Feat/coupling expansion

[LemurPwned]

Summary by Sourcery

This pull request introduces several new features, including multiple overloads for the AxialDriver class, new methods for the ScalarDriver class, and support for HDMI drivers. It also enhances documentation, refactors the Stack class, and updates plotting functions. New test cases have been added, and the documentation has been improved with new API paths. Additionally, the pre-commit configuration has been updated to exclude third-party directories.

• New Features:
  • Introduced multiple overloads for the AxialDriver class constructor to support initialization with different parameter types.
  • Added new methods to the ScalarDriver class for arithmetic operations and phase shifting.
  • Implemented new methods in the Stack class to handle phase offsets and effective coupling strengths.
  • Added support for HDMI drivers in the Layer and Junction classes.
  • Introduced new functions in the resistance module to compute GMR and handle 3D arrays for time series resistance calculations.
• Enhancements:
  • Enhanced docstrings across multiple classes and methods for better clarity and documentation.
  • Refactored the Stack class to include phase offsets and effective coupling strength calculations.
  • Improved the error handling in the Stack class for coupling strength vector size validation.
  • Updated the plotting functions in the utils/plotting.py to use consistent string formatting.
  • Refactored the LLGBJunction class to include detailed docstrings and improved method signatures.
• Documentation:
  • Updated the mkdocs configuration to include new API documentation paths.
  • Added new API documentation files for core, stack, noise, and LLGB modules.
  • Improved the main documentation index with updated installation instructions and links.
• Tests:
  • Added new test cases in test_drivers.py to validate arithmetic operations on drivers.
  • Commented out certain test assertions in test_models.py to avoid numerical errors during testing.
• Chores:
  • Updated the pre-commit configuration to exclude third-party directories from certain checks.
  • Removed outdated docgen.py script from the hooks section in mkdocs.yml.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request introduces significant enhancements and refactoring to the codebase, focusing on expanding the coupling mechanisms and improving documentation and code quality. The changes include adding new methods, improving existing ones, and enhancing the documentation with detailed docstrings. Additionally, the pull request includes various bug fixes and code style improvements.

File-Level Changes

Files	Changes
cmtj/__init__.pyi cmtj/llgb/__init__.pyi cmtj/stack/__init__.pyi	Added detailed docstrings and refactored method signatures for better readability and consistency.
core/stack.hpp core/drivers.hpp core/junction.hpp core/llgb.hpp core/reservoir.hpp core/cvector.hpp	Introduced new methods, improved error handling, and refactored method signatures for better readability.
cmtj/utils/plotting.py cmtj/utils/resistance.py cmtj/utils/__init__.py cmtj/utils/parallel.py	Standardized string formatting, added detailed docstrings, and refactored methods for better readability.
tests/test_models.py tests/test_drivers.py	Added new test cases and refactored existing ones for better readability.
docs/index.md docs/docgen.py docs/api/core.md docs/api/llgb.md docs/api/noise.md docs/api/stack.md	Updated documentation configuration, fixed broken links, and added new API references.
mkdocs.yml .pre-commit-config.yaml	Updated configuration files for better code quality checks and documentation generation.

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[sourcery-ai]

Hey @LemurPwned - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟡 General issues: 12 issues found
• 🟢 Security: all looks good
• 🟡 Testing: 5 issues found
• 🟢 Complexity: all looks good
• 🟡 Documentation: 1 issue found

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