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Update README

Najam Syed requested to merge dev/update_readme into master

@christopher.funk @benjamin.pikus @sarah.brockman

This MR updates and overhauls the README. Sections and content have been re-organized, rewritten, or both to improve clarity. A maximum line length of 79 characters is used.

The requirements.txt has also been updated to 1) present packages alphabetically and 2) add packages that were previously being installed manually per the README but can simply be pip installed. This brings the installation process in line with the Dockerfile.

Edited by Najam Syed

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