STY: Add the mypy flag to check untyped function bodies

[jhlegarreta]

Add the mypy flag to check untyped function bodies.

Fixes:

test/test_parser.py:292: note:
 By default the bodies of untyped functions are not checked,
 consider using --check-untyped-defs  [annotation-unchecked]
test/test_parser.py:294: note:
 By default the bodies of untyped functions are not checked,
 consider using --check-untyped-defs  [annotation-unchecked]
test/test_main.py:92: note:
 By default the bodies of untyped functions are not checked, consider using --check-untyped-defs  [annotation-unchecked]
test/test_main.py:94: note:
 By default the bodies of untyped functions are not checked,
 consider using --check-untyped-defs  [annotation-unchecked]
test/test_main.py:99: note:
 By default the bodies of untyped functions are not checked,
 consider using --check-untyped-defs  [annotation-unchecked]

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/18418756623/job/52488477896?pr=271#step:8:34

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 74.60%. Comparing base (9ce3492) to head (f60c07c).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #273   +/-   ##
=======================================
  Coverage   74.60%   74.60%           
=======================================
  Files          28       28           
  Lines        1764     1764           
  Branches      188      188           
=======================================
  Hits         1316     1316           
  Misses        373      373           
  Partials       75       75           

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[jhlegarreta]

The remaining errors are related to the fact that all data classes are annotated with np.ndarray, but by default they are set to None; they should be annotated with np.ndarray | None, or be initialized with an empty array. Using np.ndarray | None results in dozens of errors since for every indexing operation mypy warns about the fact that None cannot be indexed.