chore: Upgrade Python requirements

[edx-requirements-bot]

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

Deleted obsolete pull_requests:
#238

[edx-requirements-bot]

List of packages in the PR without any issue.

• astroid changes from 3.3.8 to 3.3.9
• cachetools changes from 5.5.1 to 5.5.2
• filelock changes from 3.17.0 to 3.18.0
• iniconfig changes from 2.0.0 to 2.1.0
• isort changes from 6.0.0 to 6.0.1
• numpy changes from 2.2.2 to 2.2.4
• platformdirs changes from 4.3.6 to 4.3.7
• pycodestyle changes from 2.12.1 to 2.13.0
• pylint changes from 3.3.4 to 3.3.6
• pytest changes from 8.3.4 to 8.3.5
• pytz changes from 2025.1 to 2025.2
• tox changes from 4.24.1 to 4.25.0
• virtualenv changes from 20.29.1 to 20.30.0

[edx-requirements-bot]

These Packages need manual review..

• [MAJOR] setuptools changes from 75.8.0 to 78.1.0