add an pertussis model example runnable with AlgebraicABMs.jl

also add a few help functions in StateCharts.jl

.gitignore

@@ -27,3 +27,5 @@ Manifest.toml
 .DS_Store
 .vscode
 .ipynb_checkpoints
+
+cache/

docs/Project.toml

@@ -1,4 +1,7 @@
 [deps]
-StateCharts = "BFC335C0-D564-425B-98AA-D5C699C8B7AB"
+AlgebraicABMs = "5a5e3447-9604-46e6-8d91-cb86f5f51721"
+AlgebraicRewriting = "725a01d3-f174-5bbd-84e1-b9417bad95d9"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Fleck = "5bb9b785-358c-4fee-af0f-b94a146244a8"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+StateCharts = "bfc335c0-d564-425b-98aa-d5c699c8b7ab"

docs/literate/pertussis_Hethcote_model_with_run_AlgebraicABMs.jl

@@ -0,0 +1,129 @@
+using StateCharts
+using AlgebraicABMs, AlgebraicRewriting, Catlab
+using Fleck
+using Random
+import AlgebraicRewriting.Incremental.IncrementalSum: IncSumHomSet
+ENV["JULIA_DEBUG"] = "AlgebraicABMs"; 
+
+############################################## the interface functions ####################################################
+## Functions in this section are all included in the file "StateChartsInterface.jl", but this file is not #################
+## usable yet .After the extension dependency of "StateCharts.jl" registered, just delete these functions #################
+## in this section.                                                                                       #################
+###########################################################################################################################
+const DST = :TimeOut # the transtition type for discrete hazard
+const CTT = :Rate # the transtition type for continueous hazard
+const RLT = :Pattern # the transtition type for user defined rewrite rule
+
+""" automatically generate the ABM model schema from the state chart. This schema contains one object, and the name of this object is given by the input 
+argument: obn::Symbol. And each unit state chart (with one entrance transition) contributes one attributes of the object "obn" in the schema
+
+"""
+
+function StateChartCset_SingleObject(ss::AbstractStateChart,obn::Symbol=:P)
+    attrsType = enames(ss) # the attributes' type is the name of each unit state chart
+    obns = repeat([obn], length(attrsType))
+    attrs = map((x,y)->Symbol(String(x)*String(y)),obns,attrsType) # define the name of the map from the object "obn" to each attribute type
+    attrsTuple = map((x,y,z)->(x,y,z),attrs,obns,attrsType)
+    schema = BasicSchema([obn], [], attrsType, attrsTuple)
+    tp_asgn = Dict(zip(attrsType,repeat([Symbol], length(attrsType))))
+    acset = AnonACSet(schema;type_assignment=tp_asgn)
+    acset
+end
+
+function StateChartCset_MultipleObject(ss::AbstractStateChart)   
+end
+
+function make_infectious_rule(ss::AbstractStateChart;make_acset::Function=StateChartCset_SingleObject,r::Symbol=:I,obn::Symbol=:P)
+    Lᵢ,Iᵢ,Rᵢ = [make_acset(ss,obn) for _ in 1:3]
+    # return the attribute names 
+    ## TODO: need to make "attrn" support multiple unit state chart, this needs to extend the 
+    ## schema of the state charts
+    attrn = attrs(acset_schema(Lᵢ);just_names=true)[1]
+    add_parts!(Lᵢ,obn,2;attrn=>[:S,:I])
+    add_part!(Iᵢ,obn;attrn=>:I)
+    add_parts!(Rᵢ,obn,2;attrn=>[r,:I])
+    Rule(homomorphism(Iᵢ,Lᵢ),homomorphism(Iᵢ,Rᵢ)) 
+end
+
+# currently, suppose we only have one unit state chart
+# TODO: make it support multiple unit state charts
+# generate the rewrite rule
+# t is the index of a transition
+# transitions_rules is an array with pair of (timer, rule) as its elements
+function get_rule(ss::AbstractStateChart,t,transitions_rules,obn::Symbol=:P)
+    tt = ttype(ss,t)
+    if tt == RLT
+        tidx=Int(texpr(ss,t))
+        rule = transitions_rules[tidx][2]
+    elseif tt in [DST, CTT]
+        L,I,R = LIR = [StateChartCset_SingleObject(ss,obn) for _ in 1:3]
+        # return the attribute names 
+        ## TODO: need to make "attrn" and "attrt" support multiple unit state chart, this needs to extend the 
+        ## schema of the state charts
+        attrn = attrs(acset_schema(L);just_names=true)[1]
+        attrt = attrtypes(acset_schema(L))[1]
+        add_part!(L,obn;attrn=>sname(ss,tsource(ss,t)))
+        add_part!(I,obn;attrn=>AttrVar(add_part!(I,attrt)))
+        add_part!(R,obn;attrn=>sname(ss,ttarget(ss,t)))
+        rule = Rule(homomorphism(I,L),homomorphism(I,R))  
+    else
+        tn = tname(ss,t)
+        throw("transition:$tn does not have valid transition type!")
+    end
+end
+
+function get_timer(ss::AbstractStateChart,t,obn::Symbol=:P)
+    tt=ttype(ss,t)
+    if tt == DST
+        timeout = texpr(ss,t)
+        timer = DiscreteHazard(timeout)
+    elseif tt == CTT
+        r = texpr(ss,t)
+        timer = ContinuousHazard(1/r)
+    elseif tt == RLT
+        tidx=Int(texpr(ss,t))
+        timer = transitions_rules[tidx][1]
+    else
+        tn = tname(ss,t)
+        throw("transition:$tn does not have valid transition type!")
+    end
+    timer
+end
+
+function make_ABM(ss::AbstractStateChart) 
+    return ABM(map(parts(ss, :T)) do t
+        tn = tname(ss, t)
+        ABMRule(tn, get_rule(ss, t,transitions_rules), get_timer(ss,t))
+    end, [])
+end
+
+#############################################################################################
+######################### end of the dependency function part ###############################
+
+
+### example code starts here ###
+
+totalPopulation=10.0
+β = 0.001
+
+# create the pertussis state chart
+pertussis = StateChartF((:S,:E,:I,:R₄,:V₄), # states
+(:newExposure=>(:S=>:E,:Pattern=>1),:becomingInfective=>(:E=>:I,:TimeOut=>5.0),:recovery=>(:I=>:R₄,:Rate=>1.0/21.0),:vaccinated=>(:S=>:V₄,:Rate=>0.01)), #non-start transitions
+(), # alternatives for non-start transitions
+(:PertussisStateChart=>:S), # start transitions
+(:PertussisStateChart=>((:initialInfective,1.0/totalPopulation)=>:I)) # alternatives for start transitions
+)
+
+StateCharts.Graph(pertussis)
+
+# define the new_infectious rule
+transitions_rules=[(ContinuousHazard(1/β),make_infectious_rule(pertussis,r=:E))]
+
+# Initial state
+init = StateChartCset_SingleObject(pertussis)
+add_parts!(init,:P,Int(totalPopulation-1),PPertussisStateChart=:S)
+add_part!(init,:P,PPertussisStateChart=:I)
+
+res = run!(make_ABM(pertussis), init; maxtime=20);
+
+#Makie.plot(res; Dict(o=>X->nparts(X,o) for o in [:S,:I])...)

src/StateCharts.jl

@@ -2,7 +2,10 @@
 """
 module StateCharts
 
-export StateChartF, Graph
+export StateChartF, TheoryStateChart, AbstractStateChart, StateChart,
+ns, nt, ne, neal, nal, sname, snames, tname, tnames, ename, enames, eaname, eanames, aname, anames, texpr,
+ttype, ealsource, ealsources, ealtarget, ealtargets, tsource, ttarget, etarget, alsource, alsources, altarget, altargets, 
+Graph
 
 using Catlab
 
@@ -175,6 +178,8 @@ alsources(ss::AbstractStateChart) = [alsource(ss, al) for al in 1:nal(ss)]
 altarget(ss::AbstractStateChart,al) = subpart(ss,al,:abt) 
 altargets(ss::AbstractStateChart) = [altarget(ss, al) for al in 1:nal(ss)]
 
+texpr(ss::AbstractStateChart,t) = subpart(ss,t,:texpr) 
+
 # visualization
 TTYPE=Dict(:Rate=>"📉", :TimeOut=>"⏰", :Conditional=>"❓", :Pattern=>"🚩")
 # for Pattern, it indicates pattern match. User will provide the pattern match rule, and the state chart schema structure only