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Mon, 27 Apr 2026 10:21:46 +0200 Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit From: Drew Parsons <dparsons@debian.org> To: Debian Bug Tracking System <submit@bugs.debian.org> Subject: python-anndata: tests fail with scipy 1.17: 'backed_csr_matrix' object has no attribute '_validate_indices' Message-ID: <177727810596.2851989.296378702674955879.reportbug@sandy> X-Mailer: reportbug 13.2.0 Date: Mon, 27 Apr 2026 10:21:45 +0200 X-Debian-User: dparsons Delivered-To: submit@bugs.debian.org 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. ]