FIX: Address numpy and traits deprecations

[effigies]

To unlock projects that want to support numpy 2, we need to disable our pin and fix some bugs that were probably generated in the 2to3 transition, namely using np.savetxt(..., fmt=b'...').

Started to test on Python 3.13, but we're blocked on a release of traits. Ran with latest master and addressed deprecations.

@mgxd Would you be up for a quick review?

[codecov]

Codecov Report

Attention: Patch coverage is 90.00000% with 5 lines in your changes missing coverage. Please review.

Project coverage is 72.86%. Comparing base (1ccee34) to head (ddb73ac).
Report is 15 commits behind head on master.

Files with missing lines	Patch %	Lines
nipype/algorithms/rapidart.py	25.00%	3 Missing ⚠️
nipype/algorithms/confounds.py	50.00%	1 Missing ⚠️
nipype/interfaces/fsl/epi.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #3699      +/-   ##
==========================================
+ Coverage   70.81%   72.86%   +2.04%     
==========================================
  Files        1277     1278       +1     
  Lines       59153    59305     +152     
  Branches     8590        0    -8590     
==========================================
+ Hits        41890    43212    +1322     
+ Misses      16119    16093      -26     
+ Partials     1144        0    -1144     

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[effigies]

Okay, moving to tox because this CI is a pain to work with.