Avoid re-segmenting already processed subjects

[clementpoiret]

Description

This PR introduces an option to control the overwriting of already existing segmentations.
The new config is files.overwrite:

• files.overwrite=False will skip subjects with segmentations in their parent folder.

A side effect of this PR is that segmentations that are included in glob patterns are removed from the list of mris to segment, which is a good behavior.

Fixes #27

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

How Has This Been Tested?

• See tests/

Test Configuration:

• OS:
• Python version:
• Hardware:
• Any other relevant config detail:

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules

[deepsource-io]

Here's the code health analysis summary for commits 027e16f..eca176d. View details on DeepSource ↗.

Analysis Summary

Analyzer	Status	Summary	Link
Python	❌ Failure	❗ 4 occurences introduced	View Check ↗

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