Bug#1092392: python-xarray: FTBFS: make[1]: *** [debian/rules:43: override_dh_auto_test] Error 1
Lucas Nussbaum
lucas at debian.org
Tue Jan 7 19:42:25 GMT 2025
Source: python-xarray
Version: 2024.11.0-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at 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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> =================================== 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=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20250106&fusertaguser=lucas@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.
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