Bump versions, silence deprecations

[bengerman13]

warnings + plan

• this breaks ./dev watch-tests because the watcher library doesn't get toml. I'll follow up with a PR to move to the other pytest watcher later
• my plan is to work through the sqlalchemy warnings one at a time, to help lower the change size going forward

Changes proposed in this pull request:

• add function to upgrade dependencies
• upgrade dependencies
• fix one sqlalchemy deprecation warning (sqlalchemy.orm.relation -> sqlalchemy.orm.relationship)
• silence other sqlalchemy deprecation warnings

Things to check

• For any logging statements, is there any chance that they could be logging sensitive data?
• Are log statements using a logging library with a logging level set? Setting a logging level means that log statements "below" that level will not be written to the output. For example, if the logging level is set to INFO and debugging statements are written with log.debug or similar, then they won't be written to the otput, which can prevent unintentional leaks of sensitive data.

Security considerations

addresses some dependency warnings that dependabot is shouting about.