Prototype cli

[arnaudbore]

Here is a prototype of a cli: antsMouseBrainExtraction

Even tho I've been told @cookpa would take care of it, I took few minutes to give it a try. Sorry not sorry I guess 😅

#217

[ntustison]

Hey, thanks for this @arnaudbore . I'll defer to @cookpa to provide any feedback on this since it's a bit out of my wheelhouse.

[arnaudbore]

Hey @cookpa !
Any update on this side ?

[Copilot]

Pull request overview

This PR introduces a first prototype command-line interface for running ANTsPyNet’s mouse_brain_extraction utility via an installed console script, along with a unit test that verifies the CLI wiring (read → extract → write).

Changes:

• Add antspynet.cli.mouse_brain_extraction implementing an argparse-based CLI wrapper around antspynet.mouse_brain_extraction.
• Register a console script entry point in pyproject.toml.
• Add a lightweight unit test that patches I/O/model calls to validate argument routing.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 4 comments.

File	Description
antspynet/cli/mouse_brain_extraction.py	New CLI implementation (parser, run wrapper, main entry).
antspynet/cli/__init__.py	Introduces cli package and re-exports main.
pyproject.toml	Adds a console script entry point for the new CLI.
tests/test_mouse_cli.py	Adds a unit test validating CLI → mouse_brain_extraction call routing.

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[arnaudbore]

@cookpa it should be ready 👍

[cookpa]

Thanks, I will start the tests. They take a while because of data downloads

[arnaudbore]

@cookpa Ready ?

[cookpa]

I think it's almost there but there's a couple of detail comments above

[arnaudbore]

I think it's almost there but there's a couple of detail comments above

Tell me what you want me to fix please:

• The exit error issue ?

• The extra command line: ants_mouse_brain_extraction ?

[cookpa]

Sorry, my fault I did not submit the review where I wrote the comments

[arnaudbore]

Done ! 👍

[cookpa]

Test failure on Python 3.11 looks to be an infrastructure problem, works on 3.13 so I'm calling this good. Thanks @arnaudbore