refactor: turn tunables portion into a Vector{T}

src/inputoutput.jl

@@ -243,7 +243,7 @@ function generate_control_function(sys::AbstractODESystem, inputs = unbound_inpu
     end
     process = get_postprocess_fbody(sys)
     f = build_function(rhss, args...; postprocess_fbody = process,
-        expression = Val{true}, kwargs...)
+        expression = Val{true}, wrap_code = wrap_array_vars(sys, rhss; dvs, ps), kwargs...)
     f = eval_or_rgf.(f; eval_expression, eval_module)
     (; f, dvs, ps, io_sys = sys)
 end

src/systems/abstractsystem.jl

@@ -223,15 +223,29 @@ function wrap_assignments(isscalar, assignments; let_block = false)
     end
 end
 
-function wrap_array_vars(sys::AbstractSystem, exprs; dvs = unknowns(sys))
+function wrap_array_vars(
+        sys::AbstractSystem, exprs; dvs = unknowns(sys), ps = parameters(sys))
     isscalar = !(exprs isa AbstractArray)
     array_vars = Dict{Any, AbstractArray{Int}}()
-    for (j, x) in enumerate(dvs)
-        if iscall(x) && operation(x) == getindex
-            arg = arguments(x)[1]
-            inds = get!(() -> Int[], array_vars, arg)
-            push!(inds, j)
+    if dvs !== nothing
+        for (j, x) in enumerate(dvs)
+            if iscall(x) && operation(x) == getindex
+                arg = arguments(x)[1]
+                inds = get!(() -> Int[], array_vars, arg)
+                push!(inds, j)
+            end
         end
+        uind = 1
+    else
+        uind = 0
+    end
+    array_pars = Dict{Any, AbstractArray{Int}}()
+    for p in ps
+        idx = parameter_index(sys, p)
+        idx isa ParameterIndex || continue
+        idx.portion isa SciMLStructures.Tunable || continue
+        idx.idx isa AbstractArray || continue
+        array_pars[p] = idx.idx
     end
     for (k, inds) in array_vars
         if inds == (inds′ = inds[1]:inds[end])
@@ -244,7 +258,10 @@ function wrap_array_vars(sys::AbstractSystem, exprs; dvs = unknowns(sys))
                 expr.args,
                 [],
                 Let(
-                    [k ← :(view($(expr.args[1].name), $v)) for (k, v) in array_vars],
+                    vcat(
+                        [k ← :(view($(expr.args[uind].name), $v)) for (k, v) in array_vars],
+                        [k ← :(view($(expr.args[uind+1].name), $v)) for (k, v) in array_pars]
+                    ),
                     expr.body,
                     false
                 )
@@ -256,7 +273,10 @@ function wrap_array_vars(sys::AbstractSystem, exprs; dvs = unknowns(sys))
                 expr.args,
                 [],
                 Let(
-                    [k ← :(view($(expr.args[1].name), $v)) for (k, v) in array_vars],
+                    vcat(
+                        [k ← :(view($(expr.args[uind].name), $v)) for (k, v) in array_vars],
+                        [k ← :(view($(expr.args[uind+1].name), $v)) for (k, v) in array_pars]
+                    ),
                     expr.body,
                     false
                 )
@@ -267,7 +287,10 @@ function wrap_array_vars(sys::AbstractSystem, exprs; dvs = unknowns(sys))
                 expr.args,
                 [],
                 Let(
-                    [k ← :(view($(expr.args[2].name), $v)) for (k, v) in array_vars],
+                    vcat(
+                        [k ← :(view($(expr.args[uind+1].name), $v)) for (k, v) in array_vars],
+                        [k ← :(view($(expr.args[uind+2].name), $v)) for (k, v) in array_pars]
+                    ),
                     expr.body,
                     false
                 )

src/systems/callbacks.jl

@@ -354,7 +354,8 @@ function compile_condition(cb::SymbolicDiscreteCallback, sys, dvs, ps;
         condit = substitute(condit, cmap)
     end
     expr = build_function(
-        condit, u, t, p...; expression = Val{true}, wrap_code = condition_header(sys),
+        condit, u, t, p...; expression = Val{true},
+        wrap_code = condition_header(sys) .∘ wrap_array_vars(sys, condit; dvs, ps),
         kwargs...)
     if expression == Val{true}
         return expr
@@ -411,10 +412,8 @@ function compile_affect(eqs::Vector{Equation}, sys, dvs, ps; outputidxs = nothin
                 update_inds = map(sym -> unknownind[sym], update_vars)
             elseif isparameter(first(lhss)) && alleq
                 if has_index_cache(sys) && get_index_cache(sys) !== nothing
-                    ic = get_index_cache(sys)
                     update_inds = map(update_vars) do sym
-                        pind = parameter_index(sys, sym)
-                        discrete_linear_index(ic, pind)
+                        return parameter_index(sys, sym)
                     end
                 else
                     psind = Dict(reverse(en) for en in enumerate(ps))
@@ -440,7 +439,8 @@ function compile_affect(eqs::Vector{Equation}, sys, dvs, ps; outputidxs = nothin
         integ = gensym(:MTKIntegrator)
         pre = get_preprocess_constants(rhss)
         rf_oop, rf_ip = build_function(rhss, u, p..., t; expression = Val{true},
-            wrap_code = add_integrator_header(sys, integ, outvar),
+            wrap_code = add_integrator_header(sys, integ, outvar) .∘
+                        wrap_array_vars(sys, rhss; dvs, ps),
             outputidxs = update_inds,
             postprocess_fbody = pre,
             kwargs...)

src/systems/diffeqs/abstractodesystem.jl

@@ -87,7 +87,7 @@ end
 
 function generate_tgrad(
         sys::AbstractODESystem, dvs = unknowns(sys), ps = full_parameters(sys);
-        simplify = false, kwargs...)
+        simplify = false, wrap_code = identity, kwargs...)
     tgrad = calculate_tgrad(sys, simplify = simplify)
     pre = get_preprocess_constants(tgrad)
     p = if has_index_cache(sys) && get_index_cache(sys) !== nothing
@@ -97,29 +97,33 @@ function generate_tgrad(
     else
         (ps,)
     end
+    wrap_code = wrap_code .∘ wrap_array_vars(sys, tgrad; dvs, ps)
     return build_function(tgrad,
         dvs,
         p...,
         get_iv(sys);
         postprocess_fbody = pre,
+        wrap_code,
         kwargs...)
 end
 
 function generate_jacobian(sys::AbstractODESystem, dvs = unknowns(sys),
         ps = full_parameters(sys);
-        simplify = false, sparse = false, kwargs...)
+        simplify = false, sparse = false, wrap_code = identity, kwargs...)
     jac = calculate_jacobian(sys; simplify = simplify, sparse = sparse)
     pre = get_preprocess_constants(jac)
     p = if has_index_cache(sys) && get_index_cache(sys) !== nothing
         reorder_parameters(get_index_cache(sys), ps)
     else
         (ps,)
     end
+    wrap_code = wrap_code .∘ wrap_array_vars(sys, jac; dvs, ps)
     return build_function(jac,
         dvs,
         p...,
         get_iv(sys);
         postprocess_fbody = pre,
+        wrap_code,
         kwargs...)
 end
 
@@ -188,12 +192,12 @@ function generate_function(sys::AbstractODESystem, dvs = unknowns(sys),
         if implicit_dae
             build_function(rhss, ddvs, u, p..., t; postprocess_fbody = pre,
                 states = sol_states,
-                wrap_code = wrap_code .∘ wrap_array_vars(sys, rhss; dvs),
+                wrap_code = wrap_code .∘ wrap_array_vars(sys, rhss; dvs, ps),
                 kwargs...)
         else
             build_function(rhss, u, p..., t; postprocess_fbody = pre,
                 states = sol_states,
-                wrap_code = wrap_code .∘ wrap_array_vars(sys, rhss; dvs),
+                wrap_code = wrap_code .∘ wrap_array_vars(sys, rhss; dvs, ps),
                 kwargs...)
         end
     end

src/systems/diffeqs/odesystem.jl

@@ -485,6 +485,7 @@ function build_explicit_observed_function(sys, ts;
     if inputs !== nothing
         ps = setdiff(ps, inputs) # Inputs have been converted to parameters by io_preprocessing, remove those from the parameter list
     end
+    _ps = ps
     if ps isa Tuple
         ps = DestructuredArgs.(ps, inbounds = !checkbounds)
     elseif has_index_cache(sys) && get_index_cache(sys) !== nothing
@@ -505,19 +506,24 @@ function build_explicit_observed_function(sys, ts;
     end
     pre = get_postprocess_fbody(sys)
 
+    array_wrapper = if param_only
+        wrap_array_vars(sys, ts; ps = _ps, dvs = nothing)
+    else
+        wrap_array_vars(sys, ts; ps = _ps)
+    end
     # Need to keep old method of building the function since it uses `output_type`,
     # which can't be provided to `build_function`
     oop_fn = Func(args, [],
                  pre(Let(obsexprs,
                      isscalar ? ts[1] : MakeArray(ts, output_type),
-                     false))) |> wrap_array_vars(sys, ts)[1] |> toexpr
+                     false))) |> array_wrapper[1] |> toexpr
     oop_fn = expression ? oop_fn : eval_or_rgf(oop_fn; eval_expression, eval_module)
 
     if !isscalar
         iip_fn = build_function(ts,
             args...;
             postprocess_fbody = pre,
-            wrap_code = wrap_array_vars(sys, ts) .∘ wrap_assignments(isscalar, obsexprs),
+            wrap_code = array_wrapper .∘ wrap_assignments(isscalar, obsexprs),
             expression = Val{true})[2]
         if !expression
             iip_fn = eval_or_rgf(iip_fn; eval_expression, eval_module)

src/systems/discrete_system/discrete_system.jl

@@ -218,8 +218,10 @@ function flatten(sys::DiscreteSystem, noeqs = false)
 end
 
 function generate_function(
-        sys::DiscreteSystem, dvs = unknowns(sys), ps = full_parameters(sys); kwargs...)
-    generate_custom_function(sys, [eq.rhs for eq in equations(sys)], dvs, ps; kwargs...)
+        sys::DiscreteSystem, dvs = unknowns(sys), ps = full_parameters(sys); wrap_code = identity, kwargs...)
+    exprs = [eq.rhs for eq in equations(sys)]
+    wrap_code = wrap_code .∘ wrap_array_vars(sys, exprs)
+    generate_custom_function(sys, exprs, dvs, ps; wrap_code, kwargs...)
 end
 
 function process_DiscreteProblem(constructor, sys::DiscreteSystem, u0map, parammap;

src/systems/index_cache.jl

@@ -24,17 +24,19 @@ ParameterIndex(portion, idx) = ParameterIndex(portion, idx, false)
 const ParamIndexMap = Dict{BasicSymbolic, Tuple{Int, Int}}
 const UnknownIndexMap = Dict{
     BasicSymbolic, Union{Int, UnitRange{Int}, AbstractArray{Int}}}
+const TunableIndexMap = Dict{BasicSymbolic,
+    Union{Int, UnitRange{Int}, Base.ReshapedArray{Int, N, UnitRange{Int}} where {N}}}
 
 struct IndexCache
     unknown_idx::UnknownIndexMap
     discrete_idx::Dict{BasicSymbolic, Tuple{Int, Int, Int}}
-    tunable_idx::ParamIndexMap
+    tunable_idx::TunableIndexMap
     constant_idx::ParamIndexMap
     dependent_idx::ParamIndexMap
     nonnumeric_idx::ParamIndexMap
     observed_syms::Set{BasicSymbolic}
     discrete_buffer_sizes::Vector{Vector{BufferTemplate}}
-    tunable_buffer_sizes::Vector{BufferTemplate}
+    tunable_buffer_size::BufferTemplate
     constant_buffer_sizes::Vector{BufferTemplate}
     dependent_buffer_sizes::Vector{BufferTemplate}
     nonnumeric_buffer_sizes::Vector{BufferTemplate}
@@ -75,7 +77,7 @@ function IndexCache(sys::AbstractSystem)
         end
     end
 
-    observed_syms = Set{Union{Symbol, BasicSymbolic}}()
+    observed_syms = Set{BasicSymbolic}()
     for eq in observed(sys)
         if symbolic_type(eq.lhs) != NotSymbolic()
             sym = eq.lhs
@@ -236,7 +238,10 @@ function IndexCache(sys::AbstractSystem)
         haskey(dependent_buffers, ctype) && p in dependent_buffers[ctype] && continue
         insert_by_type!(
             if ctype <: Real || ctype <: AbstractArray{<:Real}
-                if istunable(p, true) && Symbolics.shape(p) !== Symbolics.Unknown()
+                if istunable(p, true) && Symbolics.shape(p) != Symbolics.Unknown &&
+                    (ctype == Real || ctype <: AbstractFloat ||
+                        ctype <: AbstractArray{Real} ||
+                        ctype <: AbstractArray{<:AbstractFloat})
                     tunable_buffers
                 else
                     constant_buffers
@@ -292,11 +297,30 @@ function IndexCache(sys::AbstractSystem)
         return idxs, buffer_sizes
     end
 
-    tunable_idxs, tunable_buffer_sizes = get_buffer_sizes_and_idxs(tunable_buffers)
     const_idxs, const_buffer_sizes = get_buffer_sizes_and_idxs(constant_buffers)
     dependent_idxs, dependent_buffer_sizes = get_buffer_sizes_and_idxs(dependent_buffers)
     nonnumeric_idxs, nonnumeric_buffer_sizes = get_buffer_sizes_and_idxs(nonnumeric_buffers)
 
+    tunable_idxs = TunableIndexMap()
+    tunable_buffer_size = 0
+    for (i, (_, buf)) in enumerate(tunable_buffers)
+        for (j, p) in enumerate(buf)
+            idx = if size(p) == ()
+                tunable_buffer_size + 1
+            else
+                reshape(
+                    (tunable_buffer_size + 1):(tunable_buffer_size + length(p)), size(p))
+            end
+            tunable_buffer_size += length(p)
+            tunable_idxs[p] = idx
+            tunable_idxs[default_toterm(p)] = idx
+            if hasname(p) && (!iscall(p) || operation(p) !== getindex)
+                symbol_to_variable[getname(p)] = p
+                symbol_to_variable[getname(default_toterm(p))] = p
+            end
+        end
+    end
+
     for sym in Iterators.flatten((keys(unk_idxs), keys(disc_idxs), keys(tunable_idxs),
         keys(const_idxs), keys(dependent_idxs), keys(nonnumeric_idxs),
         observed_syms, independent_variable_symbols(sys)))
@@ -314,7 +338,7 @@ function IndexCache(sys::AbstractSystem)
         nonnumeric_idxs,
         observed_syms,
         disc_buffer_sizes,
-        tunable_buffer_sizes,
+        BufferTemplate(Real, tunable_buffer_size),
         const_buffer_sizes,
         dependent_buffer_sizes,
         nonnumeric_buffer_sizes,
@@ -410,20 +434,6 @@ function check_index_map(idxmap, sym)
     end
 end
 
-function discrete_linear_index(ic::IndexCache, idx::ParameterIndex)
-    idx.portion isa SciMLStructures.Discrete || error("Discrete variable index expected")
-    ind = sum(temp.length for temp in ic.tunable_buffer_sizes; init = 0)
-    for clockbuftemps in Iterators.take(ic.discrete_buffer_sizes, idx.idx[1] - 1)
-        ind += sum(temp.length for temp in clockbuftemps; init = 0)
-    end
-    ind += sum(
-        temp.length
-        for temp in Iterators.take(ic.discrete_buffer_sizes[idx.idx[1]], idx.idx[2] - 1);
-        init = 0)
-    ind += idx.idx[3]
-    return ind
-end
-
 function reorder_parameters(sys::AbstractSystem, ps; kwargs...)
     if has_index_cache(sys) && get_index_cache(sys) !== nothing
         reorder_parameters(get_index_cache(sys), ps; kwargs...)
@@ -436,8 +446,12 @@ end
 
 function reorder_parameters(ic::IndexCache, ps; drop_missing = false)
     isempty(ps) && return ()
-    param_buf = Tuple(BasicSymbolic[unwrap(variable(:DEF)) for _ in 1:(temp.length)]
-    for temp in ic.tunable_buffer_sizes)
+    param_buf = if ic.tunable_buffer_size.length == 0
+        ()
+    else
+        (BasicSymbolic[unwrap(variable(:DEF))
+                              for _ in 1:(ic.tunable_buffer_size.length)],)
+    end
     disc_buf = Tuple(BasicSymbolic[unwrap(variable(:DEF)) for _ in 1:(temp.length)]
     for temp in Iterators.flatten(ic.discrete_buffer_sizes))
     const_buf = Tuple(BasicSymbolic[unwrap(variable(:DEF)) for _ in 1:(temp.length)]
@@ -453,8 +467,12 @@ function reorder_parameters(ic::IndexCache, ps; drop_missing = false)
             i, j, k = ic.discrete_idx[p]
             disc_buf[(i - 1) * disc_offset + j][k] = p
         elseif haskey(ic.tunable_idx, p)
-            i, j = ic.tunable_idx[p]
-            param_buf[i][j] = p
+            i = ic.tunable_idx[p]
+            if i isa Int
+                param_buf[1][i] = unwrap(p)
+            else
+                param_buf[1][i] = unwrap.(collect(p))
+            end
         elseif haskey(ic.constant_idx, p)
             i, j = ic.constant_idx[p]
             const_buf[i][j] = p

src/systems/jumps/jumpsystem.jl

@@ -203,6 +203,7 @@ function generate_rate_function(js::JumpSystem, rate)
     p = reorder_parameters(js, full_parameters(js))
     rf = build_function(rate, unknowns(js), p...,
         get_iv(js),
+        wrap_code = wrap_array_vars(js, rate; dvs = unknowns(js), ps = parameters(js)),
         expression = Val{true})
 end