python3Packages.anndata: init at 0.11.4 (#418562)
* python3Packages.anndata: init at 0.11.4 * Update pkgs/development/python-modules/anndata/default.nix Co-authored-by: dotlambda <nix@dotlambda.de> * Update pkgs/development/python-modules/anndata/default.nix Co-authored-by: dotlambda <nix@dotlambda.de> * Update pkgs/development/python-modules/anndata/default.nix Co-authored-by: dotlambda <nix@dotlambda.de> * Update pkgs/development/python-modules/anndata/default.nix Co-authored-by: dotlambda <nix@dotlambda.de> * Update pkgs/development/python-modules/anndata/default.nix Co-authored-by: dotlambda <nix@dotlambda.de> * python3Packages.anndata: fix build on aarch64-darwin --------- Co-authored-by: dotlambda <nix@dotlambda.de>
This commit is contained in:
Samuel Ainsworth
co-authored by
dotlambda
dotlambda
parent
07fa4d0cb8
commit
6a10970285
@@ -0,0 +1,158 @@
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{
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array-api-compat,
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awkward,
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boltons,
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buildPythonPackage,
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dask,
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distributed,
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fetchFromGitHub,
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filelock,
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h5py,
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hatch-vcs,
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hatchling,
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joblib,
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lib,
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natsort,
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numba,
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numpy,
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openpyxl,
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packaging,
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pandas,
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pyarrow,
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pytest-mock,
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pytest-xdist,
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pytestCheckHook,
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pythonOlder,
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scikit-learn,
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scipy,
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stdenv,
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typing-extensions,
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zarr,
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}:
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buildPythonPackage rec {
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pname = "anndata";
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version = "0.11.4";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "scverse";
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repo = "anndata";
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tag = version;
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hash = "sha256-9RDR0veZ8n2sq0kUbAkS2nP57u47cQxmubzuWWYBKBY=";
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};
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build-system = [
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hatch-vcs
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hatchling
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];
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dependencies = [
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array-api-compat
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h5py
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natsort
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numpy
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pandas
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scipy
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];
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nativeCheckInputs = [
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awkward
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boltons
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dask
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distributed
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filelock
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joblib
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numba
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openpyxl
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pyarrow
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pytest-mock
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pytest-xdist
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pytestCheckHook
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scikit-learn
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zarr
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];
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# Optionally disable pytest-xdist to make it easier to debug the test suite.
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# Test suite takes ~5 minutes without pytest-xdist. Note that some tests will
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# fail when running without pytest-xdist ("worker_id not found").
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# pytestFlagsArray = [ "-o" "addopts=" ];
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disabledTestPaths = [
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# Tests that require scanpy, creating a circular dependency chain
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"src/anndata/_core/anndata.py"
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"src/anndata/_core/merge.py"
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"src/anndata/_core/sparse_dataset.py"
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"src/anndata/_io/specs/registry.py"
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"src/anndata/_io/utils.py"
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"src/anndata/_warnings.py"
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"src/anndata/experimental/merge.py"
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"src/anndata/experimental/multi_files/_anncollection.py"
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"src/anndata/utils.py"
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];
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disabledTests =
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[
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# doctests that require scanpy, creating a circular dependency chain. These
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# do not work in disabledTestPaths for some reason.
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"anndata._core.anndata.AnnData.concatenate"
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"anndata._core.anndata.AnnData.obs_names_make_unique"
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"anndata._core.anndata.AnnData.var_names_make_unique"
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"anndata._core.merge.concat"
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"anndata._core.merge.gen_reindexer"
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"anndata._core.sparse_dataset.sparse_dataset"
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"anndata._io.specs.registry.read_elem_as_dask"
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"anndata._io.utils.report_read_key_on_error"
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"anndata._io.utils.report_write_key_on_error"
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"anndata._warnings.ImplicitModificationWarning"
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"anndata.experimental.merge.concat_on_disk"
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"anndata.experimental.multi_files._anncollection.AnnCollection"
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"anndata.utils.make_index_unique"
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"ci.scripts.min-deps.min_dep"
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"concatenation.rst"
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# Tests that require cupy and GPU access. Introducing cupy as a dependency
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# would make this package unfree and GPU access is not possible within the
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# nix build environment anyhow.
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"test_adata_raw_gpu"
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"test_as_cupy_dask"
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"test_as_dask_functions"
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"test_concat_different_types_dask"
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"test_concat_on_var_outer_join"
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"test_concatenate_layers_misaligned"
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"test_concatenate_layers_outer"
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"test_concatenate_layers"
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"test_concatenate_roundtrip"
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"test_dask_to_memory_unbacked"
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"test_ellipsis_index"
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"test_error_on_mixed_device"
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"test_gpu"
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"test_io_spec_cupy"
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"test_modify_view_component"
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"test_nan_merge"
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"test_pairwise_concat"
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"test_raw_gpu"
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"test_set_scalar_subset_X"
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"test_transposed_concat"
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"test_view_different_type_indices"
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"test_view_of_view"
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# Tests that are seemingly broken. See https://github.com/scverse/anndata/issues/2017.
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"test_concat_dask_sparse_matches_memory"
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]
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++ lib.optionals (stdenv.isAarch64 && stdenv.isDarwin) [
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# RuntimeError: Cluster failed to start: [Errno 1] Operation not permitted
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"test_dask_distributed_write"
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"test_read_lazy_h5_cluster"
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];
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pythonImportsCheck = [ "anndata" ];
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meta = {
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changelog = "https://github.com/scverse/anndata/blob/main/docs/release-notes/${version}.md";
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description = "Python package for handling annotated data matrices in memory and on disk";
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homepage = "https://anndata.readthedocs.io/";
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license = lib.licenses.bsd3;
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maintainers = with lib.maintainers; [ samuela ];
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};
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}
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@@ -681,6 +681,8 @@ self: super: with self; {
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anitopy = callPackage ../development/python-modules/anitopy { };
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anndata = callPackage ../development/python-modules/anndata { };
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annexremote = callPackage ../development/python-modules/annexremote { };
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annotated-types = callPackage ../development/python-modules/annotated-types { };
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