiden = [
+      igraph
+      leidenalg
+    ];
+    #louvain = [
+    #  igraph
+    #  louvain
+    #];
+    #magic = [
+    #  magic-impute
+    #];
+    paga = [
+      igraph
+    ];
+    #rapids = [
+    #  cudf
+    #  cugraph
+    #  cuml
+    #];
+    #scanorama = [
+    #  scanorama
+    #];
+    scrublet = [
+      scikit-image
+    ];
+    skmisc = [
+      scikit-misc
+    ];
+  };
+
+  nativeCheckInputs = [
+    pytestCheckHook
+    pytest-cov-stub
+    pytest-mock
+    pytest-randomly
+    pytest-rerunfailures
+    pytest-xdist
+    tuna
+    zarr
+  ];
+
+  preCheck = ''
+    export NUMBA_CACHE_DIR=$(mktemp -d);
+  '';
+
+  disabledTestPaths = [
+    # try to download data:
+    "tests/test_aggregated.py"
+    "tests/test_highly_variable_genes.py"
+    "tests/test_normalization.py"
+    "tests/test_pca.py"
+    "tests/test_plotting.py"
+    "tests/test_plotting_embedded/"
+  ];
+
+  disabledTests = [
+    # try to download data:
+    "scanpy.get._aggregated.aggregate"
+    "scanpy.plotting._tools.scatterplots.spatial"
+    "test_clip"
+    "test_download_failure"
+    "test_mean_var"
+    "test_regress_out_int"
+    "test_score_with_reference"
+
+    # fails to find the trivial test script for some reason:
+    "test_external"
+  ];
+
+  pythonImportsCheck = [
+    "scanpy"
+  ];
+
+  meta = {
+    description = "Single-cell analysis in Python which scales to >100M cells";
+    homepage = "https://scanpy.readthedocs.io";
+    changelog = "https://github.com/scverse/scanpy/releases/tag/${src.tag}";
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ bcdarwin ];
+    mainProgram = "scanpy";
+  };
+}

pkgs/development/python-modules/session-info2/default.nix

···
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  hatch-docstring-description,
+  hatch-vcs,
+  hatchling,
+  coverage,
+  ipykernel,
+  jupyter-client,
+  pytestCheckHook,
+  pytest-asyncio,
+  pytest-subprocess,
+  testing-common-database,
+  writableTmpDirAsHomeHook,
+}:
+
+buildPythonPackage rec {
+  pname = "session-info2";
+  version = "0.2";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "scverse";
+    repo = "session-info2";
+    tag = "v${version}";
+    hash = "sha256-DsI2mFM7xZgSm24yVzF6B+2aruKsjkTKZAmJPg7mWgg=";
+  };
+
+  build-system = [
+    hatch-docstring-description
+    hatch-vcs
+    hatchling
+  ];
+
+  nativeCheckInputs = [
+    coverage
+    ipykernel
+    jupyter-client
+    pytestCheckHook
+    pytest-asyncio
+    pytest-subprocess
+    testing-common-database
+    writableTmpDirAsHomeHook
+  ];
+
+  pythonImportsCheck = [
+    "session_info2"
+  ];
+
+  meta = {
+    description = "Report Python session information";
+    homepage = "https://session-info2.readthedocs.io";
+    changelog = "https://github.com/scverse/session-info2/releases/tag/${src.tag}";
+    license = lib.licenses.mpl20;
+    maintainers = with lib.maintainers; [ bcdarwin ];
+  };
+}

pkgs/top-level/python-packages.nix

···
 
   scancode-toolkit = callPackage ../development/python-modules/scancode-toolkit { };
 
+  scanpy = callPackage ../development/python-modules/scanpy { };
+
   scapy = callPackage ../development/python-modules/scapy {
     inherit (pkgs) libpcap; # Avoid confusion with python package of the same name
   };
···
   serverlessrepo = callPackage ../development/python-modules/serverlessrepo { };
 
   service-identity = callPackage ../development/python-modules/service-identity { };
+
+  session-info2 = callPackage ../development/python-modules/session-info2 { };
 
   setproctitle = callPackage ../development/python-modules/setproctitle { };