Set up package and CLI entry point

[dominiquesydow]

Description

(i) Transform scripts into package and (ii) make package main functionalities accessible via CLI entry points.

Todos

• [x] Rename the following main.py files to cli.py and add main function
  • kinase_focused_fragment_library.preprocessing.main.py
  • kinase_focused_fragment_library.fragmentation.main.py
  • kinase_focused_fragment_library.recombination.main.py
  • kinase_focused_fragment_library.analysis.ligand_analysis.main.py
• [x] Add imports to kinase_focused_fragment_library.__init__.py needed for packaging
• [x] Add sub-module __init__.py files containing imports needed for packaging
  • kinase_focused_fragment_library.preprocessing.__init__.py
  • kinase_focused_fragment_library.fragmentation.__init__.py
  • kinase_focused_fragment_library.recombination.__init__.py
  • kinase_focused_fragment_library.analysis.__init__.py
  • kinase_focused_fragment_library.ligand_analysis.__init__.py
• [x] Update imports in all files where necessary (mostly adding .)
• [x] Update setup.py
  • [x] Update author details (add Dominique Sydow and Volkamer Lab)
  • [x] Add CLI entry points :)
• [x] Update instruction in README

Status

• [x] Ready to go

[dominiquesydow]

Hi @jaimergp, thanks for this quick and insightful review! I will link all refactoring comments to our PR #8, since I intentionally did not touch these aspects in this PR. Will work on the remaining comments here, thanks!

[dominiquesydow]

We will merge this PR now and revisit @jaimergp suggestions/improvements in future PR.