From a17dac529db8d96b853752b36ed9782c50254178 Mon Sep 17 00:00:00 2001
From: Micah Halter <micah.halter@gtri.gatech.edu>
Date: Fri, 18 Sep 2020 08:52:53 -0400
Subject: [PATCH] Road to 100% Code Coverage (#19)

* Added a couple more tests to make up for missing code coverage

* Added test for base iterate

* Added some more tests

* Added some more tests

* last test addition

* Version bump
---
 Project.toml  |  2 +-
 src/Types.jl  |  1 -
 test/types.jl | 38 +++++++++++++++++++++++++++++++++-----
 3 files changed, 34 insertions(+), 7 deletions(-)

diff --git a/Project.toml b/Project.toml
index 0b691a8..c3e7019 100644
--- a/Project.toml
+++ b/Project.toml
@@ -2,7 +2,7 @@ name = "AlgebraicPetri"
 uuid = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
 license = "MIT"
 authors = ["Micah Halter <micah@mehalter.com>"]
-version = "0.4.0"
+version = "0.4.1"
 
 [deps]
 AutoHashEquals = "15f4f7f2-30c1-5605-9d31-71845cf9641f"
diff --git a/src/Types.jl b/src/Types.jl
index d7101ca..f1d148d 100644
--- a/src/Types.jl
+++ b/src/Types.jl
@@ -213,7 +213,6 @@ sname(p::Union{AbstractLabelledPetriNet, AbstractLabelledReactionNet},s) = subpa
 tname(p::Union{AbstractLabelledPetriNet, AbstractLabelledReactionNet},t) = subpart(p,t,:tname)
 
 vectorfield(pn::Union{AbstractLabelledPetriNet,AbstractLabelledReactionNet}) = begin
-  println("HELLO")
   tm = TransitionMatrices(pn)
   dt_T = transpose(tm.output - tm.input)
   f(du,u,p,t) = begin
diff --git a/test/types.jl b/test/types.jl
index 29f0827..73520d4 100644
--- a/test/types.jl
+++ b/test/types.jl
@@ -1,19 +1,47 @@
 sir_petri = PetriNet(3, ((1, 2), (2, 2)), (2, 3))
 sir_lpetri = LabelledPetriNet([:S, :I, :R], :inf=>((:S, :I), (:I, :I)), :rec=>(:I, :R))
-sir_rxn = ReactionNet{Number, Int}([990, 10, 0], (.0001)=>((1, 2)=>(2,2)), (.25)=>(2=>3))
-sir_lrxn = LabelledReactionNet{Number, Int}((:S=>990, :I=>10, :R=>0), (:inf, .0001)=>((:S, :I)=>(:I,:I)), (:rec, .25)=>(:I=>:R))
+β(u,t) = 1 / sum(u)
+γ = .25
+sir_rxn = ReactionNet{Function, Int}([990, 10, 0], (β)=>((1, 2)=>(2,2)), (t->γ)=>(2=>3))
+sir_lrxn = LabelledReactionNet{Number, Int}((:S=>990, :I=>10, :R=>0), (:inf, .001)=>((:S, :I)=>(:I,:I)), (:rec, .25)=>(:I=>:R))
 
 sir_tpetri= PetriNet(TransitionMatrices(sir_petri))
 
+next = iterate(PetriCospanOb(5))
+while next !== nothing
+    (i, state) = next
+    @test i == state && i <= 5
+    global next = iterate(PetriCospanOb(5), state)
+end
+
+pf = id(PetriFunctor)
+@test pf.F(FinSet(3))(sir_petri)
+@test !(pf.F(FinSet(5))(sir_petri))
+
 @test sir_tpetri == sir_petri
 @test Petri.Model(sir_petri) == Petri.Model(sir_rxn)
 @test Petri.Model(sir_lpetri) == Petri.Model(sir_lrxn)
 
+@test concentration(sir_rxn, 1) == 990
+@test rate(sir_rxn, 1) == β
+
 @test concentrations(sir_rxn) == [990, 10, 0]
-@test rates(sir_rxn) == [.0001, .25]
+@test typeof(rates(sir_rxn)) <: Array{Function}
 
 @test concentrations(sir_lrxn) == LVector(S=990, I=10, R=0)
-@test rates(sir_lrxn) == LVector(inf=.0001, rec=.25)
+@test rates(sir_lrxn) == LVector(inf=.001, rec=.25)
+
+du = [0.0, 0.0, 0.0]
+out = vectorfield(sir_rxn)(du, concentrations(sir_rxn), rates(sir_rxn), 0.01)
+@test out[1] ≈ -9.9
+@test out[2] ≈ 7.4
+@test out[3] ≈ 2.5
+
+du = LVector(S=0.0, I=0.0, R=0.0)
+out = vectorfield(sir_lrxn)(du, concentrations(sir_lrxn), rates(sir_lrxn), 0.01)
+@test out.S ≈ -9.9
+@test out.I ≈ 7.4
+@test out.R ≈ 2.5
 
 @test ns(sir_petri) == 3
 add_species!(sir_petri)
@@ -31,4 +59,4 @@ add_input!(sir_petri, 4, 4)
 add_output!(sir_petri, 4, 3)
 @test ni(sir_petri) == 5
 @test no(sir_petri) == 5
-@test sir_petri == PetriNet(4, ((1, 2), (2, 2)), (2, 3), (1, 4), (4, 3))
+@test sir_petri == PetriNet(4, ((1, 2), (2, 2)), (2, 3), (1, 4), (4, 3))
\ No newline at end of file