Latest version of traits (6.4.1) seems to break init_brain_extraction_wf

[ellisdg]

I am having issues using niworkflows in an environment that has the latest version of traits (traits==6.4.1) installed.

I was able to recreate the error by running the following in a brand new Anaconda environment:

conda install python=3.9 pip
pip install niworkflows==1.6.2 traits==6.4.1
python
>>> from niworkflows.anat.ants import init_brain_extraction_wf
>>> wf = init_brain_extraction_wf()

Error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/david.ellis/miniconda3/envs/nipype/lib/python3.10/site-packages/niworkflows/anat/ants.py", line 305, in init_brain_extraction_wf
    Registration(
  File "/Users/david.ellis/miniconda3/envs/nipype/lib/python3.10/site-packages/nipype/interfaces/ants/registration.py", line 1015, in __init__
    super(Registration, self).__init__(**inputs)
  File "/Users/david.ellis/miniconda3/envs/nipype/lib/python3.10/site-packages/nipype/interfaces/ants/base.py", line 77, in __init__
    super(ANTSCommand, self).__init__(**inputs)
  File "/Users/david.ellis/miniconda3/envs/nipype/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 630, in __init__
    super(CommandLine, self).__init__(**inputs)
  File "/Users/david.ellis/miniconda3/envs/nipype/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 210, in __init__
    self.load_inputs_from_json(from_file, overwrite=True)
  File "/Users/david.ellis/miniconda3/envs/nipype/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 489, in load_inputs_from_json
    setattr(self.inputs, key, inputs_dict[key])
  File "/Users/david.ellis/miniconda3/envs/nipype/lib/python3.10/site-packages/traits/trait_types.py", line 2695, in validate
    return TraitListObject(self, object, name, value)
  File "/Users/david.ellis/miniconda3/envs/nipype/lib/python3.10/site-packages/traits/trait_list_object.py", line 584, in __init__
    super().__init__(
  File "/Users/david.ellis/miniconda3/envs/nipype/lib/python3.10/site-packages/traits/trait_list_object.py", line 213, in __init__
    super().__init__(self.item_validator(item) for item in iterable)
  File "/Users/david.ellis/miniconda3/envs/nipype/lib/python3.10/site-packages/traits/trait_list_object.py", line 213, in <genexpr>
    super().__init__(self.item_validator(item) for item in iterable)
  File "/Users/david.ellis/miniconda3/envs/nipype/lib/python3.10/site-packages/traits/trait_list_object.py", line 867, in _item_validator
    return trait_validator(object, self.name, value)
  File "/Users/david.ellis/miniconda3/envs/nipype/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: Each element of the 'transform_parameters' trait of a _FixHeaderRegistrationInputSpec instance must be a tuple of the form: (a float) or a tuple of the form: (a float, a float, a float) or a tuple of the form: (a float, an integer, an integer, an integer) or a tuple of the form: (a float, an integer, a float, a float, a float, a float) or a tuple of the form: (a float, a float, a float, an integer) or a tuple of the form: (a float, an integer, an integer, an integer, an integer), but a value of [0.1] <class 'list'> was specified.

But when I revert back to traits==6.3.2, the error is avoided:

pip install traits==6.3.2
python
>>> from niworkflows.anat.ants import init_brain_extraction_wf
>>> wf = init_brain_extraction_wf()

Therefore, it seems that the latest version of traits causes the loading of the data json files in niworkflows to fail, at least for _FixHeaderRegistrationInputSpec.

[effigies]

Yes. Traits 6.4 is breaking all of nipype. We need to set a hard upper bound, IMO. The next release of nipype will include nipy/nipype#3501, but downstream projects probably need it too.

[mgxd]

This has been incorporated in 1.6.3 and above