Merge pull request #82 from COBREXA/sew-generalize-enzymes

Generalize enzymes
COBREXA · Jan 7, 2025 · d6004be · d6004be · exaexa · Jan 8, 2025
2 parents ed2e260 + 04c054b
commit d6004be
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Showing 5 changed files with 30 additions and 23 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -15,7 +15,7 @@ jobs:
       matrix:
         version:
           - '1' # This is always the latest stable release in the 1.X series
-          - '1.6' # LTS
+          - '1.10' # LTS
           #- 'nightly'
         os:
           - ubuntu-latest

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -15,8 +15,6 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
-        with:
-          version: '1.9'
       - uses: julia-actions/cache@v2
       - name: Install dependencies
         run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "COBREXA"
 uuid = "babc4406-5200-4a30-9033-bf5ae714c842"
 authors = ["The developers of COBREXA.jl"]
-version = "2.4.0"
+version = "2.5.0"
 
 [deps]
 AbstractFBCModels = "5a4f3dfa-1789-40f8-8221-69268c29937c"
@@ -19,7 +19,7 @@ StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 AbstractFBCModels = "1"
 Aqua = "0.7"
 Clarabel = "0.6"
-ConstraintTrees = "1.1"
+ConstraintTrees = "1.4"
 DocStringExtensions = "0.8, 0.9"
 Downloads = "1"
 HiGHS = "1.9"

diff --git a/src/builders/enzymes.jl b/src/builders/enzymes.jl
@@ -212,8 +212,8 @@ function enzyme_constraints(;
            ) *
            gene_product_amounts_name^gene_product_amounts *
            gene_product_capacity_name^C.ConstraintTree(
-               id => C.Constraint(;
-                   value = C.sum(
+               id => C.Constraint(
+                   C.sum(
                        gene_product_amounts[gp].value * gpmm for
                        (gp, gpmm) in ((gp, gene_product_molar_mass(gp)) for gp in gps) if
                        !isnothing(gpmm) && haskey(gene_product_amounts, gp);
@@ -292,10 +292,10 @@ function simplified_enzyme_constraints(;
         id => C.Constraint(;
             value = C.sum(
                 contribution(fluxes_forward, mass_cost_forward, f) for f in fs;
-                init = zero(C.LinearValue),
+                init = zero(C.LinearValue), # TODO not type stable if LinearValueT{not Float64}
             ) + C.sum(
                 contribution(fluxes_reverse, mass_cost_reverse, f) for f in fs;
-                init = zero(C.LinearValue),
+                init = zero(C.LinearValue), # TODO not type stable if LinearValueT{not Float64}
             ),
             bound,
         ) for (id, fs, bound) in capacity_limits

diff --git a/src/frontend/enzymes.jl b/src/frontend/enzymes.jl
@@ -24,22 +24,31 @@ subunit stoichiometry and turnover numbers. Use with
 # Fields
 $(TYPEDFIELDS)
 """
-Base.@kwdef mutable struct Isozyme
+Base.@kwdef mutable struct IsozymeT{T<:Real}
     """
     Mapping of gene product identifiers ("genes" in FBC model nomenclature)
     to their relative amount required to construct one unit of the isozyme.
     """
-    gene_product_stoichiometry::Dict{String,Float64}
+    gene_product_stoichiometry::Dict{String,T}
 
     "Turnover number for this isozyme catalyzing the forward direction of the
     reaction."
-    kcat_forward::Maybe{Float64} = nothing
+    kcat_forward::Maybe{T} = nothing
 
     "Turnover number for this isozyme catalyzing the reverse direction of the
     reaction."
-    kcat_reverse::Maybe{Float64} = nothing
+    kcat_reverse::Maybe{T} = nothing
 end
 
+export IsozymeT
+
+"""
+$(TYPEDEF)
+
+Shortcut for `[IsozymeT](@ref){Float64}`.
+"""
+const Isozyme = IsozymeT{Float64}
+
 export Isozyme
 
 """
@@ -68,12 +77,12 @@ that limits the total sum of the listed genes to the given limit.
 """
 function enzyme_constrained_flux_balance_constraints(
     model::A.AbstractFBCModel;
-    reaction_isozymes::Dict{String,Dict{String,Isozyme}},
+    reaction_isozymes::Dict{String,Dict{String,IsozymeT{R}}},
     gene_product_molar_masses::Dict{String,Float64},
-    capacity::Union{Vector{Tuple{String,Vector{String},Float64}},Float64},
+    capacity::Union{Vector{Tuple{String,Vector{String},R}},R},
     interface::Maybe{Symbol} = nothing,
     interface_name = :interface,
-)
+) where {R<:Real}
     # prepare some accessor functions for the later stuff
     # TODO: might be nicer to somehow parametrize the fwd/rev directions out.
     # Also there is a lot of conversion between symbols and strings, might be
@@ -129,9 +138,9 @@ function enzyme_constrained_flux_balance_constraints(
         isozyme_gene_product_stoichiometry,
         gene_product_molar_mass,
         capacity_limits = capacity isa Real ?
-                          [(:total_capacity, gene_ids, C.Between(0, capacity))] :
+                          [(:total_capacity, gene_ids, (zero(capacity), capacity))] :
                           [
-            (Symbol(k), Symbol.(gs), C.Between(0, cap)) for (k, gs, cap) in capacity
+            (Symbol(k), Symbol.(gs), (zero(cap), cap)) for (k, gs, cap) in capacity
         ],
     )
 end
@@ -177,12 +186,12 @@ products, but identifiers of reactions.
 """
 function simplified_enzyme_constrained_flux_balance_constraints(
     model;
-    reaction_isozymes::Dict{String,Dict{String,Isozyme}},
+    reaction_isozymes::Dict{String,Dict{String,IsozymeT{R}}},
     gene_product_molar_masses::Dict{String,Float64},
-    capacity::Union{Vector{Tuple{String,Vector{String},Float64}},Float64},
+    capacity::Union{Vector{Tuple{String,Vector{String},R}},R},
     interface::Maybe{Symbol} = nothing,
     interface_name = :interface,
-)
+) where {R<:Real}
     # TODO this deserves a rewrite once more -- Isozyme struct is hiding a bit
     # too much of uncertainty for the code of this thing to be short and
     # concise...maybe we should have an isozyme with only one kcat which is
@@ -245,10 +254,10 @@ function simplified_enzyme_constrained_flux_balance_constraints(
                                  [(
                    :total_capacity,
                    keys(constraints.fluxes),
-                   C.Between(0, capacity),
+                   (zero(capacity), capacity),
                )] :
                                  [
-                   (Symbol(k), Symbol.(fs), C.Between(0, cap)) for (k, fs, cap) in capacity
+                   (Symbol(k), Symbol.(fs), (zero(cap), cap)) for (k, fs, cap) in capacity
                ],
            ) *
            :gene_product_amounts^simplified_isozyme_gene_product_amount_constraints(