Mokapot sub commands and brew() restructuring

[gessulat]

Mokapot is a workflow that broadly consists of the following steps

• data preprocessing: optionally subsetting the input data and then doing a 3-fold split to tho generate training data
• model training: using the semi-supervised Percolator algorithm to train a classification model on the training data
• confidence assignment: the models scores are used to calculate q-values and assign confidence values to the input

As a user it is convenient to have the workflow in a single CLI that executes all steps end-to-end.
As a developer it would be convenient to have the option to run the three steps separately.
This would allow for easier separation in integration tests and easier evaluate ideas such as: How well does this pretrained model perform for a different dataset?

One way would be to introduce sub commands:

• mokapot preprocess /input/data.x /preprocessed/training/data [--max_subset]
• mokapot train /preprocessed/training/data /trained/model [--max_iterations]
• mokapot confidence /trained/model /output/results.x

Tasks

• scout which python module can help with adding sub-commands to clis
• spec out input and outputs for each sub-command and document it
• break down mokapot.brew into the three steps
• re-use the steps in mokapot.brew to add them as separate sub-commands, respectively