refactor: limit usage of scipy and skilearn dependencies

[nathan-weinberg]

Impact

This PR does the following:

• Removes some unused dependencies
• Moves all imports of scipy and skilearn
• Moves duplicated function weighted_f1_score into lm_eval.utils and does relative importing into local task utils so as to not break YAML files

This is all meant to resolve #2059

Testing

@haileyschoelkopf I could use some advice on how to test these changes - I attempted to run the unit tests after doing pip install lm_eval[all] per the CONTRIBUTING doc but was unable to do so. I can also remove the second commit to minimize the impact of this PR if we are unable to test/the maintainers prefer it.

(venv) [nathan@nathan-redhat lm-evaluation-harness (dep-update)]$ python -m pytest --ignore=tests/tests_master --ignore=tests/extra
=========================================================================== test session starts ============================================================================
platform linux -- Python 3.11.9, pytest-8.2.2, pluggy-1.5.0
rootdir: /home/nathan/instructlab/repos/lm-evaluation-harness
configfile: pyproject.toml
plugins: xdist-3.6.1, cov-5.0.0
collected 74 items / 1 error / 1 skipped                                                                                                                                   

================================================================================== ERRORS ==================================================================================
______________________________________________________________ ERROR collecting tests/models/test_openvino.py ______________________________________________________________
ImportError while importing test module '/home/nathan/instructlab/repos/lm-evaluation-harness/tests/models/test_openvino.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/models/test_openvino.py:6: in <module>
    from optimum.intel import OVModelForCausalLM
E   ModuleNotFoundError: No module named 'optimum'
========================================================================= short test summary info ==========================================================================
ERROR tests/models/test_openvino.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
======================================================================= 1 skipped, 1 error in 27.48s =======================================================================

[CLAassistant]

All committers have signed the CLA.

[nathan-weinberg]

I ran the same pytest command as the CI locally and had a successful run

(venv) [nathan@nathan-redhat lm-evaluation-harness (dep-update)]$ python -m pytest --showlocals -s -vv -n=auto --ignore=tests/models/test_neuralmagic.py --ignore=tests/models/test_openvino.py
=========================================================================== test session starts ============================================================================
platform linux -- Python 3.11.9, pytest-8.2.2, pluggy-1.5.0 -- /home/nathan/instructlab/repos/lm-evaluation-harness/venv/bin/python

...

============================================================================= warnings summary =============================================================================
tests/models/test_neuron_optimum.py::test_wrap_constant_batch_size
  /home/nathan/instructlab/repos/lm-evaluation-harness/tests/models/test_neuron_optimum.py:21: FutureWarning: `torch.testing.assert_allclose()` is deprecated since 1.12 and will be removed in a future release. Please use `torch.testing.assert_close()` instead. You can find detailed upgrade instructions in https://github.com/pytorch/pytorch/issues/61844.
    torch.testing.assert_allclose(out, tensor)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================================================== 69 passed, 1 skipped, 1 warning in 160.69s (0:02:40) ===========================================================

Will retry after fixing lint errors

[tiran]

@nathan-weinberg Your PR has lots of unrelated changes. I recommend to move code reformatting and newline at EOF fixes to a separate PR.

[nathan-weinberg]

@nathan-weinberg Your PR has lots of unrelated changes. I recommend to move code reformatting and newline at EOF fixes to a separate PR.

Will wait to hear from the maintainers - seems these issues are present in the current upstream codebase so I commited a fix just so I could continue working on it - can cherry-pick the commit and put it in a new PR for sure, thoughts @haileyschoelkopf @lintangsutawika?

[lintangsutawika]

Sorry bout that.
#2104 should fix this and then you can pull the latest main.

[haileyschoelkopf]

Thanks @nathan-weinberg for the PR, will merge once tests pass! (And thanks for adding the note about which tests to exclude in the contributor guide!)

I moved weighted_f1_score into lm_eval.api.metrics .

[nathan-weinberg]

Is any additional testing needed?

[nathan-weinberg]

Hi @haileyschoelkopf just checking in to see if this can be merged - if you need anything from my side please let me know!

I think I may have lost your commit when rebasing, feel free to readd it, sorry about that.

[haileyschoelkopf]

Hey! Sorry, no idea how this got lost, swear I merged this at the time--anyway, back from ICML now, and doing so now. Thanks for this fix!