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Jul 31, 2025
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Update code formatting with JuliaFormatter #1305

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7 changes: 4 additions & 3 deletions docs/make.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -39,9 +39,10 @@ makedocs(sitename = "Catalyst.jl",
collapselevel = 1,
assets = ["assets/favicon.ico"],
canonical = "https://docs.sciml.ai/Catalyst/stable/"),
modules = [Catalyst, ModelingToolkit,
isdefined(Base, :get_extension) ? Base.get_extension(Catalyst, :CatalystGraphMakieExtension) :
Catalyst.CatalystGraphMakieExtension],
modules = [Catalyst, ModelingToolkit,
isdefined(Base, :get_extension) ?
Base.get_extension(Catalyst, :CatalystGraphMakieExtension) :
Catalyst.CatalystGraphMakieExtension],
doctest = false,
clean = true,
pages = pages,
Expand Down
159 changes: 78 additions & 81 deletions docs/pages.jl
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Original file line number Diff line number Diff line change
@@ -1,83 +1,80 @@
pages = Any[
"Home" => "index.md",
"Introduction to Catalyst" => Any[
"introduction_to_catalyst/catalyst_for_new_julia_users.md",
"introduction_to_catalyst/introduction_to_catalyst.md",
"introduction_to_catalyst/math_models_intro.md"
],
"Model creation and properties" => Any[
"model_creation/dsl_basics.md",
"model_creation/dsl_advanced.md",
"model_creation/programmatic_CRN_construction.md",
"model_creation/compositional_modeling.md",
"model_creation/constraint_equations.md",
"model_creation/conservation_laws.md",
"model_creation/parametric_stoichiometry.md",
"model_creation/functional_parameters.md",
"model_creation/model_file_loading_and_export.md",
"model_creation/model_visualisation.md",
"model_creation/reactionsystem_content_accessing.md",
"model_creation/chemistry_related_functionality.md",
"Examples" => Any[
"model_creation/examples/basic_CRN_library.md",
"model_creation/examples/programmatic_generative_linear_pathway.md",
"model_creation/examples/hodgkin_huxley_equation.md",
"model_creation/examples/smoluchowski_coagulation_equation.md",
"model_creation/examples/noise_modelling_approaches.md",
]
],
"Model simulation and visualization" => Any[
"model_simulation/simulation_introduction.md",
"model_simulation/simulation_plotting.md",
"model_simulation/simulation_structure_interfacing.md",
"model_simulation/ensemble_simulations.md",
"model_simulation/ode_simulation_performance.md",
"model_simulation/sde_simulation_performance.md",
"model_simulation/finite_state_projection_simulation.md",
"Examples" => Any[
"model_simulation/examples/periodic_events_simulation.md",
"model_simulation/examples/activation_time_distribution_measurement.md",
"model_simulation/examples/interactive_brusselator_simulation.md"
]
],
"Network Analysis" => Any[
"network_analysis/odes.md",
"network_analysis/crn_theory.md",
"network_analysis/network_properties.md"
],
"Steady state analysis" => Any[
"steady_state_functionality/homotopy_continuation.md",
"steady_state_functionality/nonlinear_solve.md",
"steady_state_functionality/steady_state_stability_computation.md",
"steady_state_functionality/bifurcation_diagrams.md",
"steady_state_functionality/dynamical_systems.md",
"Examples" => Any[
"steady_state_functionality/examples/nullcline_plotting.md",
"steady_state_functionality/examples/bifurcationkit_periodic_orbits.md",
"steady_state_functionality/examples/bifurcationkit_codim2.md"
]
],
"Inverse problems" => Any[
"inverse_problems/petab_ode_param_fitting.md",
"inverse_problems/optimization_ode_param_fitting.md",
"inverse_problems/behaviour_optimisation.md",
"inverse_problems/structural_identifiability.md",
"inverse_problems/global_sensitivity_analysis.md",
#"Examples" => Any[
# "inverse_problems/examples/ode_fitting_oscillation.md"
#]
],
"Spatial modelling" => Any[
"spatial_modelling/lattice_reaction_systems.md",
"spatial_modelling/lattice_simulation_structure_ interaction.md",
"spatial_modelling/lattice_simulation_plotting.md",
"spatial_modelling/spatial_ode_simulations.md",
"spatial_modelling/spatial_jump_simulations.md"
],
"FAQs" => "faqs.md",
"API" => Any[
"api/core_api.md",
"api/network_analysis_api.md"
],
"Developer Documentation" => "devdocs/dev_guide.md"
"Home" => "index.md",
"Introduction to Catalyst" => Any[
"introduction_to_catalyst/catalyst_for_new_julia_users.md",
"introduction_to_catalyst/introduction_to_catalyst.md",
"introduction_to_catalyst/math_models_intro.md"
],
"Model creation and properties" => Any[
"model_creation/dsl_basics.md",
"model_creation/dsl_advanced.md",
"model_creation/programmatic_CRN_construction.md",
"model_creation/compositional_modeling.md",
"model_creation/constraint_equations.md",
"model_creation/conservation_laws.md",
"model_creation/parametric_stoichiometry.md",
"model_creation/functional_parameters.md",
"model_creation/model_file_loading_and_export.md",
"model_creation/model_visualisation.md",
"model_creation/reactionsystem_content_accessing.md",
"model_creation/chemistry_related_functionality.md",
"Examples" => Any[
"model_creation/examples/basic_CRN_library.md",
"model_creation/examples/programmatic_generative_linear_pathway.md",
"model_creation/examples/hodgkin_huxley_equation.md",
"model_creation/examples/smoluchowski_coagulation_equation.md",
"model_creation/examples/noise_modelling_approaches.md"
]
],
"Model simulation and visualization" => Any[
"model_simulation/simulation_introduction.md",
"model_simulation/simulation_plotting.md",
"model_simulation/simulation_structure_interfacing.md",
"model_simulation/ensemble_simulations.md",
"model_simulation/ode_simulation_performance.md",
"model_simulation/sde_simulation_performance.md",
"model_simulation/finite_state_projection_simulation.md",
"Examples" => Any[
"model_simulation/examples/periodic_events_simulation.md",
"model_simulation/examples/activation_time_distribution_measurement.md",
"model_simulation/examples/interactive_brusselator_simulation.md"
]
],
"Network Analysis" => Any[
"network_analysis/odes.md",
"network_analysis/crn_theory.md",
"network_analysis/network_properties.md"
],
"Steady state analysis" => Any[
"steady_state_functionality/homotopy_continuation.md",
"steady_state_functionality/nonlinear_solve.md",
"steady_state_functionality/steady_state_stability_computation.md",
"steady_state_functionality/bifurcation_diagrams.md",
"steady_state_functionality/dynamical_systems.md",
"Examples" => Any[
"steady_state_functionality/examples/nullcline_plotting.md",
"steady_state_functionality/examples/bifurcationkit_periodic_orbits.md",
"steady_state_functionality/examples/bifurcationkit_codim2.md"
]
],
"Inverse problems" => Any[
"inverse_problems/petab_ode_param_fitting.md",
"inverse_problems/optimization_ode_param_fitting.md",
"inverse_problems/behaviour_optimisation.md",
"inverse_problems/structural_identifiability.md",
"inverse_problems/global_sensitivity_analysis.md" #"Examples" => Any[ # "inverse_problems/examples/ode_fitting_oscillation.md" #]
],
"Spatial modelling" => Any[
"spatial_modelling/lattice_reaction_systems.md",
"spatial_modelling/lattice_simulation_structure_ interaction.md",
"spatial_modelling/lattice_simulation_plotting.md",
"spatial_modelling/spatial_ode_simulations.md",
"spatial_modelling/spatial_jump_simulations.md"
],
"FAQs" => "faqs.md",
"API" => Any[
"api/core_api.md",
"api/network_analysis_api.md"
],
"Developer Documentation" => "devdocs/dev_guide.md"
]
3 changes: 2 additions & 1 deletion ext/CatalystBifurcationKitExtension/bifurcation_kit_extension.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ function bkext_make_nsys(rs, u0)
cons_default = [cons_eq.rhs for cons_eq in cons_eqs]
cons_default = Catalyst.get_networkproperties(rs).conservedconst => cons_default
defaults = Dict([u0; cons_default])
nsys = convert(NonlinearSystem, rs; defaults, remove_conserved = true, conseqs_remake_warn = false)
nsys = convert(
NonlinearSystem, rs; defaults, remove_conserved = true, conseqs_remake_warn = false)
return complete(nsys)
end
9 changes: 6 additions & 3 deletions ext/CatalystCairoMakieExtension/cairo_makie_extension_spatial_modelling.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,8 @@ function lattice_animation(
vals, plot_min, plot_max = Catalyst.extract_vals(sol, sp, lrs, plot_min, plot_max, t)

# Creates the base figure (which is modified in the animation).
fig, ax, plt = scatterlines(vals[1];
fig, ax,
plt = scatterlines(vals[1];
axis = (xlabel = "Compartment", ylabel = "$(sp)",
limits = (nothing, nothing, plot_min, plot_max)),
markersize = markersize, kwargs...)
Expand Down Expand Up @@ -100,8 +101,10 @@ function lattice_animation(
x_vals, y_vals = Catalyst.extract_grid_axes(lrs)

# Creates the base figure (which is modified in the animation).
fig, ax, hm = heatmap(x_vals, y_vals, vals[1];
axis = (xgridvisible = false, ygridvisible = false, xlabel = "Compartment", ylabel = "Compartment"),
fig, ax,
hm = heatmap(x_vals, y_vals, vals[1];
axis = (xgridvisible = false, ygridvisible = false,
xlabel = "Compartment", ylabel = "Compartment"),
Comment on lines -103 to +107
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Things likes this are not a reasonable reformat, and are why Catalyst no longer uses JuliaFormatter. Please revert this PR. Is this even correct syntactically now?

colormap, colorrange = (plot_min, plot_max),
kwargs...)
ttitle && (ax.title = "Time: $(round(t[1]; sigdigits = 3))")
Expand Down
3 changes: 2 additions & 1 deletion ext/CatalystGraphMakieExtension/graph_makie_extension_spatial_modelling.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,8 @@ function lattice_animation(
vals, plot_min, plot_max = Catalyst.extract_vals(sol, sp, lrs, plot_min, plot_max, t)

# Creates the base figure (which is modified in the animation).
fig, ax, plt = graphplot(plot_graph; node_color = vals[1],
fig, ax,
plt = graphplot(plot_graph; node_color = vals[1],
node_attr = (colorrange = (plot_min, plot_max), colormap), node_size, kwargs...
)
ttitle && (ax.title = "Time: $(round(t[1]; sigdigits = 3))")
Expand Down
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