FIX: Select Eddy command at runtime

[effigies]

Follow-up to #1711

[satra]

lgtm

[mgxd]

whoops, good catch!

[codecov-io]

Codecov Report

Merging #1871 into master will decrease coverage by <.01%.
The diff coverage is 50%.

@@            Coverage Diff             @@
##           master    #1871      +/-   ##
==========================================
- Coverage   72.92%   72.91%   -0.01%     
==========================================
  Files        1061     1061              
  Lines       53749    53756       +7     
  Branches     7728     7728              
==========================================
+ Hits        39194    39197       +3     
- Misses      13341    13345       +4     
  Partials     1214     1214

Flag	Coverage Δ
#smoketests	72.91% <50%> (-0.01%)	⬇️
#unittests	70.35% <50%> (-0.01%)	⬇️

Impacted Files	Coverage Δ
nipype/interfaces/fsl/epi.py	65.54% <50%> (-0.42%)	⬇️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update cf2b1f8...33f5db1. Read the comment docs.

[effigies]

Actually, if use_cuda is in the input_spec, it should be editable after instantiation, IMO. Pushed a change that just defines _cmd as a property. Is that reasonable, or does something need for _cmd to be accessible for the class as well?

[satra]

@effigies - for many things we have class level assignments and instance level assignments. we could potentially support both in this case, but it's less of an issue here. i'm fine with your current changes.

[alexsavio]

Thanks for this. I will remove the other issue I've just created: #1876.

How are you installing Eddy? The copy I've got is from the Debian version of the Neurodebian package:
http://neuro.debian.net/pkgs/fsl-5.0-eddy-nonfree.html

[satra]

@yarikoptic, @mih - does the neurodebian version still distribute eddy separately? the fsl installer no longer does.

[effigies]

What's the best way to do a version check? Input spec? And what would be the check? The latest release seems to be 5.0.9, which is what's in Neurodebian.

If it's easier, someone feel free to build on my branch and start a new PR.

[alexsavio]

For version checking, the interfaces.fsl.Info.version static method is your best friend. :)

[satra]

@alexsavio - do you not have an eddy_openmp command with neurodebian?

[alexsavio]

@satra - no I don't. I looked for it, I tried to update my installed package...nothing. I am using the Ubuntu xenial version.

[satra]

@alexsavio - it looks like indeed eddy_openmp is not distributed via neurodebian or osx, which have eddy. however, it is available as part of the fsl centos download.

@effigies - we should think about adjusting this interface.

[effigies]

@satra is eddy equivalent to eddy_openmp? And can we assume or require a properly defined $FSL_BIN?

[satra]

shouldn't the and clause be on a separate line? otherwise if cuda is not found it will default to one of openmp or plain eddy.

[satra]

i see how this is problematic for a lot of things, but the only thing i was hoping for was to replace eddy_openmp with eddy on systems that have eddy but not eddy_openmp at runtime. (so in an overloaded run_interface call.

the previous deleted _use_cuda seems reasonable here and can also be used in doctests without requiring fsl to be present.

[satra]

looks good

[alexsavio]

👍 LGTM