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fix performance of stoichiometry conversion in flux_balance_constraints #27

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merged 3 commits into from
Apr 22, 2024
Merged

fix performance of stoichiometry conversion in flux_balance_constraints #27

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28891bc
fix performance of stoichiometry conversion in flux_balance_constraints
exaexa Apr 22, 2024
34aef05
LTS compatibility fix: replace findnz.eachrow by manual CSC matrix walk
exaexa Apr 22, 2024
4b74a2d
julia c'mon we've been here a few times.
exaexa Apr 22, 2024
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13 changes: 11 additions & 2 deletions src/frontend/balance.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -53,13 +53,22 @@ function flux_balance_constraints(
bal = A.balance(model)
obj = A.objective(model)

# The iteration through stoichiometry would be better done with eachrow(),
# unfortunately it seems to be enormously inefficient on column-major
# matrix formats, and findnz() on eachrow&eachcol output isn't very
# backwards compatible (at least not to 1.6). We thus enforce having a
# SparseMatrixCSC here and walk it manually.
stoiT = SparseArrays.SparseMatrixCSC(stoi')

constraints = C.ConstraintTree(
:fluxes^C.variables(keys = rxns, bounds = zip(lbs, ubs)) *
:flux_stoichiometry^C.ConstraintTree(
met => C.Constraint(
value = C.LinearValue(SparseArrays.sparse(row)),
value = let i = stoiT.colptr[row_idx], e = stoiT.colptr[row_idx+1] - 1
C.LinearValue(idxs = stoiT.rowval[i:e], weights = stoiT.nzval[i:e])
end,
bound = C.EqualTo(b),
) for (met, row, b) in zip(mets, eachrow(stoi), bal)
) for (met, row_idx, b) in zip(mets, 1:stoiT.n, bal)
) *
:objective^C.Constraint(C.LinearValue(SparseArrays.sparse(obj))),
)
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