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Some interfaces breaking as MapNodes with py2 + Traits 5.0.0 #2913

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mgxd opened this issue Apr 9, 2019 · 3 comments
Closed

Some interfaces breaking as MapNodes with py2 + Traits 5.0.0 #2913

mgxd opened this issue Apr 9, 2019 · 3 comments

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@mgxd
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mgxd commented Apr 9, 2019

Summary

It looks like there is some incompatibility currently with FSL interfaces (and possibly others) with py2 and traits 5.0

https://neurostars.org/t/cant-pickle-instancemethod-when-using-mapnode-in-nipype/4052/4?u=mgxd

#2910 #2882

Actual behavior

from nipype import MapNode, Workflow
from nipype.interfaces.fsl import BET

better = MapNode(BET(), iterfield=['in_file'], name='better')
better.inputs.in_file = ['/path/to/some/image'] * 2
wf = Workflow('testwf')
wf.add_nodes([better])
wf.run()
...
...
TypeError: can't pickle instancemethod objects

Expected behavior

[Node] Finished "testwf.better".

Platform details:

{'commit_hash': 'ec7457c23',
 'commit_source': 'installation',
 'networkx_version': '2.2',
 'nibabel_version': '2.3.0',
 'nipype_version': '1.1.3',
 'numpy_version': '1.15.2',
 'pkg_path': '/om2/user/mathiasg/miniconda/envs/py2/lib/python2.7/site-packages/nipype',
 'scipy_version': '1.1.0',
 'sys_executable': '/om2/user/mathiasg/miniconda/envs/py2/bin/python',
 'sys_platform': 'linux2',
 'sys_version': '2.7.14 |Anaconda, Inc.| (default, Mar 12 2018, 12:37:12) \n[GCC 7.2.0]',
 'traits_version': '5.0.0'}

Execution environment

Choose one

  • My python environment outside container
@mgxd
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mgxd commented Apr 9, 2019

Related: enthought/traits#452

I think our best bet is to pin py2 installs to traits 4.6.0 until it is resolved upstream
WDYT @satra @effigies

@effigies
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effigies commented Apr 9, 2019

I thought we had pinned that...

@mgxd
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mgxd commented Apr 16, 2019

btw- this has been fixed in traits 5.1

sebastientourbier added a commit to connectomicslab/connectomemapper3 that referenced this issue Apr 26, 2019
@mgxd mgxd closed this as completed May 2, 2019
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