Develop

[kavanase]

Summary by CodeRabbit

• New Features

  • Added a verbose option to various functions for enhanced output detail.
  • Introduced logic to handle bulk oxidation states in defect analysis.
  • Enhanced defect identification by automatically determining oxidation states if not provided.

• Bug Fixes

  • Fixed ordering in the apply_dimer_distortion function to ensure specific operations sequence.

• Documentation

  • Updated publication links and references in README and documentation to reflect current information.
  • Updated release version in documentation configuration.

• Refactor

  • Refactored test setup and test functions for improved readability and consistency.
  • Modified several functions to include a verbose parameter for conditional output.

• Tests

  • Enhanced test coverage with additional checks and a new testing function.
  • Introduced a custom decorator for image comparison in plotting tests.

• Chores

  • Updated workflow actions to newer versions and refined CI/CD pipeline configurations.
  • Updated Python versions and operating systems in workflow and documentation configurations.

[coderabbitai[bot]]

Walkthrough

This update weaves a tapestry of improvements throughout the project, enhancing functionality, maintainability, and user experience. From upgrading Python versions to refining workflows, handling errors gracefully, and enriching documentation and testing, these changes aim to elevate the project's quality and efficiency.

Changes

File Path	Change Summary
.github/workflows/...	Updated Python version, upgraded GitHub Actions, refined triggers, and modified test commands.
.readthedocs.yaml	Updated OS version to ubuntu-22.04 and Python version to 3.11.
CHANGELOG.rst	Version 3.3.2: Added verbose options, improved oxi-state guessing, efficiency updates.
README.md, docs/index.rst	Updated publication link for K. Li et al.'s paper.
setup.py, docs/conf.py	Version number updated from '3.3.1' to '3.3.2'.
shakenbreak/...	Enhanced functionality with verbose options, improved error handling, and updated function calls.
tests/...	Improved test setups, added custom decorators, and refined test functions.

🐰✨ In the warren, beneath the moon's glow, Changes whisper through the code's flow. Upgraded, refined, a dance of lines, A rabbit's touch in digital signs. Celebrate the craft, hop and twirl, In the burrow of bytes, a new world unfurls. 🌟🐇

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