Import error for nipype.interfaces.dipy.base

[koenhelwegen]

Summary

import nipype.interfaces.dipy generates an error for me, with Python 3.9 and 3.8, Dipy 4.12 (latest release) and latest release or current master of nipype.

Actual behavior

Running the above import generates the error TypeError: 'NoneType' object is not iterable generated from dipy_to_nipype_interface at:

nipype/nipype/interfaces/dipy/base.py

Line 200 in f756b71

for args, val in zip(parser.output_parameters, default_values[start:])

This function is executed during import in interfaces.dipy.preprocess. It seems this works correctly for several workflows (LabelsBundles, MedianOtsu, RecoBundles, LocalFiberTrackingPAM, PFTrackingPAM) but crashes for GibbsRingingFlow because default_values is None.

How to replicate the behavior

• create a fresh venv
• pip install the latest dipy and nipype packages
• open python and run import nipype.interfaces.dipy

Expected behavior

A working import. This seems an easy fix, if others can reproduce the issue I would be happy to make a PR replacing

nipype/nipype/interfaces/dipy/base.py

Line 192 in f756b71

default_values = inspect.getfullargspec(flow.run).defaults

with:

    default_values = inspect.getfullargspec(flow.run).defaults or []

Platform details:

{'commit_hash': 'f756b7111',
 'commit_source': 'repository',
 'networkx_version': '2.6.3',
 'nibabel_version': '3.2.1',
 'nipype_version': '1.7.1-dev+gf756b7111',
 'numpy_version': '1.21.4',
 'pkg_path': '/home/.../basedir/nipype/nipype',
 'scipy_version': '1.7.2',
 'sys_executable': '/home/.../basedir/venv/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.9.9 (main, Nov 16 2021, 03:08:02) \n[GCC 9.3.0]',
 'traits_version': '6.3.2'}

(Error is the same for Python 3.8)

Execution environment

• My python environment outside container

[effigies]

Please also report upstream to dipy. We need to make these imports more resilient to API breakages.

cc @skoudoro

[koenhelwegen]

On closer inspection I realize the bug is actually a bit more complicated. The run() method on GibbsRingingFlow does have default arguments, but inspect.getfullargspec() breaks here because of a decorator that was added a few months ago (https://github.com/dipy/dipy/blob/61a6f14015b8cd58b48501e1ef6fc853e55b6807/dipy/workflows/denoise.py#L311). So it is not really an API change from dipy.

[skoudoro]

Thank you for pinging me. It is strange that the decorator does not keep the same function signature. I need to improve the new decorator management in Nipype.

Otherwise, it will break each time we deprecate an argument. I have a quite busy period but I will have a deeper look into it for sure.

[skoudoro]

I suppose I should use inspect.signature() instead of inspect.getfullargspec()