STY: Apply ruff/refurb rules

[DimitriPapadopoulos]

Summary

Partially apply FURB rules, where they make sense, except FURB101 (26 errors), FURB103 (21 errors), FURB113 (2 errors), FURB118 (3 errors), FURB140 (2 errors), FURB171 (25 errors).

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

• STY: Apply ruff/refurb rule FURB113 FURB113 Use list.extend(...) instead of repeatedly calling list.append()
• STY: Apply ruff/refurb rule FURB129 FURB129 Instead of calling readlines(), iterate over file object directly
• STY: Apply ruff/refurb rule FURB136 FURB136 Replace 20 if len(nodiffidx) >= 20 else len(nodiffidx) with min(20, len(nodiffidx))
• STY: Apply ruff/refurb rule FURB148 FURB148 enumerate index is unused, use for x in y instead
• STY: Apply ruff/refurb rule FURB167 FURB167 Use of regular expression alias re.X FURB167 Use of regular expression alias re.M

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 21.27660% with 37 lines in your changes are missing coverage. Please review.

Project coverage is 70.90%. Comparing base (d52a62d) to head (7774e3f).

:exclamation: Current head 7774e3f differs from pull request most recent head cfcbc6d. Consider uploading reports for the commit cfcbc6d to get more accurate results

Files	Patch %	Lines
nipype/interfaces/fsl/model.py	0.00%	21 Missing and 5 partials :warning:
nipype/interfaces/io.py	25.00%	3 Missing :warning:
nipype/algorithms/misc.py	0.00%	1 Missing :warning:
nipype/interfaces/cmtk/nx.py	0.00%	1 Missing :warning:
nipype/interfaces/dipy/reconstruction.py	0.00%	1 Missing :warning:
nipype/interfaces/elastix/registration.py	0.00%	0 Missing and 1 partial :warning:
nipype/interfaces/nipy/preprocess.py	0.00%	1 Missing :warning:
nipype/pipeline/engine/workflows.py	85.71%	1 Missing :warning:
nipype/pipeline/plugins/somaflow.py	0.00%	1 Missing :warning:
nipype/sphinxext/plot_workflow.py	0.00%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #3648 +/- ## ======================================= Coverage 70.90% 70.90% ======================================= Files 1277 1277 Lines 59477 59455 -22 Branches 9819 9824 +5 ======================================= - Hits 42172 42157 -15 + Misses 16134 16122 -12 - Partials 1171 1176 +5 ```

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