chore: Upgrade Python requirements

[edx-requirements-bot]

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

Deleted obsolete pull_requests:
#196

[edx-requirements-bot]

List of packages in the PR without any issue.

• build changes from 1.4.0 to 1.4.4
• cachetools changes from 7.0.3 to 7.0.6
• certifi changes from 2026.2.25 to 2026.4.22
• charset-normalizer changes from 3.4.5 to 3.4.7
• click changes from 8.3.1 to 8.3.3
• coverage changes from 7.13.4 to 7.13.5
• coverage[toml] changes from 7.13.4 to 7.13.5
• filelock changes from 3.25.0 to 3.29.0
• idna changes from 3.11 to 3.13
• lxml changes from 6.0.2 to 6.1.0
• numpy changes from 2.4.2 to 2.4.4
• packaging changes from 26.0 to 26.2
• pip changes from 26.0.1 to 26.1
• platformdirs changes from 4.9.4 to 4.9.6
• pygments changes from 2.19.2 to 2.20.0
• pytest changes from 9.0.2 to 9.0.3
• python-discovery changes from 1.1.1 to 1.2.2
• requests changes from 2.32.5 to 2.33.1
• setuptools changes from 82.0.0 to 82.0.1
• tox changes from 4.49.0 to 4.53.0
• typer changes from 0.24.1 to 0.25.0
• virtualenv changes from 21.1.0 to 21.2.4
• wheel changes from 0.46.3 to 0.47.0

[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
• [MAJOR] rich changes from 14.3.3 to 15.0.0

[edx-requirements-bot]

Closing obsolete PR.