[Debian-med-packaging] Bug#1123524: python-anndata: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13
Santiago Vila
sanvila at debian.org
Wed Dec 17 10:52:15 GMT 2025
Package: src:python-anndata
Version: 0.12.6-1
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/202512/
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.
--------------------------------------------------------------------------------
[...]
tests/test_concatenate_disk.py::test_concatenate_xxxm[zarr-inner]
[gw0] [ 99%] PASSED tests/test_concatenate_disk.py::test_concatenate_xxxm[zarr-inner]
tests/test_concatenate_disk.py::test_concatenate_xxxm[zarr-outer]
[gw0] [ 99%] PASSED tests/test_concatenate_disk.py::test_concatenate_xxxm[zarr-outer]
tests/test_concatenate_disk.py::test_concatenate_xxxm[h5ad-inner]
[gw0] [100%] PASSED tests/test_concatenate_disk.py::test_concatenate_xxxm[h5ad-inner]
=============================== warnings summary ===============================
tests/test_readwrite.py:17
tests/test_readwrite.py:17
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/tests/test_readwrite.py:17: ZarrDeprecationWarning: zarr.convenience is deprecated. Import these functions from the top level zarr. namespace instead.
import zarr.convenience
tests/lazy/test_concat.py: 1440 warnings
tests/test_concatenate.py: 1106 warnings
tests/test_concatenate_disk.py: 490 warnings
tests/test_utils.py: 1 warning
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_anndata/build/anndata/_core/anndata.py:1796: 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_dask.py: 17 warnings
tests/test_io_backwards_compat.py: 1 warning
tests/test_io_elementwise.py: 1 warning
tests/test_io_partial.py: 2 warnings
tests/test_readwrite.py: 20 warnings
tests/test_structured_arrays.py: 1 warning
tests/test_x.py: 1 warning
/usr/lib/python3/dist-packages/zarr/api/asynchronous.py:247: 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_readwrite.py: 18 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: 75 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: 919 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:1798: 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: 187 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_concatenate_disk.py: 5 warnings
tests/test_dask.py: 5 warnings
tests/test_io_elementwise.py: 12 warnings
/usr/lib/python3/dist-packages/zarr/core/array.py:4682: ZarrUserWarning: Automatic shard shape inference is experimental and may change without notice.
shard_shape_parsed, chunk_shape_parsed = _auto_partition(
tests/test_dask.py: 20 warnings
/usr/lib/python3/dist-packages/dask/base.py:1103: UserWarning: Running on a single-machine scheduler when a distributed client is active might lead to unexpected results.
warnings.warn(
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_helpers.py::test_assert_equal_raw
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]
/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_io_elementwise.py::test_io_spec[zarr3-anndata]
/usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:318: UnstableSpecificationWarning: The data type (Structured(fields=(('BzaQf', FixedLengthUTF32(length=3, endianness='little')), ('YWfSl', FixedLengthUTF32(length=4, endianness='little')), ('lNvsp', FixedLengthUTF32(length=4, endianness='little')), ('QCMTl', FixedLengthUTF32(length=4, endianness='little')), ('ejqlc', 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[zarr3-anndata]
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_write_to_root[zarr3-anndata]
tests/test_io_elementwise.py::test_io_pd_cow[zarr3-True]
tests/test_io_elementwise.py::test_io_pd_cow[zarr3-False]
tests/test_readwrite.py::test_adata_in_uns[zarr3]
tests/test_readwrite.py::test_adata_in_uns[zarr3]
/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: 9 warnings
tests/test_readwrite.py: 7 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:318: UnstableSpecificationWarning: The data type (Structured(fields=(('Fvyza', FixedLengthUTF32(length=4, endianness='little')), ('PMpLt', FixedLengthUTF32(length=3, endianness='little')), ('omEvc', FixedLengthUTF32(length=3, endianness='little')), ('QYaGI', FixedLengthUTF32(length=4, endianness='little')), ('tQbcV', 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_anndata_to_root[zarr3]
/usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:318: UnstableSpecificationWarning: The data type (Structured(fields=(('MwAEq', FixedLengthUTF32(length=4, endianness='little')), ('TNGRt', FixedLengthUTF32(length=4, endianness='little')), ('GaaNJ', FixedLengthUTF32(length=3, endianness='little')), ('pDlPF', FixedLengthUTF32(length=4, endianness='little')), ('WldzO', 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:318: UnstableSpecificationWarning: The data type (Structured(fields=(('ypGop', FixedLengthUTF32(length=4, endianness='little')), ('Iceuk', FixedLengthUTF32(length=4, endianness='little')), ('RHeDW', FixedLengthUTF32(length=4, endianness='little')), ('gvvgh', FixedLengthUTF32(length=4, endianness='little')), ('Vbbyt', 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:318: UnstableSpecificationWarning: The data type (Structured(fields=(('RUVSM', FixedLengthUTF32(length=4, endianness='little')), ('XtaJZ', FixedLengthUTF32(length=4, endianness='little')), ('BnIbu', FixedLengthUTF32(length=4, endianness='little')), ('MFgtq', FixedLengthUTF32(length=4, endianness='little')), ('ztWgK', 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:318: UnstableSpecificationWarning: The data type (Structured(fields=(('IDaRQ', FixedLengthUTF32(length=4, endianness='little')), ('TZaXG', FixedLengthUTF32(length=3, endianness='little')), ('zhrZk', FixedLengthUTF32(length=4, endianness='little')), ('CWQTT', FixedLengthUTF32(length=4, endianness='little')), ('XjgyN', 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-True]
/usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:318: UnstableSpecificationWarning: The data type (Structured(fields=(('WsLHl', FixedLengthUTF32(length=4, endianness='little')), ('FNZgb', FixedLengthUTF32(length=4, endianness='little')), ('wksaS', FixedLengthUTF32(length=3, endianness='little')), ('AjCwf', FixedLengthUTF32(length=4, endianness='little')), ('wOPIW', 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-False]
/usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:318: UnstableSpecificationWarning: The data type (Structured(fields=(('zfsrH', FixedLengthUTF32(length=4, endianness='little')), ('QOmQJ', FixedLengthUTF32(length=3, endianness='little')), ('OGAlM', FixedLengthUTF32(length=3, endianness='little')), ('vRPIj', FixedLengthUTF32(length=4, endianness='little')), ('xaksx', 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_auto_sharded
/usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:318: UnstableSpecificationWarning: The data type (Structured(fields=(('tmJzG', FixedLengthUTF32(length=4, endianness='little')), ('XAYWn', FixedLengthUTF32(length=4, endianness='little')), ('wjcVZ', FixedLengthUTF32(length=4, endianness='little')), ('eghcf', FixedLengthUTF32(length=4, endianness='little')), ('YdfXd', 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_readwrite.py::test_zarr_compression[3]
/usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:318: UnstableSpecificationWarning: The data type (Structured(fields=(('ffexM', FixedLengthUTF32(length=4, endianness='little')), ('lCduE', FixedLengthUTF32(length=4, endianness='little')), ('olecj', FixedLengthUTF32(length=4, endianness='little')), ('XtQUv', FixedLengthUTF32(length=4, endianness='little')), ('yCpba', 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_readwrite.py::test_changed_obs_var_names[zarr3]
/usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:318: UnstableSpecificationWarning: The data type (Structured(fields=(('AvLuF', FixedLengthUTF32(length=4, endianness='little')), ('lLKJG', FixedLengthUTF32(length=4, endianness='little')), ('MhrPn', FixedLengthUTF32(length=4, endianness='little')), ('ZlfUY', FixedLengthUTF32(length=4, endianness='little')), ('CNyLX', 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_readwrite.py::test_adata_in_uns[zarr3]
tests/test_readwrite.py::test_adata_in_uns[zarr3]
/usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:318: UnstableSpecificationWarning: The data type (Structured(fields=(('viDDf', FixedLengthUTF32(length=4, endianness='little')), ('IObkx', FixedLengthUTF32(length=4, endianness='little')), ('NjEMq', FixedLengthUTF32(length=4, endianness='little')), ('DgxkL', FixedLengthUTF32(length=4, endianness='little')), ('gMWdI', 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_readwrite.py::test_adata_in_uns[zarr3]
tests/test_readwrite.py::test_adata_in_uns[zarr3]
/usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:318: UnstableSpecificationWarning: The data type (Structured(fields=(('QTObC', FixedLengthUTF32(length=3, endianness='little')), ('xKHPi', FixedLengthUTF32(length=4, endianness='little')), ('IPLbk', FixedLengthUTF32(length=4, endianness='little')), ('hdcuW', FixedLengthUTF32(length=4, endianness='little')), ('MGMiq', 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_readwrite.py::test_adata_in_uns[zarr3]
tests/test_readwrite.py::test_adata_in_uns[zarr3]
/usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:318: UnstableSpecificationWarning: The data type (Structured(fields=(('tKlBJ', FixedLengthUTF32(length=4, endianness='little')), ('veSlQ', FixedLengthUTF32(length=4, endianness='little')), ('pJbFz', FixedLengthUTF32(length=4, endianness='little')), ('imVcm', FixedLengthUTF32(length=4, endianness='little')), ('Ynzpq', 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_readwrite.py::test_adata_in_uns[zarr3]
tests/test_readwrite.py::test_adata_in_uns[zarr3]
/usr/lib/python3/dist-packages/zarr/core/dtype/npy/structured.py:318: UnstableSpecificationWarning: The data type (Structured(fields=(('bCGtU', FixedLengthUTF32(length=4, endianness='little')), ('TmmmR', FixedLengthUTF32(length=4, endianness='little')), ('jkfVH', FixedLengthUTF32(length=4, endianness='little')), ('CYmtW', FixedLengthUTF32(length=4, endianness='little')), ('AdMrk', 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:318: UnstableSpecificationWarning: The data type (Structured(fields=(('enUAF', FixedLengthUTF32(length=4, endianness='little')), ('QbmFB', FixedLengthUTF32(length=4, endianness='little')), ('dnOJb', FixedLengthUTF32(length=4, endianness='little')), ('QRdOC', FixedLengthUTF32(length=4, endianness='little')), ('JLFXS', 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:318: UnstableSpecificationWarning: The data type (Structured(fields=(('enUAF', FixedLengthUTF32(length=10, endianness='little')), ('QbmFB', FixedLengthUTF32(length=10, endianness='little')), ('dnOJb', FixedLengthUTF32(length=10, endianness='little')), ('QRdOC', FixedLengthUTF32(length=10, endianness='little')), ('JLFXS', 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:318: UnstableSpecificationWarning: The data type (Structured(fields=(('enUAF', NullTerminatedBytes(length=10)), ('QbmFB', NullTerminatedBytes(length=10)), ('dnOJb', NullTerminatedBytes(length=10)), ('QRdOC', NullTerminatedBytes(length=10)), ('JLFXS', 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_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:389: 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:577: 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:579: 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:583: 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:585: 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:318: UnstableSpecificationWarning: The data type (Structured(fields=(('GRJAF', FixedLengthUTF32(length=4, endianness='little')), ('QJgEY', FixedLengthUTF32(length=4, endianness='little')), ('YmyvB', FixedLengthUTF32(length=4, endianness='little')), ('wyJfR', FixedLengthUTF32(length=4, endianness='little')), ('LZTEP', 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)
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
== 6902 passed, 965 skipped, 163 xfailed, 5194 warnings in 762.03s (0:12:42) ===
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
--------------------------------------------------------------------------------
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