fix: update Pydantic version

Description

Update range of supported Pydantic versions (>=2, <3)
Replace json method with model_dump_json, remove dumps_kwargs argument
Convert tmpdir path to str before passing as arg by adding .strpath attribute to tmpdir in test_htsinfer.py, as pydantic was not recognizing at as a valid path

Type of change

[X] Bug fix (non-breaking change which fixes an issue)

Checklist

Please carefully read these items and tick them off if the statements are true or do not apply.

[X] I have performed a self-review of my own code
[X] My code follows the existing coding style, lints and generates no new warnings
[X] I have added type annotations to all function/method signatures, and I have added type annotations for any local variables that are non-trivial, potentially ambiguous or might otherwise benefit from explicit typing.
[X] I have commented my code in hard-to-understand areas
[X] I have added ["Google-style docstrings"] to all new modules, classes, methods/functions or updated previously existing ones
[X] I have added tests that prove my fix is effective or that my feature works
[X] New and existing unit tests pass locally with my changes and I have not reduced the code coverage relative to the previous state
[X] I have updated any sections of the app's documentation that are affected by the proposed changes

If for some reason you are unable to tick off all boxes, please leave a comment explaining the issue you are facing so that we can work on it together.

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (67bb506) 100.00% compared to head (e6d4ba3) 100.00%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #146 +/- ## ========================================= Coverage 100.00% 100.00% ========================================= Files 13 13 Lines 1078 1078 ========================================= Hits 1078 1078 ``` | [Files](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/146?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab) | Coverage Δ | | |---|---|---| | [htsinfer/htsinfer.py](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/146?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-aHRzaW5mZXIvaHRzaW5mZXIucHk=) | `100.00% <ø> (ø)` | |

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zavolanlab / htsinfer