Harmonize and improve docstrings and documentation

[famosab]

Change the docstrings in the following modules:

• [x] analysis_biocyc
• [x] analysis_db
• [x] analysis_kegg
• [x] charges
• [x] comparison
• [x] curate
• [x] cvterms
• [x] databases
• [x] entities
• [x] gapfill
• [x] growth
• [x] investigate
• [x] io
• [x] modelseed
• [x] pathways
• [x] polish
• [x] sboann

We can also take the time to transfer larger docstrings to .rst files and shorten the docstrings if possible.

The following modules / concepts need a single page in the docs:

• [x] gapfill (include manual gapfill here)
• [x] growth
• [x] pathways
• [x] sboann
• [x] polish (include curate manual here)

The docs can be restructured to make sense, I propose the following structure:

  - Installation
+ - Usage 
     - As standalone
     - As python module 
! - Main modules (here we need a better title)
     - gapfill
     - growth
     - pathways
     - sboann
     - polish
  - API
+ - Pipeline 
+ - Development

---

Changes ToDo

• Enter - into Args
• Explicitly name libSBML and cobra loaded models:

from libsbml import Model as libModel
from cobra import Model as cobraModel

• Remove * imports and explicitly import what is needed for the module.
• Ensure that all dosctrings start with capitals
• Update function signatures to contain explicit types if possible
• Remove unused imports
• Ensure that all write to file commands only take place in main.py and not in the submodules
• Check if file is valid
• Check if file contains correct authors
• Add #!/usr/bin/env python to the top of the file if not present
• Add docstring to module if not present
• Change libsbml to libSBML and cobrapy to COBRApy
• Change tuple returns to:

  """
  Returns:
   tuple: Two tables (1) & (2)
       (1) pd.DataFrame: Table with charge mismatches
       (2) pd.DataFrame: Table with formula mismatches
  """

[famosab]

The growth.py modlue holds three functions that are currently not used in the main:

• get_essential_reactions
• get_essential_reactions_via_bounds
• find_additives

I did not include them since they seemed too specific for me. I would just showcase them in the documentation when we talk about growth simulation.

[GwennyGit]

The doc strings were updated for all functions belonging to gapfill, io and databases. However, for tuples the doc strings were left as they were for now and no doc strings were shortened. I will do that as soon as gapfill-update is ready to be merged in dev and merged into dev.