Merge pull request #143 from JuliaDiffEq/solve

Remove solve warning

src/DiffEqBiological.jl

@@ -5,7 +5,9 @@ module DiffEqBiological
 using Compat, DataStructures, MacroTools, Parameters, Reexport, SparseArrays, SymEngine
 using DiffEqBase, DiffEqJump
 @reexport using DiffEqBase, DiffEqJump
-using HomotopyContinuation, DynamicPolynomials, LinearAlgebra, RecipesBase
+using DynamicPolynomials, LinearAlgebra, RecipesBase
+
+import HomotopyContinuation
 
 import Base: (==)
 

src/equilibrate_utils.jl

@@ -13,9 +13,9 @@ mutable struct EquilibrateContent
 end
 
 function EquilibrateContent(make_polynomial,n_vars,n_params)
-    pvus = (@polyvar internal___polyvar___u[1:n_vars])[1]
-    pvps = (@polyvar internal___polyvar___p[1:n_params])[1]
-    pvt = (@polyvar internal___polyvar___t)[1]
+    pvus = (HomotopyContinuation.@polyvar internal___polyvar___u[1:n_vars])[1]
+    pvps = (HomotopyContinuation.@polyvar internal___polyvar___p[1:n_params])[1]
+    pvt = (HomotopyContinuation.@polyvar internal___polyvar___t)[1]
     is_polynomial_system = try
         make_polynomial(pvus,pvt,pvps,internal___var___paramvals=fill(1,length(pvps)))
         true
@@ -197,7 +197,7 @@ function make_hc_template!(rn::DiffEqBase.AbstractReactionNetwork)
     check_has_polynomial(rn)
     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))
+    solution_template = HomotopyContinuation.solutions(HomotopyContinuation.solve(f_template, show_progress=false))
     reset_hc_templates!(rn)
     push_hc_template!(rn,p_template,solution_template)
 end
@@ -213,7 +213,7 @@ end
 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))
+    solution_template = HomotopyContinuation.solutions(HomotopyContinuation.solve(f_template, show_progress=false))
     if (isempty(get_hc_templates(rn))) || (length(solution_template) == length(get_hc_templates(rn)[1]))
         push_hc_template!(rn,p_template,solution_template)
     elseif length(solution_template) > length(get_hc_templates(rn)[1])
@@ -272,21 +272,21 @@ end
 #Finds steady states of a system using homotopy continuation.
 function steady_states(rn::DiffEqBase.AbstractReactionNetwork, solver::HCSteadyStateSolver, p=Vector{Float64}())
     using_temp_poly  = initialise_solver!(rn,p)
-    (length(p)==0) && (return positive_real_solutions(solutions(HomotopyContinuation.solve(get_equi_poly(rn),show_progress=false))))
+    (length(p)==0) && (return positive_real_solutions(HomotopyContinuation.solutions(HomotopyContinuation.solve(get_equi_poly(rn),show_progress=false))))
     result = hc_solve_at(rn,p)
     using_temp_poly && finalise_solver!(rn)
     return positive_real_solutions(result)
 end
 # Solves the reaction networks at the specific parameter values using Homotopy Continuation.
 function hc_solve_at(rn::DiffEqBase.AbstractReactionNetwork,p::Vector{Float64})
     for hc_template in get_hc_templates(rn)
-        result = solutions(HomotopyContinuation.solve(get_equi_poly(rn), hc_template.sol, parameters=get_polyvars(rn).p, p₁=hc_template.p, p₀=p, show_progress=false))
+        result = HomotopyContinuation.solutions(HomotopyContinuation.solve(get_equi_poly(rn), hc_template.sol, parameters=get_polyvars(rn).p, p₁=hc_template.p, p₀=p, show_progress=false))
         (length(result) == length(hc_template.sol)) && (return result)
     end
     @warn "While solving the system using homotopy continuation some solutions were lost."
     best_length = 0; best_solution = [];
     for hc_template in get_hc_templates(rn)
-        result = solutions(HomotopyContinuation.solve(get_equi_poly(rn), hc_template.sol, parameters=get_polyvars(rn).p, p₁=hc_template.p, p₀=p, show_progress=false))
+        result = HomotopyContinuation.solutions(HomotopyContinuation.solve(get_equi_poly(rn), hc_template.sol, parameters=get_polyvars(rn).p, p₁=hc_template.p, p₀=p, show_progress=false))
         (length(result) > best_length) && (best_length = length(result); best_solution = result;)
     end
     return best_solution
@@ -560,7 +560,7 @@ function solve_bifurcation(
     paths_incomplete = Vector{NamedTuple{(:p, :u),Tuple{Vector{Float64},Vector{Vector{Complex{Float64}}}}}}()
     for sol in sol1
         path = track_path(sol,tracker1,range...)
-        if (tracker1.state.status == CoreTrackerStatus.success)
+        if (tracker1.state.status == HomotopyContinuation.CoreTrackerStatus.success)
             remove_sol!(sol2,path.u[end],d_sol)
             push!(paths_complete,path)
         else
@@ -569,7 +569,7 @@ function solve_bifurcation(
     end
     for sol in sol2
         path = track_path(sol,tracker2,reverse(range)...)
-        (tracker2.state.status == CoreTrackerStatus.success) && remove_path!(paths_incomplete,path.u[end],d_sol)
+        (tracker2.state.status == HomotopyContinuation.CoreTrackerStatus.success) && remove_path!(paths_incomplete,path.u[end],d_sol)
         push!(paths_complete,path)
     end
     append!(paths_complete,paths_incomplete)
@@ -663,12 +663,12 @@ end
 #--- Bifurcation functions used by both solvers ---#
 #Makes a coretracker from the given information
 function make_coretracker(rn,sol,p1,p2,Δt)
-    return coretracker(get_equi_poly(rn), sol, parameters=get_polyvars(rn).p, p₁=p1, p₀=p2, max_step_size=Δt)
+    return HomotopyContinuation.coretracker(get_equi_poly(rn), sol, parameters=get_polyvars(rn).p, p₁=p1, p₀=p2, max_step_size=Δt)
 end
 #Tracks a path for the given coretracker, returns the path.
 function track_path(solution,coretracker,p_start,p_end)
     P = Vector{Float64}(); U = Vector{Vector{ComplexF64}}();
-    for (u,t) in iterator(coretracker, solution)
+    for (u,t) in HomotopyContinuation.iterator(coretracker, solution)
         push!(P,t2p(t,p_start,p_end)); push!(U,u);
     end
     return (p=P,u=U)