From 4988ee10da32d305e3c74b9cdc0888ff68dcb9e8 Mon Sep 17 00:00:00 2001
From: Benjamin Chung <ckfinite@gmail.com>
Date: Mon, 17 Feb 2025 17:51:46 -0800
Subject: [PATCH 01/14] Early work on the new discrete backend for MTK

---
 src/systems/clock_inference.jl | 11 ++++++++-
 src/systems/systems.jl         |  7 +++++-
 src/systems/systemstructure.jl | 43 +++++++++++++++++++++++++---------
 3 files changed, 48 insertions(+), 13 deletions(-)

diff --git a/src/systems/clock_inference.jl b/src/systems/clock_inference.jl
index 42fe28f7c7..86fe7e85ac 100644
--- a/src/systems/clock_inference.jl
+++ b/src/systems/clock_inference.jl
@@ -100,7 +100,7 @@ function infer_clocks!(ci::ClockInference)
         c = BitSet(c′)
         idxs = intersect(c, inferred)
         isempty(idxs) && continue
-        if !allequal(var_domain[i] for i in idxs)
+        if !allequal(iscontinuous(var_domain[i]) for i in idxs)
             display(fullvars[c′])
             throw(ClockInferenceException("Clocks are not consistent in connected component $(fullvars[c′])"))
         end
@@ -155,6 +155,9 @@ function split_system(ci::ClockInference{S}) where {S}
     cid_to_var = Vector{Int}[]
     # cid_counter = number of clocks
     cid_counter = Ref(0)
+
+    # populates clock_to_id and id_to_clock
+    # checks if there is a continuous_id (for some reason? clock to id does this too)
     for (i, d) in enumerate(eq_domain)
         cid = let cid_counter = cid_counter, id_to_clock = id_to_clock,
             continuous_id = continuous_id
@@ -174,9 +177,13 @@ function split_system(ci::ClockInference{S}) where {S}
         resize_or_push!(cid_to_eq, i, cid)
     end
     continuous_id = continuous_id[]
+    # for each clock partition what are the input (indexes/vars)
     input_idxs = map(_ -> Int[], 1:cid_counter[])
     inputs = map(_ -> Any[], 1:cid_counter[])
+    # var_domain corresponds to fullvars/all variables in the system
     nvv = length(var_domain)
+    # put variables into the right clock partition
+    # keep track of inputs to each partition
     for i in 1:nvv
         d = var_domain[i]
         cid = get(clock_to_id, d, 0)
@@ -190,6 +197,7 @@ function split_system(ci::ClockInference{S}) where {S}
         resize_or_push!(cid_to_var, i, cid)
     end
 
+    # breaks the system up into a continous and 0 or more discrete systems
     tss = similar(cid_to_eq, S)
     for (id, ieqs) in enumerate(cid_to_eq)
         ts_i = system_subset(ts, ieqs)
@@ -199,6 +207,7 @@ function split_system(ci::ClockInference{S}) where {S}
         end
         tss[id] = ts_i
     end
+    # put the continous system at the back
     if continuous_id != 0
         tss[continuous_id], tss[end] = tss[end], tss[continuous_id]
         inputs[continuous_id], inputs[end] = inputs[end], inputs[continuous_id]
diff --git a/src/systems/systems.jl b/src/systems/systems.jl
index ff455fb811..c6b9d78f97 100644
--- a/src/systems/systems.jl
+++ b/src/systems/systems.jl
@@ -36,7 +36,7 @@ function mtkcompile(
     isscheduled(sys) && throw(RepeatedStructuralSimplificationError())
     newsys′ = __mtkcompile(sys; simplify,
         allow_symbolic, allow_parameter, conservative, fully_determined,
-        inputs, outputs, disturbance_inputs,
+        inputs, outputs, disturbance_inputs, additional_passes,
         kwargs...)
     if newsys′ isa Tuple
         @assert length(newsys′) == 2
@@ -292,3 +292,8 @@ function map_variables_to_equations(sys::AbstractSystem; rename_dummy_derivative
 
     return mapping
 end
+
+"""
+Mark whether an extra pass `p` can support compiling discrete systems.
+"""
+discrete_compile_pass(p) = false
diff --git a/src/systems/systemstructure.jl b/src/systems/systemstructure.jl
index 5dfd36a6fc..a5401c9f9b 100644
--- a/src/systems/systemstructure.jl
+++ b/src/systems/systemstructure.jl
@@ -820,19 +820,40 @@ function mtkcompile!(state::TearingState; simplify = false,
     time_domains = merge(Dict(state.fullvars .=> ci.var_domain),
         Dict(default_toterm.(state.fullvars) .=> ci.var_domain))
     tss, clocked_inputs, continuous_id, id_to_clock = ModelingToolkit.split_system(ci)
+    if continuous_id == 0
+        # do a trait check here - handle fully discrete system
+        additional_passes = get(kwargs, :additional_passes, nothing)
+        if !isnothing(additional_passes) && any(discrete_compile_pass, additional_passes)
+            # take the first discrete compilation pass given for now
+            discrete_pass_idx = findfirst(discrete_compile_pass, additional_passes)
+            discrete_compile = additional_passes[discrete_pass_idx]
+            deleteat!(additional_passes, discrete_pass_idx)
+            return discrete_compile(tss, clocked_inputs)
+        end
+        throw(HybridSystemNotSupportedException("""
+        Discrete systems with multiple clocks are not supported with the standard \
+        MTK compiler.
+        """))
+    end
     if length(tss) > 1
-        if continuous_id == 0
-            throw(HybridSystemNotSupportedException("""
-            Discrete systems with multiple clocks are not supported with the standard \
-            MTK compiler.
-            """))
-        else
-            throw(HybridSystemNotSupportedException("""
-            Hybrid continuous-discrete systems are currently not supported with \
-            the standard MTK compiler. This system requires JuliaSimCompiler.jl, \
-            see https://help.juliahub.com/juliasimcompiler/stable/
-            """))
+        # simplify as normal
+        sys = _mtkcompile!(tss[continuous_id]; simplify,
+            inputs = [inputs; clocked_inputs[continuous_id]], outputs, disturbance_inputs,
+            check_consistency, fully_determined,
+            kwargs...)
+        if !isnothing(additional_passes) && any(discrete_compile_pass, additional_passes)
+            discrete_pass_idx = findfirst(discrete_compile_pass, additional_passes)
+            discrete_compile = additional_passes[discrete_pass_idx]
+            deleteat!(additional_passes, discrete_pass_idx)
+            # in the case of a hybrid system, the discrete_compile pass should take the currents of sys.discrete_subsystems
+            # and modifies discrete_subsystems to bea tuple of the io and anything else, while adding or manipulating the rest of sys as needed
+            return discrete_compile(sys, tss[2:end], inputs)
         end
+        throw(HybridSystemNotSupportedException("""
+        Hybrid continuous-discrete systems are currently not supported with \
+        the standard MTK compiler. This system requires JuliaSimCompiler.jl, \
+        see https://help.juliahub.com/juliasimcompiler/stable/
+        """))
     end
     if get_is_discrete(state.sys) ||
        continuous_id == 1 && any(Base.Fix2(isoperator, Shift), state.fullvars)

From ed0612b33c3d112498095a75f08b9ccb6e9d2cef Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Thu, 20 Feb 2025 14:52:14 +0530
Subject: [PATCH 02/14] feat: retain original equations of the system in
 `TearingState`

---
 src/systems/systems.jl         |  4 ++--
 src/systems/systemstructure.jl | 21 ++++++++++++++++++++-
 2 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/src/systems/systems.jl b/src/systems/systems.jl
index c6b9d78f97..bdca6ff71a 100644
--- a/src/systems/systems.jl
+++ b/src/systems/systems.jl
@@ -80,7 +80,6 @@ function __mtkcompile(sys::AbstractSystem; simplify = false,
 
     @unpack structure, fullvars = state
     @unpack graph, var_to_diff, var_types = structure
-    eqs = equations(state)
     brown_vars = Int[]
     new_idxs = zeros(Int, length(var_types))
     idx = 0
@@ -98,7 +97,8 @@ function __mtkcompile(sys::AbstractSystem; simplify = false,
         Is = Int[]
         Js = Int[]
         vals = Num[]
-        new_eqs = copy(eqs)
+        make_eqs_zero_equals!(state)
+        new_eqs = copy(equations(state))
         dvar2eq = Dict{Any, Int}()
         for (v, dv) in enumerate(var_to_diff)
             dv === nothing && continue
diff --git a/src/systems/systemstructure.jl b/src/systems/systemstructure.jl
index a5401c9f9b..c3ff82478e 100644
--- a/src/systems/systemstructure.jl
+++ b/src/systems/systemstructure.jl
@@ -203,6 +203,7 @@ end
 mutable struct TearingState{T <: AbstractSystem} <: AbstractTearingState{T}
     """The system of equations."""
     sys::T
+    original_eqs::Vector{Equation}
     """The set of variables of the system."""
     fullvars::Vector{BasicSymbolic}
     structure::SystemStructure
@@ -219,6 +220,7 @@ end
 TransformationState(sys::AbstractSystem) = TearingState(sys)
 function system_subset(ts::TearingState, ieqs::Vector{Int})
     eqs = equations(ts)
+    @set! ts.original_eqs = ts.original_eqs[ieqs]
     @set! ts.sys.eqs = eqs[ieqs]
     @set! ts.original_eqs = ts.original_eqs[ieqs]
     @set! ts.structure = system_subset(ts.structure, ieqs)
@@ -524,7 +526,7 @@ function TearingState(sys; quick_cancel = false, check = true, sort_eqs = true)
 
     eq_to_diff = DiffGraph(nsrcs(graph))
 
-    ts = TearingState(sys, fullvars,
+    ts = TearingState(sys, original_eqs, fullvars,
         SystemStructure(complete(var_to_diff), complete(eq_to_diff),
             complete(graph), nothing, var_types, false),
         Any[], param_derivative_map, original_eqs, Equation[])
@@ -810,6 +812,22 @@ function Base.show(io::IO, mime::MIME"text/plain", ms::MatchedSystemStructure)
     printstyled(io, " SelectedState")
 end
 
+function make_eqs_zero_equals!(ts::TearingState)
+    neweqs = map(enumerate(get_eqs(ts.sys))) do kvp
+        i, eq = kvp
+        isalgeq = true
+        for j in 𝑠neighbors(ts.structure.graph, i)
+            isalgeq &= invview(ts.structure.var_to_diff)[j] === nothing
+        end
+        if isalgeq
+            return 0 ~ eq.rhs - eq.lhs
+        else
+            return eq
+        end
+    end
+    copyto!(get_eqs(ts.sys), neweqs)
+end
+
 function mtkcompile!(state::TearingState; simplify = false,
         check_consistency = true, fully_determined = true, warn_initialize_determined = true,
         inputs = Any[], outputs = Any[],
@@ -836,6 +854,7 @@ function mtkcompile!(state::TearingState; simplify = false,
         """))
     end
     if length(tss) > 1
+        make_eqs_zero_equals!(tss[continuous_id])
         # simplify as normal
         sys = _mtkcompile!(tss[continuous_id]; simplify,
             inputs = [inputs; clocked_inputs[continuous_id]], outputs, disturbance_inputs,

From 7f8b8f260efd0ea7c067baea118c16f40263c091 Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Fri, 14 Mar 2025 14:50:31 +0530
Subject: [PATCH 03/14] feat: allow namespacing statemachine equations

---
 src/systems/abstractsystem.jl |  1 +
 src/systems/state_machines.jl | 33 +++++++++++++++++++++++++++++++++
 src/utils.jl                  |  6 ++++++
 3 files changed, 40 insertions(+)

diff --git a/src/systems/abstractsystem.jl b/src/systems/abstractsystem.jl
index 70e7b06bfe..34dfb5283e 100644
--- a/src/systems/abstractsystem.jl
+++ b/src/systems/abstractsystem.jl
@@ -1228,6 +1228,7 @@ function namespace_expr(
         O
     end
 end
+
 _nonum(@nospecialize x) = x isa Num ? x.val : x
 
 """
diff --git a/src/systems/state_machines.jl b/src/systems/state_machines.jl
index 347f92e6f8..ea65981804 100644
--- a/src/systems/state_machines.jl
+++ b/src/systems/state_machines.jl
@@ -153,3 +153,36 @@ entry
 
 When used in a finite state machine, this operator returns `true` if the queried state is active and false otherwise. 
 """ activeState
+
+function vars!(vars, O::Transition; op = Differential)
+    vars!(vars, O.from)
+    vars!(vars, O.to)
+    vars!(vars, O.cond; op)
+    return vars
+end
+function vars!(vars, O::InitialState; op = Differential)
+    vars!(vars, O.s; op)
+    return vars
+end
+function vars!(vars, O::StateMachineOperator; op = Differential)
+    error("Unhandled state machine operator")
+end
+
+function namespace_expr(
+        O::Transition, sys, n = nameof(sys); ivs = independent_variables(sys))
+    return Transition(
+        O.from === nothing ? O.from : renamespace(sys, O.from),
+        O.to === nothing ? O.to : renamespace(sys, O.to),
+        O.cond === nothing ? O.cond : namespace_expr(O.cond, sys),
+        O.immediate, O.reset, O.synchronize, O.priority
+    )
+end
+
+function namespace_expr(
+        O::InitialState, sys, n = nameof(sys); ivs = independent_variables(sys))
+    return InitialState(O.s === nothing ? O.s : renamespace(sys, O.s))
+end
+
+function namespace_expr(O::StateMachineOperator, sys, n = nameof(sys); kwargs...)
+    error("Unhandled state machine operator")
+end
diff --git a/src/utils.jl b/src/utils.jl
index e96f31f533..d028d4ed18 100644
--- a/src/utils.jl
+++ b/src/utils.jl
@@ -391,6 +391,12 @@ vars(eq::Equation; op = Differential) = vars!(Set(), eq; op = op)
 function vars!(vars, eq::Equation; op = Differential)
     (vars!(vars, eq.lhs; op = op); vars!(vars, eq.rhs; op = op); vars)
 end
+function vars!(vars, O::AbstractSystem; op = Differential)
+    for eq in equations(O)
+        vars!(vars, eq; op)
+    end
+    return vars
+end
 function vars!(vars, O; op = Differential)
     if isvariable(O)
         if iscall(O) && operation(O) === getindex && iscalledparameter(first(arguments(O)))

From 7cf774d0bd4d355b9f696def2246988b49265d87 Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Fri, 14 Mar 2025 14:56:00 +0530
Subject: [PATCH 04/14] feat: propagate state machines in structural
 simplification

---
 src/systems/systems.jl         |  4 +-
 src/systems/systemstructure.jl | 81 ++++++++++++++++++++++++++++++----
 2 files changed, 76 insertions(+), 9 deletions(-)

diff --git a/src/systems/systems.jl b/src/systems/systems.jl
index bdca6ff71a..9769d42e96 100644
--- a/src/systems/systems.jl
+++ b/src/systems/systems.jl
@@ -75,8 +75,10 @@ function __mtkcompile(sys::AbstractSystem; simplify = false,
         return simplify_optimization_system(sys; kwargs..., sort_eqs, simplify)
     end
 
+    sys, statemachines = extract_top_level_statemachines(sys)
     sys = expand_connections(sys)
-    state = TearingState(sys; sort_eqs)
+    state = TearingState(sys)
+    append!(state.statemachines, statemachines)
 
     @unpack structure, fullvars = state
     @unpack graph, var_to_diff, var_types = structure
diff --git a/src/systems/systemstructure.jl b/src/systems/systemstructure.jl
index c3ff82478e..f072dc3f52 100644
--- a/src/systems/systemstructure.jl
+++ b/src/systems/systemstructure.jl
@@ -203,7 +203,6 @@ end
 mutable struct TearingState{T <: AbstractSystem} <: AbstractTearingState{T}
     """The system of equations."""
     sys::T
-    original_eqs::Vector{Equation}
     """The set of variables of the system."""
     fullvars::Vector{BasicSymbolic}
     structure::SystemStructure
@@ -215,6 +214,7 @@ mutable struct TearingState{T <: AbstractSystem} <: AbstractTearingState{T}
     are not used in the rest of the system.
     """
     additional_observed::Vector{Equation}
+    statemachines::Vector{T}
 end
 
 TransformationState(sys::AbstractSystem) = TearingState(sys)
@@ -224,6 +224,22 @@ function system_subset(ts::TearingState, ieqs::Vector{Int})
     @set! ts.sys.eqs = eqs[ieqs]
     @set! ts.original_eqs = ts.original_eqs[ieqs]
     @set! ts.structure = system_subset(ts.structure, ieqs)
+    if all(eq -> eq.rhs isa StateMachineOperator, get_eqs(ts.sys))
+        names = Symbol[]
+        for eq in get_eqs(ts.sys)
+            if eq.lhs isa Transition
+                push!(names, first(namespace_hierarchy(nameof(eq.rhs.from))))
+                push!(names, first(namespace_hierarchy(nameof(eq.rhs.to))))
+            elseif eq.lhs isa InitialState
+                push!(names, first(namespace_hierarchy(nameof(eq.rhs.s))))
+            else
+                error("Unhandled state machine operator")
+            end
+        end
+        @set! ts.statemachines = filter(x -> nameof(x) in names, ts.statemachines)
+    else
+        @set! ts.statemachines = eltype(ts.statemachines)[]
+    end
     ts
 end
 
@@ -277,6 +293,49 @@ function symbolic_contains(var, set)
             all(x -> x in set, Symbolics.scalarize(var))
 end
 
+"""
+    $(TYPEDSIGNATURES)
+
+Descend through the system hierarchy and look for statemachines. Remove equations from
+the inner statemachine systems. Return the new `sys` and an array of top-level
+statemachines.
+"""
+function extract_top_level_statemachines(sys::AbstractSystem)
+    eqs = get_eqs(sys)
+
+    if !isempty(eqs) && all(eq -> eq.lhs isa StateMachineOperator, eqs)
+        # top-level statemachine
+        with_removed = @set sys.systems = map(remove_child_equations, get_systems(sys))
+        return with_removed, [sys]
+    elseif !isempty(eqs) && any(eq -> eq.lhs isa StateMachineOperator, eqs)
+        # error: can't mix
+        error("Mixing statemachine equations and standard equations in a top-level statemachine is not allowed.")
+    else
+        # descend
+        subsystems = get_systems(sys)
+        newsubsystems = eltype(subsystems)[]
+        statemachines = eltype(subsystems)[]
+        for subsys in subsystems
+            newsubsys, sub_statemachines = extract_top_level_statemachines(subsys)
+            push!(newsubsystems, newsubsys)
+            append!(statemachines, sub_statemachines)
+        end
+        @set! sys.systems = newsubsystems
+        return sys, statemachines
+    end
+end
+
+"""
+    $(TYPEDSIGNATURES)
+
+Return `sys` with all equations (including those in subsystems) removed.
+"""
+function remove_child_equations(sys::AbstractSystem)
+    @set! sys.eqs = eltype(get_eqs(sys))[]
+    @set! sys.systems = map(remove_child_equations, get_systems(sys))
+    return sys
+end
+
 function TearingState(sys; quick_cancel = false, check = true, sort_eqs = true)
     # flatten system
     sys = flatten(sys)
@@ -342,9 +401,16 @@ function TearingState(sys; quick_cancel = false, check = true, sort_eqs = true)
             # change the equation if the RHS is `missing` so the rest of this loop works
             eq = 0.0 ~ coalesce(eq.rhs, 0.0)
         end
-        rhs = quick_cancel ? quick_cancel_expr(eq.rhs) : eq.rhs
-        if !_iszero(eq.lhs)
+        is_statemachine_equation = false
+        if eq.lhs isa StateMachineOperator
+            is_statemachine_equation = true
+            eq = eq
+            rhs = eq.rhs
+        elseif _iszero(eq.lhs)
+            rhs = quick_cancel ? quick_cancel_expr(eq.rhs) : eq.rhs
+        else
             lhs = quick_cancel ? quick_cancel_expr(eq.lhs) : eq.lhs
+            rhs = quick_cancel ? quick_cancel_expr(eq.rhs) : eq.rhs
             eq = 0 ~ rhs - lhs
         end
         empty!(varsbuf)
@@ -408,8 +474,7 @@ function TearingState(sys; quick_cancel = false, check = true, sort_eqs = true)
                 addvar!(v, VARIABLE)
             end
         end
-
-        if isalgeq
+        if isalgeq || is_statemachine_equation
             eqs[i] = eq
         else
             eqs[i] = eqs[i].lhs ~ rhs
@@ -526,11 +591,10 @@ function TearingState(sys; quick_cancel = false, check = true, sort_eqs = true)
 
     eq_to_diff = DiffGraph(nsrcs(graph))
 
-    ts = TearingState(sys, original_eqs, fullvars,
+    ts = TearingState(sys, fullvars,
         SystemStructure(complete(var_to_diff), complete(eq_to_diff),
             complete(graph), nothing, var_types, false),
-        Any[], param_derivative_map, original_eqs, Equation[])
-
+        Any[], param_derivative_map, original_eqs, Equation[], typeof(sys)[])
     return ts
 end
 
@@ -860,6 +924,7 @@ function mtkcompile!(state::TearingState; simplify = false,
             inputs = [inputs; clocked_inputs[continuous_id]], outputs, disturbance_inputs,
             check_consistency, fully_determined,
             kwargs...)
+        additional_passes = get(kwargs, :additional_passes, nothing)
         if !isnothing(additional_passes) && any(discrete_compile_pass, additional_passes)
             discrete_pass_idx = findfirst(discrete_compile_pass, additional_passes)
             discrete_compile = additional_passes[discrete_pass_idx]

From c081a34b30549b7f2bff9ae5feff11a57067a4ca Mon Sep 17 00:00:00 2001
From: Benjamin Chung <ckfinite@gmail.com>
Date: Fri, 14 Mar 2025 18:24:11 -0700
Subject: [PATCH 05/14] Handle nothing updates better

---
 src/systems/imperative_affect.jl | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/systems/imperative_affect.jl b/src/systems/imperative_affect.jl
index 7b1a9fb286..f3d45e258a 100644
--- a/src/systems/imperative_affect.jl
+++ b/src/systems/imperative_affect.jl
@@ -262,7 +262,9 @@ function compile_functional_affect(
             upd_vals = user_affect(upd_component_array, obs_component_array, ctx, integ)
 
             # write the new values back to the integrator
-            _generated_writeback(integ, upd_funs, upd_vals)
+            if !isnothing(upd_vals)
+                _generated_writeback(integ, upd_funs, upd_vals)
+            end
 
             reset_jumps && reset_aggregated_jumps!(integ)
         end

From b60be7975ee056f2458340e75332b0f01eb89229 Mon Sep 17 00:00:00 2001
From: Benjamin Chung <ckfinite@gmail.com>
Date: Fri, 14 Mar 2025 18:24:24 -0700
Subject: [PATCH 06/14] Redefine the discrete_compile interface a bit

---
 src/systems/systemstructure.jl | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/systems/systemstructure.jl b/src/systems/systemstructure.jl
index f072dc3f52..06f8ccc639 100644
--- a/src/systems/systemstructure.jl
+++ b/src/systems/systemstructure.jl
@@ -897,6 +897,9 @@ function mtkcompile!(state::TearingState; simplify = false,
         inputs = Any[], outputs = Any[],
         disturbance_inputs = Any[],
         kwargs...)
+    # split_system returns one or two systems and the inputs for each
+    # mod clock inference to be binary
+    # if it's continous keep going, if not then error unless given trait impl in additional passes
     ci = ModelingToolkit.ClockInference(state)
     ci = ModelingToolkit.infer_clocks!(ci)
     time_domains = merge(Dict(state.fullvars .=> ci.var_domain),
@@ -910,7 +913,7 @@ function mtkcompile!(state::TearingState; simplify = false,
             discrete_pass_idx = findfirst(discrete_compile_pass, additional_passes)
             discrete_compile = additional_passes[discrete_pass_idx]
             deleteat!(additional_passes, discrete_pass_idx)
-            return discrete_compile(tss, clocked_inputs)
+            return discrete_compile(tss, clocked_inputs, ci)
         end
         throw(HybridSystemNotSupportedException("""
         Discrete systems with multiple clocks are not supported with the standard \
@@ -931,7 +934,7 @@ function mtkcompile!(state::TearingState; simplify = false,
             deleteat!(additional_passes, discrete_pass_idx)
             # in the case of a hybrid system, the discrete_compile pass should take the currents of sys.discrete_subsystems
             # and modifies discrete_subsystems to bea tuple of the io and anything else, while adding or manipulating the rest of sys as needed
-            return discrete_compile(sys, tss[2:end], inputs)
+            return discrete_compile(sys, tss[[i for i in eachindex(tss) if i != continuous_id]], clocked_inputs, ci)
         end
         throw(HybridSystemNotSupportedException("""
         Hybrid continuous-discrete systems are currently not supported with \

From 405aafabfba1af39bee6f81d6506f004c943dff4 Mon Sep 17 00:00:00 2001
From: Benjamin Chung <ckfinite@gmail.com>
Date: Wed, 14 May 2025 13:43:00 -0700
Subject: [PATCH 07/14] Change the external synchronous signature to include
 the id/clock map

---
 src/systems/systemstructure.jl | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/systems/systemstructure.jl b/src/systems/systemstructure.jl
index 06f8ccc639..66f3a4b6f9 100644
--- a/src/systems/systemstructure.jl
+++ b/src/systems/systemstructure.jl
@@ -934,7 +934,9 @@ function mtkcompile!(state::TearingState; simplify = false,
             deleteat!(additional_passes, discrete_pass_idx)
             # in the case of a hybrid system, the discrete_compile pass should take the currents of sys.discrete_subsystems
             # and modifies discrete_subsystems to bea tuple of the io and anything else, while adding or manipulating the rest of sys as needed
-            return discrete_compile(sys, tss[[i for i in eachindex(tss) if i != continuous_id]], clocked_inputs, ci)
+            return discrete_compile(
+                sys, tss[[i for i in eachindex(tss) if i != continuous_id]],
+                clocked_inputs, ci, id_to_clock)
         end
         throw(HybridSystemNotSupportedException("""
         Hybrid continuous-discrete systems are currently not supported with \

From 865523b33df9a36698879f85e7e68d32eb659623 Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Fri, 20 Jun 2025 17:15:07 +0530
Subject: [PATCH 08/14] feat: add `zero_crossing_id` to
 `SymbolicContinuousCallback`

---
 src/systems/callbacks.jl | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/src/systems/callbacks.jl b/src/systems/callbacks.jl
index a4f39243d9..f05e455cbc 100644
--- a/src/systems/callbacks.jl
+++ b/src/systems/callbacks.jl
@@ -165,6 +165,7 @@ struct SymbolicContinuousCallback <: AbstractCallback
     finalize::Union{Affect, Nothing}
     rootfind::Union{Nothing, SciMLBase.RootfindOpt}
     reinitializealg::SciMLBase.DAEInitializationAlgorithm
+    zero_crossing_id::Symbol
 
     function SymbolicContinuousCallback(
             conditions::Union{Equation, Vector{Equation}},
@@ -174,6 +175,7 @@ struct SymbolicContinuousCallback <: AbstractCallback
             finalize = nothing,
             rootfind = SciMLBase.LeftRootFind,
             reinitializealg = nothing,
+            zero_crossing_id = gensym(),
             kwargs...)
         conditions = (conditions isa AbstractVector) ? conditions : [conditions]
 
@@ -190,7 +192,7 @@ struct SymbolicContinuousCallback <: AbstractCallback
             make_affect(affect_neg; kwargs...),
             make_affect(initialize; kwargs...), make_affect(
                 finalize; kwargs...),
-            rootfind, reinitializealg)
+            rootfind, reinitializealg, zero_crossing_id)
     end # Default affect to nothing
 end
 
@@ -466,7 +468,8 @@ function namespace_callback(cb::SymbolicContinuousCallback, s)::SymbolicContinuo
         affect_neg = namespace_affects(affect_negs(cb), s),
         initialize = namespace_affects(initialize_affects(cb), s),
         finalize = namespace_affects(finalize_affects(cb), s),
-        rootfind = cb.rootfind, reinitializealg = cb.reinitializealg)
+        rootfind = cb.rootfind, reinitializealg = cb.reinitializealg,
+        zero_crossing_id = cb.zero_crossing_id)
 end
 
 function namespace_conditions(condition, s)
@@ -490,6 +493,8 @@ function Base.hash(cb::AbstractCallback, s::UInt)
     s = hash(finalize_affects(cb), s)
     !is_discrete(cb) && (s = hash(cb.rootfind, s))
     hash(cb.reinitializealg, s)
+    !is_discrete(cb) && (s = hash(cb.zero_crossing_id, s))
+    return s
 end
 
 ###########################
@@ -524,13 +529,16 @@ function finalize_affects(cbs::Vector{<:AbstractCallback})
 end
 
 function Base.:(==)(e1::AbstractCallback, e2::AbstractCallback)
-    (is_discrete(e1) === is_discrete(e2)) || return false
-    (isequal(e1.conditions, e2.conditions) && isequal(e1.affect, e2.affect) &&
-     isequal(e1.initialize, e2.initialize) && isequal(e1.finalize, e2.finalize)) &&
-        isequal(e1.reinitializealg, e2.reinitializealg) ||
-        return false
-    is_discrete(e1) ||
-        (isequal(e1.affect_neg, e2.affect_neg) && isequal(e1.rootfind, e2.rootfind))
+    is_discrete(e1) === is_discrete(e2) || return false
+    isequal(e1.conditions, e2.conditions) && isequal(e1.affect, e2.affect) || return false
+    isequal(e1.initialize, e2.initialize) || return false
+    isequal(e1.finalize, e2.finalize) || return false
+    isequal(e1.reinitializealg, e2.reinitializealg) || return false
+    if !is_discrete(e1)
+        isequal(e1.affect_neg, e2.affect_neg) || return false
+        isequal(e1.rootfind, e2.rootfind) || return false
+        isequal(e1.zero_crossing_id, e2.zero_crossing_id) || return false
+    end
 end
 
 Base.isempty(cb::AbstractCallback) = isempty(cb.conditions)

From aeefc8abcfd6c00170352459d55f132b6ecfba1a Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Fri, 20 Jun 2025 17:25:53 +0530
Subject: [PATCH 09/14] feat: add `ZeroCrossing` and `EventClock` from zero
 crossing

---
 src/discretedomain.jl | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/src/discretedomain.jl b/src/discretedomain.jl
index da8417de4e..370d93d894 100644
--- a/src/discretedomain.jl
+++ b/src/discretedomain.jl
@@ -365,3 +365,14 @@ function input_timedomain(x)
         throw(ArgumentError("$x of type $(typeof(x)) is not an operator expression"))
     end
 end
+
+function ZeroCrossing(expr; name = gensym(), up = true, down = true, kwargs...)
+    return SymbolicContinuousCallback(
+        [expr ~ 0], up ? ImperativeAffect(Returns(nothing)) : nothing;
+        affect_neg = down ? ImperativeAffect(Returns(nothing)) : nothing,
+        kwargs..., zero_crossing_id = name)
+end
+
+function SciMLBase.Clocks.EventClock(cb::SymbolicContinuousCallback)
+    return SciMLBase.Clocks.EventClock(cb.zero_crossing_id)
+end

From fbef1a8bd5f27080b8d40c1100c5eb30764b50e0 Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Fri, 27 Jun 2025 13:10:21 +0530
Subject: [PATCH 10/14] feat: subset variables appropriately in clock inference

---
 src/systems/clock_inference.jl |  4 ++--
 src/systems/systemstructure.jl | 30 +++++++++++++++++++++---------
 2 files changed, 23 insertions(+), 11 deletions(-)

diff --git a/src/systems/clock_inference.jl b/src/systems/clock_inference.jl
index 86fe7e85ac..ff2d77f19b 100644
--- a/src/systems/clock_inference.jl
+++ b/src/systems/clock_inference.jl
@@ -199,8 +199,8 @@ function split_system(ci::ClockInference{S}) where {S}
 
     # breaks the system up into a continous and 0 or more discrete systems
     tss = similar(cid_to_eq, S)
-    for (id, ieqs) in enumerate(cid_to_eq)
-        ts_i = system_subset(ts, ieqs)
+    for (id, (ieqs, ivars)) in enumerate(zip(cid_to_eq, cid_to_var))
+        ts_i = system_subset(ts, ieqs, ivars)
         if id != continuous_id
             ts_i = shift_discrete_system(ts_i)
             @set! ts_i.structure.only_discrete = true
diff --git a/src/systems/systemstructure.jl b/src/systems/systemstructure.jl
index 66f3a4b6f9..3a0e0584d3 100644
--- a/src/systems/systemstructure.jl
+++ b/src/systems/systemstructure.jl
@@ -218,12 +218,12 @@ mutable struct TearingState{T <: AbstractSystem} <: AbstractTearingState{T}
 end
 
 TransformationState(sys::AbstractSystem) = TearingState(sys)
-function system_subset(ts::TearingState, ieqs::Vector{Int})
+function system_subset(ts::TearingState, ieqs::Vector{Int}, ivars::Vector{Int})
     eqs = equations(ts)
     @set! ts.original_eqs = ts.original_eqs[ieqs]
     @set! ts.sys.eqs = eqs[ieqs]
     @set! ts.original_eqs = ts.original_eqs[ieqs]
-    @set! ts.structure = system_subset(ts.structure, ieqs)
+    @set! ts.structure = system_subset(ts.structure, ieqs, ivars)
     if all(eq -> eq.rhs isa StateMachineOperator, get_eqs(ts.sys))
         names = Symbol[]
         for eq in get_eqs(ts.sys)
@@ -240,22 +240,33 @@ function system_subset(ts::TearingState, ieqs::Vector{Int})
     else
         @set! ts.statemachines = eltype(ts.statemachines)[]
     end
+    @set! ts.fullvars = ts.fullvars[ivars]
     ts
 end
 
-function system_subset(structure::SystemStructure, ieqs::Vector{Int})
-    @unpack graph, eq_to_diff = structure
+function system_subset(structure::SystemStructure, ieqs::Vector{Int}, ivars::Vector{Int})
+    @unpack graph = structure
     fadj = Vector{Int}[]
     eq_to_diff = DiffGraph(length(ieqs))
+    var_to_diff = DiffGraph(length(ivars))
+
     ne = 0
+    old_to_new_var = zeros(Int, ndsts(graph))
+    for (i, iv) in enumerate(ivars)
+        old_to_new_var[iv] = i
+        structure.var_to_diff[iv] === nothing && continue
+        var_to_diff[i] = old_to_new_var[structure.var_to_diff[iv]]
+    end
     for (j, eq_i) in enumerate(ieqs)
-        ivars = copy(graph.fadjlist[eq_i])
-        ne += length(ivars)
-        push!(fadj, ivars)
+        var_adj = [old_to_new_var[i] for i in graph.fadjlist[eq_i]]
+        @assert all(!iszero, var_adj)
+        ne += length(var_adj)
+        push!(fadj, var_adj)
         eq_to_diff[j] = structure.eq_to_diff[eq_i]
     end
-    @set! structure.graph = complete(BipartiteGraph(ne, fadj, ndsts(graph)))
+    @set! structure.graph = complete(BipartiteGraph(ne, fadj, length(ivars)))
     @set! structure.eq_to_diff = eq_to_diff
+    @set! structure.var_to_diff = complete(var_to_diff)
     structure
 end
 
@@ -440,7 +451,8 @@ function TearingState(sys; quick_cancel = false, check = true, sort_eqs = true)
             isdelay(v, iv) && continue
 
             if !symbolic_contains(v, dvs)
-                isvalid = iscall(v) && (operation(v) isa Shift || is_transparent_operator(operation(v)))
+                isvalid = iscall(v) &&
+                          (operation(v) isa Shift || is_transparent_operator(operation(v)))
                 v′ = v
                 while !isvalid && iscall(v′) && operation(v′) isa Union{Differential, Shift}
                     v′ = arguments(v′)[1]

From ea917fc060bc6beb695c1a649302162565efa978 Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Fri, 27 Jun 2025 14:24:24 +0530
Subject: [PATCH 11/14] feat: add hook during problem construction

---
 src/systems/problem_utils.jl | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/systems/problem_utils.jl b/src/systems/problem_utils.jl
index ecba542fd0..a35b3b1663 100644
--- a/src/systems/problem_utils.jl
+++ b/src/systems/problem_utils.jl
@@ -1272,6 +1272,8 @@ function get_p_constructor(p_constructor, pType::Type, floatT::Type)
     end
 end
 
+abstract type ProblemConstructionHook end
+
 """
     $(TYPEDSIGNATURES)
 
@@ -1324,6 +1326,8 @@ function process_SciMLProblem(
 
     check_inputmap_keys(sys, op)
 
+    op = getmetadata(sys, ProblemConstructionHook, identity)(op)
+
     defs = add_toterms(recursive_unwrap(defaults(sys)); replace = is_discrete_system(sys))
     kwargs = NamedTuple(kwargs)
 

From 66d5b0760e382aebb7a8a04fcbbfca8449ce6c77 Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Mon, 7 Jul 2025 15:40:07 +0530
Subject: [PATCH 12/14] fixup! feat: retain original equations of the system in
 `TearingState`

---
 src/systems/systemstructure.jl | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/systems/systemstructure.jl b/src/systems/systemstructure.jl
index 3a0e0584d3..1a76fc88c0 100644
--- a/src/systems/systemstructure.jl
+++ b/src/systems/systemstructure.jl
@@ -220,7 +220,6 @@ end
 TransformationState(sys::AbstractSystem) = TearingState(sys)
 function system_subset(ts::TearingState, ieqs::Vector{Int}, ivars::Vector{Int})
     eqs = equations(ts)
-    @set! ts.original_eqs = ts.original_eqs[ieqs]
     @set! ts.sys.eqs = eqs[ieqs]
     @set! ts.original_eqs = ts.original_eqs[ieqs]
     @set! ts.structure = system_subset(ts.structure, ieqs, ivars)

From 6e6138087614d0341c9b4be9c7f2237ddd89ff2f Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Fri, 6 Jun 2025 15:22:42 +0530
Subject: [PATCH 13/14] fix: fix `get_mtkparameters_reconstructor` handling of
 nonnumerics

---
 src/systems/problem_utils.jl | 40 ++++++++++++++++++++++++++++--------
 1 file changed, 32 insertions(+), 8 deletions(-)

diff --git a/src/systems/problem_utils.jl b/src/systems/problem_utils.jl
index a35b3b1663..1f5c021a3b 100644
--- a/src/systems/problem_utils.jl
+++ b/src/systems/problem_utils.jl
@@ -711,7 +711,8 @@ end
     $(TYPEDEF)
 
 A callable struct which applies `p_constructor` to possibly nested arrays. It also
-ensures that views (including nested ones) are concretized.
+ensures that views (including nested ones) are concretized. This is implemented manually
+of using `narrow_buffer_type` to preserve type-stability.
 """
 struct PConstructorApplicator{F}
     p_constructor::F
@@ -721,10 +722,18 @@ function (pca::PConstructorApplicator)(x::AbstractArray)
     pca.p_constructor(x)
 end
 
+function (pca::PConstructorApplicator)(x::AbstractArray{Bool})
+    pca.p_constructor(BitArray(x))
+end
+
 function (pca::PConstructorApplicator{typeof(identity)})(x::SubArray)
     collect(x)
 end
 
+function (pca::PConstructorApplicator{typeof(identity)})(x::SubArray{Bool})
+    BitArray(x)
+end
+
 function (pca::PConstructorApplicator{typeof(identity)})(x::SubArray{<:AbstractArray})
     collect(pca.(x))
 end
@@ -749,6 +758,7 @@ takes a value provider of `srcsys` and a value provider of `dstsys` and returns
 """
 function get_mtkparameters_reconstructor(srcsys::AbstractSystem, dstsys::AbstractSystem;
         initials = false, unwrap_initials = false, p_constructor = identity)
+    _p_constructor = p_constructor
     p_constructor = PConstructorApplicator(p_constructor)
     # if we call `getu` on this (and it were able to handle empty tuples) we get the
     # fields of `MTKParameters` except caches.
@@ -802,14 +812,24 @@ function get_mtkparameters_reconstructor(srcsys::AbstractSystem, dstsys::Abstrac
         Base.Fix1(broadcast, p_constructor) ∘
         getu(srcsys, syms[3])
     end
-    rest_getters = map(Base.tail(Base.tail(Base.tail(syms)))) do buf
-        if buf == ()
-            return Returns(())
-        else
-            return Base.Fix1(broadcast, p_constructor) ∘ getu(srcsys, buf)
-        end
+    const_getter = if syms[4] == ()
+        Returns(())
+    else
+        Base.Fix1(broadcast, p_constructor) ∘ getu(srcsys, syms[4])
     end
-    getters = (tunable_getter, initials_getter, discs_getter, rest_getters...)
+    nonnumeric_getter = if syms[5] == ()
+        Returns(())
+    else
+        ic = get_index_cache(dstsys)
+        buftypes = Tuple(map(ic.nonnumeric_buffer_sizes) do bufsize
+            Vector{bufsize.type}
+        end)
+        # nonnumerics retain the assigned buffer type without narrowing
+        Base.Fix1(broadcast, _p_constructor) ∘
+        Base.Fix1(Broadcast.BroadcastFunction(call), buftypes) ∘ getu(srcsys, syms[5])
+    end
+    getters = (
+        tunable_getter, initials_getter, discs_getter, const_getter, nonnumeric_getter)
     getter = let getters = getters
         function _getter(valp, initprob)
             oldcache = parameter_values(initprob).caches
@@ -822,6 +842,10 @@ function get_mtkparameters_reconstructor(srcsys::AbstractSystem, dstsys::Abstrac
     return getter
 end
 
+function call(f, args...)
+    f(args...)
+end
+
 """
     $(TYPEDSIGNATURES)
 

From bcd21af0562582cdb8495453d8790fb902afb345 Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Fri, 6 Jun 2025 14:23:30 +0530
Subject: [PATCH 14/14] test: test nonnumerics aren't narrowed in `ODEProblem`
 and `init`

---
 test/initializationsystem.jl | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/test/initializationsystem.jl b/test/initializationsystem.jl
index 3be3e400c3..8f37ca905b 100644
--- a/test/initializationsystem.jl
+++ b/test/initializationsystem.jl
@@ -1670,3 +1670,23 @@ end
     prob = ODEProblem(sys, [x[1] => nothing, x[2] => 1], (0.0, 1.0))
     @test SciMLBase.initialization_status(prob) == SciMLBase.FULLY_DETERMINED
 end
+
+@testset "Nonnumerics aren't narrowed" begin
+    @mtkmodel Foo begin
+        @variables begin
+            x(t) = 1.0
+        end
+        @parameters begin
+            p::AbstractString
+            r = 1.0
+        end
+        @equations begin
+            D(x) ~ r * x
+        end
+    end
+    @mtkbuild sys = Foo(p = "a")
+    prob = ODEProblem(sys, [], (0.0, 1.0))
+    @test prob.p.nonnumeric[1] isa Vector{AbstractString}
+    integ = init(prob)
+    @test integ.p.nonnumeric[1] isa Vector{AbstractString}
+end