[BUG] Need traits>=4.5: unicode string problems

[oesteban]

Summary

Traits error checking strings. I think this is duplicated of #1621.

Actual behavior

Traits errors are raised for most of the interfaces, particularly FSL interfaces check and set dictionaries that are prone to reproduce this error.

python -c "from nipype.interfaces.fsl import BET; BET()"

.
.
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traits.trait_errors.TraitError: Each key of the 'environ' trait of a BETInputSpec instance must be an implementor of, or can be adapted to implement, newbytes or None or an implementor of, or can be adapted to implement, newstr or None, but a value of u'FSLOUTPUTTYPE' <type 'unicode'> was specified.

Expected behavior

No errors

python -c "from nipype.interfaces.fsl import BET; BET()"
170210-18:07:18,599 interface WARNING:
	 FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI

How to replicate the behavior

pip install "traits==4.4" --user
Collecting traits==4.4
  Downloading traits-4.4.0.tar.gz (226kB)
    100% |████████████████████████████████| 229kB 1.3MB/s 
Building wheels for collected packages: traits
  Running setup.py bdist_wheel for traits
  Stored in directory: /scratch/users/oesteban/.cache/pip/wheels/cc/8e/0f/5a1d87bc760cd08234133ce38b5737859839c94473eacd452d
Successfully built traits
Installing collected packages: traits
  Found existing installation: traits 4.5.0
    Uninstalling traits-4.5.0:
      Successfully uninstalled traits-4.5.0
Successfully installed traits-4.4.0
You are using pip version 7.1.2, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.


[oesteban@sherlock-ln02 login_node ~]$ python -c "from nipype.interfaces.fsl import BET; BET()"
170210-18:11:48,650 interface WARNING:
	 FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
Exception occurred in traits notification handler.
Please check the log file for details.
Exception occurred in traits notification handler for object: 
args = <undefined>
center = <undefined>
environ = {}
frac = <undefined>
functional = <undefined>
ignore_exception = False
in_file = <undefined>
mask = <undefined>
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
terminal_output = stream
threshold = <undefined>
vertical_gradient = <undefined>
, trait: output_type, old value: <undefined>, new value: NIFTI
Traceback (most recent call last):
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_notifiers.py", line 520, in _dispatch_change_event
    self.dispatch( handler, *args )
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_notifiers.py", line 483, in dispatch
    handler( *args )
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/nipype/interfaces/fsl/base.py", line 174, in _output_update
    self.inputs.environ.update({'FSLOUTPUTTYPE': self.inputs.output_type})
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_handlers.py", line 3206, in update
    new_dic = self._validate_dic( dic )
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_handlers.py", line 3304, in _validate_dic
    raise excp
TraitError: Each key of the 'environ' trait of a BETInputSpec instance must be an implementor of, or can be adapted to implement, newbytes or None or an implementor of, or can be adapted to implement, newstr or None, but a value of u'FSLOUTPUTTYPE' <type 'unicode'> was specified.
170210-18:11:48,650 traits ERROR:
	 Exception occurred in traits notification handler for object: 
args = <undefined>
center = <undefined>
environ = {}
frac = <undefined>
functional = <undefined>
ignore_exception = False
in_file = <undefined>
mask = <undefined>
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
terminal_output = stream
threshold = <undefined>
vertical_gradient = <undefined>
, trait: output_type, old value: <undefined>, new value: NIFTI
Traceback (most recent call last):
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_notifiers.py", line 520, in _dispatch_change_event
    self.dispatch( handler, *args )
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_notifiers.py", line 483, in dispatch
    handler( *args )
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/nipype/interfaces/fsl/base.py", line 174, in _output_update
    self.inputs.environ.update({'FSLOUTPUTTYPE': self.inputs.output_type})
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_handlers.py", line 3206, in update
    new_dic = self._validate_dic( dic )
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_handlers.py", line 3304, in _validate_dic
    raise excp
TraitError: Each key of the 'environ' trait of a BETInputSpec instance must be an implementor of, or can be adapted to implement, newbytes or None or an implementor of, or can be adapted to implement, newstr or None, but a value of u'FSLOUTPUTTYPE' <type 'unicode'> was specified.
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/nipype/interfaces/fsl/base.py", line 168, in __init__
    self.inputs.output_type = self._output_type
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_notifiers.py", line 475, in __call__
    self.notify_listener( self, object, trait_name, old, new )
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_notifiers.py", line 546, in _notify_method_listener
    listener )
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_notifiers.py", line 527, in _dispatch_change_event
    handle_exception( object, trait_name, old, new )
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_notifiers.py", line 520, in _dispatch_change_event
    self.dispatch( handler, *args )
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_notifiers.py", line 483, in dispatch
    handler( *args )
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/nipype/interfaces/fsl/base.py", line 174, in _output_update
    self.inputs.environ.update({'FSLOUTPUTTYPE': self.inputs.output_type})
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_handlers.py", line 3206, in update
    new_dic = self._validate_dic( dic )
  File "/scratch/users/oesteban/.local/lib/python2.7/site-packages/traits/trait_handlers.py", line 3304, in _validate_dic
    raise excp
traits.trait_errors.TraitError: Each key of the 'environ' trait of a BETInputSpec instance must be an implementor of, or can be adapted to implement, newbytes or None or an implementor of, or can be adapted to implement, newstr or None, but a value of u'FSLOUTPUTTYPE' <type 'unicode'> was specified.

Platform details:

{'nibabel_version': '2.0.1', 'networkx_version': '1.10', 'numpy_version': '1.9.3', 'sys_platform': 'linux2', 'sys_version': '2.7.10 |Continuum Analytics, Inc.| (default, Oct 19 2015, 18:04:42) \n[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]', 'commit_source': u'installation', 'commit_hash': u'61978ad', 'pkg_path': '/scratch/users/oesteban/.local/lib/python2.7/site-packages/nipype', 'sys_executable': '/share/PI/russpold/software/anaconda/bin/python', 'traits_version': '4.4.0', 'scipy_version': '0.16.0'}

Fix

Installing traits>=4.5 seems to fix the problem.

[oesteban]

I assume this will be fixed with #1791