[From nobody Thu May 28 11:37:08 2026 Received: (at submit) by bugs.debian.org; 16 May 2026 16:27:59 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-120.5 required=4.0 tests=BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FROMDEVELOPER,FVGT_m_MULTI_ODD,HAS_PACKAGE, RCVD_IN_DNSWL_MED,SPF_HELO_PASS,SPF_PASS,USER_IN_DKIM_WELCOMELIST, X_DEBBUGS_CC autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 273; hammy, 150; neutral, 363; spammy, 0. spammytokens: hammytokens:0.000-+--python3, 0.000-+--pkgbuilddir, 0.000-+--PKGBUILDDIR, 0.000-+--forky, 0.000-+--HTo:N*Debian Return-path: <sanvila@debian.org> Received: from mitropoulos.debian.org ([2001:648:2ffc:deb:216:61ff:fe9d:958d]:47552) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1wOHrq-002EzI-2e for submit@bugs.debian.org; Sat, 16 May 2026 16:27:59 +0000 Received: via submission from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA, CN=paradis.debian.org, EMAIL=hostmaster@paradis.debian.org (verified) by mitropoulos.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1wOHro-0002x3-2m for submit@bugs.debian.org; Sat, 16 May 2026 16:27:57 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.paradis; h=Date:Message-Id:Subject:To:From:Reply-To:Cc: MIME-Version:Content-Type:Content-Transfer-Encoding:Content-ID: Content-Description:In-Reply-To:References; bh=PPP/FwaxXzDD4UyY1GJX1hImrHKa88N8nmMn67oMwa8=; b=YI46gI0CVOHHmNAHZBKE8TZPMO TT1GIB++1kpfKSChFQWOC4miMREc17i0m6ySQYzA2p7bFHiqm2uZCY0cgLco8bKvZzb/sqCLleE8F +BHEOiTXZnnspIXnD0ruzSXfhPyi3LiB3bHKLSqJVNm9wBx4DKpBHo+2bWIVHtsDxLfvv+SyISyyJ k96B42iZKciU1f6ZFIXleUhXQEjAMT8eK3nvBVmB6+pkDR9lRQxKe3igH96ouBC6Lc046Zvf3y6vN shqih/oW1u23FJlmzOSlX5SwssuKmWtcQqmiuqWhCpJrEDjjs3o5S4+U0xVv29UZvaAH9WMExD3t1 kkFGCXsQ==; Received: from sanvila by paradis.debian.org with local (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1wOHrn-000BNU-0z for submit@bugs.debian.org; Sat, 16 May 2026 16:27:55 +0000 From: Santiago Vila <sanvila@debian.org> To: Debian BTS <submit@bugs.debian.org> Subject: python-anndata: FTBFS: E ModuleNotFoundError: No module named 'zarr.convenience' X-Debbugs-Cc: sanvila@debian.org Message-Id: <E1wOHrn-000BNU-0z@paradis.debian.org> Date: Sat, 16 May 2026 16:27:55 +0000 Delivered-To: submit@bugs.debian.org Package: src:python-anndata Version: 0.12.7-1 Severity: serious Tags: ftbfs forky sid Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202605/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:python-anndata, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:142: Building wheel for python3.14 with "build" module I: pybuild base:385: python3.14 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_anndata * Building wheel... Successfully built anndata-0.12.7-py3-none-any.whl [... snipped ...] backoff = random.uniform(0, upper_cap) attempt += 1 logger.debug( "Could not connect to %s, waiting for %s before retrying", loc, backoff ) await asyncio.sleep(backoff) else: > raise OSError( f"Timed out trying to connect to {addr} after {timeout} s" ) from active_exception E OSError: Timed out trying to connect to tcp://127.0.0.1:37269 after 30 s /usr/lib/python3/dist-packages/distributed/comm/core.py:368: OSError =============================== warnings summary =============================== tests/lazy/test_concat.py: 1372 warnings tests/test_concatenate.py: 1110 warnings tests/test_concatenate_disk.py: 494 warnings tests/test_utils.py: 1 warning /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/anndata/_core/anndata.py:1806: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`. utils.warn_names_duplicates("obs") tests/test_backed_sparse.py: 136 warnings tests/test_io_elementwise.py: 1 warning tests/test_io_partial.py: 2 warnings tests/test_structured_arrays.py: 1 warning tests/test_x.py: 1 warning tests/test_dask.py: 17 warnings tests/test_io_backwards_compat.py: 1 warning /usr/lib/python3/dist-packages/zarr/api/asynchronous.py:231: ZarrUserWarning: Consolidated metadata is currently not part in the Zarr format 3 specification. It may not be supported by other zarr implementations and may change in the future. warnings.warn( tests/test_base.py: 6 warnings tests/test_annot.py: 1 warning tests/test_io_elementwise.py: 6 warnings tests/test_views.py: 1 warning /usr/lib/python3.13/functools.py:934: ImplicitModificationWarning: Transforming to str index. return dispatch(args[0].__class__)(*args, **kw) tests/test_concatenate.py: 24 warnings tests/test_concatenate_disk.py: 74 warnings /usr/lib/python3/dist-packages/scipy/sparse/_index.py:210: SparseEfficiencyWarning: Changing the sparsity structure of a csc_matrix is expensive. lil and dok are more efficient. self._set_arrayXarray(i, j, x) tests/test_concatenate.py: 923 warnings tests/test_utils.py: 1 warning tests/test_concatenate_disk.py: 480 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/anndata/_core/anndata.py:1808: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`. utils.warn_names_duplicates("var") tests/test_concatenate.py: 26 warnings tests/test_concatenate_disk.py: 178 warnings /usr/lib/python3/dist-packages/scipy/sparse/_index.py:210: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil and dok are more efficient. self._set_arrayXarray(i, j, x) tests/test_concatenate.py::test_concatenate_fill_value[nan] tests/test_concatenate.py::test_concatenate_fill_value[3.141592653589793] /usr/lib/python3/dist-packages/scipy/sparse/_index.py:210: SparseEfficiencyWarning: Changing the sparsity structure of a csc_array is expensive. lil and dok are more efficient. self._set_arrayXarray(i, j, x) tests/test_backed_dense.py::test_assign_x_subset[h5ad] tests/test_backed_dense.py::test_assign_x_subset[zarr2] tests/test_backed_dense.py::test_assign_x_subset[zarr3] /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/tests/test_backed_dense.py:84: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden view.X = np.zeros((4, 2)) tests/test_io_elementwise.py::test_io_spec[zarr3-anndata] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('bfmjz', FixedLengthUTF32(length=4, endianness='little')), ('RauJm', FixedLengthUTF32(length=4, endianness='little')), ('JYcqq', FixedLengthUTF32(length=4, endianness='little')), ('cBVYh', FixedLengthUTF32(length=4, endianness='little')), ('DOTzR', FixedLengthUTF32(length=4, endianness='little'))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_io_elementwise.py: 9 warnings tests/test_structured_arrays.py: 1 warning tests/test_x.py: 1 warning /usr/lib/python3/dist-packages/zarr/core/dtype/npy/string.py:249: UnstableSpecificationWarning: The data type (FixedLengthUTF32(length=4, endianness='little')) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_io_elementwise.py::test_io_spec_raw[zarr3] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('ghivi', FixedLengthUTF32(length=4, endianness='little')), ('JXKWi', FixedLengthUTF32(length=4, endianness='little')), ('wJYsn', FixedLengthUTF32(length=4, endianness='little')), ('JTwHO', FixedLengthUTF32(length=3, endianness='little')), ('AYCYC', FixedLengthUTF32(length=4, endianness='little'))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_io_elementwise.py::test_io_spec_raw[zarr3] tests/test_io_elementwise.py::test_write_anndata_to_root[zarr3] tests/test_io_elementwise.py::test_read_iospec_not_found[zarr3-encoding-type-floob] tests/test_io_elementwise.py::test_io_pd_cow[zarr3-cow] tests/test_io_elementwise.py::test_io_pd_cow[zarr3-nocow] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/string.py:249: UnstableSpecificationWarning: The data type (FixedLengthUTF32(length=3, endianness='little')) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_io_elementwise.py::test_write_anndata_to_root[zarr3] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('zPLgA', FixedLengthUTF32(length=4, endianness='little')), ('zBhnP', FixedLengthUTF32(length=4, endianness='little')), ('uOdlp', FixedLengthUTF32(length=4, endianness='little')), ('uoeGT', FixedLengthUTF32(length=3, endianness='little')), ('jaQgz', FixedLengthUTF32(length=4, endianness='little'))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_io_elementwise.py::test_read_iospec_not_found[zarr3-encoding-type-floob] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('VlXIA', FixedLengthUTF32(length=4, endianness='little')), ('tKEoJ', FixedLengthUTF32(length=3, endianness='little')), ('IHtyn', FixedLengthUTF32(length=4, endianness='little')), ('swaIN', FixedLengthUTF32(length=4, endianness='little')), ('dBzmZ', FixedLengthUTF32(length=4, endianness='little'))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_io_elementwise.py::test_read_iospec_not_found[zarr3-encoding-version-10000.0] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('RBuAa', FixedLengthUTF32(length=4, endianness='little')), ('Jpett', FixedLengthUTF32(length=4, endianness='little')), ('vCCTO', FixedLengthUTF32(length=4, endianness='little')), ('jwdXn', FixedLengthUTF32(length=4, endianness='little')), ('WLTjs', FixedLengthUTF32(length=4, endianness='little'))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_io_elementwise.py::test_write_to_root[zarr3-anndata] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('ZfdUX', FixedLengthUTF32(length=4, endianness='little')), ('jdLgn', FixedLengthUTF32(length=4, endianness='little')), ('UxEts', FixedLengthUTF32(length=4, endianness='little')), ('bwDdy', FixedLengthUTF32(length=4, endianness='little')), ('VbSAT', FixedLengthUTF32(length=4, endianness='little'))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_io_elementwise.py::test_io_pd_cow[zarr3-cow] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('pnrRR', FixedLengthUTF32(length=4, endianness='little')), ('JBudq', FixedLengthUTF32(length=4, endianness='little')), ('nGUYe', FixedLengthUTF32(length=4, endianness='little')), ('Yeazy', FixedLengthUTF32(length=4, endianness='little')), ('BehXe', FixedLengthUTF32(length=3, endianness='little'))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_io_elementwise.py::test_io_pd_cow[zarr3-nocow] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('vYGPP', FixedLengthUTF32(length=4, endianness='little')), ('lMMgH', FixedLengthUTF32(length=4, endianness='little')), ('QBgKZ', FixedLengthUTF32(length=3, endianness='little')), ('RzVDe', FixedLengthUTF32(length=3, endianness='little')), ('KYhdv', FixedLengthUTF32(length=4, endianness='little'))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_io_elementwise.py: 12 warnings tests/test_concatenate_disk.py: 5 warnings /usr/lib/python3/dist-packages/zarr/core/array.py:4442: ZarrUserWarning: Automatic shard shape inference is experimental and may change without notice. shard_shape_parsed, chunk_shape_parsed = _auto_partition( tests/test_io_elementwise.py::test_write_auto_sharded /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('SYSVN', FixedLengthUTF32(length=4, endianness='little')), ('hgPmd', FixedLengthUTF32(length=4, endianness='little')), ('mONpg', FixedLengthUTF32(length=4, endianness='little')), ('utOXS', FixedLengthUTF32(length=4, endianness='little')), ('PgzlH', FixedLengthUTF32(length=4, endianness='little'))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_structured_arrays.py::test_io[zarr3] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('YCpGG', FixedLengthUTF32(length=4, endianness='little')), ('bnlzr', FixedLengthUTF32(length=4, endianness='little')), ('uKODd', FixedLengthUTF32(length=4, endianness='little')), ('pyoFu', FixedLengthUTF32(length=4, endianness='little')), ('hnfcd', FixedLengthUTF32(length=4, endianness='little'))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_structured_arrays.py::test_io[zarr3] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('YCpGG', FixedLengthUTF32(length=10, endianness='little')), ('bnlzr', FixedLengthUTF32(length=10, endianness='little')), ('uKODd', FixedLengthUTF32(length=10, endianness='little')), ('pyoFu', FixedLengthUTF32(length=10, endianness='little')), ('hnfcd', FixedLengthUTF32(length=10, endianness='little'))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_structured_arrays.py::test_io[zarr3] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/string.py:249: UnstableSpecificationWarning: The data type (FixedLengthUTF32(length=10, endianness='little')) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_structured_arrays.py::test_io[zarr3] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('YCpGG', NullTerminatedBytes(length=10)), ('bnlzr', NullTerminatedBytes(length=10)), ('uKODd', NullTerminatedBytes(length=10)), ('pyoFu', NullTerminatedBytes(length=10)), ('hnfcd', NullTerminatedBytes(length=10))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_structured_arrays.py::test_io[zarr3] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/bytes.py:386: UnstableSpecificationWarning: The data type (NullTerminatedBytes(length=10)) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_views.py::test_views /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/tests/test_views.py:129: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden adata[:2, 0].X = [0, 0] tests/test_views.py::test_modify_view_component[scipy_csr_matrix-obsm] tests/test_views.py::test_modify_view_component[scipy_csr_matrix-layers] tests/test_views.py::test_modify_view_component[scipy_csr_matrix-varm] tests/test_views.py::test_modify_view_component[sparse_dask_matrix-varm] tests/test_views.py::test_modify_view_component[sparse_dask_matrix-obsm] tests/test_views.py::test_modify_view_component[sparse_dask_matrix-layers] tests/test_helpers.py::test_assert_equal_raw /usr/lib/python3/dist-packages/scipy/sparse/_index.py:168: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil and dok are more efficient. self._set_intXint(row, col, x.flat[0]) tests/test_views.py::test_modify_view_component[scipy_csc_matrix-varm] tests/test_views.py::test_modify_view_component[scipy_csc_matrix-obsm] tests/test_views.py::test_modify_view_component[scipy_csc_matrix-layers] /usr/lib/python3/dist-packages/scipy/sparse/_index.py:168: SparseEfficiencyWarning: Changing the sparsity structure of a csc_matrix is expensive. lil and dok are more efficient. self._set_intXint(row, col, x.flat[0]) tests/test_views.py: 77 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/tests/test_views.py:390: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden adata_subset.X = 1 tests/test_views.py::test_modify_view_component[scipy_csr_array-varm] tests/test_views.py::test_modify_view_component[scipy_csr_array-obsm] tests/test_views.py::test_modify_view_component[scipy_csr_array-layers] /usr/lib/python3/dist-packages/scipy/sparse/_index.py:168: SparseEfficiencyWarning: Changing the sparsity structure of a csr_array is expensive. lil and dok are more efficient. self._set_intXint(row, col, x.flat[0]) tests/test_views.py::test_modify_view_component[scipy_csc_array-varm] tests/test_views.py::test_modify_view_component[scipy_csc_array-obsm] tests/test_views.py::test_modify_view_component[scipy_csc_array-layers] /usr/lib/python3/dist-packages/scipy/sparse/_index.py:168: SparseEfficiencyWarning: Changing the sparsity structure of a csc_array is expensive. lil and dok are more efficient. self._set_intXint(row, col, x.flat[0]) tests/test_views.py::test_view_of_view_modification /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/tests/test_views.py:578: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden adata[0, :][:, 5:].X = np.ones(5) tests/test_views.py::test_view_of_view_modification /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/tests/test_views.py:580: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden adata[[1, 2], :][:, [1, 2]].X = np.ones((2, 2)) tests/test_views.py::test_view_of_view_modification /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/tests/test_views.py:584: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden adata[0, :][:, 5:].X = np.ones(5) * 2 tests/test_views.py::test_view_of_view_modification /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/tests/test_views.py:586: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden adata[[1, 2], :][:, [1, 2]].X = np.ones((2, 2)) * 2 tests/test_x.py::test_repeat_indices_view /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/tests/test_x.py:48: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden subset.X = mat tests/test_x.py: 21 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/tests/test_x.py:61: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden view.X = to_assign tests/test_x.py::test_setter_view[csr-csr] tests/test_x.py::test_setter_view[csc-csr] tests/test_x.py::test_setter_view[csr_array-csr] tests/test_x.py::test_setter_view[csc_array-csr] tests/test_x.py::test_setter_view[ndarray-csr] /usr/lib/python3/dist-packages/scipy/sparse/_index.py:201: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil and dok are more efficient. self._set_arrayXarray_sparse(i, j, x) tests/test_x.py::test_setter_view[csr-csc] tests/test_x.py::test_setter_view[csc-csc] tests/test_x.py::test_setter_view[csr_array-csc] tests/test_x.py::test_setter_view[csc_array-csc] tests/test_x.py::test_setter_view[ndarray-csc] /usr/lib/python3/dist-packages/scipy/sparse/_index.py:201: SparseEfficiencyWarning: Changing the sparsity structure of a csc_matrix is expensive. lil and dok are more efficient. self._set_arrayXarray_sparse(i, j, x) tests/test_x.py::test_setter_view[csr-csr_array] tests/test_x.py::test_setter_view[csc-csr_array] tests/test_x.py::test_setter_view[csr_array-csr_array] tests/test_x.py::test_setter_view[csc_array-csr_array] tests/test_x.py::test_setter_view[ndarray-csr_array] /usr/lib/python3/dist-packages/scipy/sparse/_index.py:201: SparseEfficiencyWarning: Changing the sparsity structure of a csr_array is expensive. lil and dok are more efficient. self._set_arrayXarray_sparse(i, j, x) tests/test_x.py::test_setter_view[csr-csc_array] tests/test_x.py::test_setter_view[csc-csc_array] tests/test_x.py::test_setter_view[csr_array-csc_array] tests/test_x.py::test_setter_view[csc_array-csc_array] tests/test_x.py::test_setter_view[ndarray-csc_array] /usr/lib/python3/dist-packages/scipy/sparse/_index.py:201: SparseEfficiencyWarning: Changing the sparsity structure of a csc_array is expensive. lil and dok are more efficient. self._set_arrayXarray_sparse(i, j, x) tests/test_x.py::test_io_missing_X[zarr3] /usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:591: UnstableSpecificationWarning: The data type (Struct(fields=(('FlvnS', FixedLengthUTF32(length=4, endianness='little')), ('IEJSM', FixedLengthUTF32(length=4, endianness='little')), ('CrayJ', FixedLengthUTF32(length=4, endianness='little')), ('Iiefh', FixedLengthUTF32(length=4, endianness='little')), ('CbviL', FixedLengthUTF32(length=4, endianness='little'))))) does not have a Zarr V3 specification. That means that the representation of arrays saved with this data type may change without warning in a future version of Zarr Python. Arrays stored with this data type may be unreadable by other Zarr libraries. Use this data type at your own risk! Check https://github.com/zarr-developers/zarr-extensions/tree/main/data-types for the status of data type specifications for Zarr V3. v3_unstable_dtype_warning(self) tests/test_io_backwards_compat.py::test_backwards_compat_files[v0.5.0] tests/test_io_backwards_compat.py::test_no_diff[v0.5.0] /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/anndata/_io/specs/registry.py:286: FutureWarning: Moving element from .uns['neighbors']['distances'] to .obsp['distances']. This is where adjacency matrices should go now. return self.callback(read_func, elem.name, elem, iospec=iospec) tests/test_io_backwards_compat.py::test_backwards_compat_files[v0.5.0] tests/test_io_backwards_compat.py::test_no_diff[v0.5.0] /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/anndata/_io/specs/registry.py:286: FutureWarning: Moving element from .uns['neighbors']['connectivities'] to .obsp['connectivities']. This is where adjacency matrices should go now. return self.callback(read_func, elem.name, elem, iospec=iospec) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_dask.py::test_dask_distributed_write[h5ad-sizes0-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[h5ad-sizes1-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[h5ad-sizes2-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[h5ad-sizes3-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[h5ad-sizes4-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[zarr2-sizes0-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[zarr2-sizes1-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[zarr2-sizes2-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[zarr2-sizes3-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[zarr2-sizes4-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[zarr3-sizes0-shard] - ... FAILED tests/test_dask.py::test_dask_distributed_write[zarr3-sizes0-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[zarr3-sizes1-shard] - ... FAILED tests/test_dask.py::test_dask_distributed_write[zarr3-sizes1-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[zarr3-sizes2-shard] - ... FAILED tests/test_dask.py::test_dask_distributed_write[zarr3-sizes2-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[zarr3-sizes3-shard] - ... FAILED tests/test_dask.py::test_dask_distributed_write[zarr3-sizes3-no-shard] FAILED tests/test_dask.py::test_dask_distributed_write[zarr3-sizes4-shard] - ... FAILED tests/test_dask.py::test_dask_distributed_write[zarr3-sizes4-no-shard] ERROR tests/test_readwrite.py - ImportError while importing test module '/bui... = 20 failed, 6774 passed, 945 skipped, 164 xfailed, 5053 warnings, 1 error in 1265.52s (0:21:05) = E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build; python3.13 -m pytest -v tests/ -k 'not test_dataset_2d_set_extension_array' -n2 dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14 3.13" --parallel=2 returned exit code 13 make: *** [debian/rules:10: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 -------------------------------------------------------------------------------- ]