Naming standards for inputs to algorithms

[oliverfanderson]

An index of each method and the type of input that it accepts would be very helpful. Perhaps we could add it to a README in the /SPRAS/spras/ directory.

In addition, multiple input types appear to be the same. Is there a difference between ['sources', 'targets', 'edges'] and ['nodetypes', 'network'] inputs? Or can we condense these into just ['nodetypes', 'network']?

Along these same lines, what is the difference between 'network' and 'edges' when mentioned here? Are these the same things?

Here is a picture for context:

[agitter]

I believe the required inputs variables current match the naming convention of the target software at the expense of being consistent across algorithms. Some of these like edges and network are essentially synonymous so it may not be confusing if we merge them and pick one term to use consistently. Others like sources, targets, and nodetypes have slightly different meanings. A nodetypes file is one file that designates sources and targets as opposed to a file listing sources and a file listing targets.

Whatever we decide, we should document more of our decisions and conventions somewhere in https://github.com/Reed-CompBio/spras/tree/master/doc.