chore: Upgrade Python requirements

[edx-requirements-bot]

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

[edx-requirements-bot]

List of packages in the PR without any issue.

• asgiref changes from 3.11.1 to 3.12.1
• beautifulsoup4 changes from 4.14.3 to 4.15.0
• cachetools changes from 7.1.2 to 7.1.4
• certifi changes from 2026.4.22 to 2026.6.17
• cffi changes from 2.0.0 to 2.1.0
• charset-normalizer changes from 3.4.7 to 3.4.9
• click changes from 8.4.0 to 8.4.2
• coverage changes from 7.14.0 to 7.15.2
• distlib changes from 0.4.0 to 0.4.3
• django - python_full_version < '3.13' changes from 5.2.14 to 5.2.16
• django - python_full_version >= '3.13' changes from 5.2.14 to 5.2.16
• edx-submissions changes from 4.0.0 to 4.0.1
• filelock changes from 3.29.0 to 3.31.0
• idna changes from 3.15 to 3.18
• lxml changes from 6.1.0 to 6.1.1
• nh3 changes from 0.3.5 to 0.3.6
• nltk changes from 3.9.4 to 3.10.0
• numpy changes from 2.4.5 to 2.5.1
• pillow changes from 12.2.0 to 12.3.0
• platformdirs changes from 4.9.6 to 4.10.1
• pydata-sphinx-theme changes from 0.16.1 to 0.20.0
• pyjwt changes from 2.12.1 to 2.13.0
• pyproject-api changes from 1.10.0 to 1.10.1
• pytest changes from 9.0.3 to 9.1.1
• python-discovery changes from 1.3.1 to 1.4.4
• regex changes from 2026.5.9 to 2026.7.19
• ruff changes from 0.15.18 to 0.15.22
• scipy changes from 1.17.1 to 1.18.0
• snowballstemmer changes from 3.0.1 to 3.1.1
• soupsieve changes from 2.8.3 to 2.9
• sphinx-book-theme changes from 1.2.0 to 1.4.0
• stevedore changes from 5.7.0 to 5.9.0
• tox changes from 4.54.0 to 4.57.0
• tqdm changes from 4.67.3 to 4.69.0
• typing-extensions changes from 4.15.0 to 4.16.0
• tzdata changes from 2026.2 to 2026.3
• uv changes from 0.11.14 to 0.11.29
• virtualenv changes from 21.3.3 to 21.6.1
• webob changes from 1.8.9 to 1.8.10
• wrapt changes from 2.1.2 to 2.2.2
• xblock changes from 6.1.0 to 6.3.1

[edx-requirements-bot]

These Packages need manual review..

• [MAJOR] cryptography changes from 48.0.0 to 49.0.0
• [MAJOR] edxval changes from 4.0.1 to 5.0.1
• [REMOVED] web-fragments (4.0.0) removed from the requirements