FIX caching of afni allineate when out_matrix is specified

[salma1601]

Summary

Fixes #3140 .

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

added name_template, name_source and kepp_extension to out_matrix

Acknowledgment

• (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]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 64.86%. Comparing base (523dad9) to head (85aeffc).
⚠️ Report is 1305 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #3141   +/-   ##
=======================================
  Coverage   64.86%   64.86%           
=======================================
  Files         299      299           
  Lines       39493    39493           
  Branches     5219     5219           
=======================================
  Hits        25618    25618           
  Misses      12826    12826           
  Partials     1049     1049           

Flag	Coverage Δ
unittests	64.79% <ø> (ø)

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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...