Merge pull request #825 from LCSB-BioCore/mk-workaround-coupling-equa…

…lities

work-around equalities in coupling bounds in MAT

src/base/solver.jl

@@ -24,8 +24,16 @@ function make_optimization_model(model::MetabolicModel, optimizer; sense = MAX_S
     C = coupling(model) # empty if no coupling
     isempty(C) || begin
         cl, cu = coupling_bounds(model)
-        @constraint(optimization_model, c_lbs, cl .<= C * x) # coupling lower bounds
-        @constraint(optimization_model, c_ubs, C * x .<= cu) # coupling upper bounds
+        @constraint(
+            optimization_model,
+            c_lbs,
+            cl[isfinite.(cl)] .<= C[isfinite.(cl), :] * x
+        ) # coupling lower bounds
+        @constraint(
+            optimization_model,
+            c_ubs,
+            C[isfinite.(cu), :] * x .<= cu[isfinite.(cu)]
+        ) # coupling upper bounds
     end
 
     return optimization_model

src/base/types/MATModel.jl

@@ -104,14 +104,23 @@ Extracts the coupling constraints. Currently, there are several accepted ways to
 function coupling_bounds(m::MATModel)
     nc = n_coupling_constraints(m)
     if _mat_has_squashed_coupling(m.mat)
+        c = reshape(m.mat["b"], length(m.mat["b"]))[n_reactions(m)+1:end]
+        csense = reshape(m.mat["csense"], length(m.mat["csense"]))[n_reactions(m)+1:end],
         (
-            sparse(fill(-Inf, nc)),
-            sparse(reshape(m.mat["b"], length(m.mat["b"]))[n_reactions(m)+1:end]),
+            [sense in ["G", "E"] ? val : -Inf for (val, sense) in zip(c, csense)],
+            [sense in ["L", "E"] ? val : Inf for (val, sense) in zip(c, csense)],
+        )
+    elseif haskey(m.mat, "d") && haskey(m.mat, "dsense")
+        d = reshape(m.mat["d"], nc)
+        dsense = reshape(m.mat["dsense"], nc)
+        (
+            [sense in ["G", "E"] ? val : -Inf for (val, sense) in zip(d, dsense)],
+            [sense in ["L", "E"] ? val : Inf for (val, sense) in zip(d, dsense)],
         )
     else
         (
-            sparse(reshape(get(m.mat, "cl", fill(-Inf, nc, 1)), nc)),
-            sparse(reshape(get(m.mat, "cu", fill(Inf, nc, 1)), nc)),
+            reshape(get(m.mat, "cl", fill(-Inf, nc, 1)), nc),
+            reshape(get(m.mat, "cu", fill(Inf, nc, 1)), nc),
         )
     end
 end