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get stuff to hie properly
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docs/src/introduction_to_catalyst/introduction_to_catalyst.md

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -196,7 +196,7 @@ jprob = JumpProblem(repressilator, dprob, Direct(), save_positions=(false,false)
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# now, let's solve and plot the jump process:
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sol = solve(jprob, SSAStepper(), saveat=10.)
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plot(sol)
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plot(sol, plotdensity = 1000, fmt =:png) # hide
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plot(sol, plotdensity = 1000, fmt = :png) # hide
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```
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We see that oscillations remain, but become much noisier. Note, in constructing

docs/src/model_creation/examples/basic_CRN_library.md

Lines changed: 9 additions & 9 deletions
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@@ -115,11 +115,11 @@ using Plots
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oplt = plot(osol; title = "Reaction rate equation (ODE)")
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splt = plot(ssol; title = "Chemical Langevin equation (SDE)")
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jplt = plot(jsol; title = "Stochastic chemical kinetics (Jump)")
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plot(oplt, splt, jplt; lw = 2, size=(800,800), layout = (3,1))
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plot(plot(osol; title = "Reaction rate equation (ODE)", plotdensity = 1000, fmt =:png),
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plot(ssol; title = "Chemical Langevin equation (SDE)", plotdensity = 1000, fmt =:png),
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plot(jsol; title = "Stochastic chemical kinetics (Jump)", plotdensity = 1000, fmt =:png);
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lw = 2, size=(800,800), layout = (3,1), bottom_margin = 3Plots.Measures.mm) # hide
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plot(oplt, splt, jplt; lw = 2, size=(800,800), layout = (3,1)) # hide
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oplt = plot(osol; title = "Reaction rate equation (ODE)", plotdensity = 1000, fmt = :png) # hide
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splt = plot(ssol; title = "Chemical Langevin equation (SDE)", plotdensity = 1000, fmt = :png) # hide
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jplt = plot(jsol; title = "Stochastic chemical kinetics (Jump)", plotdensity = 1000, fmt = :png) # hide
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plot(oplt, splt, jplt; lw = 2, size=(800,800), layout = (3,1))
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```
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## [SIR infection model](@id basic_CRN_library_sir)
@@ -160,10 +160,10 @@ jplt1 = plot(jsol1; title = "Outbreak")
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jplt2 = plot(jsol2; title = "Outbreak")
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jplt3 = plot(jsol3; title = "No outbreak")
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plot(jplt1, jplt2, jplt3; lw = 3, size=(800,700), layout = (3,1))
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plot(plot(jsol1; title = "Outbreak", plotdensity = 1000, fmt =:png),
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plot(jsol2; title = "Outbreak", plotdensity = 1000, fmt =:png),
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plot(jsol3; title = "No outbreak", plotdensity = 1000, fmt =:png);
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lw = 3, size=(800,700), layout = (3,1)) # hide
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jplt1 = plot(jsol1; title = "Outbreak", plotdensity = 1000, fmt = :png) # hide
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jplt2 = plot(jsol2; title = "Outbreak", plotdensity = 1000, fmt = :png) # hide
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jplt3 = plot(jsol3; title = "No outbreak", plotdensity = 1000, fmt = :png) # hide
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plot(jplt1, jplt2, jplt3; lw = 3, size=(800,700), layout = (3,1), plotdensity = 1000, fmt = :png) # hide
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```
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## [Chemical cross-coupling](@id basic_CRN_library_cc)

docs/src/model_simulation/ode_simulation_performance.md

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ oprob = ODEProblem(brusselator, u0, tspan, ps)
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sol1 = solve(oprob, Tsit5())
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plot(sol1)
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plot(sol1, plotdensity = 1000, fmt =:png) # hide
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plot(sol1, plotdensity = 1000, fmt = :png) # hide
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```
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We get a warning, indicating that the simulation was terminated. Furthermore, the resulting plot ends at $t ≈ 12$, meaning that the simulation was not completed (as the simulation's endpoint is $t = 20$). Indeed, we can confirm this by checking the *return code* of the solution object:

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