Enforce type hinting and remove redundant numpydoc type annotations

[Copilot]

• Configure ruff to enforce type hinting (add ANN to ruff select, ignore ANN401)
• Add missing type hints to pyrenew/ source files
• Verify numpydoc config already ignores PR04
• Remove type annotations from numpydoc docstring Parameters sections
• Change **kwargs: Any / *args: Any to use object instead of Any
• Remove now-unused from typing import Any imports
• Apply reviewer suggestions (better types for censorednormal.py, multisignal_model.py, pyrenew_builder.py, observation/base.py, ar.py, math.py)
• Fix remaining ANN401 error with # noqa: ANN401 for genuinely-Any argument in differencedprocess.py
• Exclude test/ from ANN ruff checks via [tool.ruff.lint.per-file-ignores]
• All ruff checks pass for both pyrenew/ and test/

Original prompt

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This section details on the original issue you should resolve

<issue_title>Enforce type hinting and remove redundant type annotations from numpydoc docstrings</issue_title>
<issue_description>Steps to implement

• Ensure ruff is configured to enforce type hinting
• Add type hints to functions wherever they are missing
• Configure numpydoc pre-commit hook not to require type annotation in docstrings
• Remove type hints from docstrings</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Enforce type hinting and remove redundant type annotations from numpydoc docstrings #716

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.91%. Comparing base (923fda8) to head (356341c).
⚠️ Report is 8 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #717   +/-   ##
=======================================
  Coverage   97.91%   97.91%           
=======================================
  Files          51       51           
  Lines        1580     1583    +3     
=======================================
+ Hits         1547     1550    +3     
  Misses         33       33           

Flag	Coverage Δ
unittests	97.91% <100.00%> (+<0.01%)	⬆️

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[dylanhmorris]

@copilot please revise so that **kwargs are type-hinted as object rather than as Any

[Copilot]

@copilot please revise so that **kwargs are type-hinted as object rather than as Any

Done in 4c767e9. All **kwargs (and *args) across pyrenew/ are now typed as object instead of Any. The now-unused from typing import Any imports were also removed (kept only where Any is genuinely needed, e.g. dict[str, Any] in pyrenew_builder.py and differencing_order: Any in differencedprocess.py).

[dylanhmorris]

@copilot please run ruff-check and resolve any remaining errors. If there are instances in which an argument should genuinely be typed as Any, add a one-off ignore for ANN401

[Copilot]

@copilot please run ruff-check and resolve any remaining errors. If there are instances in which an argument should genuinely be typed as Any, add a one-off ignore for ANN401

Done in d2b026a. The only remaining ANN401 was in differencedprocess.py:73 — assert_valid_differencing_order(differencing_order: Any) — where Any is intentional (the function exists to validate whatever type is passed). Added # noqa: ANN401 there. All other ruff checks now pass cleanly.

[dylanhmorris]

@damonbayer @cdc-mitzimorris pre-commit is now failing because of lack of type annotation in the test suite. Going back and forth on whether we should enforce it. Thoughts before I we either turn off that rule for the tests or ask copilot to type-annotate the test suite?

[damonbayer]

either turn off that rule for the tests or ask copilot to type-annotate the test suite?

I think we can exclude the tests.

[dylanhmorris]

That was my inclination too.

@copilot, please exclude all files within the tests directory from the ANN ruff check for type annotation, but retain other ruff checks for those files.

[Copilot]

That was my inclination too.

@copilot, please exclude all files within the tests directory from the ANN ruff check for type annotation, but retain other ruff checks for t...

Done in 356341c. Added [tool.ruff.lint.per-file-ignores] to pyproject.toml to suppress ANN checks for test/**, while all other ruff rules remain enforced for those files.

[dylanhmorris]

I have reviewed all changes. This LGTM.