wip: Adding all configuration options as arguments

[ns-rse]

• Renames toposats.run_topostats > topostats.run_modules as its more descriptive of what the submodule is doing.
• Moves generic command line options to be arguments of the parser.
• Adds arguments to each sub-parser for all module options.
• Adds tests to check that each argument is correctly returned.
• Updated and made a few names consistent.

This is still a Work In Progress but it shouldn't break anything (tests have all passed locally).

Whether to merge this depends perhaps on the desire to tag and make a release and whether there is anything else pending that is considered essential to be in that release (e.g. documentation). If so then don't merge this.

[ns-rse]

Merge conflict resolved and a temporary fix to get around a problem with pytest-regtest-2.3.2 under OSX. This is now ready for review again.