Clean up requirements to avoid listing extra dependencies

[egrace479]

I think this could be cleaned up to avoid listing extra dependencies (eg., numpy can be installed through pandas), but we can add generate clear requirements without added dependencies to our issues for package creation.

Originally posted by @egrace479 in #4 (comment)

[egrace479]

This includes having pytest listed as an optional dependency:

[project.optional-dependencies]
dev = [
    "pytest",
    "ruff"
]

[thompsonmj]

environment.yaml as well