just reformat everything

...to be able to continue pushing formatted code sanely

src/base/types/CoreModel.jl

@@ -99,8 +99,11 @@ end
 Return the reaction equation of reaction with id `rxn_id` in model. The reaction
 equation maps metabolite ids to their stoichiometric coefficients.
 """
-function reaction_stoichiometry(m::CoreModel, rxn_id::String)::Dict{String, Float64}
-    Dict(m.mets[k]=>v for (k, v) in zip(findnz(m.S[:, first(indexin([rxn_id], m.rxns))])...))
+function reaction_stoichiometry(m::CoreModel, rxn_id::String)::Dict{String,Float64}
+    Dict(
+        m.mets[k] => v for
+        (k, v) in zip(findnz(m.S[:, first(indexin([rxn_id], m.rxns))])...)
+    )
 end
 
 """
@@ -109,8 +112,8 @@ end
 Return the reaction equation of reaction with id `rxn_ind` in model. The reaction
 equation maps metabolite ids to their stoichiometric coefficients.
 """
-function reaction_stoichiometry(m::CoreModel, rxn_ind::Int)::Dict{String, Float64}
-    Dict(m.mets[k]=>v for (k, v) in zip(findnz(m.S[:, rxn_ind])...))
+function reaction_stoichiometry(m::CoreModel, rxn_ind::Int)::Dict{String,Float64}
+    Dict(m.mets[k] => v for (k, v) in zip(findnz(m.S[:, rxn_ind])...))
 end
 
 """

src/base/types/CoreModelCoupled.jl

@@ -110,7 +110,7 @@ end
 Return the reaction equation of reaction with id `rxn_id` in model. The reaction
 equation maps metabolite ids to their stoichiometric coefficients.
 """
-function reaction_stoichiometry(m::CoreModelCoupled, rxn_id::String)::Dict{String, Float64}
+function reaction_stoichiometry(m::CoreModelCoupled, rxn_id::String)::Dict{String,Float64}
     reaction_stoichiometry(m.lm, rxn_id)
 end
 
@@ -120,7 +120,7 @@ end
 Return the reaction equation of reaction with id `rxn_ind` in model. The reaction
 equation maps metabolite ids to their stoichiometric coefficients.
 """
-function reaction_stoichiometry(m::CoreModelCoupled, rxn_ind::Int)::Dict{String, Float64}
+function reaction_stoichiometry(m::CoreModelCoupled, rxn_ind::Int)::Dict{String,Float64}
     reaction_stoichiometry(m.lm, rxn_ind)
 end
 

src/base/types/JSONModel.jl

@@ -282,7 +282,7 @@ end
 Return the reaction equation of reaction with id `rxn_id` in model. The reaction
 equation maps metabolite ids to their stoichiometric coefficients.
 """
-function reaction_stoichiometry(m::JSONModel, rxn_id::String)::Dict{String, Float64}
+function reaction_stoichiometry(m::JSONModel, rxn_id::String)::Dict{String,Float64}
     ind = findfirst(x -> x["id"] == rxn_id, m.json["reactions"])
     m.json["reactions"][ind]["metabolites"]
 end

src/base/types/MATModel.jl

@@ -174,7 +174,7 @@ metabolite_compartment(m::MATModel, mid::String) = _maybemap(
 Return the reaction equation of reaction with id `rxn_id` in model. The reaction
 equation maps metabolite ids to their stoichiometric coefficients.
 """
-function reaction_stoichiometry(m::MATModel, rxn_id::String)::Dict{String, Float64}
+function reaction_stoichiometry(m::MATModel, rxn_id::String)::Dict{String,Float64}
     rxn_ind = first(indexin([rxn_id], m.mat["rxns"]))
     reaction_stoichiometry(m, rxn_ind)
 end
@@ -186,7 +186,7 @@ Return the reaction equation of reaction with index `rxn_index` in model. The re
 equation maps metabolite ids to their stoichiometric coefficients. Note, `rxn_index` can 
 be any suitable type that can index into an array.
 """
-function reaction_stoichiometry(m::MATModel, rxn_ind)::Dict{String, Float64}
+function reaction_stoichiometry(m::MATModel, rxn_ind)::Dict{String,Float64}
     met_inds = findall(m.mat["S"][:, rxn_ind] .!= 0.0)
     Dict(m.mat["mets"][met_ind] => m.mat["S"][met_ind, rxn_ind] for met_ind in met_inds)
 end

src/base/types/SBMLModel.jl

@@ -143,7 +143,7 @@ _sbml_export_notes = _sbml_export_annotation
 Return the reaction equation of reaction with id `rxn_id` in model. The reaction
 equation maps metabolite ids to their stoichiometric coefficients.
 """
-function reaction_stoichiometry(m::SBMLModel, rxn_id::String)::Dict{String, Float64}
+function reaction_stoichiometry(m::SBMLModel, rxn_id::String)::Dict{String,Float64}
     m.sbml.reactions[rxn_id].stoichiometry
 end
 

src/base/types/StandardModel.jl

@@ -288,7 +288,7 @@ end
 Return the reaction equation of reaction with id `rxn_id` in model. The reaction
 equation maps metabolite ids to their stoichiometric coefficients.
 """
-function reaction_stoichiometry(m::StandardModel, rxn_id::String)::Dict{String, Float64}
+function reaction_stoichiometry(m::StandardModel, rxn_id::String)::Dict{String,Float64}
     m.reactions[rxn_id].metabolites
 end
 

src/base/types/abstract/MetabolicModel.jl

@@ -312,9 +312,12 @@ end
 Return the reaction equation of reaction with id `rxn_id` in model. The reaction
 equation maps metabolite ids to their stoichiometric coefficients.
 """
-function reaction_stoichiometry(m::MetabolicModel, rxn_id::String)::Dict{String, Float64}
+function reaction_stoichiometry(m::MetabolicModel, rxn_id::String)::Dict{String,Float64}
     mets = metabolites(m)
-    Dict(mets[k] => v for (k, v) in zip(findnz(stoichiometry(m)[:, first(indexin([rxn_id], reactions(m)))])...))
+    Dict(
+        mets[k] => v for (k, v) in
+        zip(findnz(stoichiometry(m)[:, first(indexin([rxn_id], reactions(m)))])...)
+    )
 end
 
 """

src/base/utils/StandardModel.jl

@@ -59,7 +59,8 @@ function atom_exchange(flux_dict::Dict{String,Float64}, model::StandardModel)
             for (met, stoich_rxn) in model.reactions[rxn_id].metabolites
                 adict = get_atoms(model.metabolites[met])
                 for (atom, stoich_molecule) in adict
-                    atom_flux[atom] = get(atom_flux, atom, 0.0) + flux * stoich_rxn * stoich_molecule
+                    atom_flux[atom] =
+                        get(atom_flux, atom, 0.0) + flux * stoich_rxn * stoich_molecule
                 end
             end
         end

src/reconstruction/CoreModelCoupled.jl

@@ -21,20 +21,12 @@ function add_reactions(
     xu::AbstractFloat;
     check_consistency = false,
 ) where {V1<:VecType,V2<:VecType}
-    new_lm = add_reactions(
-                m.lm,
-                s,
-                b,
-                c,
-                xl,
-                xu,
-                check_consistency = check_consistency,
-            )
+    new_lm = add_reactions(m.lm, s, b, c, xl, xu, check_consistency = check_consistency)
     return CoreModelCoupled(
         new_lm,
-        hcat(m.C, spzeros(size(m.C, 1), n_reactions(new_lm)-n_reactions(m.lm))),
+        hcat(m.C, spzeros(size(m.C, 1), n_reactions(new_lm) - n_reactions(m.lm))),
         m.cl,
-        m.cu
+        m.cu,
     )
 end
 
@@ -64,21 +56,21 @@ function add_reactions(
     check_consistency = false,
 ) where {V1<:VecType,V2<:VecType,K<:StringVecType}
     new_lm = add_reactions(
-                m.lm,
-                s,
-                b,
-                c,
-                xl,
-                xu,
-                rxn,
-                mets,
-                check_consistency = check_consistency
-            )
+        m.lm,
+        s,
+        b,
+        c,
+        xl,
+        xu,
+        rxn,
+        mets,
+        check_consistency = check_consistency,
+    )
     return CoreModelCoupled(
         new_lm,
-        hcat(m.C, spzeros(size(m.C, 1), n_reactions(new_lm)-n_reactions(m.lm))),
+        hcat(m.C, spzeros(size(m.C, 1), n_reactions(new_lm) - n_reactions(m.lm))),
         m.cl,
-        m.cu
+        m.cu,
     )
 end
 
@@ -103,20 +95,12 @@ function add_reactions(
     xu::V;
     check_consistency = false,
 ) where {M<:MatType,V<:VecType}
-    new_lm = add_reactions(
-                m.lm,
-                Sp,
-                b,
-                c,
-                xl,
-                xu,
-                check_consistency = check_consistency,
-            )
+    new_lm = add_reactions(m.lm, Sp, b, c, xl, xu, check_consistency = check_consistency)
     return CoreModelCoupled(
         new_lm,
-        hcat(m.C, spzeros(size(m.C, 1), n_reactions(new_lm)-n_reactions(m.lm))),
+        hcat(m.C, spzeros(size(m.C, 1), n_reactions(new_lm) - n_reactions(m.lm))),
         m.cl,
-        m.cu
+        m.cu,
     )
 end
 
@@ -127,16 +111,12 @@ Add all reactions from `m2` to `m1`.
 
 """
 function add_reactions(m1::CoreModelCoupled, m2::CoreModel; check_consistency = false)
-    new_lm = add_reactions(
-                m1.lm,
-                m2,
-                check_consistency=check_consistency
-            )
+    new_lm = add_reactions(m1.lm, m2, check_consistency = check_consistency)
     return CoreModelCoupled(
         new_lm,
-        hcat(m1.C, spzeros(size(m1.C, 1), n_reactions(new_lm)-n_reactions(m1.lm))),
+        hcat(m1.C, spzeros(size(m1.C, 1), n_reactions(new_lm) - n_reactions(m1.lm))),
         m1.cl,
-        m1.cu
+        m1.cu,
     )
 end
 
@@ -166,21 +146,21 @@ function add_reactions(
     check_consistency = false,
 ) where {M<:MatType,V<:VecType,K<:StringVecType}
     new_lm = add_reactions(
-            m.lm,
-            Sp,
-            b,
-            c,
-            xl,
-            xu,
-            rxns,
-            mets,
-            check_consistency = check_consistency
-        )
+        m.lm,
+        Sp,
+        b,
+        c,
+        xl,
+        xu,
+        rxns,
+        mets,
+        check_consistency = check_consistency,
+    )
     return CoreModelCoupled(
         new_lm,
-        hcat(m.C, spzeros(size(m.C, 1), n_reactions(new_lm)-n_reactions(m.lm))),
+        hcat(m.C, spzeros(size(m.C, 1), n_reactions(new_lm) - n_reactions(m.lm))),
         m.cl,
-        m.cu
+        m.cu,
     )
 end
 
@@ -194,11 +174,11 @@ Also removes any metabolites not involved in any reaction after the deletion.
 """
 function remove_reactions(m::CoreModelCoupled, rxns::Vector{Int})
     return CoreModelCoupled(
-                remove_reactions(m.lm, rxns),
-                m.C[:, filter(e -> e ∉ rxns, 1:n_reactions(m))],
-                m.cl,
-                m.cu
-            )
+        remove_reactions(m.lm, rxns),
+        m.C[:, filter(e -> e ∉ rxns, 1:n_reactions(m))],
+        m.cl,
+        m.cu,
+    )
 end
 
 """
@@ -222,7 +202,8 @@ end
 
 """
 function remove_reactions(m::CoreModelCoupled, rxns::Vector{String})
-    rxn_indices = [findfirst(isequal(name), m.lm.rxns) for name in intersect(rxns, m.lm.rxns)]
+    rxn_indices =
+        [findfirst(isequal(name), m.lm.rxns) for name in intersect(rxns, m.lm.rxns)]
     if isempty(rxn_indices)
         return m
     else
@@ -398,12 +379,7 @@ function change_bounds!(
     xl::V = Float64[],
     xu::V = Float64[],
 ) where {V<:VecType}
-    change_bounds!(
-        model.lm,
-        rxns,
-        xl = xl,
-        xu = xu
-    )
+    change_bounds!(model.lm, rxns, xl = xl, xu = xu)
 end
 
 """
@@ -421,10 +397,5 @@ function change_bounds!(
     xl::V = Float64[],
     xu::V = Float64[],
 ) where {V<:VecType}
-    change_bounds!(
-        model.lm,
-        rxns,
-        xl = xl,
-        xu = xu
-    )
+    change_bounds!(model.lm, rxns, xl = xl, xu = xu)
 end

src/reconstruction/StandardModel.jl

@@ -32,8 +32,8 @@ end
 
 Add `met` to `model` based on metabolite `id`.
 """
-add_metabolite!(model::StandardModel, met::Metabolite) =  add_metabolites!(model, [met])
-    
+add_metabolite!(model::StandardModel, met::Metabolite) = add_metabolites!(model, [met])
+
 """
     add_genes!(model::StandardModel, genes::Vector{Gene})
 
@@ -50,7 +50,7 @@ end
 
 Add `gene` to `model` based on gene `id`.
 """
-add_gene!(model::StandardModel, gene::Gene) = add_genes!(model, [gene]) 
+add_gene!(model::StandardModel, gene::Gene) = add_genes!(model, [gene])
 
 """
     @add_reactions!(model::Symbol, ex::Expr)
@@ -130,7 +130,7 @@ Remove reaction with `id` from `model`. Note, may result in orphan metabolites.
 remove_reaction!(model, "EX_glc__D_e")
 ```
 """
-remove_reaction!(model::StandardModel, id::String) = remove_reactions!(model, [id]) 
+remove_reaction!(model::StandardModel, id::String) = remove_reactions!(model, [id])
 
 """
     remove_metabolites!(model::StandardModel, ids::Vector{String})
@@ -145,7 +145,7 @@ remove_metabolites!(model, ["atp_c", "adp_c"])
 ```
 """
 function remove_metabolites!(model::StandardModel, ids::Vector{String})
-    pop!.(Ref(model.metabolites), ids)    
+    pop!.(Ref(model.metabolites), ids)
 end
 
 """
@@ -160,7 +160,7 @@ require the deleted metabolite, in which case analysis functions will error.
 remove_metabolite!(model, "atp_c")
 ```
 """
-remove_metabolite!(model::StandardModel, id::String) = remove_metabolites!(model, [id]) 
+remove_metabolite!(model::StandardModel, id::String) = remove_metabolites!(model, [id])
 
 """
     remove_genes!(
@@ -210,7 +210,8 @@ constrain reactions that require the genes to function to carry zero flux.
 remove_gene!(model, "g1")
 ```
 """
-remove_gene!(model::StandardModel, gid::String; knockout_reactions::Bool = false) = remove_genes!(model, [gid]; knockout_reactions = knockout_reactions)
+remove_gene!(model::StandardModel, gid::String; knockout_reactions::Bool = false) =
+    remove_genes!(model, [gid]; knockout_reactions = knockout_reactions)
 
 function set_bound(model::StandardModel, reaction_id::String; ub, lb)
     reaction = model.reactions[reaction_id]

src/reconstruction/community.jl

@@ -151,8 +151,7 @@ function add_model_with_exchanges(
 
     rxnsadd = "$(model_name)_" .* reactions(model)
     if !isnothing(biomass_id)
-        metsadd =
-            ["$(model_name)_" .* metabolites(model); "$(model_name)_" * biomass_id]
+        metsadd = ["$(model_name)_" .* metabolites(model); "$(model_name)_" * biomass_id]
     else
         metsadd = "$(model_name)_" .* metabolites(model)
     end
@@ -247,7 +246,7 @@ function join_with_exchanges(
     add_biomass_objective = true,
     biomass_ids = String[],
     model_names = String[],
-)::CoreModel where M <: MetabolicModel
+)::CoreModel where {M<:MetabolicModel}
 
     if add_biomass_objective && isempty(biomass_ids)
         throw(
@@ -284,7 +283,8 @@ function join_with_exchanges(
     nnz_total =
         sum(length(first(nnz)) for nnz in nnzs) +
         length(models) * length(exchange_rxn_ids) +
-        length(exchange_met_ids) + nnz_add
+        length(exchange_met_ids) +
+        nnz_add
     n_reactions_metabolic = sum(reaction_lengths)
     n_reactions_total = n_reactions_metabolic + length(exchange_rxn_ids) + column_add
     n_metabolites_metabolic = sum(metabolite_lengths)

test/analysis/flux_balance_analysis.jl

@@ -19,8 +19,8 @@
     lp = flux_balance_analysis(cp, Tulip.Optimizer)
     @test termination_status(lp) == MOI.OPTIMAL
     sol = JuMP.value.(lp[:x])
-    @test isapprox(objective_value(lp), expected_optimum, atol=TEST_TOLERANCE)
-    @test isapprox(cp.c' * sol, expected_optimum, atol=TEST_TOLERANCE)
+    @test isapprox(objective_value(lp), expected_optimum, atol = TEST_TOLERANCE)
+    @test isapprox(cp.c' * sol, expected_optimum, atol = TEST_TOLERANCE)
 
     # test the "nicer output" variants
     fluxes_vec = flux_balance_analysis_vec(cp, Tulip.Optimizer)

test/analysis/knockouts.jl

@@ -5,7 +5,10 @@
 
     add_gene!(m, Gene("g1"))
     add_gene!(m, Gene("g2"))
-    add_reaction!(m, Reaction("v1", metabolites = Dict("A" => -1.0, "B" => 1.0), grr = [["g1"]]))
+    add_reaction!(
+        m,
+        Reaction("v1", metabolites = Dict("A" => -1.0, "B" => 1.0), grr = [["g1"]]),
+    )
     add_reaction!(
         m,
         Reaction("v2", metabolites = Dict("A" => -1.0, "B" => 1.0), grr = [["g1", "g2"]]),

test/base/utils/StandardModel.jl

@@ -12,14 +12,18 @@
 
     # atom tracker
     atom_fluxes = atom_exchange(sol, model)
-    @test isapprox(atom_fluxes["C"], 37.19016648975907; atol=TEST_TOLERANCE)
+    @test isapprox(atom_fluxes["C"], 37.19016648975907; atol = TEST_TOLERANCE)
     @test atom_exchange("FBA", model)["C"] == 0.0
-    @test isapprox(atom_exchange("BIOMASS_Ecoli_core_w_GAM", model)["C"], -42.5555; atol=TEST_TOLERANCE)
-    
+    @test isapprox(
+        atom_exchange("BIOMASS_Ecoli_core_w_GAM", model)["C"],
+        -42.5555;
+        atol = TEST_TOLERANCE,
+    )
+
     # metabolite trackers
     consuming, producing = metabolite_fluxes(sol, model)
-    @test isapprox(consuming["atp_c"]["PFK"], -7.47738; atol=TEST_TOLERANCE)
-    @test isapprox(producing["atp_c"]["PYK"], 1.75818; atol=TEST_TOLERANCE)
+    @test isapprox(consuming["atp_c"]["PFK"], -7.47738; atol = TEST_TOLERANCE)
+    @test isapprox(producing["atp_c"]["PYK"], 1.75818; atol = TEST_TOLERANCE)
 
     # set bounds
     cbm = make_optimization_model(model, optimizer)

test/base/utils/looks_like.jl

@@ -25,17 +25,29 @@
         ["EX_m1"; "Exch_m3"; "Ex_m2"],
         ["m1"; "m2"; "m3_e"],
     )
-    @test filter(looks_like_exchange_reaction, reactions(cp)) == ["EX_m1", "Exch_m3", "Ex_m2"]
-    @test filter(x -> looks_like_exchange_reaction(x; exchange_prefixes = ["Exch_"]), reactions(cp)) == ["Exch_m3"]
+    @test filter(looks_like_exchange_reaction, reactions(cp)) ==
+          ["EX_m1", "Exch_m3", "Ex_m2"]
+    @test filter(
+        x -> looks_like_exchange_reaction(x; exchange_prefixes = ["Exch_"]),
+        reactions(cp),
+    ) == ["Exch_m3"]
 
     # this is originally the "toyModel1.mat"
     cp = test_toyModel()
 
-    @test filter(looks_like_exchange_reaction, reactions(cp)) == ["EX_m1(e)", "EX_m3(e)", "EX_biomass(e)"]
-    @test filter(x -> looks_like_exchange_reaction(x; exclude_biomass=true), reactions(cp)) == ["EX_m1(e)", "EX_m3(e)"]
+    @test filter(looks_like_exchange_reaction, reactions(cp)) ==
+          ["EX_m1(e)", "EX_m3(e)", "EX_biomass(e)"]
+    @test filter(
+        x -> looks_like_exchange_reaction(x; exclude_biomass = true),
+        reactions(cp),
+    ) == ["EX_m1(e)", "EX_m3(e)"]
     @test filter(looks_like_exchange_metabolite, metabolites(cp)) == ["m1[e]", "m3[e]"]
-    @test filter(looks_like_biomass_reaction, reactions(cp)) == ["EX_biomass(e)", "biomass1"]
-    @test filter(x -> looks_like_biomass_reaction(x; exclude_exchanges=true), reactions(cp)) == ["biomass1"] 
+    @test filter(looks_like_biomass_reaction, reactions(cp)) ==
+          ["EX_biomass(e)", "biomass1"]
+    @test filter(
+        x -> looks_like_biomass_reaction(x; exclude_exchanges = true),
+        reactions(cp),
+    ) == ["biomass1"]
 end
 
 @testset "Looks like functions, basic" begin
@@ -43,25 +55,25 @@ end
     @test length(filter(looks_like_exchange_reaction, reactions(model))) == 20
     @test length(filter(looks_like_exchange_metabolite, metabolites(model))) == 20
     @test length(filter(looks_like_biomass_reaction, reactions(model))) == 1
-    
+
     model = load_model(model_paths["e_coli_core.xml"])
     @test length(filter(looks_like_exchange_reaction, reactions(model))) == 20
     @test length(filter(looks_like_exchange_metabolite, metabolites(model))) == 20
     @test length(filter(looks_like_biomass_reaction, reactions(model))) == 1
-    
+
     model = load_model(model_paths["e_coli_core.mat"])
     @test length(filter(looks_like_exchange_reaction, reactions(model))) == 20
     @test length(filter(looks_like_exchange_metabolite, metabolites(model))) == 20
     @test length(filter(looks_like_biomass_reaction, reactions(model))) == 1
-    
+
     model = convert(StandardModel, model)
     @test length(filter(looks_like_exchange_reaction, reactions(model))) == 20
     @test length(filter(looks_like_exchange_metabolite, metabolites(model))) == 20
     @test length(filter(looks_like_biomass_reaction, reactions(model))) == 1
-    
+
     model = convert(CoreModelCoupled, model)
     @test length(filter(looks_like_exchange_reaction, reactions(model))) == 20
     @test length(filter(looks_like_exchange_metabolite, metabolites(model))) == 20
     @test length(filter(looks_like_biomass_reaction, reactions(model))) == 1
-    
+
 end

test/reconstruction/CoreModel.jl

@@ -175,10 +175,10 @@ end
 
     lp = CoreModel(
         [1.0 1 1 0; 1 1 1 0; 1 1 1 0; 0 0 0 1],
-        collect(1.:4),
-        collect(1.:4),
-        collect(1.:4),
-        collect(1.:4),
+        collect(1.0:4),
+        collect(1.0:4),
+        collect(1.0:4),
+        collect(1.0:4),
         ["r1"; "r2"; "r3"; "r4"],
         ["m1"; "m2"; "m3"; "m4"],
     )

test/reconstruction/CoreModelCoupled.jl

@@ -54,7 +54,16 @@ end
     @test cp.cl == new_cp.cl
     @test cp.cu == new_cp.cu
 
-    new_cp = add_reactions(cp, 2.0 * ones(4), 3 .* ones(4), 2.0, -1.0, 1.0, "r4", ["m$i" for i in 1:4])
+    new_cp = add_reactions(
+        cp,
+        2.0 * ones(4),
+        3 .* ones(4),
+        2.0,
+        -1.0,
+        1.0,
+        "r4",
+        ["m$i" for i = 1:4],
+    )
     @test cp.C == new_cp.C[:, 1:end-1]
     @test cp.cl == new_cp.cl
     @test cp.cu == new_cp.cu
@@ -78,34 +87,28 @@ end
         2 .* ones(10),
         -ones(10),
         ones(10),
-        ["r$i" for i in 1:10],
-        ["m$i" for i in 1:4]
+        ["r$i" for i = 1:10],
+        ["m$i" for i = 1:4],
     )
     @test cp.C == new_cp.C[:, 1:end-7] # 3 reactions were already present
     @test cp.cl == new_cp.cl
     @test cp.cu == new_cp.cu
 
-    new_cp = add_reactions(
-            cp,
-            2.0 * sprand(4000, 0.5),
-            3 .* sprand(4000, 0.5),
-            2.0,
-            -1.0,
-            1.0
-        )
+    new_cp =
+        add_reactions(cp, 2.0 * sprand(4000, 0.5), 3 .* sprand(4000, 0.5), 2.0, -1.0, 1.0)
     @test cp.C == new_cp.C[:, 1:end-1]
     @test cp.cl == new_cp.cl
     @test cp.cu == new_cp.cu
 
     cm = CoreModel(
-            2.0 * ones(4, 10),
-            3 .* ones(4),
-            2 .* ones(10),
-            -ones(10),
-            ones(10),
-            ["r$i" for i in 1:10],
-            ["m$i" for i in 1:4]
-        )
+        2.0 * ones(4, 10),
+        3 .* ones(4),
+        2 .* ones(10),
+        -ones(10),
+        ones(10),
+        ["r$i" for i = 1:10],