Update linting tools and and workflows

[jmmshn]

Summary

Updates GitHub Actions workflows with modernized configurations and dependency updates:

• Python publishing: Switch to trusted publishing using OIDC tokens instead of API tokens
• Testing workflow: Add Python 3.12 support and update action versions (codecov v4, gh-pages v4)
• Pre-commit updates: Modernize workflow with latest action versions and Python 3.11 default

Changes

• .github/workflows/python-publish.yml: Enable trusted publishing with id-token: write permission, remove deprecated password parameter
• .github/workflows/testing.yml: Add Python 3.12 to test matrix, update codecov action to v4, update gh-pages action to v4
• .github/workflows/update-precommit.yml: Update all actions to latest versions (checkout v4, setup-python v5, create-pull-request v6)

Benefits

• More secure package publishing using OpenID Connect
• Extended Python version support (3.10, 3.11, 3.12)
• Latest GitHub Actions with improved security and features

🤖 Generated with Claude Code

[codecov]

Codecov Report

Attention: Patch coverage is 92.30769% with 1 line in your changes missing coverage. Please review.

Project coverage is 90.94%. Comparing base (a3bb39b) to head (52e203c).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
pymatgen/analysis/defects/plotting/thermo.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #217   +/-   ##
=======================================
  Coverage   90.94%   90.94%           
=======================================
  Files          14       14           
  Lines        2264     2265    +1     
  Branches      287      287           
=======================================
+ Hits         2059     2060    +1     
  Misses        118      118           
  Partials       87       87           

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[Copilot]

Pull Request Overview

This PR modernizes linting tools and GitHub Actions workflows while also cleaning up code quality issues identified by updated linters. The changes improve code maintainability, security, and Python version support.

Key changes:

• Updates GitHub Actions workflows with modern security practices (OIDC tokens) and Python 3.12 support
• Updates pre-commit hook versions for ruff, mypy, and codespell
• Fixes various code quality issues including deprecated NumPy functions, import organization, and string formatting

Reviewed Changes

Copilot reviewed 19 out of 20 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
.github/workflows/python-publish.yml	Adds OIDC token support for secure package publishing
.github/workflows/testing.yml	Adds Python 3.12 support and updates action versions
.github/workflows/update-precommit.yml	Updates action versions and Python version
.pre-commit-config.yaml	Updates ruff, mypy, and codespell to latest versions
pyproject.toml	Adds new lint rule ignores and notebook-specific exceptions
pymatgen/analysis/defects/utils.py	Removes unnecessary int() casting
pymatgen/analysis/defects/recombination.py	Replaces deprecated np.trapz with np.trapezoid
Various Python files	Import organization, string formatting, and logging improvements
Notebook files	Removes unused imports and improves code formatting