Merge pull request #1006 from isaacsas/long_jump_plotting_fix

Long jump plotting fix

docs/src/api.md

@@ -68,11 +68,12 @@ jumpsys = convert(JumpSystem, rs)
 jumpsys = complete(jumpsys)
 u₀map    = [S => 999, I => 1, R => 0]
 dprob = DiscreteProblem(jumpsys, u₀map, tspan, parammap)
-jprob = JumpProblem(jumpsys, dprob, Direct(); save_positions = (false,false))
-sol = solve(jprob, SSAStepper(), saveat = 2.0)
+jprob = JumpProblem(jumpsys, dprob, Direct())
+sol = solve(jprob, SSAStepper())
+sol = solve(jprob, SSAStepper(), seed = 1234) # hide
 p3 = plot(sol, title = "jump")
-
 plot(p1, p2, p3; layout = (3,1))
+Catalyst.PNG(plot(p1, p2, p3; layout = (3,1), fmt = :png, dpi = 200)) # hide
 ```
 
 ```@docs
@@ -85,19 +86,19 @@ ReactionSystem
 ```
 
 ## [Options for the `@reaction_network` DSL](@id api_dsl_options)
-We have [previously described](@ref dsl_advanced_options) how options permits the user to supply non-reaction information to [`ReactionSystem`](@ref) created through the DSL. Here follows a list 
+We have [previously described](@ref dsl_advanced_options) how options permits the user to supply non-reaction information to [`ReactionSystem`](@ref) created through the DSL. Here follows a list
 of all options currently available.
-- [`parameters`]:(@ref dsl_advanced_options_declaring_species_and_parameters) Allows the designation of a set of symbols as system parameter. 
+- [`parameters`]:(@ref dsl_advanced_options_declaring_species_and_parameters) Allows the designation of a set of symbols as system parameter.
 - [`species`](@ref dsl_advanced_options_declaring_species_and_parameters): Allows the designation of a set of symbols as system species.
-- [`variables`](@ref dsl_advanced_options_declaring_species_and_parameters): Allows the designation of a set of symbols as system non-species variables. 
+- [`variables`](@ref dsl_advanced_options_declaring_species_and_parameters): Allows the designation of a set of symbols as system non-species variables.
 - [`ivs`](@ref dsl_advanced_options_ivs): Allows the designation of a set of symbols as system independent variables.
 - [`compounds`](@ref chemistry_functionality_compounds): Allows the designation of compound species.
-- [`observables`](@ref dsl_advanced_options_observables): Allows the designation of compound observables. 
+- [`observables`](@ref dsl_advanced_options_observables): Allows the designation of compound observables.
 - [`default_noise_scaling`](@ref simulation_intro_SDEs_noise_saling): Enables the setting of a default noise scaling expression.
-- [`differentials`](@ref constraint_equations_coupling_constraints): Allows the designation of differentials. 
-- [`equations`](@ref constraint_equations_coupling_constraints): Allows the creation of algebraic and/or differential equations. 
-- [`continuous_events`](@ref constraint_equations_events): Allows the creation of continuous events. 
-- [`discrete_events`](@ref constraint_equations_events): Allows the creation of discrete events.  
+- [`differentials`](@ref constraint_equations_coupling_constraints): Allows the designation of differentials.
+- [`equations`](@ref constraint_equations_coupling_constraints): Allows the creation of algebraic and/or differential equations.
+- [`continuous_events`](@ref constraint_equations_events): Allows the creation of continuous events.
+- [`discrete_events`](@ref constraint_equations_events): Allows the creation of discrete events.
 - [`combinatoric_ratelaws`](@ref faq_combinatoric_ratelaws): Takes a single option (`true` or `false`), which sets whether to use combinatorial rate laws.
 
 ## [ModelingToolkit and Catalyst accessor functions](@id api_accessor_functions)
@@ -186,7 +187,7 @@ isautonomous
 ```
 
 ## Coupled reaction/equation system properties
-The following system property accessor functions are primarily relevant to reaction system [coupled 
+The following system property accessor functions are primarily relevant to reaction system [coupled
 to differential and/or algebraic equations](@ref constraint_equations).
 ```@docs
 ModelingToolkit.has_alg_equations

docs/src/introduction_to_catalyst/introduction_to_catalyst.md

@@ -211,7 +211,7 @@ jprob = JumpProblem(rn, dprob, Direct())
 # now, let's solve and plot the jump process:
 sol = solve(jprob, SSAStepper())
 plot(sol)
-plot(sol, density = 10000, fmt = :png) # hide
+Catalyst.PNG(plot(sol; fmt = :png, dpi = 200)) # hide
 ```
 
 We see that oscillations remain, but become much noisier. Note, in constructing

docs/src/model_creation/examples/basic_CRN_library.md

@@ -116,11 +116,9 @@ oplt = plot(osol; title = "Reaction rate equation (ODE)")
 splt = plot(ssol; title = "Chemical Langevin equation (SDE)")
 jplt = plot(jsol; title = "Stochastic chemical kinetics (Jump)")
 plot(oplt, splt, jplt; lw = 2, size=(800,800), layout = (3,1))
-oplt = plot(osol; title = "Reaction rate equation (ODE)", plotdensity = 1000, fmt = :png) # hide
-splt = plot(ssol; title = "Chemical Langevin equation (SDE)", plotdensity = 1000, fmt = :png) # hide
-jplt = plot(jsol; title = "Stochastic chemical kinetics (Jump)", plotdensity = 1000, fmt = :png) # hide
-plot(oplt, splt, jplt; lw = 2, size=(800,800), layout = (3,1), plotdensity = 1000, fmt = :png) # hide
-plot!(bottom_margin = 3Plots.Measures.mm) # hide
+fullplt = plot(oplt, splt, jplt; lw = 2, size=(800,800), layout = (3,1), fmt = :png,
+    dpi = 200, bottom_margin = 3Plots.Measures.mm) # hide
+Catalyst.PNG(fullplt) # hide
 ```
 
 ## [SIR infection model](@id basic_CRN_library_sir)
@@ -148,23 +146,21 @@ Next, we perform 3 different Jump simulations. Note that for the stochastic mode
 ```@example crn_library_sir
 using JumpProcesses
 dprob = DiscreteProblem(sir_model, u0, tspan, ps)
-jprob = JumpProblem(sir_model, dprob, Direct(); save_positions = (false, false))
+jprob = JumpProblem(sir_model, dprob, Direct())
 
-jsol1 = solve(jprob, SSAStepper(); saveat = 1.0)
-jsol2 = solve(jprob, SSAStepper(); saveat = 1.0)
-jsol3 = solve(jprob, SSAStepper(); saveat = 1.0)
-jsol1 = solve(jprob, SSAStepper(); saveat = 1.0, seed = 1) # hide
-jsol2 = solve(jprob, SSAStepper(); saveat = 1.0, seed = 2) # hide
-jsol3 = solve(jprob, SSAStepper(); saveat = 1.0, seed = 3) # hide
+jsol1 = solve(jprob, SSAStepper())
+jsol2 = solve(jprob, SSAStepper())
+jsol3 = solve(jprob, SSAStepper())
+jsol1 = solve(jprob, SSAStepper(), seed = 1) # hide
+jsol2 = solve(jprob, SSAStepper(), seed = 2) # hide
+jsol3 = solve(jprob, SSAStepper(), seed = 3) # hide
 
 jplt1 = plot(jsol1; title = "Outbreak")
 jplt2 = plot(jsol2; title = "Outbreak")
 jplt3 = plot(jsol3; title = "No outbreak")
 plot(jplt1, jplt2, jplt3; lw = 3, size=(800,700), layout = (3,1))
-jplt1 = plot(jsol1; title = "Outbreak", plotdensity = 1000, fmt = :png) # hide
-jplt2 = plot(jsol2; title = "Outbreak", plotdensity = 1000, fmt = :png) # hide
-jplt3 = plot(jsol3; title = "No outbreak", plotdensity = 1000, fmt = :png) # hide
-plot(jplt1, jplt2, jplt3; lw = 3, size=(800,700), layout = (3,1), plotdensity = 1000, fmt = :png) # hide
+fullplt = plot(jplt1, jplt2, jplt3; lw = 3, size=(800,700), layout = (3,1), fmt = :png, dpi = 200) # hide
+Catalyst.PNG(fullplt) # hide
 ```
 
 ## [Chemical cross-coupling](@id basic_CRN_library_cc)
@@ -186,7 +182,7 @@ In two separate plots.
 using OrdinaryDiffEq, Plots
 u0 = [:S₁ => 1.0, :C => 0.05, :S₂ => 1.2, :S₁C => 0.0, :CP => 0.0, :P => 0.0]
 tspan = (0., 15.)
-ps = [:k₁ => 5.0, :k₂ => 5.0, :k₃ => 100.0] 
+ps = [:k₁ => 5.0, :k₂ => 5.0, :k₃ => 100.0]
 
 # solve ODEs
 oprob = ODEProblem(cc_system, u0, tspan, ps)
@@ -208,7 +204,7 @@ wilhelm_model = @reaction_network begin
     k4, X --> 0
 end
 ```
-We can simulate the model for two different initial conditions, demonstrating the existence of two different stable steady states. 
+We can simulate the model for two different initial conditions, demonstrating the existence of two different stable steady states.
 ```@example crn_library_wilhelm
 using OrdinaryDiffEq, Plots
 u0_1 = [:X => 1.5, :Y => 0.5]
@@ -234,7 +230,7 @@ sa_loop = @reaction_network begin
     d, X --> ∅
 end
 ```
-A simple example of such a loop is a transcription factor which activates its own gene. Here, $v₀$ represents a basic transcription rate (leakage) in the absence of the transcription factor. 
+A simple example of such a loop is a transcription factor which activates its own gene. Here, $v₀$ represents a basic transcription rate (leakage) in the absence of the transcription factor.
 
 We simulate the self-activation loop from a single initial condition using both deterministic (ODE) and stochastic (jump) simulations. We note that while the deterministic simulation reaches a single steady state, the stochastic one switches between two different states.
 ```@example crn_library_self_activation
@@ -247,13 +243,15 @@ oprob = ODEProblem(sa_loop, u0, tspan, ps)
 osol = solve(oprob)
 
 dprob = DiscreteProblem(sa_loop, u0, tspan, ps)
-jprob = JumpProblem(sa_loop, dprob, Direct(); save_positions = (false,false))
-jsol = solve(jprob, SSAStepper(); saveat = 10.0)
-jsol = solve(jprob, SSAStepper(); saveat = 10.0, seed = 12) # hide
+jprob = JumpProblem(sa_loop, dprob, Direct())
+jsol = solve(jprob, SSAStepper())
+jsol = solve(jprob, SSAStepper(), seed = 12) # hide
 
-plot(osol; lw = 3, label = "Reaction rate equation (ODE)")
-plot!(jsol; lw = 3, label = "Stochastic chemical kinetics (Jump)", yguide = "X", size = (800,350))
-plot!(bottom_margin = 3Plots.Measures.mm, left_margin=3Plots.Measures.mm) # hide
+fplt = plot(osol; lw = 3, label = "Reaction rate equation (ODE)")
+plot!(fplt, jsol; lw = 3, label = "Stochastic chemical kinetics (Jump)", yguide = "X", size = (800,350))
+plot!(fplt, bottom_margin = 3Plots.Measures.mm, left_margin=3Plots.Measures.mm) # hide
+plot!(fplt; fmt = :png, dpi = 200) # hide
+Catalyst.PNG(fplt) # hide
 ```
 
 ## [The Brusselator](@id basic_CRN_library_brusselator)

docs/src/model_creation/parametric_stoichiometry.md

@@ -165,7 +165,7 @@ show(stdout, MIME"text/plain"(), equations(jsys)[4].rate) # hide
 equations(jsys)[4].affect!
 show(stdout, MIME"text/plain"(), equations(jsys)[4].affect!) # hide
 ```
-Finally, we can now simulate our jumpsystem
+Finally, we can now simulate our `JumpSystem`
 ```@example s1
 pmean = 200
 bval = 70

src/Catalyst.jl

@@ -141,7 +141,8 @@ export mm, mmr, hill, hillr, hillar
 # for Latex printing of ReactionSystems
 include("latexify_recipes.jl")
 
-# for making and saving graphs
+# for making and saving graphs/plots
+include("plotting.jl")
 include("graphs.jl")
 export Graph, savegraph, complexgraph
 

src/plotting.jl

@@ -0,0 +1,73 @@
+#######################################################################################
+"""
+The following code is taken from the MIT licensed https://github.com/tkf/DisplayAs.jl
+
+Copyright (c) 2019 Takafumi Arakaki <aka.tkf@gmail.com>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this
+software and associated documentation files (the "Software"), to deal in the Software
+without restriction, including without limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons
+to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or
+substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
+PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE
+FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+
+------------------------------------------------------------------------------------
+In Catalyst this code is considered **internal**, and solely used for forcing a given image
+type in documentation due to limitations in Documenter.jl and Plots.jl. It should never be
+used for any other purpose or exported.
+"""
+
+# _showables = [
+#     (:Text, "text/plain")
+#     (:MD, "text/markdown")
+#     (:HTML, "text/html")
+#     (:JSON, "application/json")
+#     (:SVG, "image/svg+xml")
+#     (:PNG, "image/png")
+#     (:GIF, "image/gif")
+#     (:PDF, "application/pdf")
+#     (:EPS, "application/eps")
+#     (:JPEG, "image/jpeg")
+#     (:PS, "application/postscript")
+#     (:LaTeX, "text/latex")
+#     (:CSV, "text/csv")
+#     (:TSV, "text/tab-separated-values")
+# ]
+
+# currently we only use PNG conversion, but others can be added from above as needed
+_showables = [(:PNG, "image/png")]
+
+struct Showable{mime <: MIME}
+    content::Any
+    options::NamedTuple
+end
+
+function Showable{T}(content; options...) where {T <: MIME}
+    @nospecialize
+    return Showable{T}(content, (; options...))
+end
+
+for (_, mime) in _showables
+    MIMEType = typeof(MIME(mime))
+    @eval Base.show(io::IO, ::$MIMEType, s::Showable{>:$MIMEType}; options...) = show(
+        io, $MIMEType(), s.content; s.options..., options...)
+end
+
+macro mime_str(s)
+    :(Showable{MIME{Symbol($s)}})
+end
+
+for (name, mime) in _showables
+    @eval const $name = @mime_str $mime
+end
+
+#######################################################################################