Evaluate & add entry points

[GwennyGit]

Gather & evaluate entry points

Module	Submodule	Possible entry points	Notes	Status1
analysis	comparison	❓	Annotation/SBO report?	🟥
	core_pan	generate_core_pan compare_to_core_pan	1. setup, 2. analyse	🟩; untested
	growth	growth_analysis test_auxotrophies test_growth_with_source model_minimal_medium	Sum all test modules to one entry point up? - done 4	🟩 , partially not tested
	investigate	❓	A new function as entry point?	🟫
classes	egcs	❓	One call with flags	🟩
	medium	❓	Are there any feasible/necessary entry points?	🟫
	reports	❓	got 'em covered	🟩
curation	db_access	compare_to_modelseed	Make wider comparable with more namespaces?	🟥
	biomass	check_normalise_biomass		🟩
	charges	correct_charges_modelseed	correct_charges_from_database $\rightarrow$ Extension? As a replacement for correct_charges_modelseed?	🟦 / 🟩
	curate	❓	Which function(s) to add as entry point(s)?	🟫
	gapfill	gapfill	one call	🟩
	pathways	kegg_pathways	in sth. like 'refine'	🟩
	polish	check_direction polish	One function for add_gp_ids_from_... as an entry point? polish_annotations + change_all_qualifiers as one entry point/separate ones?	🟥
utility	cvterms	None	$\textcolor{magenta}{\text{Possible for future release}}$	🟫
	databases	initialise_database		🟩 2
	io	save_user_input	put together with other configs?	🟫 -> moved to SPECIMEN (draeger-lab/SPECIMEN/issues/8)
	set_up	download_config	one for all or one for each	🟥 what about rg config? / 🟩 media config

What to do about data & examples?

Footnotes

1. 🟥 = under discussion; 🟦 = needs to be implemented; 🟩 = implemented; 🟫 = will not be implemented ↩

2. for further information and TODOs/IDEAs, see comments in code ↩