[ENH]: Introduce run_ext_cmd for running external commands

[synchon]

• description of feature/fix
• tests added/passed
• add an entry for the latest changes

This PR introduces a helper function run_ext_cmd to run external commands like those from FSL, ANTs and others.

[github-actions]

PR Preview Action v1.4.6
Preview removed because the pull request was closed.
2024-01-16 11:17 UTC

[codecov]

Codecov Report

Attention: 12 lines in your changes are missing coverage. Please review.

Comparison is base (69ebbcd) 88.11% compared to head (ed448c4) 89.23%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #295      +/-   ##
==========================================
+ Coverage   88.11%   89.23%   +1.12%     
==========================================
  Files          99      100       +1     
  Lines        4517     4449      -68     
  Branches      865      853      -12     
==========================================
- Hits         3980     3970      -10     
+ Misses        396      341      -55     
+ Partials      141      138       -3     

Flag	Coverage Δ
docs	100.00% <ø> (ø)
junifer	89.23% <72.72%> (+1.12%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
junifer/markers/falff/falff_estimator.py	95.50% <100.00%> (+1.56%)	⬆️
junifer/markers/reho/reho_estimator.py	68.30% <100.00%> (+0.12%)	⬆️
junifer/utils/__init__.py	100.00% <100.00%> (ø)
junifer/utils/helpers.py	100.00% <100.00%> (ø)
junifer/data/coordinates.py	63.38% <33.33%> (+7.28%)	⬆️
junifer/data/masks.py	81.37% <33.33%> (+5.09%)	⬆️
junifer/data/parcellations.py	88.16% <33.33%> (+1.89%)	⬆️
...er/preprocess/ants/ants_apply_transforms_warper.py	47.50% <25.00%> (+9.03%)	⬆️
junifer/preprocess/fsl/apply_warper.py	47.50% <25.00%> (+9.03%)	⬆️