From 10b79ec111925f1236b15ce06fcad9fdc4419d0b Mon Sep 17 00:00:00 2001
From: slwu89 <slwu89@users.noreply.github.com>
Date: Mon, 28 Aug 2023 17:42:34 -0700
Subject: [PATCH 1/4] rebase onto main

---
 src/AlgebraicPetri.jl        | 22 ++++++++++++++-
 test/algebraicpetri/types.jl | 53 ++++++++++++++++++++++++++++++++++++
 2 files changed, 74 insertions(+), 1 deletion(-)

diff --git a/src/AlgebraicPetri.jl b/src/AlgebraicPetri.jl
index 743b769e..28ecba78 100644
--- a/src/AlgebraicPetri.jl
+++ b/src/AlgebraicPetri.jl
@@ -5,7 +5,7 @@ module AlgebraicPetri
 export SchPetriNet, PetriNet, OpenPetriNetOb, AbstractPetriNet,
   ns, nt, ni, no, os, ot, is, it,
   add_species!, add_transition!, add_transitions!,
-  add_input!, add_inputs!, add_output!, add_outputs!, inputs, outputs,
+  add_input!, add_inputs!, add_output!, add_outputs!, inputs, outputs, induced_subnet,
   TransitionMatrices, vectorfield, vectorfield_expr, flatten_labels,
   SchLabelledPetriNet, LabelledPetriNet, AbstractLabelledPetriNet, sname, tname, snames, tnames,
   SchReactionNet, ReactionNet, AbstractReactionNet, concentration, concentrations, rate, rates,
@@ -272,6 +272,26 @@ inputs(p::AbstractPetriNet, t) = subpart(p, incident(p, t, :it), :is)
 """
 outputs(p::AbstractPetriNet, t) = subpart(p, incident(p, t, :ot), :os)
 
+""" induced_subnet(p::T, t)
+
+Return the induced subnet consisting of the transition `t`, all input
+places and input arcs, and all output places and output arcs. The returned
+object will be of the same type as `p`.
+"""
+function induced_subnet(p::T, t) where {T <: AbstractPetriNet}
+  @assert t ∈ parts(p, :T)
+
+  input_arcs = incident(p, t, :it)
+  output_arcs = incident(p, t, :ot)
+
+  input_places = subpart(p, input_arcs, :is)
+  output_places = subpart(p, output_arcs, :os)
+
+  subnet = T()
+  copy_parts!(subnet, p, T=t, I=input_arcs, O=output_arcs, S=union(input_places, output_places))
+  return subnet
+end
+
 valueat(x::Number, u, t) = x
 valueat(f::Function, u, t) =
   try
diff --git a/test/algebraicpetri/types.jl b/test/algebraicpetri/types.jl
index 441a8f63..568c0451 100644
--- a/test/algebraicpetri/types.jl
+++ b/test/algebraicpetri/types.jl
@@ -176,4 +176,57 @@ for p in [sir_proplpetri, sir_proplrxn]
   @test Open(p, [:S], [:I], [:R]) == Open(p)
 end
 
+# test subnet for each type of net
+for net in [sir_petri, sir_rxn]
+  si_net = induced_subnet(net, 1)
+
+  @test ns(si_net) == 2
+  @test nt(si_net) == 1
+  @test is(si_net) == [1,2]
+  @test os(si_net) == [2,2]
+  
+  r_net = induced_subnet(net, 2)
+  
+  @test ns(r_net) == 2
+  @test nt(r_net) == 1
+  @test is(r_net) == [1]
+  @test os(r_net) == [2]
+end
+
+for net in [sir_lpetri, sir_lrxn]
+  si_net = induced_subnet(sir_lpetri, 1)
+
+  @test ns(si_net) == 2
+  @test nt(si_net) == 1
+  @test is(si_net) == [1,2]
+  @test os(si_net) == [2,2]
+  @test only(si_net[:tname]) == :inf
+  @test si_net[:sname] == [:S,:I]
+  
+  r_net = induced_subnet(sir_lpetri, 2)
+  
+  @test ns(r_net) == 2
+  @test nt(r_net) == 1
+  @test is(r_net) == [1]
+  @test os(r_net) == [2]
+  @test only(r_net[:tname]) == :rec
+  @test r_net[:sname] == [:I,:R]  
+end
+
+sir_net = induced_subnet(sir_petri, [1,2])
+sir_net == sir_petri
+
+test_petri = PetriNet(
+  6,
+  1 => (3,4),
+  1 => 2,
+  5 => 6
+)
+
+test_net = induced_subnet(test_petri, [1,2])
+@test ns(test_net) == 4
+@test nt(test_net) == 2
+@test is(test_net) == [1,1]
+@test os(test_net) == [2,3,4]
+
 end

From 93faedf0114ab8644ce2c62c34da758ec35be941 Mon Sep 17 00:00:00 2001
From: slwu89 <10673535+slwu89@users.noreply.github.com>
Date: Mon, 27 Mar 2023 18:48:05 -0700
Subject: [PATCH 2/4] generalize subnet to any number of transitions; add tests

---
 src/AlgebraicPetri.jl | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/AlgebraicPetri.jl b/src/AlgebraicPetri.jl
index 28ecba78..67dd9e1b 100644
--- a/src/AlgebraicPetri.jl
+++ b/src/AlgebraicPetri.jl
@@ -279,16 +279,20 @@ places and input arcs, and all output places and output arcs. The returned
 object will be of the same type as `p`.
 """
 function induced_subnet(p::T, t) where {T <: AbstractPetriNet}
-  @assert t ∈ parts(p, :T)
+  induced_subnet(p, [t])
+end
+
+function induced_subnet(p::T, t::AbstractVector{Int}) where {T <: AbstractPetriNet}
+  @assert all([tt ∈ parts(p,:T) for tt in t])
 
   input_arcs = incident(p, t, :it)
   output_arcs = incident(p, t, :ot)
 
-  input_places = subpart(p, input_arcs, :is)
-  output_places = subpart(p, output_arcs, :os)
+  input_places = [subpart(p, input_i, :is) for input_i in input_arcs]
+  output_places = [subpart(p, output_i, :os) for output_i in output_arcs]
 
   subnet = T()
-  copy_parts!(subnet, p, T=t, I=input_arcs, O=output_arcs, S=union(input_places, output_places))
+  copy_parts!(subnet, p, T=t, I=vcat(input_arcs...), O=vcat(output_arcs...), S=union(input_places..., output_places...))
   return subnet
 end
 

From ea215165dd5abdc8b39298097cb391be17fdf41f Mon Sep 17 00:00:00 2001
From: slwu89 <10673535+slwu89@users.noreply.github.com>
Date: Mon, 27 Mar 2023 18:49:07 -0700
Subject: [PATCH 3/4] clarify docstring

---
 src/AlgebraicPetri.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/AlgebraicPetri.jl b/src/AlgebraicPetri.jl
index 67dd9e1b..6642af7c 100644
--- a/src/AlgebraicPetri.jl
+++ b/src/AlgebraicPetri.jl
@@ -274,7 +274,7 @@ outputs(p::AbstractPetriNet, t) = subpart(p, incident(p, t, :ot), :os)
 
 """ induced_subnet(p::T, t)
 
-Return the induced subnet consisting of the transition `t`, all input
+Return the induced subnet consisting of the transition(s) in `t`, all input
 places and input arcs, and all output places and output arcs. The returned
 object will be of the same type as `p`.
 """

From 13f861832f82eba46016c5eeae0be92f307bde0f Mon Sep 17 00:00:00 2001
From: slwu89 <slwu89@users.noreply.github.com>
Date: Sat, 4 May 2024 16:16:08 -0700
Subject: [PATCH 4/4] use subobj interface

---
 src/AlgebraicPetri.jl        | 13 ++-----------
 test/algebraicpetri/types.jl |  4 ++--
 2 files changed, 4 insertions(+), 13 deletions(-)

diff --git a/src/AlgebraicPetri.jl b/src/AlgebraicPetri.jl
index 6642af7c..e050e6f2 100644
--- a/src/AlgebraicPetri.jl
+++ b/src/AlgebraicPetri.jl
@@ -283,17 +283,8 @@ function induced_subnet(p::T, t) where {T <: AbstractPetriNet}
 end
 
 function induced_subnet(p::T, t::AbstractVector{Int}) where {T <: AbstractPetriNet}
-  @assert all([tt ∈ parts(p,:T) for tt in t])
-
-  input_arcs = incident(p, t, :it)
-  output_arcs = incident(p, t, :ot)
-
-  input_places = [subpart(p, input_i, :is) for input_i in input_arcs]
-  output_places = [subpart(p, output_i, :os) for output_i in output_arcs]
-
-  subnet = T()
-  copy_parts!(subnet, p, T=t, I=vcat(input_arcs...), O=vcat(output_arcs...), S=union(input_places..., output_places...))
-  return subnet
+  subnet = Subobject(p, T=t)
+  return dom(hom(~(¬subnet)))
 end
 
 valueat(x::Number, u, t) = x
diff --git a/test/algebraicpetri/types.jl b/test/algebraicpetri/types.jl
index 568c0451..f477097b 100644
--- a/test/algebraicpetri/types.jl
+++ b/test/algebraicpetri/types.jl
@@ -226,7 +226,7 @@ test_petri = PetriNet(
 test_net = induced_subnet(test_petri, [1,2])
 @test ns(test_net) == 4
 @test nt(test_net) == 2
-@test is(test_net) == [1,1]
-@test os(test_net) == [2,3,4]
+@test ni(test_net) == 2
+@test no(test_net) == 3
 
 end