Bug#1114394: specreduce: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13

Fri, 05 Sep 2025 11:44:51 -0700 

Package: src:specreduce
Version: 1.6.0-1
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build.

Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202509/

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 could not 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:specreduce, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --with python3 --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary
dh binary --with python3 --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:129: Building wheel for python3.13 with "build" 
module
I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation 
--wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13  
* Building wheel...

[... snipped ...]

        # Attempt to parse the spectral axis. If none is given, try 
instead to
        # parse a given wcs. This is put into a GWCS object 
to
        # then be used behind-the-scenes for all specutils 
operations.
        if spectral_axis is not 
None:
            # Ensure that the spectral axis is an astropy 
Quantity
            if not 
isinstance(spectral_axis, u.Quantity):
                raise 
ValueError("Spectral axis must be a 
`Quantity` or "
                                 "`SpectralAxis` 
object.")
    
            # If spectral axis is provided as an astropy Quantity, convert 
it
            # to a specutils SpectralAxis 
object.
            if not 
isinstance(spectral_axis, SpectralAxis):
                self._spectral_axis = 
SpectralAxis(
                    spectral_axis, redshift=redshift,
                    radial_velocity=radial_velocity, 
doppler_rest=rest_value,
                    doppler_convention=velocity_convention,
                    bin_specification=bin_specification)
            # If a SpectralAxis object is provided, we assume it doesn't 
need
            # information from other keywords 
added
            else:
                for a in [radial_velocity, 
redshift]:
                    if a is not 
None:
                        raise 
ValueError("Cannot separately set redshift 
or "
                                         "radial_velocity 
if a SpectralAxis "
                                         "object is input 
to spectral_axis")
    
                self._spectral_axis = 
spectral_axis
    
            if wcs is 
None:
                wcs = 
gwcs_from_array(self._spectral_axis,
                                      flux.shape,
                                      
spectral_axis_index=self.spectral_axis_index
                                      )
    
        elif wcs is 
None:
            # If no spectral axis or wcs information is provided, 
initialize
            # with an empty gwcs based on the 
flux.
            if self.spectral_axis_index 
is None:
                if flux.ndim == 
1:
                    self._spectral_axis_index = 
0
                else:
>                   raise 
> ValueError("Must specify 
> spectral_axis_index if no WCS or 
> spectral"
                                     " axis is 
input.")
E                   ValueError: Must specify spectral_axis_index if no 
WCS or spectral axis is input.

/usr/lib/python3/dist-packages/specutils/spectra/spectrum.py:351: 
ValueError
____________ TestMeasureCrossDispersionProfile.test_errors_warnings 
____________

self = <specreduce.tests.test_utils.TestMeasureCrossDispersionProfile object at 
0x7f8286e22050>

    def 
test_errors_warnings(self):
        img = mk_gaussian_img(nrows=10, 
ncols=10)
        with 
pytest.raises(ValueError,
                           match='`crossdisp_axis` must be 
0 or 1'):
            measure_cross_dispersion_profile(img, 
crossdisp_axis=2)
    
        with pytest.raises(ValueError, 
match='`trace` must be Trace object, 
'
                                             'number to 
specify the location '
                                             'of a 
FlatTrace, or None to use '
                                             'center of 
image.'):
>           measure_cross_dispersion_profile(img, 
> trace='not a trace or a 
> number')

specreduce/tests/test_utils.py:147: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
specreduce/utils/utils.py:92: in measure_cross_dispersion_profile
    image = parser._parse_image(image, disp_axis=disp_axis)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
specreduce/core.py:95: in _parse_image
    return self._get_data_from_image(image, 
disp_axis=disp_axis, mask_treatment=mask_treatment)
           
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
specreduce/core.py:155: in _get_data_from_image
    img = Spectrum(
/usr/lib/python3/dist-packages/astropy/utils/decorators.py:143: in 
deprecated_func
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
/usr/lib/python3/dist-packages/specutils/spectra/spectrum.py:960: 
in __init__
    super().__init__(*args, 
**kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <[AttributeError("'Spectrum1D' object has no attribute '_data'") raised 
in repr()] Spectrum1D object at 0x7f8286c854f0>
flux = <Quantity [[0.04393693, 0.04393693, 0.04393693, 0.04393693, 0.04393693,
            0.04393693, 0.04393693, 0.04393693...23323, 0.96923323, 0.96923323, 
0.96923323,
            0.96923323, 0.96923323, 0.96923323, 0.96923323, 0.96923323]] DN>
spectral_axis = <Quantity [0., 1., 2., 3., 4., 5., 6., 7., 8., 9.] pix>
spectral_axis_index = None, wcs = None, velocity_convention = None
rest_value = None, redshift = None, radial_velocity = None
bin_specification = None, move_spectral_axis = None
kwargs = {'mask': array([[False, False, False, False, False, False, False, 
False, False,
        False],
       [False, False, ..., 1., 1., 1., 1., 1., 1., 1., 1.],
                     [1., 1., 1., 1., 1., 1., 1., 1., 1., 1.]]), 'unit': 
Unit("DN")}
unknown_kwargs = set(), matching_axes = [0, 1], add_elements = [0, 1], i = 1
add_element = 1

    def __init__(self, 
flux=None, spectral_axis=None, 
spectral_axis_index=None,
                 wcs=None, 
velocity_convention=None, 
rest_value=None,
                 redshift=None, 
radial_velocity=None, 
bin_specification=None,
                 move_spectral_axis=None, 
**kwargs):
    
        if spectral_axis_index == 
-1:
            spectral_axis_index = flux.ndim - 1
    
        # If the flux (data) argument is already a Spectrum (as it 
would
        # be for internal arithmetic operations), avoid setup 
entirely.
        if isinstance(flux, 
Spectrum):
            self._spectral_axis_index = 
flux.spectral_axis_index
            self._spectral_axis = 
flux.spectral_axis
            
super().__init__(flux)
            return
    
        self._spectral_axis_index = 
spectral_axis_index
        # Might as well handle this right away
        if spectral_axis_index is 
None and flux is 
not None:
            if flux.ndim == 1:
                self._spectral_axis_index = 
0
        elif flux is 
None:
            self._spectral_axis_index = 
0
    
        # Check for pre-defined entries in the kwargs 
dictionary.
        unknown_kwargs = set(kwargs).difference(
            {'data', 
'unit', 
'uncertainty', 
'meta', 
'mask', 
'copy',
             
'extra_coords'})
    
        if len(unknown_kwargs) > 
0:
            raise 
ValueError("Initializer contains unknown 
arguments(s): 
{}."
                             
"".format(', 
'.join(map(str, 
unknown_kwargs))))
    
        # Handle initializing from NDCube 
objects
        elif isinstance(flux, 
NDCube):
            if flux.unit is 
None:
                raise 
ValueError("Input NDCube missing unit 
parameter")
    
            # Change the flux array from bare ndarray to a 
Quantity
            q_flux = flux.data << u.Unit(flux.unit)
    
            self.__init__(flux=q_flux, 
wcs=flux.wcs, mask=flux.mask,
                          uncertainty=flux.uncertainty)
            return
    
        # If the mask kwarg is not passed to the constructor, but the flux 
array
        # contains NaNs, add the NaN locations to the 
mask.
        if 
"mask" not 
in kwargs and flux is 
not None:
            nan_mask = np.isnan(flux)
            if nan_mask.any():
                if 
hasattr(self, 
"mask"):
                    
kwargs["mask"] = 
np.logical_or(nan_mask, self.mask)
                else:
                    
kwargs["mask"] = 
nan_mask.copy()
            del nan_mask
    
        # Ensure that the flux argument is an astropy 
quantity
        if flux is not 
None:
            if not 
isinstance(flux, u.Quantity):
                raise 
ValueError("Flux must be a `Quantity` 
object.")
            elif flux.isscalar:
                flux = u.Quantity([flux])
    
        # Ensure that only one or neither of these parameters is 
set
        if redshift is not 
None and radial_velocity is 
not None:
            raise 
ValueError("Cannot set both 
radial_velocity and redshift at "
                             "the same 
time.")
    
        # In cases of slicing, new objects will be initialized with 
`data`
        # instead of ``flux``. Ensure we grab the `data` 
argument.
        if flux is None 
and 'data' 
in kwargs:
            flux = 
kwargs.pop('data')
    
        # Ensure that the unit information codified in the quantity object 
is
        # the One True Unit.
        
kwargs.setdefault('unit', 
flux.unit if isinstance(flux, 
u.Quantity)
                                            else 
kwargs.get('unit'))
    
        # In the case where the arithmetic operation is being performed 
with
        # a single float, int, or array object, just go ahead and ignore 
wcs
        # requirements
        if np.ndim(flux) == 0 
and spectral_axis is None 
and wcs is None:
            super(Spectrum, 
self).__init__(data=flux, wcs=wcs, 
**kwargs)
            return
    
        if rest_value is 
None:
            if hasattr(wcs, 
'rest_frequency') 
and wcs.rest_frequency != 0:
                rest_value = wcs.rest_frequency * u.Hz
            elif hasattr(wcs, 
'rest_wavelength') 
and wcs.rest_wavelength != 0:
                rest_value = wcs.rest_wavelength * u.AA
            elif hasattr(wcs, 
'wcs') and 
hasattr(wcs.wcs, 
'restfrq') and 
wcs.wcs.restfrq > 0:
                rest_value = wcs.wcs.restfrq * u.Hz
            elif hasattr(wcs, 
'wcs') and 
hasattr(wcs.wcs, 
'restwav') and 
wcs.wcs.restwav > 0:
                rest_value = wcs.wcs.restwav * u.m
            else:
                rest_value = None
        else:
            if not 
isinstance(rest_value, u.Quantity):
                warnings.warn("No unit information 
provided with rest value. "
                              f"Assuming 
units of spectral axis 
('{spectral_axis.unit}').")
                rest_value = u.Quantity(rest_value, 
spectral_axis.unit)
            elif not 
rest_value.unit.is_equivalent(u.AA, equivalencies=u.spectral()):
                raise u.UnitsError("Rest 
value must be "
                                   
"energy/wavelength/frequency 
equivalent.")
    
        # If flux and spectral axis are both specified, check that their 
lengths
        # match or are off by one (implying the spectral axis stores bin 
edges).
        # If we can't determine which flux axis corresponds to the 
spectral axis
        # we raise an error.
        if flux is not 
None and spectral_axis is 
not None:
            if spectral_axis_index is 
None:
                if flux.ndim == 
1:
                    self._spectral_axis_index = 
0
                else:
                    matching_axes = []
                    if bin_specification == 
"centers":
                        add_elements = [0,]
                    elif bin_specification == 
"edges":
                        add_elements = [1,]
                    elif bin_specification is 
None:
                        add_elements = 
[0,1]
                    for i in 
range(flux.ndim):
                        for add_element in 
add_elements:
                            if 
spectral_axis.shape[0] == flux.shape[i] + 
add_element:
                                matching_axes.append(i)
    
                    if len(matching_axes) == 
1:
                        self._spectral_axis_index = 
matching_axes[0]
                    else:
>                       raise 
> ValueError("Unable to determine which 
> flux axis corresponds to "
                                         "the spectral 
axis. Please specify 
spectral_axis_index"
                                         " or provide a 
spectral_axis matching a flux axis.")
E                       ValueError: Unable to determine which flux 
axis corresponds to the spectral axis. Please specify spectral_axis_index or 
provide a spectral_axis matching a flux axis.

/usr/lib/python3/dist-packages/specutils/spectra/spectrum.py:213: 
ValueError

During handling of the above exception, another exception occurred:

self = <specreduce.tests.test_utils.TestMeasureCrossDispersionProfile object at 
0x7f8286e22050>

    def 
test_errors_warnings(self):
        img = mk_gaussian_img(nrows=10, 
ncols=10)
        with 
pytest.raises(ValueError,
                           match='`crossdisp_axis` must be 
0 or 1'):
            measure_cross_dispersion_profile(img, 
crossdisp_axis=2)
    
>       with pytest.raises(ValueError, 
> match='`trace` must be Trace object, 
> '
                                             'number to 
specify the location '
                                             'of a 
FlatTrace, or None to use '
                                             'center of 
image.'):
E                                            AssertionError: Regex 
pattern did not match.
E                                             Regex: '`trace` must be 
Trace object, number to specify the location of a FlatTrace, or None to use 
center of image.'
E                                             Input: 'Unable to 
determine which flux axis corresponds to the spectral axis. Please specify 
spectral_axis_index or provide a spectral_axis matching a flux axis.'

specreduce/tests/test_utils.py:143: AssertionError
=========================== short test summary info 
============================
FAILED 
specreduce/tests/test_background.py::TestMasksBackground::test_fully_masked_column[apply]
 - ValueError: Unable to determine which flux axis corresponds to the 
spectral...
FAILED 
specreduce/tests/test_background.py::TestMasksBackground::test_fully_masked_column[propagate]
 - ValueError: Unable to determine which flux axis corresponds to the 
spectral...
FAILED 
specreduce/tests/test_background.py::TestMasksBackground::test_fully_masked_column[zero_fill]
 - ValueError: Unable to determine which flux axis corresponds to the 
spectral...
FAILED 
specreduce/tests/test_background.py::TestMasksBackground::test_fully_masked_image[apply]
 - AssertionError: Regex pattern did not match.
FAILED 
specreduce/tests/test_background.py::TestMasksBackground::test_fully_masked_image[propagate]
 - AssertionError: Regex pattern did not match.
FAILED 
specreduce/tests/test_background.py::TestMasksBackground::test_mask_treatment_bkg_img_spectrum[apply-expected0]
 - ValueError: Unable to determine which flux axis corresponds to the 
spectral...
FAILED 
specreduce/tests/test_background.py::TestMasksBackground::test_mask_treatment_bkg_img_spectrum[propagate-expected1]
 - ValueError: Unable to determine which flux axis corresponds to the 
spectral...
FAILED 
specreduce/tests/test_background.py::TestMasksBackground::test_mask_treatment_bkg_img_spectrum[zero_fill-expected2]
 - ValueError: Unable to determine which flux axis corresponds to the 
spectral...
FAILED 
specreduce/tests/test_background.py::TestMasksBackground::test_sub_bkg_image
 - ValueError: Unable to determine which flux axis corresponds to the 
spectral...
FAILED 
specreduce/tests/test_tracing.py::TestMasksTracing::test_flat_and_basic_trace_mask
 - ValueError: Unable to determine which flux axis corresponds to the 
spectral...
FAILED 
specreduce/tests/test_tracing.py::TestMasksTracing::test_array_trace_masking
 - ValueError: Unable to determine which flux axis corresponds to the 
spectral...
FAILED 
specreduce/tests/test_tracing.py::TestMasksTracing::test_fit_trace_fully_masked_cols[apply]
 - ValueError: Unable to determine which flux axis corresponds to the 
spectral...
FAILED 
specreduce/tests/test_tracing.py::TestMasksTracing::test_fit_trace_fully_masked_cols[propagate]
 - ValueError: Unable to determine which flux axis corresponds to the 
spectral...
FAILED 
specreduce/tests/test_tracing.py::TestMasksTracing::test_fit_trace_fully_masked_cols[apply_nan_only]
 - ValueError: Unable to determine which flux axis corresponds to the 
spectral...
FAILED 
specreduce/tests/test_utils.py::TestMeasureCrossDispersionProfile::test_measure_cross_dispersion_profile[10-None]
 - ValueError: Must specify spectral_axis_index if no WCS or spectral axis is 
...
FAILED 
specreduce/tests/test_utils.py::TestMeasureCrossDispersionProfile::test_measure_cross_dispersion_profile[10-1]
 - ValueError: Must specify spectral_axis_index if no WCS or spectral axis is 
...
FAILED 
specreduce/tests/test_utils.py::TestMeasureCrossDispersionProfile::test_measure_cross_dispersion_profile[10-pixel2]
 - ValueError: Must specify spectral_axis_index if no WCS or spectral axis is 
...
FAILED 
specreduce/tests/test_utils.py::TestMeasureCrossDispersionProfile::test_measure_cross_dispersion_profile[9-None]
 - ValueError: Must specify spectral_axis_index if no WCS or spectral axis is 
...
FAILED 
specreduce/tests/test_utils.py::TestMeasureCrossDispersionProfile::test_measure_cross_dispersion_profile[9-1]
 - ValueError: Must specify spectral_axis_index if no WCS or spectral axis is 
...
FAILED 
specreduce/tests/test_utils.py::TestMeasureCrossDispersionProfile::test_measure_cross_dispersion_profile[9-pixel2]
 - ValueError: Must specify spectral_axis_index if no WCS or spectral axis is 
...
FAILED 
specreduce/tests/test_utils.py::TestMeasureCrossDispersionProfile::test_errors_warnings
 - AssertionError: Regex pattern did not match.
ERROR specreduce/tests/test_background.py::test_background - 
ValueError: Must specify spectral_axis_index if no WCS or spectral axis is ...
ERROR 
specreduce/tests/test_background.py::test_warnings_errors - ValueError: 
Must specify spectral_axis_index if no WCS or spectral axis is ...
ERROR 
specreduce/tests/test_image_parsing.py::test_parse_general - 
ValueError: Must specify spectral_axis_index if no WCS or spectral axis is ...
ERROR specreduce/tests/test_image_parsing.py::test_parse_horne 
- ValueError: Must specify spectral_axis_index if no WCS or spectral axis is ...
============= 21 failed, 55 passed, 24 
skipped, 4 errors in 2.95s ==============
E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=1: cd 
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build; python3.13 -m pytest 
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 
returned exit code 13
make: *** [debian/rules:7: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

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