Update the `growth` module

[GwennyGit]

The growth module works and contains excellent ideas. However, a new and less confusing setup would be beneficial. The following ideas should improve the setup and add better handling of flux values.

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Improvement/rearranging of already existing functions (-> #79)

Main changes

• [x] Change existing functions:
  • [x] Rename set_fluxes_to_simulate -> set_bounds_to_default
  • [x] Change/add default parameter for upper & lower bound from COBRApy/user-specified
  • [x] Merge get_default_uptake (renamed to get_model_uptake) & get_minimal_uptake -> Name function get_uptake
  • [x] Replace get_missing_exchanges & modify_medium with medium.add_medium_to_model
  • [x] Merge find_missing_essential & find_minimum_essential -> find_essential?
  • [x] Further ideas for medium.add_medium_to_model -> ❗ name changed to medium_to_model:
  • [x] Integrate functionality of find_essential ❓
  • [x] Add a parameter to return the resulting medium
  • [x] Add the possibility to load medium as anaerobic ❓
  • [x] Extend usable namespaces from BiGG-specific to more namespaces
    • 🔴 this function can already do that, but not the wrappers in growth etc. -> see "still missing" below
  • [x] Rename simulate_minimal_essential -> simulate_growth
  • [x] Add parameter to enable growth with or without supplements
  • [x] Merge growth_one_medium_from_default & growth_one_medium_from_minimal -> growth_on_one_medium
  • [x] Check output of growth_on_one_medium & get_growth_selected_media
  • [x] Remove get_growth_selected_media -> Now handled by medium.add_medium_to_model!
• [x] Check connections in/to:
  • [x] medium.py
  • [x] main.py
  • [x] SPECIMEN (#99)
• [x] Check pseudo algorithm

  Additional ideas

• [x] Check model.optimize & model.slim_optimize -> Possibility for faster run time?
• [x] growth_on_one_medium:
  • [x] Allow growth without supplementation -> default!
  • [x] Allow user-specified supplementation -> #79
• [x] Add possibility to add:
  • [x] medium-specific fluxes from medium2substance table in data.db,
  • [x] default flux (Currently: 10),
  • [x] user-specific default flux and
  • [x] user-specific fluxes -> 🟠 oxygen percentage can be set only currently
• [x] Improve handling of anaerobic simulations

  Isolated functions

• [x] Change function get_default_secretion -> Wrong description for what it currently really does!
• [x] get_all_minimum_essential -> Do we need this? Is it correct? 🤔 -> Removed!
• [x] Rename get_essential_reactions -> get_single_ko_essential_reacs ❓
• [x] Rename get_essential_reactions_via_bounds -> get_single_deletion_essential_reacs ❓
• [x] Rename find_additives -> find_additives_to_enhance_growth/ find_growth_enhancing_additives ❓

  ---

  Improvement/addition of new functions:

• [x] Add the possibility of changing carbon sources -> Function to variate carbon sources -> #79
• [x] namespace parameter or independency -> #79

Still missing

• [x] function for reading external media: missing a 'file' option 🟠 written, only needs testing
• [x] adding superoxide to a medium to enable growth e.g. important for Klebsiella (either via subset or new category to add different substances) -> #16

[cb-Hades]

Notes from the Whiteboard:

[cb-Hades]

get_default_secretion changed to one function for returning ID for reactions secreting compounds (get_secretion) and a second for for returning functions that produce a compound called get_production.

[cb-Hades]

Added functions to plot and save the growth simulation results.

[GwennyGit]

All tasks are either done or transferred to a new issue -- closing issue (#16, #79).