Merge pull request #1160 from SciML/qqy/fit_parameters

Allow fit_parameters keyword

Author: ChrisRackauckas

ext/DiffEqBaseChainRulesCoreExt.jl

@@ -2,7 +2,8 @@ module DiffEqBaseChainRulesCoreExt
 
 using DiffEqBase
 using DiffEqBase.SciMLBase
-import DiffEqBase: numargs, AbstractSensitivityAlgorithm, AbstractDEProblem, set_mooncakeoriginator_if_mooncake
+import DiffEqBase: numargs, AbstractSensitivityAlgorithm, AbstractDEProblem,
+                   set_mooncakeoriginator_if_mooncake
 
 import ChainRulesCore
 import ChainRulesCore: NoTangent
@@ -15,7 +16,8 @@ function ChainRulesCore.frule(::typeof(DiffEqBase.solve_up), prob,
         u0, p, args...;
         kwargs...)
     DiffEqBase._solve_forward(
-        prob, sensealg, u0, p, set_mooncakeoriginator_if_mooncake(SciMLBase.ChainRulesOriginator()), args...;
+        prob, sensealg, u0, p,
+        set_mooncakeoriginator_if_mooncake(SciMLBase.ChainRulesOriginator()), args...;
         kwargs...)
 end
 
@@ -24,7 +26,8 @@ function ChainRulesCore.rrule(::typeof(DiffEqBase.solve_up), prob::AbstractDEPro
         u0, p, args...;
         kwargs...)
     DiffEqBase._solve_adjoint(
-        prob, sensealg, u0, p, set_mooncakeoriginator_if_mooncake(SciMLBase.ChainRulesOriginator()), args...;
+        prob, sensealg, u0, p,
+        set_mooncakeoriginator_if_mooncake(SciMLBase.ChainRulesOriginator()), args...;
         kwargs...)
 end
 

ext/DiffEqBaseMooncakeExt.jl

@@ -3,33 +3,29 @@ module DiffEqBaseMooncakeExt
 using DiffEqBase, Mooncake
 using DiffEqBase: SciMLBase
 using SciMLBase: ADOriginator, MooncakeOriginator
-Mooncake.@from_rrule(
-    Mooncake.MinimalCtx,
+Mooncake.@from_rrule(Mooncake.MinimalCtx,
     Tuple{
         typeof(DiffEqBase.solve_up),
         DiffEqBase.AbstractDEProblem,
         Union{Nothing, DiffEqBase.AbstractSensitivityAlgorithm},
         Any,
         Any,
-        Any,
+        Any
     },
-    true,
-    )
+    true,)
 
 # Dispatch for auto-alg
-Mooncake.@from_rrule(
-    Mooncake.MinimalCtx,
+Mooncake.@from_rrule(Mooncake.MinimalCtx,
     Tuple{
         typeof(DiffEqBase.solve_up),
         DiffEqBase.AbstractDEProblem,
         Union{Nothing, DiffEqBase.AbstractSensitivityAlgorithm},
         Any,
-        Any,
+        Any
     },
-    true,
-    )
+    true,)
 
 Mooncake.@zero_adjoint Mooncake.MinimalCtx Tuple{typeof(DiffEqBase.numargs), Any}
 Mooncake.@mooncake_overlay DiffEqBase.set_mooncakeoriginator_if_mooncake(x::ADOriginator) = MooncakeOriginator
 
-end
+end

src/solve.jl

@@ -99,7 +99,9 @@ const allowedkeywords = (:dense,
     # Termination condition for solvers
     :termination_condition,
     # For AbstractAliasSpecifier
-    :alias)
+    :alias,
+    # Parameter estimation with BVP
+    :fit_parameters)
 
 const KWARGWARN_MESSAGE = """
                           Unrecognized keyword arguments found.
@@ -541,7 +543,8 @@ end
 Get the innermost index provider using `SII.symbolic_container`.
 """
 function _get_root_indp(indp)
-    if hasmethod(SII.symbolic_container, Tuple{typeof(indp)}) && (sc = SII.symbolic_container(indp)) !== indp
+    if hasmethod(SII.symbolic_container, Tuple{typeof(indp)}) &&
+       (sc = SII.symbolic_container(indp)) !== indp
         return _get_root_indp(sc)
     end
     return indp
@@ -748,7 +751,7 @@ function build_null_solution(prob::AbstractDEProblem, args...;
 
     prob, success = hack_null_solution_init(prob)
     retcode = success ? ReturnCode.Success : ReturnCode.InitialFailure
-    build_solution(prob, nothing, ts, timeseries; dense=true, retcode)
+    build_solution(prob, nothing, ts, timeseries; dense = true, retcode)
 end
 
 function build_null_solution(
@@ -1139,7 +1142,6 @@ function solve(prob::NonlinearProblem, args...; sensealg = nothing,
         sensealg = prob.kwargs[:sensealg]
     end
 
-    
     if haskey(prob.kwargs, :alias_u0)
         @warn "The `alias_u0` keyword argument is deprecated. Please use a NonlinearAliasSpecifier, e.g. `alias = NonlinearAliasSpecifier(alias_u0 = true)`."
         alias_spec = NonlinearAliasSpecifier(alias_u0 = prob.kwargs[:alias_u0])
@@ -1152,7 +1154,7 @@ function solve(prob::NonlinearProblem, args...; sensealg = nothing,
         alias_spec = NonlinearAliasSpecifier(alias = prob.kwargs[:alias])
     elseif haskey(kwargs, :alias) && kwargs[:alias] isa Bool
         alias_spec = NonlinearAliasSpecifier(alias = kwargs[:alias])
-    end   
+    end
 
     if haskey(prob.kwargs, :alias) && prob.kwargs[:alias] isa NonlinearAliasSpecifier
         alias_spec = prob.kwargs[:alias]

test/downstream/unitful.jl

@@ -5,5 +5,5 @@ intg = init(prob, Tsit5())
 @test_nowarn step!(intg, 0.02u"s", true)
 
 @test DiffEqBase.unitfulvalue(u"1/s") == u"1/s"
-@test DiffEqBase.value(ForwardDiff.Dual(1)*u"1/s") == 1
-@test DiffEqBase.unitfulvalue(ForwardDiff.Dual(1)*u"1/s") == u"1/s"
+@test DiffEqBase.value(ForwardDiff.Dual(1) * u"1/s") == 1
+@test DiffEqBase.unitfulvalue(ForwardDiff.Dual(1) * u"1/s") == u"1/s"

test/static/static_checks.jl

@@ -1,5 +1,5 @@
 using DiffEqBase, ComponentArrays, AllocCheck, Test
 
-u = ComponentArray(x=1.0, y=0.0, z=0.0)
+u = ComponentArray(x = 1.0, y = 0.0, z = 0.0)
 t = 0.0
-@test length(check_allocs(DiffEqBase.ODE_DEFAULT_NORM, (typeof(u), typeof(t)))) == 0
+@test length(check_allocs(DiffEqBase.ODE_DEFAULT_NORM, (typeof(u), typeof(t)))) == 0