FIX caching of afni allineate when out_matrix is specified

[salma1601]

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Summary

Fixes #3140 .

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

added name_template, name_source and kepp_extension to out_matrix

Acknowledgment

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

[satra]

@salma1601 - one of the doctests needs to be updated with this: -1Dmatrix_save functional_allineated.aff12

[codecov[bot]]

Codecov Report

Merging #3141 into master will decrease coverage by 2.75%. The diff coverage is 72.97%.

@@            Coverage Diff             @@
##           master    #3141      +/-   ##
==========================================
- Coverage   67.62%   64.86%   -2.76%     
==========================================
  Files         299      299              
  Lines       39480    39493      +13     
  Branches     5220     5219       -1     
==========================================
- Hits        26698    25618    -1080     
- Misses      12070    12826     +756     
- Partials      712     1049     +337

Flag	Coverage Δ
#smoketests	?
#unittests	64.86% <72.97%> (-0.03%)	:arrow_down:

Impacted Files	Coverage Δ
nipype/pipeline/plugins/tools.py	78.94% <ø> (-1.32%)	:arrow_down:
nipype/interfaces/base/core.py	83.85% <0%> (-3.12%)	:arrow_down:
nipype/pipeline/plugins/sgegraph.py	14.94% <0%> (ø)	:arrow_up:
nipype/pipeline/engine/nodes.py	78.15% <100%> (-5.16%)	:arrow_down:
nipype/pipeline/plugins/multiproc.py	78.78% <100%> (-2.47%)	:arrow_down:
nipype/info.py	92.3% <100%> (-1.54%)	:arrow_down:
nipype/interfaces/fsl/model.py	55.14% <100%> (-25.44%)	:arrow_down:
nipype/pipeline/plugins/legacymultiproc.py	68.81% <100%> (+5.99%)	:arrow_up:
nipype/__init__.py	34.37% <33.33%> (-24.36%)	:arrow_down:
nipype/interfaces/io.py	56.41% <42.85%> (-3.27%)	:arrow_down:
... and 40 more

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[effigies]

@salma1601 You might have an old version of black installed. I merged master and reran make specs for you. Is this ready to go otherwise?

[effigies]

Just checking back in on this in the run-up to another release. Apologies for the short notice...