chore: Upgrade Python requirements

[edx-requirements-bot]

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

Deleted obsolete pull_requests:
#1139

[edx-requirements-bot]

List of packages in the PR without any issue.

• asgiref changes from 3.10.0 to 3.11.0
• billiard changes from 4.2.2 to 4.2.3
• cachetools changes from 6.2.1 to 6.2.2
• certifi changes from 2025.10.5 to 2025.11.12
• click changes from 8.3.0 to 8.3.1
• coverage[toml] changes from 7.11.2 to 7.12.0
• datadog-api-client changes from 2.45.0 to 2.46.0
• diff-cover changes from 9.7.1 to 9.7.2
• keyring changes from 25.6.0 to 25.7.0
• pip-tools changes from 7.5.1 to 7.5.2
• pymongo changes from 4.15.3 to 4.15.4
• pynacl changes from 1.6.0 to 1.6.1
• pytest changes from 9.0.0 to 9.0.1
• secretstorage changes from 3.4.0 to 3.4.1
• stevedore changes from 5.5.0 to 5.6.0

[edx-requirements-bot]

These Packages need manual review..

• [MAJOR] ddtrace changes from 3.18.1 to 4.0.0
• [REMOVED] protobuf (6.33.0) removed from the requirements
• [MAJOR] restructuredtext-lint changes from 1.4.0 to 2.0.0