Modernize tooling

[daneah]

This change is a: (check at least one)

• Bugfix
• Feature addition
• Code style update
• Refactor
• Release activity

Is this a breaking change? (check one)

• Yes
• No

Is the:

• Title of this pull request clear, concise, and indicative of the issue number it addresses, if any?
• Test suite passing?
• Code coverage maximal?
• Changelog up to date?

What does this change address?

We want to keep relatively up to date with latest versions of tooling packages, language syntax, and internal practices and preferences.

How does this change work?

• Replace pyflakes with ruff
• Add isort to manage import ordering
• Update versions of pre-commit hooks and make parity with tox envs
• Run all hooks against all files
  • isort reordered imports
  • pyupgrade replaced primitives like List, Dict, and Set with
    their literals, allowed in Python 3.9+, removing need for imports
  • pyupgrade moved Iterable from typing to collections.abc
  • Fix type checking failures
    • Remove unused settings in docs/conf.py
    • Add Protocol for resolver classes

[drewgingerich]

What do you think about replacing black with ruff as well? I don't have experience with ruff's formatting, but it looks like it's designed to be able to replace Black.

[daneah]

Haven't had enough experience with it yet, but last I used it it was fairly compliant but the CLI interface was slightly different in a bothersome way. Don't want to do so at this juncture, but definitely something we could align on eventually. Black is generally fast enough not to bother me, but one less tool could be good. I think ruff can handle isort's job too.