Feature: Add predict command to CLI

[melisande-c]

Description

• What: Implement CLI predict command.
• Why: Previously calling the CLI predict command would raise NotImplementedError.
• How: A given checkpoint is loaded, then the CAREamist.predict_to_disk is called with optional parameters. Using Typer.

Changes Made

• Added:
  • CLI predict command in careamics/cli/main.py.
  • Tests for CLI predict command.
• Modified:
  • CAREamist.predict_to_disk: fixed bug relating to prediction output directory structure for a single file + some reorganisation.
  • For CLI replaced patch_size_callback with handle_2D_3D_callback, moved to careamics/cli/utils.py. (Typer can only handle fixed sized inputs so this callback is used for a parameter like tile_size that can be 2D or 3D).
  • predict_to_disk tests. Predictions are saved directly to the selected predictions output directory (Not in a second level internal directory).

Additional Notes and Examples

Calling the train and predict command (for a N2V config) is as follows

$ careamics train <CONFIG PATH> -ts <TRAIN DATA PATH>
$ careamics predict checkpoints/<EXPERIMENT NAME>.ckpt <TEST DATA PATH>

Also, please note that CAREamist.predict_to_disk is quite messy but it should be replaced soon when the `PredictionWriterCallback is complete.

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• Code builds and passes tests locally, including doctests
• New tests have been added (for bug fixes/features)
• Pre-commit passes
• PR to the documentation exists (for bug fixes / features)