[Bug]: TypeError: dumps_kwargs keyword arguments are no longer supported. when running tests on pynwb 2.5.0

[TheChymera]

What happened?

Full build log including tests: https://ppb.chymera.eu/345788.log

Steps to Reproduce

python3.11 -m pytest -vv -ra -l -Wdefault --color=yes -o console_output_style=count -p no:cov -p no:flake8 -p no:flakes -p no:pylint -p no:markdown -p no:sugar -p no:xvfb -p no:pytest-describe -p no:plus -p no:tavern --deselect tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached --deselect tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_bad_ns --deselect tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_core --deselect tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension --deselect tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension_pass_ns --deselect tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_hdmf_common --deselect tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_ignore --deselect tests/validation/test_validate.py::TestValidateCLI::test_validate_file_invalid --deselect tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_core --deselect tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension --deselect tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache --deselect tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns

Traceback

No response

Operating System

Linux

Python Executable

Python

Python Version

3.11

Package Versions

No response

Code of Conduct

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• Have you checked the Contributing document?
• Have you ensured this bug was not already reported?

[oruebel]

Thanks for sharing the log. As far as I can tell from the log, this looks like an error in the DANDIAPI related to the use of pydantic. From a quick google search, it looks pydantic removed in version 2 the option to pass custom options to json dumps https://stackoverflow.com/questions/77076597/is-it-possible-to-get-pydantic-v2-to-dump-json-with-sorted-keys

PyNWB does not have pydantic as a dependency, so this gets probably installed via the dandi python package. I don't think this is an issue we can fix in PyNWB, but is something that I think will need to be fixed in dandi. A possible workaround may be to install v1.10.13 of `pydantic.

I would recommend creating an issue on https://github.com/dandi/dandi-cli for this.

[oruebel]

Actually, I think the issue may be https://github.com/dandi/dandi-schema instead

[oruebel]

Looking at the requirements for dandi-schema, it actually requires pydantic[email] >= 1.8.1, < 2.0 (see
https://github.com/dandi/dandi-schema/blob/36753193205198b7855aed842af76d5e5829816f/setup.cfg#L33). I.e., it looks like the only solution is to either downgrade pydantic to version 1.10x. or to update dandi-schema to support pydantic >2.0.

It looks like there is already an open issue for this here dandi/dandi-schema#176 . I'll close this issue for now here, since we can't fix this on our end, and leave a note about this issue there.

[TheChymera]

Thank you for the clarification!