Merge pull request #420 from LCSB-BioCore/mo-tiny-fixes

Mo tiny fixes

src/analysis/modifications/generic.jl

@@ -25,19 +25,19 @@ change_constraint(id::String, lb, ub) =
     end
 
 """
-    change_objective(new_objective::Union{String,Vector{String}}; weights=[], sense=MOI.MAX_SENSE)
+    change_objective(new_objective::Union{String,Vector{String}}; weights=[], sense=MAX_SENSE)
 
 Modification that changes the objective function used in a constraint based
 analysis function.  `new_objective` can be a single reaction identifier, or an
 array of reactions identifiers.
 
 Optionally, the objective can be weighted by a vector of `weights`, and a
-optimization `sense` can be set.
+optimization `sense` can be set to either `MAX_SENSE` or `MIN_SENSE`.
 """
 change_objective(
     new_objective::Union{String,Vector{String}};
     weights = [],
-    sense = MOI.MAX_SENSE,
+    sense = MAX_SENSE,
 ) =
     (model, opt_model) -> begin
 

src/base/types/FluxSummary.jl

@@ -11,6 +11,20 @@ struct FluxSummary
     unbounded_fluxes::OrderedDict{String,Float64}
 end
 
+"""
+    FluxSummary()
+
+A default empty constructor for `FluxSummary`.
+"""
+function FluxSummary()
+    FluxSummary(
+        OrderedDict{String,Float64}(),
+        OrderedDict{String,Float64}(),
+        OrderedDict{String,Float64}(),
+        OrderedDict{String,Float64}(),
+    )
+end
+
 """
     flux_summary(flux_result::Dict{String, Float64};
                 exclude_exchanges = false,
@@ -49,7 +63,7 @@ Export:
 ```
 """
 function flux_summary(
-    flux_result::Dict{String,Float64};
+    flux_result::Maybe{Dict{String,Float64}};
     exclude_exchanges = false,
     exchange_prefixes = _constants.exchange_prefixes,
     biomass_strings = _constants.biomass_strings,
@@ -58,6 +72,8 @@ function flux_summary(
     large_flux_bound = _constants.default_reaction_bound,
     keep_unbounded = false,
 )
+    isnothing(flux_result) && return FluxSummary()
+
     rxn_ids = collect(keys(flux_result))
     ex_rxns = filter(
         x -> looks_like_exchange_reaction(

src/base/types/FluxVariabilitySummary.jl

@@ -9,6 +9,18 @@ struct FluxVariabilitySummary
     exchange_fluxes::Dict{String,Vector{Union{Float64,Nothing}}}
 end
 
+"""
+    FluxVariabilitySummary()
+
+A default empty constructor for `FluxVariabilitySummary`
+"""
+function FluxVariabilitySummary()
+    FluxVariabilitySummary(
+        Dict{String,Vector{Union{Float64,Nothing}}}(),
+        Dict{String,Vector{Union{Float64,Nothing}}}(),
+    )
+end
+
 """
     flux_variability_summary(flux_result::Tuple{Dict{String, Dict{String, Float64}}, Dict{String, Dict{String, Float64}}};
         exclude_exchanges = false,
@@ -50,6 +62,7 @@ function flux_variability_summary(
     biomass_strings = _constants.biomass_strings,
     exclude_biomass = false,
 )
+    isnothing(flux_result) && return FluxVariabilitySummary()
 
     rxn_ids = keys(flux_result[1])
     ex_rxns = filter(

src/base/utils/fluxes.jl

@@ -14,14 +14,13 @@ function metabolite_fluxes(model::MetabolicModel, flux_dict::Dict{String,Float64
     for (row, mid) in enumerate(mids)
         for (col, rid) in enumerate(rids)
             mf = flux_dict[rid] * S[row, col]
-            # ignore zero flux
-            if mf < -_constants.tolerance # consuming rxn
+            if mf < 0 # consuming rxn
                 if haskey(consuming, mid)
                     consuming[mid][rid] = mf
                 else
                     consuming[mid] = Dict(rid => mf)
                 end
-            elseif mf > _constants.tolerance
+            elseif mf >= 0 # producing rxn
                 if haskey(producing, mid)
                     producing[mid][rid] = mf
                 else

src/io/show/FluxSummary.jl

@@ -5,9 +5,10 @@ end
 _pad_spaces(str::String, maxlen::Int) = _pad_spaces(length(str), maxlen)
 
 function Base.show(io::IO, ::MIME"text/plain", flux_res::FluxSummary)
-    longest_biomass_len = maximum([length(k) for k in keys(flux_res.biomass_fluxes)])
-    longest_import_len = maximum([length(k) for k in keys(flux_res.import_fluxes)])
-    longest_export_len = maximum([length(k) for k in keys(flux_res.export_fluxes)])
+    longest_biomass_len =
+        maximum(length(k) for k in keys(flux_res.biomass_fluxes); init = 0)
+    longest_import_len = maximum(length(k) for k in keys(flux_res.import_fluxes); init = 0)
+    longest_export_len = maximum(length(k) for k in keys(flux_res.export_fluxes); init = 0)
 
     if !isempty(flux_res.unbounded_fluxes)
         longest_unbounded_len =

src/io/show/FluxVariabilitySummary.jl

 function Base.show(io::IO, ::MIME"text/plain", flux_res::FluxVariabilitySummary)
 
-    longest_biomass_len = maximum([length(k) for k in keys(flux_res.biomass_fluxes)])
-    longest_exchange_len = maximum([length(k) for k in keys(flux_res.exchange_fluxes)])
+    longest_biomass_len =
+        maximum(length(k) for k in keys(flux_res.biomass_fluxes); init = 0)
+    longest_exchange_len =
+        maximum(length(k) for k in keys(flux_res.exchange_fluxes); init = 0)
     word_pad_len = max(longest_biomass_len, longest_exchange_len)
 
-    longest_biomass_flux_len = maximum([
-        length(string(round(v[1], digits = 4))) for v in values(flux_res.biomass_fluxes)
-    ])
+    longest_biomass_flux_len = maximum(
+        length(string(round(v[1], digits = 4))) for v in values(flux_res.biomass_fluxes);
+        init = 0,
+    )
     longest_exchange_flux_len = max(
-        maximum([
+        maximum(
             length(string(round(v[1], digits = 4))) for
-            v in values(flux_res.exchange_fluxes)
-        ]),
+            v in values(flux_res.exchange_fluxes);
+            init = 0,
+        ),
         length("Lower bound  "),
     )
     number_pad_len = max(longest_biomass_flux_len, longest_exchange_flux_len)

test/reconstruction/community.jl

@@ -53,7 +53,7 @@ end
 
     exchange_rxn_mets = Dict(
         ex_rxn => first(keys(reaction_stoichiometry(m2, ex_rxn))) for
-        ex_rxn in filter(looks_like_exchange_reaction, reactions(m2))
+        ex_rxn in reactions(m2) if looks_like_exchange_reaction(ex_rxn)
     )
 
     biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ecoli_core_w_GAM"]
@@ -91,7 +91,7 @@ end
 
     exchange_rxn_mets = Dict(
         ex_rxn => first(keys(reaction_stoichiometry(m2, ex_rxn))) for
-        ex_rxn in filter(looks_like_exchange_reaction, reactions(m2))
+        ex_rxn in reactions(m2) if looks_like_exchange_reaction(ex_rxn)
     )
 
     biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ec_iJO1366_core_53p95M"]
@@ -143,7 +143,7 @@ end
 
     exchange_rxn_mets = Dict(
         ex_rxn => first(keys(reaction_stoichiometry(m1, ex_rxn))) for
-        ex_rxn in filter(looks_like_exchange_reaction, reactions(m1))
+        ex_rxn in reactions(m1) if looks_like_exchange_reaction(ex_rxn)
     )
 
     biomass_ids = ["BIOMASS_Ecoli_core_w_GAM"]