Extend community model #696
Conversation
|
/format |
|
✔️ Auto-formatting triggered by this comment succeeded, commited as b439fc8 |
|
/format |
|
✔️ Auto-formatting triggered by this comment succeeded, commited as 0b51955 |
Codecov ReportBase: 90.21% // Head: 89.93% // Decreases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## next #696 +/- ##
==========================================
- Coverage 90.21% 89.93% -0.29%
==========================================
Files 82 84 +2
Lines 2106 1977 -129
==========================================
- Hits 1900 1778 -122
+ Misses 206 199 -7
Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here. ☔ View full report at Codecov. |
|
/format |
|
✔️ Auto-formatting triggered by this comment succeeded, commited as 9dead6f |
| @@ -0,0 +1,333 @@ | |||
| @testset "BalancedGrowthCommunityModel: simple model" begin | |||
| m1 = ObjectModel(id = "Model1") | |||
There was a problem hiding this comment.
could you technically reuse some of the models in data_static ? (possibly just adding a few genes to them?)
| A helper function to get the unique environmental metabolites. | ||
| """ | ||
| get_env_mets(cm::BalancedGrowthCommunityModel) = | ||
| unique(hcat([get_exchange_mets(m) for m in cm.members]...)) |
There was a problem hiding this comment.
get_env_mets is pretty slow and it's repeated everywhere, it might be much better to cache the result in the model structure directly
| appended as a prefix with the delimiter `#`. | ||
| """ | ||
| Accessors.genes(cm::BalancedGrowthCommunityModel) = | ||
| [m.id * "#" * gid for m in cm.members for gid in genes(m.model)] |
There was a problem hiding this comment.
| [m.id * "#" * gid for m in cm.members for gid in genes(m.model)] | |
| ["$(m.id)#$gid" for m in cm.members for gid in genes(m.model)] |
| delimiter `#`. The environmental metabolites have no prefix. | ||
| """ | ||
| function Accessors.metabolites(cm::BalancedGrowthCommunityModel) | ||
| mets = [m.id * "#" * mid for m in cm.members for mid in metabolites(m.model)] |
There was a problem hiding this comment.
| mets = [m.id * "#" * mid for m in cm.members for mid in metabolites(m.model)] | |
| mets = ["$(m.id)#$mid" for m in cm.members for mid in metabolites(m.model)] |
| io, | ||
| "A balanced growth community model comprised of $(length(cm.members)) underlying models.", | ||
| ) | ||
| end |
There was a problem hiding this comment.
this isn't very useful, I guess the generic show will suffice for now. I'll eventually make a bigger PR with MultiModelWrapper that fixes this forever
There was a problem hiding this comment.
(as in, pls remove the custom shows here)
| """ | ||
| Base.@kwdef mutable struct CommunityMember | ||
| "Name of model appended to intracellular reactions and metabolites." | ||
| id::String |
There was a problem hiding this comment.
TODO for myself, for later:
id should be outside of the community member, making the members a dict.
| "List of all exchange reactions in model." | ||
| exchange_reaction_ids::Vector{String} | ||
| "ID of biomass metabolite." | ||
| biomass_metabolite_id::String |
There was a problem hiding this comment.
TODO for myself later: biomass balancing is a function of the class that provides the balance, so the metabolite (= equality constraint) should be created externally, not by the community member.
Currently our community model framework is rather fragile. Let's extend it to: