Merge pull request #142 from JuliaDiffEq/add_!_after_some_functions

Add ! after function names

Author: ChrisRackauckas

src/DiffEqBiological.jl

@@ -41,7 +41,7 @@ export ODEProblem, SDEProblem, DiscreteProblem, JumpProblem, SteadyStateProblem
 
 # tolls for finding equilibrium solutions and bifurcation diagrams.
 export EquilibrateContent
-export @add_constraint, @add_constraints, internal___add___constraint!, fix_parameters, @make_hc_template, make_hc_template, @add_hc_template, add_hc_template
+export @add_constraint, @add_constraints, internal___add___constraint!, fix_parameters, @make_hc_template, make_hc_template!, @add_hc_template, add_hc_template!
 export steady_states, stability
 export bifurcations, bifurcation_grid, bifurcation_grid_2d, bifurcation_grid_diagram, SimpleHCBifurcationSolver, HCBifurcationSolver, HCSteadyStateSolver
 

src/equilibrate_utils.jl

@@ -192,7 +192,7 @@ end
 ## args
 -  reaction_network: a reaction network.
 """
-function make_hc_template(rn::DiffEqBase.AbstractReactionNetwork)
+function make_hc_template!(rn::DiffEqBase.AbstractReactionNetwork)
     check_is_polynomial(rn)
     check_has_polynomial(rn)
     p_template = randn(ComplexF64, length(rn.params))
@@ -210,7 +210,7 @@ end
 ## args
 -  reaction_network: a reaction network.
 """
-function add_hc_template(rn::DiffEqBase.AbstractReactionNetwork)
+function add_hc_template!(rn::DiffEqBase.AbstractReactionNetwork)
     p_template = randn(ComplexF64, length(rn.params))
     f_template = DynamicPolynomials.subs.(get_equi_poly(rn), Ref(get_polyvars(rn).p => p_template))
     solution_template = solutions(HomotopyContinuation.solve(f_template, show_progress=false))
@@ -234,7 +234,7 @@ end
 -  reaction_network: a reaction network.
 """
 macro make_hc_template(rn::Symbol)
-    return Expr(:escape,:(make_hc_template($rn)))
+    return Expr(:escape,:(make_hc_template!($rn)))
 end
 #Macro running the HC template function.
 """
@@ -246,7 +246,7 @@ end
 -  reaction_network: a reaction network.
 """
 macro add_hc_template(rn::Symbol)
-    return Expr(:escape,:(add_hc_template($rn)))
+    return Expr(:escape,:(add_hc_template!($rn)))
 end
 
 
@@ -297,7 +297,7 @@ function initialise_solver!(rn::DiffEqBase.AbstractReactionNetwork, p::Vector{Fl
     check_is_polynomial(rn)
     using_temp_poly = !has_equi_poly(rn)
     using_temp_poly && fix_parameters(rn, p, full_vector_exemption=bifurcation_exception_parameter)
-    !has_hc_templates(rn) && make_hc_template(rn)
+    !has_hc_templates(rn) && make_hc_template!(rn)
     return using_temp_poly
 end
 # In case a temporary equilibrium polynomial were used, this one resets it.

test/equilibrate_test_4.jl

@@ -38,8 +38,8 @@ bif_brusselator = bifurcations(brusselator_network,brusselator_p,:B,(1.,4.))
 end v0 v K n kD kB kC deg S;
 fix_parameters(σ_network,n=4)
 σ_p = [0.005, 0.1, 2.8, 4, 10, 100, 0.1, 0.01, 0.5]
-make_hc_template(σ_network)
-add_hc_template(σ_network)
+make_hc_template!(σ_network)
+add_hc_template!(σ_network)
 ss_σ = steady_states(σ_network,σ_p)
 @test(length(ss_σ)==3)
 stabs_σ = stability(ss_σ,σ_network,σ_p)
@@ -58,7 +58,7 @@ cc_network = @reaction_network begin
 end k1 k2p k2pp k3p k3pp A J3 k4 m J4
 cc_p = [0.04,0.04,1.,1.,10.0,0.,0.04,35.,.3,.04]
 @add_constraint cc_network P+Po=1
-add_hc_template(cc_network)
+add_hc_template!(cc_network)
 @add_hc_template cc_network
 ss_cc = steady_states(cc_network,cc_p)
 @test(length(ss_cc)==3)