chore: Upgrade Python requirements

[edx-requirements-bot]

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

Deleted obsolete pull_requests:
#141

[edx-requirements-bot]

List of packages in the PR without any issue.

• astroid changes from 3.3.5 to 3.3.8
• cachetools changes from 5.5.0 to 5.5.1
• charset-normalizer changes from 3.4.0 to 3.4.1
• click changes from 8.1.7 to 8.1.8
• coverage changes from 7.6.8 to 7.6.12
• coverage[toml] changes from 7.6.8 to 7.6.12
• edx-lint changes from 5.4.1 to 5.6.0
• filelock changes from 3.16.1 to 3.17.0
• jinja2 changes from 3.1.4 to 3.1.5
• lxml changes from 5.3.0 to 5.3.1
• numpy changes from 2.1.3 to 2.2.3
• pbr changes from 6.1.0 to 6.1.1
• pylint changes from 3.3.1 to 3.3.4
• pyparsing changes from 3.2.0 to 3.2.1
• pyproject-api changes from 1.8.0 to 1.9.0
• pytest changes from 8.3.3 to 8.3.4
• scipy changes from 1.14.1 to 1.15.2
• setuptools changes from 75.6.0 to 75.8.0
• six changes from 1.16.0 to 1.17.0
• tox changes from 4.23.2 to 4.24.1
• virtualenv changes from 20.27.1 to 20.29.2

[edx-requirements-bot]

These Packages need manual review..

• [MAJOR] certifi changes from 2024.8.30 to 2025.1.31
• [MAJOR] code-annotations changes from 1.8.2 to 2.2.0
• [MAJOR] isort changes from 5.13.2 to 6.0.0

[edx-requirements-bot]

Closing obsolete PR.