I just realized that slice-to-volume motion correction is only implemented when use_cuda is True. The options that are included in this are: mporder, s2v_niter, s2v_lambda, s2v_interp, slspec and json. Any ideas on how to add a check for this?

requires=['use_cuda']?

use_cuda can be made to be True or False. Does requires=['use_cuda']work if use_cuda is False?

I'd check!

Cool! Thanks, I'll try it out

Codecov Report

Merging #3034 into master will increase coverage by 0.61%.
The diff coverage is 56%.

@@            Coverage Diff             @@
##           master    #3034      +/-   ##
==========================================
+ Coverage   67.23%   67.84%   +0.61%     
==========================================
  Files         294      295       +1     
  Lines       39245    39310      +65     
  Branches     5162     5181      +19     
==========================================
+ Hits        26386    26671     +285     
+ Misses      12185    11933     -252     
- Partials      674      706      +32

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requires=['use_cuda'] doesn't quite work. The doctests will still pass if I make use_cuda = False.

Actually, all of the requires might need some finessing.
requires=['repol'] actually needs repol = True
requires=['mporder'] needs mporder > 0
requires=['estimate_move_by_susceptibility'] needs estimate_move_by_susceptibility = True

converting some of the former Bool traits to Enum ended up passing the doctests but fail to run in a workflow:

  File "/scratch/mjoseph/.pyenv/versions/dmriprep_venv/lib/python3.7/site-packages/nipype-1.2.3-py3.7.egg/nipype/interfaces/base/core.py", line 801, in _format_arg
    return argstr % value
TypeError: not all arguments converted during string formatting

Hmm. This is somewhat frustrating. I guess I'd revert to traits.Bool, and then just raise a warning (or an error, if you think it's worth it) in _format_arg() for those that require a Bool that's False, and then return None.

Hi @josephmje, sorry to do this to you, but we just merged some pretty huge changes. Could you re-apply these changes on the latest master? You'll want to re-run make specs entirely, and we're now using the Black formatter. You can run it manually, or use pre-commit to have it automatically run every time you commit.

Please let me know if you need any help or clarifications.

@effigies Sorry my rebase didn't go so well. Do you know what I can do to fix this?

I'll see what I can do.

I rebased, selecting your changes, and running black/make specs before committing each revision. It looks like this doubled up a bunch of commits. I'm not really clear on how that happened.

To update your local branch use git fetch origin && git reset --hard origin/update_eddy.

Thanks for this.