FIX: Return afni.Qwarp outputs as absolute paths

[effigies]

Summary

afni.QwarpPlusMinus provides a default out_file as a relative path, causing afni.Qwarp._list_outputs to return all outputs as relative. This PR always gets the absolute path of the prefix directory, and places all outputs there.

Follow-up to #2674.
Reported in nipreps/fmriprep#1287.

List of changes proposed in this PR (pull-request)

• Fix _gen_filename, which used a missing input
• Locate all specified outputs in the absolute path of the directory implied by -prefix.

Acknowledgment

• (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

[effigies]

Resolves issues on our end. Anybody up for a quick review?

[satra]

@effigies - the code looks fine - but perhaps an afni person (@rmarkello) can take a quick look?

[codecov-io]

Codecov Report

Merging #2705 into master will increase coverage by <.01%.
The diff coverage is 0%.

@@            Coverage Diff             @@
##           master    #2705      +/-   ##
==========================================
+ Coverage    67.6%   67.61%   +<.01%     
==========================================
  Files         340      340              
  Lines       43152    43153       +1     
  Branches     5351     5351              
==========================================
+ Hits        29174    29176       +2     
+ Misses      13276    13275       -1     
  Partials      702      702

Flag	Coverage Δ
#smoketests	50.57% <ø> (ø)	⬆️
#unittests	65.1% <0%> (+0.02%)	⬆️

Impacted Files	Coverage Δ
nipype/interfaces/afni/preprocess.py	81.39% <0%> (-0.1%)	⬇️
nipype/utils/profiler.py	45.4% <0%> (+1.14%)	⬆️

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[rmarkello]

Looks alright to me! Good catch on the source_file name change, too. 👍

[effigies]

Thanks for the reviews, @rmarkello and @satra!

I'll merge when the CI is idle or we have a batch of mergeable PRs.