Use optional-dependencies for third-party packages

[donbarbos]

• tqdm: https://github.com/tqdm/tqdm/blob/master/pyproject.toml
• pyogrio: https://github.com/geopandas/pyogrio/blob/main/pyproject.toml
• docker: https://github.com/docker/docker-py/blob/main/pyproject.toml
• pygments: https://github.com/pygments/pygments/blob/master/pyproject.toml
• gunicorn: https://github.com/benoitc/gunicorn/blob/master/pyproject.toml
• pony: https://github.com/ponyorm/pony/blob/main/setup.py

I left some dependencies in the dependencies field because they appeared to be used fairly frequently throughout the typeshed stubs. For example, numpy is used by stubs/networkx/, even though it's only an optional dependency of networkx.