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?
[^1]: 🟥 = under discussion; 🟦 = needs to be implemented; 🟩 = implemented; 🟫 = will not be implemented
[^2]: for further information and TODOs/IDEAs, see comments in code
Gather & evaluate entry points
generate_core_pan
compare_to_core_pan
growth_analysis
test_auxotrophies
test_growth_with_source
model_minimal_medium
compare_to_modelseed
check_normalise_biomass
correct_charges_modelseed
correct_charges_from_database
$\rightarrow$ Extension? As a replacement forcorrect_charges_modelseed
?gapfill
kegg_pathways
check_direction
polish
add_gp_ids_from_...
as an entry point?polish_annotations
+change_all_qualifiers
as one entry point/separate ones?initialise_database
save_user_input
download_config
What to do about data & examples?
[^1]: 🟥 = under discussion; 🟦 = needs to be implemented; 🟩 = implemented; 🟫 = will not be implemented [^2]: for further information and TODOs/IDEAs, see comments in code