chore: Upgrade Python requirements

[edx-requirements-bot]

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

Deleted obsolete pull_requests:
#204

[edx-requirements-bot]

List of packages in the PR without any issue.

• build changes from 1.4.0 to 1.5.0
• cachetools changes from 7.0.3 to 7.1.4
• certifi changes from 2026.2.25 to 2026.5.20
• charset-normalizer changes from 3.4.5 to 3.4.7
• click changes from 8.3.1 to 8.4.1
• coverage changes from 7.13.4 to 7.14.1
• coverage[toml] changes from 7.13.4 to 7.14.1
• distlib changes from 0.4.0 to 0.4.1
• filelock changes from 3.25.0 to 3.29.1
• idna changes from 3.11 to 3.18
• lxml changes from 6.0.2 to 6.1.1
• markdown-it-py changes from 4.0.0 to 4.2.0
• numpy changes from 2.4.2 to 2.4.6
• packaging changes from 26.0 to 26.2
• pip changes from 26.0.1 to 26.1.2
• platformdirs changes from 4.9.4 to 4.10.0
• pygments changes from 2.19.2 to 2.20.0
• pyproject-api changes from 1.10.0 to 1.10.1
• pytest changes from 9.0.2 to 9.0.3
• python-discovery changes from 1.1.1 to 1.4.0
• requests changes from 2.32.5 to 2.34.2
• setuptools changes from 82.0.0 to 82.0.1
• stevedore changes from 5.7.0 to 5.8.0
• tomlkit changes from 0.14.0 to 0.15.0
• tox changes from 4.49.0 to 4.55.1
• typer changes from 0.24.1 to 0.26.7
• urllib3 changes from 2.6.3 to 2.7.0
• virtualenv changes from 21.1.0 to 21.4.2
• wheel changes from 0.46.3 to 0.47.0

[edx-requirements-bot]

These Packages need manual review..

• [REMOVED] click (8.3.1) removed from the requirements
• [MAJOR] code-annotations changes from 2.3.2 to 3.0.0
• [MAJOR] edx-lint changes from 5.6.0 to 6.1.0
• [MAJOR] rich changes from 14.3.3 to 15.0.0