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What happens if I push all of nixpkgs
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Nix
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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"). # 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" ];
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 ]; };}