Replace general asserts with specific exceptions

[dmdunla]

Suggestion: Replace general asserts with specific exceptions based on context.

We currently use a lot of general asserts in the following pattern:

if (<condition>):
    assert False, "<str>"

Using specific exceptions -- e.g., ValueError, IndexError, etc. -- could be more helpful to users.

[ntjohnson1]

I think there is some nuance to the asserts. I think specific exceptions are more helpful for things that couldn't POSSIBLY be correct. However, in this PR I used an assert intentionally so if someone wanted to load larger data and didn't care about the guardrails they could using python -O to simply ignore the check entirely. I think that may be a cleaner logical separation. What should always halt at exception, and what are nice to have checks that we want to optimize away when running larger problems.