Replace pre-commit with Tox and Fix Documentation Generation

[tikhomirovd]

Replace pre-commit with Tox and Fix Documentation Generation

Description

This Pull Request introduces the following major changes to the repository:

1. Replaced pre-commit with Tox:

   • Removed .pre-commit-config.yaml file and all related configurations.
   • Added a comprehensive tox.ini file for managing:
     • Testing across Python versions (py38, py39, py310, py311, py312).
     • Linting with flake8, black, and isort.
     • Documentation generation using Sphinx.
     • Type checking with mypy.
     • Code formatting.
     • Checking for spelling errors with codespell.

2. Fixed Sphinx Documentation Generation:

   • Addressed issues in _templates/autosummary/module.rst, ensuring proper formatting and resolving doc8 validation errors.
   • Updated tox.ini to handle Sphinx builds seamlessly with dependencies like doc8, nbsphinx, and IPython.
   • Ensured successful HTML generation with make clean html.

---

Key Changes

1. Removed Files:

   • .pre-commit-config.yaml (no longer required as Tox replaces its functionality).

2. Added/Updated Files:

   • tox.ini:
     • Configured Tox for testing, linting, formatting, type checking, documentation generation, and more.

3. Dependencies Updated:

   • Updated pyproject.toml to reflect dependencies required for Tox and documentation generation.

---

How to Test

1. Run Tox Locally:

   tox