Updated doc string (to test git functions)
Revert "Updated doc string (to test git functions)"

This reverts commit f4564e104950804e71ae1dcee009584b26633221.
Update get_neighbor_throats to return an ndarray rather than a list when flatten if False
Cleanup of GenericNetwork:  added flatten functionality to several methods, expanded doc strings
Update of gitignore; recommit of my script file (JTG)
Revert "Changed GenericGenerator to no longer call "return self._net" in the generator step, instead requiring a netowork object to be assigned explicity with the get_net function"

This reverts commit 0a22d8f7811702a3327364e79894913f48d00f6c.
Update run_script to work with reverted .generate() which now returns the network rather than requiring a call to get_net
Small changes:
- environment script
- documnetation layout
Updates to gitignore for branch
Merge branch 'develop' into feature/CustomGenerator
Some cosmetic changes to CustomGenerator, and corresponding changes to the run script.