chore: Upgrade Python requirements

[edx-requirements-bot]

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

Deleted obsolete pull_requests:
#105

[edx-requirements-bot]

List of packages in the PR without any issue.

• astroid changes from 3.2.2 to 3.3.5
• build changes from 1.2.1 to 1.2.2.post1
• cachetools changes from 5.3.3 to 5.5.0
• coverage changes from 7.5.4 to 7.6.4
• dill changes from 0.3.8 to 0.3.9
• distlib changes from 0.3.8 to 0.3.9
• filelock changes from 3.15.4 to 3.16.1
• nltk changes from 3.8.1 to 3.9.1
• platformdirs changes from 4.2.2 to 4.3.6
• pycodestyle changes from 2.12.0 to 2.12.1
• pylint changes from 3.2.3 to 3.3.1
• pyparsing changes from 3.1.2 to 3.2.0
• pyproject-api changes from 1.7.1 to 1.8.0
• pyproject-hooks changes from 1.1.0 to 1.2.0
• regex changes from 2024.5.15 to 2024.9.11
• scipy changes from 1.10.1 to 1.14.1
• tomlkit changes from 0.12.5 to 0.13.2
• tox changes from 4.15.1 to 4.23.2
• tqdm changes from 4.66.4 to 4.66.6
• virtualenv changes from 20.26.3 to 20.27.1
• wheel changes from 0.43.0 to 0.44.0

[edx-requirements-bot]

These Packages need manual review..

• [REMOVED] importlib-metadata (6.11.0) removed from the requirements
• [MAJOR] markupsafe changes from 2.1.5 to 3.0.2
• [MAJOR] numpy changes from 1.24.4 to 2.1.3
• [REMOVED] tomli (2.0.1) removed from the requirements
• [REMOVED] typing-extensions (4.12.2) removed from the requirements
• [REMOVED] zipp (3.19.2) removed from the requirements