chore: Upgrade Python requirements

[edx-requirements-bot]

Python requirements update. Please review the changelogs for the upgraded packages.

Deleted obsolete pull_requests:
#214

[edx-requirements-bot]

List of packages in the PR without any issue.

• cachetools changes from 7.0.3 to 7.0.5
• chardet changes from 7.0.1 to 7.2.0
• charset-normalizer changes from 3.4.5 to 3.4.6
• coverage[toml] changes from 7.13.4 to 7.13.5
• filelock changes from 3.25.0 to 3.25.2
• jaraco-context changes from 6.1.0 to 6.1.2
• pydata-sphinx-theme changes from 0.15.4 to 0.16.1
• pytest-cov changes from 7.0.0 to 7.1.0
• python-discovery changes from 1.1.0 to 1.2.0
• setuptools changes from 82.0.0 to 82.0.1
• sphinx-book-theme changes from 1.1.4 to 1.2.0
• tox changes from 4.48.1 to 4.50.3
• virtualenv changes from 21.1.0 to 21.2.0

[edx-requirements-bot]

These Packages need manual review..

• [MAJOR] code-annotations changes from 2.3.2 to 3.0.0
• [MAJOR] edx-lint changes from 5.6.0 to 6.0.0