Update pyproject.toml, including stricter linting rules

[drbenvincent]

This PR modernizes our pyproject.toml configuration and enables stricter linting rules to catch potential bugs and improve code quality.

Changes to pyproject.toml

• Added project URLs: Documentation, Changelog, and Discussions links for better discoverability
• Enhanced coverage settings: Added source, branch, show_missing, and fail_under=80 threshold
• Expanded ruff linting: Added rules to catch bugs (F, B), modernize syntax (UP), and improve code style (C4, SIM)
• Improved mypy config: Added python_version and check_untyped_defs settings
• Cleaned up dependencies: Removed pathlib from dev dependencies (standard library)

Code Fixes

Fixed 27 linting errors across the codebase to comply with new stricter rules:

• B008, B006: Fixed mutable default arguments (common Python pitfall)
• B028: Added proper stacklevel to warnings
• B905: Added strict= parameter to zip() calls
• UP038: Modernized isinstance() calls to use | syntax (Python 3.10+)
• SIM102, SIM105: Simplified nested conditionals and exception handling
• C405: Converted list literals to set literals where appropriate

Pre-commit Configuration

• Added exclude: ^docs/ to ruff pre-commit hook to avoid applying strict rules to example notebooks
• All pre-commit checks now pass

Testing

• All 197 tests pass
• Code coverage threshold set to 80%
• No breaking changes to public APIs

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📚 Documentation preview 📚: https://causalpy--571.org.readthedocs.build/en/571/

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[juanitorduz]

Does this one need a rebase?

[drbenvincent]

Remote tests failing saying test coverage is 0%, which is obviously not true. Debugging...

[codecov]

Codecov Report

❌ Patch coverage is 52.80000% with 59 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.72%. Comparing base (c1cd88f) to head (bcc7f46).

Files with missing lines	Patch %	Lines
...salpy/tests/test_integration_its_new_timeseries.py	26.47%	50 Missing ⚠️
causalpy/pymc_models.py	73.07%	4 Missing and 3 partials ⚠️
causalpy/data/simulate_data.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #571      +/-   ##
==========================================
- Coverage   91.95%   88.72%   -3.24%     
==========================================
  Files          33       33              
  Lines        4776     4844      +68     
  Branches        0      352     +352     
==========================================
- Hits         4392     4298      -94     
- Misses        384      428      +44     
- Partials        0      118     +118     

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