[Debian-med-packaging] Bug#959138: Error in build time tests (Was: numpy breaks nipy autopkgtest: No module named 'numpy.testing.decorators')

[Andreas Tille]

Control: tags -1 pending
Control: tags -1 help

Hi,

I've updated nipy Git[1] to version 0.4.3~rc1 which solves the
originally reported issue.  However, there are some remaining failures
in the build time test:

...
======================================================================
ERROR: Failure: TypeError (unsupported operand type(s) for *: 'GreaterThan' and 'Add')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/usr/lib/python3/dist-packages/nose/loader.py", line 416, in loadTestsFromName
    module = self.importer.importFromPath(
  File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python3.9/imp.py", line 234, in load_module
    return load_source(name, filename, file)
  File "/usr/lib/python3.9/imp.py", line 171, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 711, in _load
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 790, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/build/nipy-0.4.3~rc1/.pybuild/cpython3_3.9_nipy/build/nipy/modalities/fmri/design.py", line 20, in <module>
    from .hrf import glover
  File "/build/nipy-0.4.3~rc1/.pybuild/cpython3_3.9_nipy/build/nipy/modalities/fmri/hrf.py", line 123, in <module>
    _gexpr = gamma_expr(5.4, 5.2) - 0.35 * gamma_expr(10.8, 7.35)
  File "/build/nipy-0.4.3~rc1/.pybuild/cpython3_3.9_nipy/build/nipy/modalities/fmri/hrf.py", line 106, in gamma_expr
    coef * ((T >= 0) * (T+1.0e-14))**(shape-1)
TypeError: unsupported operand type(s) for *: 'GreaterThan' and 'Add'

======================================================================
ERROR: Failure: TypeError (unsupported operand type(s) for *: 'GreaterThan' and 'Add')
----------------------------------------------------------------------

... (more of this type) ...

======================================================================
FAIL: Doctest: nipy.modalities.fmri.utils.convolve_functions
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3.9/doctest.py", line 2204, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for nipy.modalities.fmri.utils.convolve_functions
  File "/build/nipy-0.4.3~rc1/.pybuild/cpython3_3.9_nipy/build/nipy/modalities/fmri/utils.py", line 494, in convolve_functions

----------------------------------------------------------------------
File "/build/nipy-0.4.3~rc1/.pybuild/cpython3_3.9_nipy/build/nipy/modalities/fmri/utils.py", line 533, in nipy.modalities.fmri.utils.convolve_functions
Failed example:
    f1 = (t > 0) * (t < 1)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.9/doctest.py", line 1336, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest nipy.modalities.fmri.utils.convolve_functions[2]>", line 1, in <module>
        f1 = (t > 0) * (t < 1)
    TypeError: unsupported operand type(s) for *: 'StrictGreaterThan' and 'StrictLessThan'
----------------------------------------------------------------------
File "/build/nipy-0.4.3~rc1/.pybuild/cpython3_3.9_nipy/build/nipy/modalities/fmri/utils.py", line 538, in nipy.modalities.fmri.utils.convolve_functions
Failed example:
    tri = convolve_functions(f1, f1, [0, 2], [0, 2], 1.0e-3, name='conv')
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.9/doctest.py", line 1336, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest nipy.modalities.fmri.utils.convolve_functions[3]>", line 1, in <module>
        tri = convolve_functions(f1, f1, [0, 2], [0, 2], 1.0e-3, name='conv')
    NameError: name 'f1' is not defined
----------------------------------------------------------------------
...
----------------------------------------------------------------------
File "/build/nipy-0.4.3~rc1/.pybuild/cpython3_3.9_nipy/build/nipy/modalities/fmri/utils.py", line 549, in nipy.modalities.fmri.utils.convolve_functions
Failed example:
    y = ftri(x)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.9/doctest.py", line 1336, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest nipy.modalities.fmri.utils.convolve_functions[7]>", line 1, in <module>
        y = ftri(x)
    NameError: name 'ftri' is not defined
----------------------------------------------------------------------
File "/build/nipy-0.4.3~rc1/.pybuild/cpython3_3.9_nipy/build/nipy/modalities/fmri/utils.py", line 552, in nipy.modalities.fmri.utils.convolve_functions
Failed example:
    x[np.argmax(y)]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.9/doctest.py", line 1336, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest nipy.modalities.fmri.utils.convolve_functions[8]>", line 1, in <module>
        x[np.argmax(y)]
    NameError: name 'y' is not defined


----------------------------------------------------------------------
Ran 4508 tests in 172.252s

FAILED (SKIP=6, errors=9, failures=1)


Any idea how to fix this?

Kind regards

      Andreas.


[1] https://salsa.debian.org/med-team/nipy

-- 
http://fam-tille.de