Bug#1092392: marked as done (python-xarray: FTBFS: make[1]: *** [debian/rules:43: override_dh_auto_test] Error 1)

[Debian Bug Tracking System]

Your message dated Fri, 17 Jan 2025 15:09:26 +0000
with message-id <e1tynyq-0016qx...@fasolo.debian.org>
and subject line Bug#1092392: fixed in python-xarray 2025.01.1-1
has caused the Debian Bug report #1092392,
regarding python-xarray: FTBFS: make[1]: *** [debian/rules:43: 
override_dh_auto_test] Error 1
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
1092392: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1092392
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Source: python-xarray
Version: 2024.11.0-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20250106 ftbfs-trixie

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.


Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> #for p in python3.13 python3.12; do \
> #     PY3VERNUM=`echo $p | sed -e 's/python//' `; \
> #     pybuild --test --test-pytest -i $p -p $PY3VERNUM  ;  \
> #     done
> # Tests fail for 3.11, but we ship 3.12 in trixie
> python3.12 -m pytest .
> Fontconfig error: No writable cache directories
> ============================= test session starts 
> ==============================
> platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0
> rootdir: /<<PKGBUILDDIR>>
> configfile: pyproject.toml
> plugins: typeguard-4.4.1, hypothesis-6.122.1
> collected 17186 items / 5 skipped
> 
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> 0%]
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> 
> =================================== FAILURES 
> ===================================
> ________________________ test_dask_da_groupby_quantile 
> _________________________
> 
>     @requires_dask
>     def test_dask_da_groupby_quantile() -> None:
>         # Only works when the grouped reduction can run blockwise
>         # Scalar quantile
>         expected = xr.DataArray(
>             data=[2, 5], coords={"x": [1, 2], "quantile": 0.5}, dims="x"
>         )
>         array = xr.DataArray(
>             data=[1, 2, 3, 4, 5, 6], coords={"x": [1, 1, 1, 2, 2, 2]}, 
> dims="x"
>         )
> >       with pytest.raises(ValueError):
> E       Failed: DID NOT RAISE <class 'ValueError'>
> 
> /<<PKGBUILDDIR>>/xarray/tests/test_groupby.py:295: Failed
> _______________ TestVariableWithDask.test_datetime64_conversion 
> ________________
> 
> self = <xarray.tests.test_variable.TestVariableWithDask object at 
> 0x7f13b1f108c0>
> 
>     @pytest.mark.filterwarnings("ignore:Converting non-nanosecond")
>     def test_datetime64_conversion(self):
>         times = pd.date_range("2000-01-01", periods=3)
>         for values, preserve_source in [
>             (times, True),
>             (times.values, True),
>             (times.values.astype("datetime64[s]"), False),
>             (times.to_pydatetime(), False),
>         ]:
>             v = self.cls(["t"], values)
>             assert v.dtype == np.dtype("datetime64[ns]")
>             assert_array_equal(v.values, times.values)
>             assert v.values.dtype == np.dtype("datetime64[ns]")
>             same_source = source_ndarray(v.values) is source_ndarray(values)
> >           assert preserve_source == same_source
> E           assert True == False
> 
> /<<PKGBUILDDIR>>/xarray/tests/test_variable.py:292: AssertionError
> _______________ TestVariableWithDask.test_timedelta64_conversion 
> _______________
> 
> self = <xarray.tests.test_variable.TestVariableWithDask object at 
> 0x7f13b1f10b30>
> 
>     @pytest.mark.filterwarnings("ignore:Converting non-nanosecond")
>     def test_timedelta64_conversion(self):
>         times = pd.timedelta_range(start=0, periods=3)
>         for values, preserve_source in [
>             (times, True),
>             (times.values, True),
>             (times.values.astype("timedelta64[s]"), False),
>             (times.to_pytimedelta(), False),
>         ]:
>             v = self.cls(["t"], values)
>             assert v.dtype == np.dtype("timedelta64[ns]")
>             assert_array_equal(v.values, times.values)
>             assert v.values.dtype == np.dtype("timedelta64[ns]")
>             same_source = source_ndarray(v.values) is source_ndarray(values)
> >           assert preserve_source == same_source
> E           assert True == False
> 
> /<<PKGBUILDDIR>>/xarray/tests/test_variable.py:308: AssertionError
> _____________________ TestVariableWithDask.test_multiindex 
> _____________________
> 
> self = <xarray.tests.test_variable.TestVariableWithDask object at 
> 0x7f13b2469820>
> 
>     def test_multiindex(self):
> >       super().test_multiindex()
> 
> /<<PKGBUILDDIR>>/xarray/tests/test_variable.py:2370: 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> /<<PKGBUILDDIR>>/xarray/tests/test_variable.py:680: in test_multiindex
>     assert_identical(Variable((), ("a", 0)), v[0])
> /<<PKGBUILDDIR>>/xarray/core/variable.py:1840: in identical
>     return utils.dict_equiv(self.attrs, other.attrs) and self.equals(
> /<<PKGBUILDDIR>>/xarray/core/variable.py:1819: in equals
>     self._data is other._data or equiv(self.data, other.data)
> /<<PKGBUILDDIR>>/xarray/core/duck_array_ops.py:328: in array_equiv
>     return bool(flag_array.all())
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> 
> self = dask.array<all-aggregate, shape=(), dtype=bool, chunksize=(), 
> chunktype=numpy.ndarray>
> 
>     def __bool__(self):
>         if self.size > 1:
>             raise ValueError(
>                 f"The truth value of a {self.__class__.__name__} is 
> ambiguous. "
>                 "Use a.any() or a.all()."
>             )
>         else:
> >           return bool(self.compute())
> E           ValueError: The truth value of an array with more than one 
> element is ambiguous. Use a.any() or a.all()
> 
> /usr/lib/python3/dist-packages/dask/array/core.py:1876: ValueError
> =============================== warnings summary 
> ===============================
> xarray/tests/test_backends.py: 81 warnings
> xarray/tests/test_conventions.py: 6 warnings
>   /<<PKGBUILDDIR>>/xarray/coding/variables.py:348: DeprecationWarning: NumPy 
> will stop allowing conversion of out-of-bound Python integers to integer 
> arrays.  The conversion of 255 to int8 will fail in the future.
>   For the old behavior, usually:
>       np.array(value).astype(dtype)
>   will give the desired result (the cast overflows).
>     new_fill = encoded_dtype.type(fill_value)
> 
> xarray/tests/test_backends.py::TestH5NetCDFFileObject::test_open_fileobj
>   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: 
> PytestUnraisableExceptionWarning: Exception ignored in: <function 
> CachingFileManager.__del__ at 0x7f13d3061a80>
>   
>   Traceback (most recent call last):
>     File "/<<PKGBUILDDIR>>/xarray/backends/file_manager.py", line 255, in 
> __del__
>       warnings.warn(
>   RuntimeWarning: deallocating CachingFileManager(<class 
> 'h5netcdf.core.File'>, <_io.BufferedReader 
> name='/tmp/tmpusjcausw/temp-2005.nc'>, mode='r', kwargs={'invalid_netcdf': 
> None, 'decode_vlen_strings': True, 'driver': None}, 
> manager_id='1497464f-8ff0-4646-a9ff-ce539db89992'), but file is not already 
> closed. This may indicate a bug.
>   
>     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
> 
> xarray/tests/test_backends.py::test_h5netcdf_storage_options
>   /usr/lib/python3/dist-packages/_pytest/python.py:159: RuntimeWarning: 
> deallocating CachingFileManager(<class 'h5netcdf.core.File'>, 
> <fsspec.implementations.local.LocalFileOpener object at 0x7f139cd9d0f0>, 
> mode='r', kwargs={'invalid_netcdf': None, 'decode_vlen_strings': True, 
> 'driver': None}, manager_id='d1fab47f-677a-49e2-ae00-ffa3e8fb1efe'), but file 
> is not already closed. This may indicate a bug.
>     result = testfunction(**testargs)
> 
> xarray/tests/test_backends.py::test_h5netcdf_storage_options
>   /usr/lib/python3/dist-packages/_pytest/python.py:159: RuntimeWarning: 
> deallocating CachingFileManager(<class 'h5netcdf.core.File'>, 
> <fsspec.implementations.local.LocalFileOpener object at 0x7f139cbf3e20>, 
> mode='r', kwargs={'invalid_netcdf': None, 'decode_vlen_strings': True, 
> 'driver': None}, manager_id='e4324340-a4c9-4572-a407-f1727e92de2e'), but file 
> is not already closed. This may indicate a bug.
>     result = testfunction(**testargs)
> 
> xarray/tests/test_coding_times.py::test_roundtrip_datetime64_nanosecond_precision[1677-09-21T00:12:43.145225-us-int64-None-False]
> xarray/tests/test_coding_times.py::test_roundtrip_datetime64_nanosecond_precision[1970-01-01T00:00:01.000001-us-int64-None-False]
>   /<<PKGBUILDDIR>>/xarray/tests/test_coding_times.py:1268: UserWarning: 
> Converting non-nanosecond precision datetime values to nanosecond precision. 
> This behavior can eventually be relaxed in xarray, as it is an artifact from 
> pandas which is now beginning to support non-nanosecond precision values. 
> This warning is caused by passing non-nanosecond np.datetime64 or 
> np.timedelta64 values to the DataArray or Variable constructor; it can be 
> silenced by converting the values to nanosecond precision ahead of time.
>     var = Variable(["time"], times, encoding=encoding)
> 
> xarray/tests/test_computation.py::test_unified_dim_sizes
>   /<<PKGBUILDDIR>>/xarray/namedarray/core.py:264: UserWarning: Duplicate 
> dimension names present: dimensions {'x'} appear more than once in dims=('x', 
> 'x'). We do not yet support duplicate dimension names, but we do allow 
> initial construction of the object. We recommend you rename the dims 
> immediately to become distinct, as most xarray functionality is likely to 
> fail silently if you do not. To rename the dimensions you will need to set 
> the ``.dims`` attribute of each variable, ``e.g. var.dims=('x0', 'x1')``.
>     self._dims = self._parse_dimensions(dims)
> 
> xarray/tests/test_conventions.py: 1 warning
> xarray/tests/test_dataset.py: 1 warning
> xarray/tests/test_rolling.py: 36 warnings
>   /<<PKGBUILDDIR>>/xarray/core/duck_array_ops.py:228: RuntimeWarning: invalid 
> value encountered in cast
>     return data.astype(dtype, **kwargs)
> 
> xarray/tests/test_dask.py: 19 warnings
>   /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:21: UserWarning: 
> The 'dataframe.query-planning' config is now set to True, but query planning 
> is already disabled. The query-planning config can only be changed before 
> `dask.dataframe` is first imported!
>     warnings.warn(
> 
> xarray/tests/test_dask.py: 12 warnings
>   /usr/lib/python3/dist-packages/numpy/core/numeric.py:407: RuntimeWarning: 
> invalid value encountered in cast
>     multiarray.copyto(res, fill_value, casting='unsafe')
> 
> xarray/tests/test_dataset.py::TestDataset::test_to_and_from_dict_with_nan_nat[array]
>   /<<PKGBUILDDIR>>/xarray/tests/test_dataset.py:5171: UserWarning: Converting 
> non-nanosecond precision datetime values to nanosecond precision. This 
> behavior can eventually be relaxed in xarray, as it is an artifact from 
> pandas which is now beginning to support non-nanosecond precision values. 
> This warning is caused by passing non-nanosecond np.datetime64 or 
> np.timedelta64 values to the DataArray or Variable constructor; it can be 
> silenced by converting the values to nanosecond precision ahead of time.
>     roundtripped = Dataset.from_dict(ds.to_dict(data=data))
> 
> xarray/tests/test_duck_array_ops.py::test_cftime_datetime_mean[True]
>   /usr/lib/python3/dist-packages/dask/array/core.py:5083: DeprecationWarning: 
> Bitwise inversion '~' on bool is deprecated and will be removed in Python 
> 3.16. This returns the bitwise inversion of the underlying int object and is 
> usually not what you expect from negating a bool. Use the 'not' operator for 
> boolean negation or ~int(x) if you really want the bitwise inversion of the 
> underlying int.
>     result = function(*args, **kwargs)
> 
> xarray/tests/test_strategies.py::TestReduction::test_mean
> xarray/tests/test_strategies.py::TestReduction::test_mean
> xarray/tests/test_strategies.py::TestReduction::test_mean
> xarray/tests/test_strategies.py::TestReduction::test_mean
> xarray/tests/test_strategies.py::TestReduction::test_mean
> xarray/tests/test_strategies.py::TestReduction::test_mean
>   /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: 
> RuntimeWarning: invalid value encountered in reduce
>     return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
> 
> xarray/tests/test_strategies.py::TestReduction::test_mean
> xarray/tests/test_strategies.py::TestReduction::test_mean
> xarray/tests/test_strategies.py::TestReduction::test_mean
> xarray/tests/test_strategies.py::TestReduction::test_mean
> xarray/tests/test_strategies.py::TestReduction::test_mean
> xarray/tests/test_strategies.py::TestReduction::test_mean
>   /<<PKGBUILDDIR>>/xarray/tests/test_strategies.py:276: RuntimeWarning: Mean 
> of empty slice
>     expected = np.nanmean(var.data, axis=reduction_axes)
> 
> xarray/tests/test_variable.py::TestIndexVariable::test_to_index_multiindex_level
>   /<<PKGBUILDDIR>>/xarray/tests/test_variable.py:2430: FutureWarning: the 
> `pandas.MultiIndex` object(s) passed as 'x' coordinate(s) or data variable(s) 
> will no longer be implicitly promoted and wrapped into multiple indexed 
> coordinates in the future (i.e., one coordinate for each multi-index level + 
> one dimension coordinate). If you want to keep this behavior, you need to 
> first wrap it explicitly using `mindex_coords = 
> xarray.Coordinates.from_pandas_multiindex(mindex_obj, 'dim')` and pass it as 
> coordinates, e.g., `xarray.Dataset(coords=mindex_coords)`, 
> `dataset.assign_coords(mindex_coords)` or 
> `dataarray.assign_coords(mindex_coords)`.
>     ds = Dataset(coords={"x": midx})
> 
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info 
> ============================
> FAILED xarray/tests/test_groupby.py::test_dask_da_groupby_quantile - Failed: 
> ...
> FAILED 
> xarray/tests/test_variable.py::TestVariableWithDask::test_datetime64_conversion
> FAILED 
> xarray/tests/test_variable.py::TestVariableWithDask::test_timedelta64_conversion
> FAILED xarray/tests/test_variable.py::TestVariableWithDask::test_multiindex
> = 4 failed, 16209 passed, 825 skipped, 59 xfailed, 94 xpassed, 177 warnings 
> in 975.83s (0:16:15) =
> make[1]: *** [debian/rules:43: override_dh_auto_test] Error 1


The full build log is available from:
http://qa-logs.debian.net/2025/01/06/python-xarray_2024.11.0-2_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20250106;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20250106&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.

--- End Message ---

--- Begin Message ---

Source: python-xarray
Source-Version: 2025.01.1-1
Done: Alastair McKinstry <mckins...@debian.org>

We believe that the bug you reported is fixed in the latest version of
python-xarray, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1092...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Alastair McKinstry <mckins...@debian.org> (supplier of updated python-xarray 
package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


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Hash: SHA512

Format: 1.8
Date: Fri, 17 Jan 2025 13:21:13 +0000
Source: python-xarray
Architecture: source
Version: 2025.01.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Alastair McKinstry <mckins...@debian.org>
Closes: 1092392
Changes:
 python-xarray (2025.01.1-1) unstable; urgency=medium
 .
   * New upstream release
   * Enable tests for all pythons; catch but dont fail. Closes: #1092392
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