feat(nfcoreInstall): use statefiles to track installs in a library

[prototaxites]

Running nfcoreInstall on a bunch of modules takes time. If you are caching the same library between multiple tests, this means calling nf-core install for modules that are already installed. Instead, now we write a state file for each module after a successful install (hashed from name, git commit SHA and remote), and check if it exists before trying an install later.

Not sure how to test this though as I don't think I can access the nf-test stdout in its own test...

[muffato]

Essentially, I'd do:

1. fake a statefile for a given module
2. check that nfcoreInstall doesn't reinstall that module

To fake the statefile:

1. Craft one manually
2. Or install a module, remove all its files but leaving the statefile intact

To check nfcoreInstall:

1. Run the process and check no file was created
2. Or (if possible), modify and empty $PATH and check no sub-process exception is raised.

[muffato]

Also, what is it you're trying to optimise ? The time it takes for nf-core modules install to load the module list, lookup in modules.json and decide there's nothing to do ? Is it that slow ?

[prototaxites]

Also, what is it you're trying to optimise ? The time it takes for nf-core modules install to load the module list, lookup in modules.json and decide there's nothing to do ? Is it that slow ?

It was running very slowly for me on the farm, for reasons I'm not sure why. It does have to query github each time, I think, which is not so ideal in any case?

[prototaxites]

Added a test, using the install -> delete -> reinstall -> check for files method.

[maxulysse]

could you add some documentation to reflect this new feature?

[prototaxites]

I've added some documentation and improved the error handling over MD5 sums, as well as a couple other places where I spotted the functions should probably throw an error and exit rather than continue.