[Debian-med-packaging] Bug#1027550: nitime: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.11 3.10" returned exit code 13
Lucas Nussbaum
lucas at debian.org
Sun Jan 1 14:33:57 GMT 2023
Source: nitime
Version: 0.9-3
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20230101 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> 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
> I: pybuild base:240: python3.11 setup.py config
> I: pybuild base:240: python3.10 setup.py config
> dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:240: /usr/bin/python3.11 setup.py build
> I: pybuild base:240: /usr/bin/python3 setup.py build
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:240: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; python3.11 -m pytest
> ============================= test session starts ==============================
> platform linux -- Python 3.11.1, pytest-7.2.0, pluggy-1.0.0+repack
> rootdir: /<<PKGBUILDDIR>>
> collected 123 items
>
> nitime/algorithms/tests/test_autoregressive.py ..... [ 4%]
> nitime/algorithms/tests/test_coherence.py ..........s.... [ 16%]
> nitime/algorithms/tests/test_correlation.py . [ 17%]
> nitime/algorithms/tests/test_entropy.py ..... [ 21%]
> nitime/algorithms/tests/test_event_related.py . [ 21%]
> nitime/algorithms/tests/test_spectral.py ................ [ 34%]
> nitime/analysis/tests/test_base.py . [ 35%]
> nitime/analysis/tests/test_coherence.py ...... [ 40%]
> nitime/analysis/tests/test_correlation.py . [ 41%]
> nitime/analysis/tests/test_granger.py .. [ 43%]
> nitime/analysis/tests/test_snr.py . [ 43%]
> nitime/fmri/tests/test_io.py . [ 44%]
> nitime/tests/test_algorithms.py ......F. [ 51%]
> nitime/tests/test_analysis.py ....... [ 56%]
> nitime/tests/test_descriptors.py . [ 57%]
> nitime/tests/test_lazy.py .. [ 59%]
> nitime/tests/test_timeseries.py .................................... [ 88%]
> nitime/tests/test_utils.py ........... [ 97%]
> nitime/tests/test_viz.py ... [100%]
>
> =================================== FAILURES ===================================
> _______________________________ test_psd_matlab ________________________________
>
> def test_psd_matlab():
>
> """ Test the results of mlab csd/psd against saved results from Matlab"""
>
> from matplotlib import mlab
>
> test_dir_path = os.path.join(nitime.__path__[0], 'tests')
>
> ts = np.loadtxt(os.path.join(test_dir_path, 'tseries12.txt'))
>
> #Complex signal!
> ts0 = ts[1] + ts[0] * np.complex(0, 1)
>
> NFFT = 256
> Fs = 1.0
> noverlap = NFFT / 2
>
> > fxx, f = mlab.psd(ts0, NFFT=NFFT, Fs=Fs, noverlap=noverlap,
> scale_by_freq=True)
>
> nitime/tests/test_algorithms.py:154:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /usr/lib/python3/dist-packages/matplotlib/mlab.py:584: in psd
> Pxx, freqs = csd(x=x, y=None, NFFT=NFFT, Fs=Fs, detrend=detrend,
> /usr/lib/python3/dist-packages/matplotlib/mlab.py:640: in csd
> Pxy, freqs, _ = _spectral_helper(x=x, y=y, NFFT=NFFT, Fs=Fs,
> /usr/lib/python3/dist-packages/matplotlib/mlab.py:382: in _spectral_helper
> result = _stride_windows(x, NFFT, noverlap)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> x = array([ 8.8313817e+00+8.9429666e+00j, 4.3005055e+00+5.0100717e+00j,
> -4.1649119e+00-2.6816087e+00j, -6.3050160e...01-3.9449765e+00j, 4.4173569e+00+1.4387487e+00j,
> 7.1039609e+00+1.0514320e+01j, 5.4811765e+00+1.0769771e+01j])
> n = 256, noverlap = 128.0, axis = 0
>
> def _stride_windows(x, n, noverlap=0, axis=0):
> # np>=1.20 provides sliding_window_view, and we only ever use axis=0.
> if hasattr(np.lib.stride_tricks, "sliding_window_view") and axis == 0:
> if noverlap >= n:
> raise ValueError('noverlap must be less than n')
> > return np.lib.stride_tricks.sliding_window_view(
> x, n, axis=0)[::n - noverlap].T
> E TypeError: slice indices must be integers or None or have an __index__ method
>
> /usr/lib/python3/dist-packages/matplotlib/mlab.py:258: TypeError
> =============================== warnings summary ===============================
> nitime/algorithms/event_related.py:13
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/event_related.py:13: DeprecationWarning: invalid escape sequence '\h'
> """
>
> nitime/algorithms/tests/test_coherence.py:206
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_coherence.py:206: DeprecationWarning: invalid escape sequence '\c'
> """
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_coherence.py: 30 warnings
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py: 16 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/cohere.py:1008: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> Slices = np.zeros((n_slices, n_freqs), dtype=np.complex)
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_coherence.py: 6 warnings
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py: 7 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/cohere.py:1224: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> Cxy = np.zeros((channels_i, channels_j, freqs), dtype=np.complex)
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_coherence.py::test_cache_to_coherency
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_coherence.py::test_cache_to_coherency
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_coherence.py::test_cache_to_coherency
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_coherence.py::test_cache_to_coherency
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/cohere.py:1164: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> Phi_xy = np.zeros((channels_i, channels_j, freqs), dtype=np.complex)
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py:73: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig1 = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py:78: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig2 = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_periodogram
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py:121: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_periodogram_csd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py:146: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig1 = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_periodogram_csd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py:150: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig2 = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_CoherenceAnalyzer
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SparseCoherenceAnalyzer
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/coherence.py:200: RuntimeWarning: invalid value encountered in divide
> delay[i, j] = this_phase / (2 * np.pi * self.frequencies)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_CoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/coherence.py:200: RuntimeWarning: divide by zero encountered in divide
> delay[i, j] = this_phase / (2 * np.pi * self.frequencies)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_CoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/cohere.py:699: RuntimeWarning: divide by zero encountered in divide
> return (((np.abs(Rxy - Rxr * Rry)) ** 2) /
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_CoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/cohere.py:699: RuntimeWarning: invalid value encountered in divide
> return (((np.abs(Rxy - Rxr * Rry)) ** 2) /
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SparseCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/coherence.py:523: RuntimeWarning: invalid value encountered in divide
> return self.relative_phases / (2 * np.pi * self.frequencies)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/coherence.py:659: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> self.frequencies.shape[0]), dtype=np.complex)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/coherence.py:656: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> self.frequencies.shape[0]), dtype=np.complex)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/coherence.py:730: RuntimeWarning: invalid value encountered in divide
> return self.relative_phases / (2 * np.pi * self.frequencies)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/coherence.py:94: RuntimeWarning: In nitime.analysis, the provided input time-series is shorter than the requested NFFT + n_overlap. All coherence values will be set to 1.
> warnings.warn(e_s, RuntimeWarning)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_correlation.py::test_SeedCorrelationAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/correlation.py:150: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> self.target.data.shape[0]), dtype=np.float)
>
> .pybuild/cpython3_3.11/build/nitime/fmri/tests/test_io.py: 10 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/fmri/io.py:121: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
>
> * deprecated from version: 3.0
> * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
> data = im.get_data()
>
> .pybuild/cpython3_3.11/build/nitime/fmri/tests/test_io.py::test_time_series_from_file
> .pybuild/cpython3_3.11/build/nitime/fmri/tests/test_io.py::test_time_series_from_file
> .pybuild/cpython3_3.11/build/nitime/fmri/tests/test_io.py::test_time_series_from_file
> .pybuild/cpython3_3.11/build/nitime/fmri/tests/test_io.py::test_time_series_from_file
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/fmri/io.py:91: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
>
> * deprecated from version: 3.0
> * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
> data = im.get_data()
>
> .pybuild/cpython3_3.11/build/nitime/fmri/tests/test_io.py::test_time_series_from_file
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/fmri/tests/test_io.py:68: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
>
> * deprecated from version: 3.0
> * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
> data = io.load(fmri_file1).get_data()
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py::test_scipy_resample
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py:27: DeprecationWarning: Please use `resample` from the `scipy.signal` namespace, the `scipy.signal.signaltools` namespace is deprecated.
> t_up = signaltools.resample(tst, 128)
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py::test_scipy_resample
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py:30: DeprecationWarning: Please use `resample` from the `scipy.signal` namespace, the `scipy.signal.signaltools` namespace is deprecated.
> t_dn = signaltools.resample(tst, 32)
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py::test_scipy_resample
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py:36: DeprecationWarning: Please use `resample` from the `scipy.signal` namespace, the `scipy.signal.signaltools` namespace is deprecated.
> t_dn2 = signaltools.resample(tst, 48)
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py::test_psd_matlab
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py:148: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> ts0 = ts[1] + ts[0] * np.complex(0, 1)
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_analysis.py::test_MorletWaveletAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/wavelet.py:77: RuntimeWarning: divide by zero encountered in log
> wf = (2 * np.exp(-(np.log(f) - np.log(f0)) ** 2 / (2 * sfl ** 2)) *
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_analysis.py::test_MorletWaveletAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/wavelet.py:77: RuntimeWarning: invalid value encountered in log
> wf = (2 * np.exp(-(np.log(f) - np.log(f0)) ** 2 / (2 * sfl ** 2)) *
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_lazy.py::test_lazy_noreload
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/tests/test_lazy.py:40: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses
> import imp
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_viz.py::test_drawgraph_channels
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/viz.py:681: DeprecationWarning: adj_matrix is deprecated and will be removed in version 3.0.
> Use `adjacency_matrix` instead
>
> amat = nx.adj_matrix(G).A # get a normal array out of it
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_viz.py::test_drawgraph_channels
> /usr/lib/python3/dist-packages/networkx/linalg/graphmatrix.py:187: FutureWarning: adjacency_matrix will return a scipy.sparse array instead of a matrix in Networkx 3.0.
> return adjacency_matrix(G, nodelist, dtype, weight)
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_viz.py::test_drawgraph_channels
> /usr/lib/python3/dist-packages/networkx/linalg/graphmatrix.py:173: DeprecationWarning:
>
> The scipy.sparse array containers will be used instead of matrices
> in Networkx 3.0. Use `to_scipy_sparse_array` instead.
> return nx.to_scipy_sparse_matrix(G, nodelist=nodelist, dtype=dtype, weight=weight)
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> FAILED nitime/tests/test_algorithms.py::test_psd_matlab - TypeError: slice in...
> =========== 1 failed, 121 passed, 1 skipped, 113 warnings in 47.14s ============
> E: pybuild pybuild:388: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; python3.11 -m pytest
> I: pybuild base:240: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build; python3.10 -m pytest
> ============================= test session starts ==============================
> platform linux -- Python 3.10.9, pytest-7.2.0, pluggy-1.0.0+repack
> rootdir: /<<PKGBUILDDIR>>
> collected 123 items
>
> nitime/algorithms/tests/test_autoregressive.py ..... [ 4%]
> nitime/algorithms/tests/test_coherence.py ..........s.... [ 16%]
> nitime/algorithms/tests/test_correlation.py . [ 17%]
> nitime/algorithms/tests/test_entropy.py ..... [ 21%]
> nitime/algorithms/tests/test_event_related.py . [ 21%]
> nitime/algorithms/tests/test_spectral.py ................ [ 34%]
> nitime/analysis/tests/test_base.py . [ 35%]
> nitime/analysis/tests/test_coherence.py ...... [ 40%]
> nitime/analysis/tests/test_correlation.py . [ 41%]
> nitime/analysis/tests/test_granger.py .. [ 43%]
> nitime/analysis/tests/test_snr.py . [ 43%]
> nitime/fmri/tests/test_io.py . [ 44%]
> nitime/tests/test_algorithms.py ......F. [ 51%]
> nitime/tests/test_analysis.py ....... [ 56%]
> nitime/tests/test_descriptors.py . [ 57%]
> nitime/tests/test_lazy.py .. [ 59%]
> nitime/tests/test_timeseries.py .................................... [ 88%]
> nitime/tests/test_utils.py ........... [ 97%]
> nitime/tests/test_viz.py ... [100%]
>
> =================================== FAILURES ===================================
> _______________________________ test_psd_matlab ________________________________
>
> def test_psd_matlab():
>
> """ Test the results of mlab csd/psd against saved results from Matlab"""
>
> from matplotlib import mlab
>
> test_dir_path = os.path.join(nitime.__path__[0], 'tests')
>
> ts = np.loadtxt(os.path.join(test_dir_path, 'tseries12.txt'))
>
> #Complex signal!
> ts0 = ts[1] + ts[0] * np.complex(0, 1)
>
> NFFT = 256
> Fs = 1.0
> noverlap = NFFT / 2
>
> > fxx, f = mlab.psd(ts0, NFFT=NFFT, Fs=Fs, noverlap=noverlap,
> scale_by_freq=True)
>
> nitime/tests/test_algorithms.py:154:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /usr/lib/python3/dist-packages/matplotlib/mlab.py:584: in psd
> Pxx, freqs = csd(x=x, y=None, NFFT=NFFT, Fs=Fs, detrend=detrend,
> /usr/lib/python3/dist-packages/matplotlib/mlab.py:640: in csd
> Pxy, freqs, _ = _spectral_helper(x=x, y=y, NFFT=NFFT, Fs=Fs,
> /usr/lib/python3/dist-packages/matplotlib/mlab.py:382: in _spectral_helper
> result = _stride_windows(x, NFFT, noverlap)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> x = array([ 8.8313817e+00+8.9429666e+00j, 4.3005055e+00+5.0100717e+00j,
> -4.1649119e+00-2.6816087e+00j, -6.3050160e...01-3.9449765e+00j, 4.4173569e+00+1.4387487e+00j,
> 7.1039609e+00+1.0514320e+01j, 5.4811765e+00+1.0769771e+01j])
> n = 256, noverlap = 128.0, axis = 0
>
> def _stride_windows(x, n, noverlap=0, axis=0):
> # np>=1.20 provides sliding_window_view, and we only ever use axis=0.
> if hasattr(np.lib.stride_tricks, "sliding_window_view") and axis == 0:
> if noverlap >= n:
> raise ValueError('noverlap must be less than n')
> > return np.lib.stride_tricks.sliding_window_view(
> x, n, axis=0)[::n - noverlap].T
> E TypeError: slice indices must be integers or None or have an __index__ method
>
> /usr/lib/python3/dist-packages/matplotlib/mlab.py:258: TypeError
> =============================== warnings summary ===============================
> nitime/algorithms/event_related.py:13
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/event_related.py:13: DeprecationWarning: invalid escape sequence '\h'
> """
>
> nitime/algorithms/tests/test_coherence.py:206
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_coherence.py:206: DeprecationWarning: invalid escape sequence '\c'
> """
>
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_coherence.py: 30 warnings
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py: 16 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/cohere.py:1008: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> Slices = np.zeros((n_slices, n_freqs), dtype=np.complex)
>
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_coherence.py: 6 warnings
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py: 7 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/cohere.py:1224: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> Cxy = np.zeros((channels_i, channels_j, freqs), dtype=np.complex)
>
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_coherence.py::test_cache_to_coherency
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_coherence.py::test_cache_to_coherency
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_coherence.py::test_cache_to_coherency
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_coherence.py::test_cache_to_coherency
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/cohere.py:1164: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> Phi_xy = np.zeros((channels_i, channels_j, freqs), dtype=np.complex)
>
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py:73: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig1 = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py:78: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig2 = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py::test_periodogram
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py:121: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py::test_periodogram_csd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py:146: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig1 = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py::test_periodogram_csd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/tests/test_spectral.py:150: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig2 = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_CoherenceAnalyzer
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_SparseCoherenceAnalyzer
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/analysis/coherence.py:200: RuntimeWarning: invalid value encountered in divide
> delay[i, j] = this_phase / (2 * np.pi * self.frequencies)
>
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_CoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/analysis/coherence.py:200: RuntimeWarning: divide by zero encountered in divide
> delay[i, j] = this_phase / (2 * np.pi * self.frequencies)
>
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_CoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/cohere.py:699: RuntimeWarning: divide by zero encountered in divide
> return (((np.abs(Rxy - Rxr * Rry)) ** 2) /
>
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_CoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/cohere.py:699: RuntimeWarning: invalid value encountered in divide
> return (((np.abs(Rxy - Rxr * Rry)) ** 2) /
>
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_SparseCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/analysis/coherence.py:523: RuntimeWarning: invalid value encountered in divide
> return self.relative_phases / (2 * np.pi * self.frequencies)
>
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/analysis/coherence.py:659: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> self.frequencies.shape[0]), dtype=np.complex)
>
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/analysis/coherence.py:656: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> self.frequencies.shape[0]), dtype=np.complex)
>
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/analysis/coherence.py:730: RuntimeWarning: invalid value encountered in divide
> return self.relative_phases / (2 * np.pi * self.frequencies)
>
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/analysis/coherence.py:94: RuntimeWarning: In nitime.analysis, the provided input time-series is shorter than the requested NFFT + n_overlap. All coherence values will be set to 1.
> warnings.warn(e_s, RuntimeWarning)
>
> .pybuild/cpython3_3.10/build/nitime/analysis/tests/test_correlation.py::test_SeedCorrelationAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/analysis/correlation.py:150: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> self.target.data.shape[0]), dtype=np.float)
>
> .pybuild/cpython3_3.10/build/nitime/fmri/tests/test_io.py: 10 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/fmri/io.py:121: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
>
> * deprecated from version: 3.0
> * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
> data = im.get_data()
>
> .pybuild/cpython3_3.10/build/nitime/fmri/tests/test_io.py::test_time_series_from_file
> .pybuild/cpython3_3.10/build/nitime/fmri/tests/test_io.py::test_time_series_from_file
> .pybuild/cpython3_3.10/build/nitime/fmri/tests/test_io.py::test_time_series_from_file
> .pybuild/cpython3_3.10/build/nitime/fmri/tests/test_io.py::test_time_series_from_file
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/fmri/io.py:91: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
>
> * deprecated from version: 3.0
> * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
> data = im.get_data()
>
> .pybuild/cpython3_3.10/build/nitime/fmri/tests/test_io.py::test_time_series_from_file
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/fmri/tests/test_io.py:68: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
>
> * deprecated from version: 3.0
> * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
> data = io.load(fmri_file1).get_data()
>
> .pybuild/cpython3_3.10/build/nitime/tests/test_algorithms.py::test_scipy_resample
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/tests/test_algorithms.py:27: DeprecationWarning: Please use `resample` from the `scipy.signal` namespace, the `scipy.signal.signaltools` namespace is deprecated.
> t_up = signaltools.resample(tst, 128)
>
> .pybuild/cpython3_3.10/build/nitime/tests/test_algorithms.py::test_scipy_resample
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/tests/test_algorithms.py:30: DeprecationWarning: Please use `resample` from the `scipy.signal` namespace, the `scipy.signal.signaltools` namespace is deprecated.
> t_dn = signaltools.resample(tst, 32)
>
> .pybuild/cpython3_3.10/build/nitime/tests/test_algorithms.py::test_scipy_resample
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/tests/test_algorithms.py:36: DeprecationWarning: Please use `resample` from the `scipy.signal` namespace, the `scipy.signal.signaltools` namespace is deprecated.
> t_dn2 = signaltools.resample(tst, 48)
>
> .pybuild/cpython3_3.10/build/nitime/tests/test_algorithms.py::test_psd_matlab
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/tests/test_algorithms.py:148: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> ts0 = ts[1] + ts[0] * np.complex(0, 1)
>
> .pybuild/cpython3_3.10/build/nitime/tests/test_analysis.py::test_MorletWaveletAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/wavelet.py:77: RuntimeWarning: divide by zero encountered in log
> wf = (2 * np.exp(-(np.log(f) - np.log(f0)) ** 2 / (2 * sfl ** 2)) *
>
> .pybuild/cpython3_3.10/build/nitime/tests/test_analysis.py::test_MorletWaveletAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/algorithms/wavelet.py:77: RuntimeWarning: invalid value encountered in log
> wf = (2 * np.exp(-(np.log(f) - np.log(f0)) ** 2 / (2 * sfl ** 2)) *
>
> .pybuild/cpython3_3.10/build/nitime/tests/test_lazy.py::test_lazy_noreload
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/tests/test_lazy.py:40: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses
> import imp
>
> .pybuild/cpython3_3.10/build/nitime/tests/test_viz.py::test_drawgraph_channels
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/nitime/viz.py:681: DeprecationWarning: adj_matrix is deprecated and will be removed in version 3.0.
> Use `adjacency_matrix` instead
>
> amat = nx.adj_matrix(G).A # get a normal array out of it
>
> .pybuild/cpython3_3.10/build/nitime/tests/test_viz.py::test_drawgraph_channels
> /usr/lib/python3/dist-packages/networkx/linalg/graphmatrix.py:187: FutureWarning: adjacency_matrix will return a scipy.sparse array instead of a matrix in Networkx 3.0.
> return adjacency_matrix(G, nodelist, dtype, weight)
>
> .pybuild/cpython3_3.10/build/nitime/tests/test_viz.py::test_drawgraph_channels
> /usr/lib/python3/dist-packages/networkx/linalg/graphmatrix.py:173: DeprecationWarning:
>
> The scipy.sparse array containers will be used instead of matrices
> in Networkx 3.0. Use `to_scipy_sparse_array` instead.
> return nx.to_scipy_sparse_matrix(G, nodelist=nodelist, dtype=dtype, weight=weight)
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> FAILED nitime/tests/test_algorithms.py::test_psd_matlab - TypeError: slice in...
> =========== 1 failed, 121 passed, 1 skipped, 113 warnings in 47.53s ============
> E: pybuild pybuild:388: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build; python3.10 -m pytest
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.11 3.10" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2023/01/01/nitime_0.9-3_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230101;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230101&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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