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Fix sparse matrix interactions in sq.gr.utils. #891

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merged 7 commits into from
Oct 14, 2024
Merged

Fix sparse matrix interactions in sq.gr.utils. #891

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387795b
Fix sparse matrix interactions in `sq.gr.utils`.
alam-shahul Sep 23, 2024
dff6eb1
Make import depend on `anndata` version.
alam-shahul Oct 10, 2024
24940cc
Fix logic for `anndata` import.
alam-shahul Oct 10, 2024
72d601b
Merge branch 'main' into main
alam-shahul Oct 11, 2024
0e72ea5
Make comparison version correct.
alam-shahul Oct 11, 2024
b012df3
Merge branch 'main' of https://github.com/alam-shahul/squidpy into sp…
alam-shahul Oct 11, 2024
70e9bb2
Merge pull request #1 from alam-shahul/sparse-matrix-fix
alam-shahul Oct 11, 2024
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11 changes: 10 additions & 1 deletion src/squidpy/gr/_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,12 @@
from contextlib import contextmanager
from typing import TYPE_CHECKING, Any

import anndata
import numpy as np
import pandas as pd
from anndata import AnnData
from anndata._core.views import ArrayView, SparseCSCView, SparseCSRView
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from anndata.utils import make_index_unique
from packaging.version import Version
from pandas import CategoricalDtype
from pandas.api.types import infer_dtype
from scanpy import logging as logg
Expand All @@ -19,6 +20,14 @@
from squidpy._docs import d
from squidpy._utils import NDArrayA, _unique_order_preserving

CAN_USE_SPARSE_ARRAY = Version(anndata.__version__) >= Version("0.11.0rc1")
if CAN_USE_SPARSE_ARRAY:
from anndata._core.views import ArrayView
from anndata._core.views import SparseCSCMatrixView as SparseCSCView
from anndata._core.views import SparseCSRMatrixView as SparseCSRView
else:
from anndata._core.views import ArrayView, SparseCSCView, SparseCSRView


def _check_tuple_needles(
needles: Sequence[tuple[Any, Any]],
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