5821 Enhance bundle CLI entry for different bundle workflows

[Nic-Ma]

part of #5821 .

Description

This PR enhanced the bundle CLI entry to support different customized bundle workflows.

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).
• Breaking change (fix or new feature that would cause existing functionality to change).
• New tests added to cover the changes.
• Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
• Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[ericspod]

I have a few concerns with backwards compatibility with this change. I see what your intent is and that it does work correctly, but if someone has a command line python -m monai.bundle run some_expr they would need to have python -m monai.bundle run --run_id some_expr? Even besides that, because the arguments are being removed from the signature of the function the help output from Fire gives less information about what the arguments are, and what they are for, since all the important values get put into **kwargs.

[ericspod]

Also it looks like the premerge tests are failing for related reasons, that is the command line has changed.

[Nic-Ma]

Hi @ericspod ,

Thanks for your review and suggestions.
I totally updated the PR based on the comments and added tests, could you please help review it again?

Thanks in advance.

[Nic-Ma]

/black

[Nic-Ma]

/build

[Nic-Ma]

/build

[ericspod]

Looks good, I have very minor style suggestions. I see you're using pydoc.locate here and I wonder if we should have our own function in monai.utils.module for doing this. This is a topic for some other time and place but I had used something like this in the past that worked well enough:

def find_type_def(qualified_name: str):
    if "." not in qualified_name:
        modname, defname = "builtins", qualified_name
    else:
        modname, defname = qualified_name.rsplit(".", 1)

    mod = __import__(modname)
    return getattr(mod, defname)

[Nic-Ma]

Hi @ericspod ,

Thanks for your review, I updated the PR accordingly.
And for the locate suggestion, I created a ticket to discuss and track: #6275.
Because we use locate in several places of current codebase:
https://github.com/Project-MONAI/MONAI/blob/dev/monai/networks/nets/flexible_unet.py#L16

https://github.com/Project-MONAI/MONAI/blob/dev/monai/utils/module.py#L244

https://github.com/Project-MONAI/MONAI/blob/dev/monai/transforms/io/array.py#L208

If we want to change them together, maybe better to do a separate PR?

Thanks.

[Nic-Ma]

/black

[Nic-Ma]

/build

[Nic-Ma]

/build

[Nic-Ma]

/build

[ericspod]

If we want to change them together, maybe better to do a separate PR?

Thanks.

Thanks I see that issue now. It should be done separately yes.

[Nic-Ma]

/build

[Nic-Ma]

/build

[Nic-Ma]

Hi @wyli ,

Do you know the root cause of Blossom system error here?

Thanks in advance.

[wyli]

/build