--- Begin Message ---
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
--------------------------------------------------------------------------------
--- End Message ---
pgpvi31RGl1fQ.pgp
