Post-paper updates

Adding some changes and fixes that have arisen from more people testing out on their data!

New features:

• Add basic quality control for assemblies input (#37, #42).
• Generate a network and cluster assignment by applying a fitted model to a distance database (--use-model).
• Added script to calculate Rand distances between cluster assignments (calculate_rand_indices.py)
• Added script to extract .graphml files for all clusters (extract_components.py).

Bug fixes:

• More general parsing of epiData for --microreact (#35).
• Correct paths in output prefix with mash sketch.
• Removed the zero level contour in distance plots (#38).

Other:

• Updated docs (troubleshooting, installation, README.md)
• Removed n subscript on pi on x-axis of plots.
• Updated networkx version for pip (#39).
• Catch errors when curve fit fails (#41).
• Travis-CI uses conda rather than pip to install dependencies.