Fix CLI output directory type

[Vbitz]

Summary

Restore the CLI-facing output_dir annotation from str | Path to str. Typer 0.15 does not support union-typed command parameters and currently raises AssertionError: Typer Currently doesn't support Union types while constructing the command, including for preprocessor --help.

The function already converts the value with output_dir = Path(output_dir), so runtime path handling is unchanged.

Neurodesk confirmation

This investigation was started with OpenAI Codex CLI while debugging the NeuroContainers BrainLesion image, then confirmed by Neurodesk release CI:

• The NeuroContainers Preprocessor CLI renders help fulltest executes the installed console entry point.
• The unmodified upstream package failed that test: 78/79 container checks passed, with preprocessor --help as the sole failure.
• NeuroContainers temporarily applied the same annotation correction in neurodesk/neurocontainers#2955.
• The replacement image then passed all 79/79 checks, including preprocessor --help.

Local validation

Tested from this branch under Python 3.10 with the project dependency set and Typer 0.15.4:

• preprocessor --help
• preprocessor --version

Both commands exit successfully.

[Copilot]

Pull request overview

This PR fixes a Typer CLI compatibility issue by changing the output_dir command parameter annotation from str | Path to str, avoiding Typer 0.15’s unsupported Union-typed parameters while keeping runtime behavior unchanged (the value is still converted via Path(output_dir)).

Changes:

• Update output_dir CLI parameter type annotation from str | Path to str to prevent Typer AssertionError during command construction (e.g., preprocessor --help).

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[MarcelRosier]

Thanks for the fix! There's actually a better approach that avoids both the union-type issue and retains the semantic correctness of Path — Typer has native Path support via Click's Path param type.

Instead of reverting to str, you can annotate with Path directly:

output_dir: Annotated[
    Path,
    typer.Option(
        "-o",
        "--output_dir",
        help="The path to the output directory",
        exists=False,       # output dir doesn't need to exist yet
        file_okay=False,    # must be a directory, not a file
        dir_okay=True,
        resolve_path=True,
    ),
],

Typer/Click handles the str → Path conversion automatically (no union needed), so you can also remove the manual output_dir = Path(output_dir) on line 92.

This gives you the correct type annotation, Typer 0.15 compatibility, and optional path validation for free.

[neuronflow]

@Vbitz please adress @MarcelRosier's comment ;)

[Vbitz]

Thanks for your review :) Pushed a fix.