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Fixes to arg parsing#25

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DanielMDouglas wants to merge 4 commits intoDeepLearnPhysics:developfrom
DanielMDouglas:develop
Open

Fixes to arg parsing#25
DanielMDouglas wants to merge 4 commits intoDeepLearnPhysics:developfrom
DanielMDouglas:develop

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Switched from old optparse to argparse. Now supports positional and optional args without weird dependence on arg ordering.

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Sorry for the foul language

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