chore: Upgrade Python requirements

[edx-requirements-bot]

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

Deleted obsolete pull_requests:
#723

[edx-requirements-bot]

List of packages in the PR without any issue.

• alembic changes from 1.18.4 to 1.18.5
• cachetools changes from 7.0.5 to 7.1.4
• certifi changes from 2026.2.25 to 2026.6.17
• click changes from 8.3.1 to 8.4.2
• distlib changes from 0.4.0 to 0.4.3
• docutils changes from 0.22.4 to 0.23
• edx-lint changes from 6.0.0 to 6.1.0
• fastcore changes from 1.12.34 to 1.13.9
• filelock changes from 3.25.2 to 3.29.4
• fonttools changes from 4.62.1 to 4.63.0
• ghapi changes from 1.0.13 to 1.0.14
• gitpython changes from 3.1.47 to 3.1.50
• greenlet changes from 3.3.2 to 3.5.3
• idna changes from 3.11 to 3.18
• mako changes from 1.3.11 to 1.3.12
• markdown-it-py changes from 4.0.0 to 4.2.0
• matplotlib changes from 3.10.8 to 3.11.0
• more-itertools changes from 11.0.1 to 11.1.0
• moreorless changes from 0.5.0 to 0.6.0
• msgpack changes from 1.1.2 to 1.2.1
• numpy changes from 2.4.4 to 2.5.0
• packaging changes from 26.0 to 26.2
• pandas changes from 3.0.2 to 3.0.3
• pillow changes from 12.2.0 to 12.3.0
• platformdirs changes from 4.9.4 to 4.10.0
• playwright changes from 1.58.0 to 1.61.0
• pygithub changes from 2.9.0 to 2.9.1
• pyjwt changes from 2.12.1 to 2.13.0
• pylint changes from 4.0.5 to 4.0.6
• pyproject-api changes from 1.10.0 to 1.10.1
• pytest changes from 9.0.2 to 9.1.1
• python-discovery changes from 1.2.1 to 1.4.2
• requests changes from 2.33.1 to 2.34.2
• requirements-parser changes from 0.13.0 to 0.13.1
• responses changes from 0.26.0 to 0.26.1
• stevedore changes from 5.7.0 to 5.8.0
• tomlkit changes from 0.14.0 to 0.15.0
• tox changes from 4.52.0 to 4.56.1
• tqdm changes from 4.67.3 to 4.68.3
• urllib3 changes from 2.6.3 to 2.7.0
• virtualenv changes from 21.2.0 to 21.5.1

[edx-requirements-bot]

These Packages need manual review..

• [REMOVED] banal (1.0.6) removed from the requirements
• [MAJOR] cryptography changes from 46.0.6 to 49.0.0
• [MAJOR] dataset changes from 1.6.2 to 2.0.0
• [MAJOR] rich changes from 14.3.3 to 15.0.0
• [MAJOR] sqlalchemy changes from 1.4.54 to 2.0.51
• [MAJOR] tzdata changes from 2025.3 to 2026.2