Unverified Commit 2ad630fc authored by Miroslav Kratochvil's avatar Miroslav Kratochvil Committed by GitHub
Browse files

Merge pull request #448 from LCSB-BioCore/mk-sanitize-fva

slightly improve the objective value handling at FVA
parents 1a9348ef bc4bd821
Pipeline #46298 passed with stages
in 52 minutes and 57 seconds
......@@ -5,7 +5,8 @@
modifications = [],
workers = [myid()],
bounds = z -> (z,z),
optimal_objective_value = nothing,
bounds = z -> (z, Inf),
ret = objective_value,
......@@ -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(
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(
Z = bounds(
isnothing(optimal_objective_value) ?
flux_balance_analysis(model, optimizer; modifications = modifications),
) : optimal_objective_value,
return screen_optmodel_modifications(
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