rename n_classes to num_classes

[Borda]

Fixes #2841

Description

unify n_classes and num_classes across model arguments

Status

Ready/Work in progress/Hold

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.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[rijobro]

This is obviously a breaking change, but definitely a useful one.

Similarly, we use dimensions in a few places (e.g., UNet), but use spatial_dims in the majority of other cases.

We also have a couple of different ways of specifying image size if that's necessary, but it's probably more effort than it's worth to correct that.

[wyli]

this PR is probably needed, it is also a good opportunity to test and roll out the deprecated_arg utility before v1.0

MONAI/monai/utils/deprecated.py

Lines 109 to 119 in 1ffa909

	def deprecated_arg(
	name,
	since: Optional[str] = None,
	removed: Optional[str] = None,
	msg_suffix: str = "",
	version_val: str = __version__,
	):
	"""
	Marks a particular named argument of a callable as deprecated. The same conditions for `since` and `removed` as
	described in the `deprecated` decorator.

n_class user could get a specific error message @Nic-Ma

[Nic-Ma]

Looks good to me.
Please note to execute the integration tests and update related tutorials.

Thanks.

[Borda]

Please note to execute the integration

is I am new in this repository, due to GH policy I need to have approved each CI run by maintainers

update related tutorials

what steps do you suggest, as this is a breaking change, shall this be merged first and update tutorials or do it in parallel?

[Nic-Ma]

/integration-test

[Nic-Ma]

I already triggered the integration tests by command, CC @wyli .
Please try to update related tutorials or examples when this PR merged.

Thanks.

[Borda]

Similarly, we use dimensions in a few places (e.g., UNet), but use spatial_dims in the majority of other cases.

@rijobro I would address in it separate PR :]

Please try to update related tutorials or examples when this PR merged.

@wyli prepared PR here: Project-MONAI/tutorials#322

this PR is probably needed, it is also a good opportunity to test and roll out the deprecated_arg utility before v1.0

@Nic-Ma I have been using this zero dependence feature: https://pypi.org/project/pyDeprecate/

[wyli]

this will break the current pretrained model loading... (the following works for the dev branch)

import os
from monai.apps.mmars import MODEL_DESC
from monai.apps.mmars import load_from_mmar

# download the MMAR from NGC to local "./" folder
for x in MODEL_DESC:
    pretrained_model = load_from_mmar(item=x, mmar_dir="./", map_location="cpu")

mainly for the breaking changes in:

• monai/networks/nets/torchvision_fc.py
• monai/networks/nets/resnet.py

could you please help make the above two files backward compatible for now?

[Borda]

could you please help make the above two files backward compatible for now?

@wyli Are you fine with using https://pypi.org/project/pyDeprecate

[wyli]

could you please help make the above two files backward compatible for now?

@wyli Are you fine with using https://pypi.org/project/pyDeprecate

Monai aims at keeping the set of dependencies small for its core modules https://github.com/Project-MONAI/MONAI/blob/dev/requirements.txt we should consider pyDeprecate if it could be an optional dependency instead of a mandatory requirementent. cc @ericspod

[ericspod]

The deprecated annotations won't be optional so I don't think we can do an optional dependency for pyDeprecate. The idea was to define our own decorator that was just enough for our purposes without being a huge amount of code. pyDeprecate is providing a similar facility but having minimal dependencies is worth the reduplication of code in this instance.

[Borda]

@ericspod I have added back-compatibility path, mind check if I use the deprecated_arg correctly?

[Borda]

/integration-test

[Borda]

I already triggered the integration tests by command

@Nic-Ma it seems that /integration-test does not work for me :] does not start anything

[wyli]

The /integration-test is done here https://github.com/Project-MONAI/MONAI/actions/runs/1169956359

I think there are some issue with the utility function. How about we remove the decorator deprecated_arg for now and merge this PR, then have a follow-up on fixing deprecated_arg?

[Borda]

just a noob question why Flake8 CI is complaining about Isort formating?
also seems that the script does not work locally:

~/Workingspace/MONAI$ ./runtests.sh --autofix
PYTHONPATH: /home/jirka/Workingspace/MONAI:
python: /usr/bin/python
./runtests.sh: line 105: 3065342 Segmentation fault      (core dumped) ${cmdPrefix}${PY_EXE} -c "import monai"

so I just just isort . which could be easily fused with #2843

[Borda]

/build

[wyli]

looks like the pre-commit ci doesn't read the black config

MONAI/pyproject.toml

Lines 13 to 17 in ce139f6

	exclude = '''
	(
	/(
	# exclude a few common directories in the root of the project
	\.eggs

, I'll disable those for now

[madil90]

/build

[Borda]

any suggestion on this typing issue:

monai/networks/nets/resnet.py:322:5: error: Returning Any from function declared to return "ResNet"

while I have not touched any return types... could be related to using the deprecated_arg wrapper?

[wyli]

any suggestion on this typing issue:

monai/networks/nets/resnet.py:322:5: error: Returning Any from function declared to return "ResNet"

while I have not touched any return types... could be related to using the deprecated_arg wrapper?

you're right, I think the wrapper needs some enhancements, do you have time to look into deprecated_arg or please just put a "type ignore" to skip the check

[ericspod]

The decorator might have an issue with it's type or an issue with constructors but it's being used correct I believe.