Commit bc4bd821 authored by Miroslav Kratochvil's avatar Miroslav Kratochvil
Browse files

slightly improve the objective value handling at FVA

...and finally allow the whole FBA part to be successfully and easily separated
into its own efficient single-threaded step.
parent 1a9348ef
Pipeline #46297 passed with stages
in 15 minutes and 31 seconds
......@@ -5,7 +5,8 @@
optimizer;
modifications = [],
workers = [myid()],
bounds = z -> (z,z),
optimal_objective_value = nothing,
bounds = z -> (z, Inf),
ret = objective_value,
)::Matrix{Float64}
......@@ -30,7 +31,11 @@ first and second pair to remove the limit. Use [`gamma_bounds`](@ref) and
`optimizer` must be set to a `JuMP`-compatible optimizer. The computation of
the individual optimization problems is transparently distributed to `workers`
(see `Distributed.workers()`).
(see `Distributed.workers()`). The value of Z₀ can be optionally supplied in
argument `optimal_objective_value`, which prevents this function from calling
the non-parallelizable FBA. Separating the single-threaded FBA and
multithreaded variability computation can be used to improve resource
allocation efficiency in many common use-cases.
`ret` is a function used to extract results from optimized JuMP models of the
individual reactions. By default, it calls and returns the value of
......@@ -55,7 +60,8 @@ function flux_variability_analysis(
optimizer;
modifications = [],
workers = [myid()],
bounds = z -> (z, z),
optimal_objective_value = nothing,
bounds = z -> (z, Inf),
ret = objective_value,
)
if any(reactions .< 1) || any(reactions .> n_reactions(model))
......@@ -63,9 +69,10 @@ function flux_variability_analysis(
end
Z = bounds(
isnothing(optimal_objective_value) ?
objective_value(
flux_balance_analysis(model, optimizer; modifications = modifications),
),
) : optimal_objective_value,
)
return screen_optmodel_modifications(
......
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