Upgrade python dependencies

[fyliu]

Fixes #529

What changes did you make?

• auto upgrade python dependencies in pre-commmit commented out
• upgrade python dependencies
• update uv version in Dockerfile
• remove extra line in uv docs page

Why did you make the changes (we will use this info to test)?

• Commented out the auto upgrade python dependencies hook with a reason, in case one of us rediscovers and wants to add it. We can enable it if the reasoning is no longer as relevant.
• Updating software versions to for feature set and security
• Other are changes or cleanup related to the main change.

Testing

• The code should still build, run, lint, and pass all tests. So basically the precommit-check.sh script should finish without error.

[fyliu]

Converting to draft because I'm not sure if this is a good idea to have. It could generate a good amount of changes if it checks and updates requirements.txt really often. Maybe it's better as a manual script or encoded in to a GHA on a schedule.

[fyliu]

This is ready for review.
I didn't remove the automatic update hook but commented it out to show that it was considered and not used.