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More mypy fixes

Laura Lindzey (APLUW) requested to merge dev/more_mypy into master

... because apparently I can't help myself. (And I find the mypy type checking super useful...)

Builds on !31 (merged), !32 (merged), and !33 (merged), so I'd recommend dealing with those first.

@egallimore - These changes also include come questions/comments identifying possibly dead code; if it's not there as an intentional building block for immediate development, I'd be happy to push another commit removing it.

Copyright assigned to Woods Hole Oceanographic Institution.

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