Migrated pydantic v1 API to v2 API for compliance and warning reduction

[silvandeleemput]

Closes #62 Closes #64

This PR migrates the codebase to use the Pydantic v2 API instead of the deprecated v1 API.
This PR almost removes all of the Pydantic-related deprecation warnings, while still passing all the tests.

The steps that I took for the code changes:

• Installed a development virtual environment with all the dev dependencies and bump_pydantic
• I ran the bump_pydantic tool, which solved some issues, but did not solve all the issues
• I went through all the pydantic warnings, while running pytests, replacing the deprecated V1 api calls with V2 api calls.
• I re-added the comments removed by bump_pandantic

The only remaining warning is related to the following code.

dicomtrolley/dicomtrolley/mint.py

Lines 162 to 178 in bedfc40

	@model_validator(mode="after")
	def min_max_study_date_xor(cls, values): # noqa: B902, N805
	"""Min and max should both be given or both be empty"""
	min_date = values.min_study_date
	max_date = values.max_study_date
	if min_date and not max_date:
	raise ValueError(
	f"min_study_date parameter was passed"
	f"({min_date}), "
	f"but max_study_date was not. Both need to be given"
	)
	elif max_date and not min_date:
	raise ValueError(
	f"max_study_date parameter was passed ({max_date}), "
	f"but min_study_date was not. Both need to be given"
	)
	return values

The warning is:

D:\workspace\dicomtrolley\dicomtrolley\mint.py:164: PydanticDeprecatedSince212: Using `@model_validator` with mode='after' on a classmethod is deprecated. Instead, use an instance method. See the documentation at https://docs.pydantic.dev/2.12/concepts/validators/#model-after-validator. Deprecated in Pydantic V2.12 to be removed in V3.0.

I think this can be easily solved by changing the method to an instance method instead of a class method. Which seems a better fit to me based on my understanding of Pydantic. I've added the change, but please let me know if it should remain a class method for some reason, @sjoerdk.

[sjoerdk]

@silvandeleemput thanks for the work!
That migration has been on my to do list for a long time.

It's fine to make those methods instance methods. If all the tests still run we should be fine.

[sjoerdk]

This is a major change to dicomtrolley though. It will break older (maybe too old) applications.

@silvandeleemput could you do a major version bump as described here?

https://dicomtrolley.readthedocs.io/en/stable/contributing/#incrementing-the-version-number

[sjoerdk]

Looks good!
To fix the CI errors look at #64

And please bump the major version as in https://dicomtrolley.readthedocs.io/en/stable/contributing/#incrementing-the-version-number

I can't do this myself as I'm on my phone and making Christmas dinner

[silvandeleemput]

@sjoerdk Thank you for your timely reply!
I bumped the major version from 3.3.0 -> 4.0.0 in the pyproject.toml and updated the history.md
I think I solved the flake8 and the black issues using the pre-commit hooks, but let's see what the CI says, my environment is suboptimal for this.

[sjoerdk]

Thanks! For some reason github keeps this at status 'blocked, changes requested'. But you already addressed the requested changes. And all tests pass. So I'm bypassing