fix plotting, solution, log

Signed-off-by: Bíma, Jan <jan.bima@merck.com>

src/ReactiveDynamics.jl

@@ -74,7 +74,7 @@ end
 
 @acset_type FoldedReactionNetworkType(TheoryReactionNetwork)
 
-const ReactionNetwork = FoldedReactionNetworkType{
+const ReactionNetworkSchema = FoldedReactionNetworkType{
     Symbol,
     Union{String,Symbol,Missing},
     SampleableValues,
@@ -131,11 +131,11 @@ defargs = Dict(
 )
 
 compilable_attrs =
-    filter(attr -> eltype(attr) == SampleableValues, propertynames(ReactionNetwork()))
+    filter(attr -> eltype(attr) == SampleableValues, propertynames(ReactionNetworkSchema()))
 
 species_modalities = [:nonblock, :conserved, :rate]
 
-function assign_defaults!(acs::ReactionNetwork)
+function assign_defaults!(acs::ReactionNetworkSchema)
     for (_, v_) in defargs, (k, v) in v_
         for i = 1:length(subpart(acs, k))
             isnothing(acs[i, k]) && (subpart(acs, k)[i] = v)
@@ -160,12 +160,12 @@ function assign_defaults!(acs::ReactionNetwork)
     return acs
 end
 
-function ReactionNetwork(transitions, reactants, obs, events)
-    return merge_acs!(ReactionNetwork(), transitions, reactants, obs, events)
+function ReactionNetworkSchema(transitions, reactants, obs, events)
+    return merge_acs!(ReactionNetworkSchema(), transitions, reactants, obs, events)
 end
 
-function ReactionNetwork(transitions, reactants, obs)
-    return merge_acs!(ReactionNetwork(), transitions, reactants, obs, [])
+function ReactionNetworkSchema(transitions, reactants, obs)
+    return merge_acs!(ReactionNetworkSchema(), transitions, reactants, obs, [])
 end
 
 function add_obs!(acs, obs)
@@ -194,7 +194,7 @@ function add_obs!(acs, obs)
     return acs
 end
 
-function merge_acs!(acs::ReactionNetwork, transitions, reactants, obs, events)
+function merge_acs!(acs::ReactionNetworkSchema, transitions, reactants, obs, events)
     foreach(
         t -> add_part!(acs, :T; trans = t[1][2], transRate = t[1][1], t[2]...),
         transitions,

src/compilers.jl

@@ -112,12 +112,12 @@ function wrap_expr(fex, species_names, prm_names, varmap)
     )
     push!(letex.args[2].args, fex)
 
-    # the function shall be a function of the dynamic ReactiveNetwork structure: letex -> :(state -> $letex)
+    # the function shall be a function of the dynamic ReactionNetworkSchema structure: letex -> :(state -> $letex)
     # eval the expression to a Julia function, save that function into the "compiled" acset
     return eval(:(state -> $letex))
 end
 
-function get_wrap_fun(acs::ReactionNetwork)
+function get_wrap_fun(acs::ReactionNetworkSchema)
     species_names = collect(acs[:, :specName])
     prm_names = collect(acs[:, :prmName])
     varmap = Dict([name => :(state.u[$i]) for (i, name) in enumerate(species_names)])
@@ -133,7 +133,7 @@ function skip_compile(attr)
            (string(attr) == "trans")
 end
 
-function compile_attrs(acs::ReactionNetwork)
+function compile_attrs(acs::ReactionNetworkSchema)
     species_names = collect(acs[:, :specName])
     prm_names = collect(acs[:, :prmName])
     varmap = Dict([name => :(state.u[$i]) for (i, name) in enumerate(species_names)])
@@ -169,7 +169,7 @@ function compile_attrs(acs::ReactionNetwork)
     return attrs, transitions, wrap_fun
 end
 
-function remove_choose(acs::ReactionNetwork)
+function remove_choose(acs::ReactionNetworkSchema)
     acs = deepcopy(acs)
     pcs = []
     for attr in propertynames(acs.subparts)

src/interface/create.jl

@@ -1,6 +1,6 @@
 # reaction network DSL: CREATE part; reaction line and event parsing 
 
-export @ReactionNetwork
+export @ReactionNetworkSchema
 
 using MacroTools: prewalk, postwalk, striplines, isexpr
 using Symbolics: build_function, get_variables
@@ -45,7 +45,7 @@ Custom functions and sampleable objects can be used as numeric parameters. Note
 # Examples
 
 ```julia
-acs = @ReactionNetwork begin
+acs = @ReactionNetworkSchema begin
     1.0, X ⟶ Y
     1.0, X ⟶ Y, priority => 6.0, prob => 0.7, capacity => 3.0
     1.0, ∅ --> (Poisson(0.3γ)X, Poisson(0.5)Y)
@@ -57,17 +57,17 @@ end
 @solve_and_plot acs
 ```
 """
-macro ReactionNetwork end
+macro ReactionNetworkSchema end
 
-macro ReactionNetwork()
+macro ReactionNetworkSchema()
     return make_ReactionNetwork(:())
 end
 
-macro ReactionNetwork(ex)
+macro ReactionNetworkSchema(ex)
     return make_ReactionNetwork(ex; eval_module = __module__)
 end
 
-macro ReactionNetwork(ex, args...)
+macro ReactionNetworkSchema(ex, args...)
     return make_ReactionNetwork(
         generate(Expr(:braces, ex, args...); eval_module = __module__);
         eval_module = __module__,
@@ -78,7 +78,7 @@ function make_ReactionNetwork(ex::Expr; eval_module = @__MODULE__)
     blockex = generate(ex; eval_module)
     blockex = unblock_shallow!(blockex)
 
-    return :(ReactionNetwork(get_data($(QuoteNode(blockex)))...))
+    return :(ReactionNetworkSchema(get_data($(QuoteNode(blockex)))...))
 end
 
 ### Functions that process the input and rephrase it as a reaction system ###

src/interface/plots.jl

@@ -0,0 +1,19 @@
+using Plots
+
+function plot_df(df::DataFrames.DataFrame, t_ix = 1)
+    data = Matrix(df)
+    t = @view data[:, t_ix]
+    data_ = @view data[:, setdiff(1:size(data, 2), (t_ix,))]
+    colnames = reshape(DataFrames.names(df)[setdiff(1:size(data, 2), (t_ix,))], 1, :)
+
+    Plots.plot(t, data_, labels = colnames, xlabel = "t")
+end
+
+# plot reduction
+function AlgebraicAgents._draw(prob::ReactionNetworkProblem, vars = string.(prob.acs[:, :specName]); kwargs...)
+    p = plot()
+    for var in vars
+        p = plot!(p, prob.sol[!, "t"], prob.sol[!, var]; label="$var", xlabel="time", ylabel="quantity", kwargs...)
+    end
+    p
+end

src/interface/reaction_parser.jl

@@ -29,7 +29,7 @@ function recursively_choose(r_line, state)
     end
 end
 
-function extract_reactants(r_line, state::ReactiveNetwork)
+function extract_reactants(r_line, state::ReactionNetworkProblem)
     r_line = recursively_choose(r_line, state)
 
     return recursive_find_reactants!(

src/interface/solve.jl

@@ -1,56 +1,8 @@
-export @agentize, @solve, @plot
-export @optimize, @fit, @fit_and_plot, @build_solver
+export @agentize
 
 import MacroTools
 import Plots
 
-"""
-Convert a model to a `ReactiveNetwork`. If passed a problem instance, return the instance.
-
-# Examples
-
-```julia
-@agentize acs tspan = 1:100
-```
-"""
-macro agentize(acsex, args...)
-    args, kwargs = args_kwargs(args)
-    quote
-        if $(esc(acsex)) isa ReactiveNetwork
-            $(esc(acsex))
-        else
-            ReactiveNetwork($(esc(acsex)), $(args...); $(kwargs...))
-        end
-    end
-end
-
-"""
-Solve the problem. Solverargs passed at the calltime take precedence.
-
-# Examples
-
-```julia
-@solve prob
-@solve prob tspan = 1:100
-@solve prob tspan = 100
-```
-"""
-macro solve(probex, args...)
-    args, kwargs = args_kwargs(args)
-    mode = find_kwargex_delete!(kwargs, :mode, nothing)
-    !isnothing(findfirst(el -> el.args[1] == :trajectories, kwargs)) && (mode = :ensemble)
-
-    quote
-        prob = if $(esc(probex)) isa ReactiveNetwork
-            $(esc(probex))
-        else
-            ReactiveNetwork($(esc(probex)), $(args...); $(kwargs...))
-        end
-
-        simulate(prob)
-    end
-end
-
 # auxiliary plotting functions
 function plot_summary(s, labels, ixs; kwargs...)
     isempty(ixs) && return @warn "Set of species to plot must be non-empty!"

src/loadsave.jl

@@ -16,15 +16,15 @@ const objects_aliases = Dict(
     :obs => "obs",
 )
 
-const RN_attrs = string.(propertynames(ReactionNetwork().subparts))
+const RN_attrs = string.(propertynames(ReactionNetworkSchema().subparts))
 
 function get_attrs(object)
     object = object isa Symbol ? objects_aliases[object] : object
 
     return filter(x -> occursin(object, x), RN_attrs)
 end
 
-function export_network(acs::ReactionNetwork)
+function export_network(acs::ReactionNetworkSchema)
     dict = Dict()
     for (key, val) in objects_aliases
         push!(dict, val => [])
@@ -113,7 +113,7 @@ function import_network(path::AbstractString)
     end
 end
 
-function export_network(acs::ReactionNetwork, path::AbstractString)
+function export_network(acs::ReactionNetworkSchema, path::AbstractString)
     if splitext(path)[2] == ".csv"
         exported_network = export_network(acs)
         paths = DataFrame(; type = [], path = [])

src/operators/equalize.jl

@@ -21,7 +21,7 @@ function get_eqs_ff(eq)
     end
 end
 
-function equalize!(acs::ReactionNetwork, eqs = [])
+function equalize!(acs::ReactionNetworkSchema, eqs = [])
     specmap = Dict()
     for block in eqs
         block_alias = findfirst(e -> e[1] == :alias, block)

src/operators/joins.jl

@@ -59,7 +59,7 @@ end
 """
 Prepend species names with a model identifier (unless a global species name).
 """
-function prepend!(acs::ReactionNetwork, name = gensym("acs"), eqs = [])
+function prepend!(acs::ReactionNetworkSchema, name = gensym("acs"), eqs = [])
     specmap = Dict()
     for i = 1:nparts(acs, :S)
         new_name = normalize_name(name, i, acs[i, :specName], eqs)
@@ -199,7 +199,7 @@ Model variables / parameter values and metadata are propagated; the last model t
 macro join(exs...)
     callex = :(
         begin
-            acs_new = ReactionNetwork()
+            acs_new = ReactionNetworkSchema()
         end
     )
     exs = collect(exs)