[WIP] Documentation overhaul

[AntObi]

Overhauling the documentation

Description

N/A

Closes #67 Closes #297

Type of change

Please delete options that are not relevant.

• [x] New feature (non-breaking change which adds functionality)
• [x] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [x] This change requires a documentation update

How Has This Been Tested?

TBC

Test Configuration:

• Python version: 3.10
• Operating System: macOS

Reviewers

N/A

Checklist:

• [x] My code follows the style guidelines of this project
• [x] I have performed a self-review of my own code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] I have made corresponding changes to the documentation
• [x] My changes generate no new warnings
• [x] I have added tests that prove my fix is effective or that my feature works
• [x] New and existing unit tests pass locally with my changes
• [x] Any dependent changes have been merged and published in downstream modules
• [x] I have checked my code and corrected any misspellings

Summary by CodeRabbit

• New Features

  • Enhanced documentation with improved formatting and clarity in the README.md and CONTRIBUTING.md files, facilitating better user navigation and understanding.
  • Introduced support for Jupyter notebooks in documentation, enhancing accessibility for users.
  • Added a new tutorials guide to help users navigate practical applications of the smact library.
  • Expanded the introduction section to outline key features and installation instructions for the smact module.

• Documentation

  • Standardised section headers and improved overall structure in documentation files, making it easier for users to find relevant information.
  • Updated project metadata in configuration files to reflect branding consistency and enhance discoverability.
  • Changed the HTML theme and added new options for better visual presentation and navigation in documentation.

• Chores

  • Minor updates to configuration files for improved clarity and consistency.
  • Updated dependencies in project configuration to ensure compatibility with newer features.

[coderabbitai[bot]]

Walkthrough

The changes encompass various modifications across multiple files, including updates to documentation, formatting adjustments, enhancements to type hinting, and improvements in error handling. The updates also involve reorganising sections in templates, refining workflows, and expanding documentation to provide clearer guidance on functionalities. Overall, these changes aim to enhance code clarity, maintainability, and usability without altering the core logic of the existing functionalities.

Changes

Files	Change Summary
CONTRIBUTING.md, README.md, docs/*.rst	Formatting adjustments, content reorganisation, and minor textual edits for clarity.
docs/conf.py	Added myst_nb extension and updated project metadata.
docs/examples/*.ipynb, docs/tutorials/*.rst	Updated content and structure for improved clarity and accessibility.
pyproject.toml, setup.py	Significant updates for packaging, dependency management, and author information.
smact/*.py	Enhanced type hinting, updated docstrings, and improved error handling across several modules.
smact/tests/*.py	Formatting improvements in test cases and added future import for type hinting.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant System
    participant Documentation
    participant Codebase

    User->>System: Request for functionalities
    System->>Documentation: Retrieve updated documentation
    Documentation-->>User: Provide clear guidance
    User->>Codebase: Execute functions
    Codebase-->>User: Return results

🐰 "In fields of code, I hop with glee,
Changes abound, as bright as can be!
From templates to docs, all polished and neat,
A world of knowledge, oh what a treat!
With every update, I dance and I play,
Celebrating progress, hip-hip-hooray!"
🌼

Assessment against linked issues

Objective	Addressed	Explanation
Running examples from a browser (#67)	✅
Move to ruff for linting and formatting (#297)	✅

[!TIP] We have updated our review workflow to use the Anthropic's Claude family of models. Please share any feedback in the discussion post on our Discord.

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[codecov[bot]]

Codecov Report

Attention: Patch coverage is 65.20619% with 135 lines in your changes missing coverage. Please review.

Project coverage is 72.42%. Comparing base (a7946c9) to head (5167778). Report is 364 commits behind head on develop.

Files with missing lines	Patch %	Lines
smact/structure_prediction/prediction.py	21.62%	29 Missing :warning:
smact/data_loader.py	54.54%	15 Missing :warning:
smact/__init__.py	77.41%	7 Missing :warning:
smact/distorter.py	12.50%	7 Missing :warning:
smact/properties.py	46.15%	7 Missing :warning:
smact/structure_prediction/mutation.py	68.18%	7 Missing :warning:
smact/structure_prediction/structure.py	65.00%	7 Missing :warning:
smact/dopant_prediction/doper.py	64.70%	6 Missing :warning:
smact/utils/band_gap_simple.py	0.00%	6 Missing :warning:
...ls/crystal_space/download_compounds_with_mp_api.py	0.00%	6 Missing :warning:
... and 13 more

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #309      +/-   ##
===========================================
- Coverage    76.46%   72.42%   -4.05%     
===========================================
  Files           26       30       +4     
  Lines         2265     2415     +150     
===========================================
+ Hits          1732     1749      +17     
- Misses         533      666     +133     

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