Dependency updates

[jimmymathews]

A number of dependencies have updates, some quite major. For this issue, update the following if possible and refactor as necessary:

1. Python 3.11 => 3.13. Version 3.13 is supposed to be released October 1, but I think I read that this might be pushed back a week or more.
2. Postgres 14 => 17. Version 17 was very recently released. Previously I recall some minor reason that it was beneficial to hold back our postgres version, I think to take advantage of the official Postgres docker images for our test containers. Try to resolve this and upgrade everything to v17.
3. pip list --outdated reports:

   Package       Version  Latest
   ------------- -------- ------
   attrs         23.2.0   24.2.0
   bokeh         3.4.1    3.6.0
   boto3         1.35.23  1.35.29
   botocore      1.35.23  1.35.29
   fastapi       0.111.0  0.115.0
   fsspec        2023.6.0 2024.9.0
   h5py          3.10.0   3.12.1
   llvmlite      0.42.0   0.43.0
   numba         0.59.1   0.60.0
   numpy         1.26.4   2.1.1
   pandas        2.2.2    2.2.3
   Pillow        9.5.0    10.4.0
   pip           24.0     24.2
   psycopg       3.1.19   3.2.3
   pydantic      2.7.2    2.9.2
   pydantic_core 2.18.3   2.24.0
   s3fs          0.6.0    2024.9.0
   scikit-learn  1.5.0    1.5.2
   scipy         1.13.1   1.14.1
   secure        0.3.0    1.0.0
   setuptools    65.5.0   75.1.0
   squidpy       1.5.0    1.6.1
   starlette     0.37.2   0.39.2
   tables        3.9.2    3.10.1
   tqdm          4.66.4   4.66.5
   uvicorn       0.30.0   0.31.0