Missing click dependency and confusing methods interface

[daffidwilde]

Just running through a little audit on the documentation (as per @callummole's email to me some time ago now) and was stopped in my tracks straight away.

Using a clean installation of reprosyn in a conda environment, I tried to import a method and got a ModuleNotFoundError for click. It should be a simple enough fix but I don't use the CLI so defer to someone else to determine the required minimum version.

As another quick improvement, we should define an __all__ in methods/__init__.py to make it clearer which classes are usable when tab-completing (plus the COMMANDS tuple, which is used elsewhere). At the moment, you have to sift through a number of CLI commands and modules, which can be confusing. It might also be worth considering the way methods are named - using all caps is not the convention for class names unless they are acronyms.

Happy to help in implementing any of these things.