Catching too many warnings, tests fail

[ashgillman]

Hi,

I am maintaining a Nix packages for Nibabel, here:
https://github.com/NixOS/nixpkgs/blob/master/pkgs/development/python-modules/nibabel/default.nix

I have a few tests fail:

======================================================================
FAIL: nibabel.gifti.tests.test_giftiio.test_read_deprecated
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nix/store/khj4yg8583s59wyg1vijj005qvaqiqnk-python3.6-nose-1.3.7/lib/python3.6/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/tmp/nix-build-python3.6-nibabel-2.3.1.drv-0/nibabel-2.3.1/nibabel/gifti/tests/test_giftiio.py", line 36, in test_read_deprecated
    assert_equal(len(w), 1)
AssertionError: 2 != 1

======================================================================
FAIL: nibabel.gifti.tests.test_parse_gifti_fast.test_parse_dataarrays
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nix/store/khj4yg8583s59wyg1vijj005qvaqiqnk-python3.6-nose-1.3.7/lib/python3.6/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/tmp/nix-build-python3.6-nibabel-2.3.1.drv-0/nibabel-2.3.1/nibabel/gifti/tests/test_parse_gifti_fast.py", line 358, in test_parse_dataarrays
    assert_equal(len(w), 1)
AssertionError: 2 != 1

======================================================================
FAIL: test_load_file_with_wrong_information (nibabel.streamlines.tests.test_trk.TestTRK)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/nix-build-python3.6-nibabel-2.3.1.drv-0/nibabel-2.3.1/nibabel/streamlines/tests/test_trk.py", line 135, in test_load_file_with_wrong_information
    assert_equal(len(w), 1)
AssertionError: 2 != 1

======================================================================
FAIL: test_load_trk_version_1 (nibabel.streamlines.tests.test_trk.TestTRK)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/nix-build-python3.6-nibabel-2.3.1.drv-0/nibabel-2.3.1/nibabel/streamlines/tests/test_trk.py", line 186, in test_load_trk_version_1
    assert_equal(len(w), 1)
AssertionError: 2 != 1

======================================================================
FAIL: nibabel.tests.test_minc1.test_old_namespace
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nix/store/khj4yg8583s59wyg1vijj005qvaqiqnk-python3.6-nose-1.3.7/lib/python3.6/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/tmp/nix-build-python3.6-nibabel-2.3.1.drv-0/nibabel-2.3.1/nibabel/tests/test_minc1.py", line 145, in test_old_namespace
    assert_equal(warns.pop(0).category, FutureWarning)
AssertionError: <class 'DeprecationWarning'> != <class 'FutureWarning'>

======================================================================
FAIL: nibabel.tests.test_nifti1.test_extension_io
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nix/store/khj4yg8583s59wyg1vijj005qvaqiqnk-python3.6-nose-1.3.7/lib/python3.6/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/tmp/nix-build-python3.6-nibabel-2.3.1.drv-0/nibabel-2.3.1/nibabel/tests/test_nifti1.py", line 1167, in test_extension_io
    assert_equal(len(warns), 1)
AssertionError: 2 != 1

----------------------------------------------------------------------
Ran 7625 tests in 116.361s

They seem to be all related to catching warnings. Any idea what the issue may be?

Cheers,
Ash

[effigies]

Hi @ashgillman, sorry for the extremely slow response. I'm going to guess, based on the 5th entry, that some non-nibabel-related DeprecationWarning is getting raised in addition to the warnings we're expecting. I'd also guess that it's going to be a numpy issue. Are you still seeing this with the latest release and current master?

[ashgillman]

Yes, I believe this has been taken care of. Thanks :)