Your message dated Thu, 28 May 2026 10:34:26 +0000
with message-id <[email protected]>
and subject line Bug#1135061: fixed in python-anndata 0.12.16-1
has caused the Debian Bug report #1135061,
regarding python-anndata: tests fail with scipy 1.17: 'backed_csr_matrix'
object has no attribute '_validate_indices'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1135061: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1135061
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: python-anndata
Version: 0.12.7-1
Severity: normal
python-anndata is failing debci tests with scipy 1.17,
currently available in experimental
e.g. https://ci.debian.net/packages/p/python-anndata/unstable/amd64/70575515/
234s _____ test_read_array[zarr3-array_bool_subset-slice_int_subset-csr_matrix]
_____
234s [gw42] linux -- Python 3.14.4 /usr/bin/python3.14
234s
234s tmp_path =
PosixPath('/tmp/pytest-of-debci/pytest-0/popen-gw42/test_read_array_zarr3_array_bo0')
234s sparse_format = <class 'scipy.sparse._csr.csr_matrix'>, diskfmt = 'zarr'
234s subset_func = <function array_bool_subset at 0x7f5c7c0da4b0>
234s subset_func2 = <function slice_int_subset at 0x7f5c7c0db110>
234s
234s @pytest.mark.parametrize("sparse_format", [sparse.csr_matrix,
sparse.csc_matrix])
234s @pytest.mark.parametrize(
234s ("subset_func", "subset_func2"),
234s product(
234s [
234s test_helpers.array_subset,
234s test_helpers.slice_int_subset,
234s test_helpers.array_int_subset,
234s test_helpers.array_bool_subset,
234s ],
234s repeat=2,
234s ),
234s )
234s def test_read_array(
234s tmp_path: Path,
234s sparse_format: Callable[[ArrayLike], CSMatrix],
234s diskfmt: Literal["h5ad", "zarr"],
234s subset_func,
234s subset_func2,
234s ):
234s path = tmp_path / f"test.{diskfmt.replace('ad', '')}"
234s a = sparse_format(sparse.random(100, 100))
234s obs_idx = subset_func(np.arange(100))
234s var_idx = subset_func2(np.arange(100))
234s f = open_write_group(path, mode="a") if diskfmt == "zarr" else
h5py.File(path, "a")
234s ad.io.write_elem(f, "mtx", a)
234s diskmtx = sparse_dataset(f["mtx"])
234s ad.settings.use_sparse_array_on_read = True
234s > assert issubclass(type(diskmtx[obs_idx, var_idx]), CSArray)
234s ^^^^^^^^^^^^^^^^^^^^^^^^^
234s
234s tests/test_backed_sparse.py:336:
234s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _
234s /usr/lib/python3/dist-packages/anndata/_core/sparse_dataset.py:461: in
__getitem__
234s row_sp_matrix_validated, col_sp_matrix_validated = validate_indices(
234s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _
234s
234s mtx = <Compressed Sparse Row sparse matrix of dtype 'float64'
234s with 100 stored elements and shape (100, 100)>
234s indices = (array([ True, True, True, False, True, True, False, True,
False,
234s False, False, True, False, False, True... False, False, False,
False, False, False, False, False, False,
234s False]), slice(np.int64(3), np.int64(43), None))
234s
234s def validate_indices(
234s mtx: BackedSparseMatrix, indices: tuple[Index1D, Index1D]
234s ) -> tuple[Index1D, Index1D]:
234s > res = mtx._validate_indices(indices)
234s ^^^^^^^^^^^^^^^^^^^^^
234s E AttributeError: 'backed_csr_matrix' object has no attribute
'_validate_indices'. Did you mean: '_prepare_indices'?
234s
234s /usr/lib/python3/dist-packages/anndata/_core/sparse_dataset.py:395:
AttributeError
This bug will become RC severity: serious later once scipy 1.17 is
uploaded to unstable.
--- End Message ---
--- Begin Message ---
Source: python-anndata
Source-Version: 0.12.16-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-anndata, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated python-anndata package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 28 May 2026 12:19:45 +0200
Source: python-anndata
Architecture: source
Version: 0.12.16-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1135061 1136868
Changes:
python-anndata (0.12.16-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
Closes: #1136868, #1135061
* d/watch: Do not report RC candidates
* Standards-Version: 4.7.4 (routine-update)
* Build-Depends: python3-scverse-misc
* Fix test for Pandas >= 2.3
* Skip dask_distributed tests
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