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ChrisRackauckasChrisRackauckas
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Merge pull request #1305 from SciML/julia-formatter-update
Update code formatting with JuliaFormatter
2 parents 10e7af5 + a164b3f commit e718736

23 files changed

+328
-281
lines changed

‎docs/make.jl

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -39,9 +39,10 @@ makedocs(sitename = "Catalyst.jl",
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collapselevel = 1,
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assets = ["assets/favicon.ico"],
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canonical = "https://docs.sciml.ai/Catalyst/stable/"),
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modules = [Catalyst, ModelingToolkit,
43-
isdefined(Base, :get_extension) ? Base.get_extension(Catalyst, :CatalystGraphMakieExtension) :
44-
Catalyst.CatalystGraphMakieExtension],
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modules = [Catalyst, ModelingToolkit,
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isdefined(Base, :get_extension) ?
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Base.get_extension(Catalyst, :CatalystGraphMakieExtension) :
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Catalyst.CatalystGraphMakieExtension],
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doctest = false,
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clean = true,
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pages = pages,

‎docs/pages.jl

Lines changed: 78 additions & 81 deletions
Original file line numberDiff line numberDiff line change
@@ -1,83 +1,80 @@
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pages = Any[
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"Home" => "index.md",
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"Introduction to Catalyst" => Any[
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"introduction_to_catalyst/catalyst_for_new_julia_users.md",
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"introduction_to_catalyst/introduction_to_catalyst.md",
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"introduction_to_catalyst/math_models_intro.md"
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],
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"Model creation and properties" => Any[
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"model_creation/dsl_basics.md",
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"model_creation/dsl_advanced.md",
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"model_creation/programmatic_CRN_construction.md",
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"model_creation/compositional_modeling.md",
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"model_creation/constraint_equations.md",
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"model_creation/conservation_laws.md",
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"model_creation/parametric_stoichiometry.md",
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"model_creation/functional_parameters.md",
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"model_creation/model_file_loading_and_export.md",
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"model_creation/model_visualisation.md",
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"model_creation/reactionsystem_content_accessing.md",
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"model_creation/chemistry_related_functionality.md",
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"Examples" => Any[
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"model_creation/examples/basic_CRN_library.md",
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"model_creation/examples/programmatic_generative_linear_pathway.md",
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"model_creation/examples/hodgkin_huxley_equation.md",
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"model_creation/examples/smoluchowski_coagulation_equation.md",
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"model_creation/examples/noise_modelling_approaches.md",
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]
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],
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"Model simulation and visualization" => Any[
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"model_simulation/simulation_introduction.md",
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"model_simulation/simulation_plotting.md",
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"model_simulation/simulation_structure_interfacing.md",
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"model_simulation/ensemble_simulations.md",
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"model_simulation/ode_simulation_performance.md",
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"model_simulation/sde_simulation_performance.md",
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"model_simulation/finite_state_projection_simulation.md",
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"Examples" => Any[
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"model_simulation/examples/periodic_events_simulation.md",
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"model_simulation/examples/activation_time_distribution_measurement.md",
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"model_simulation/examples/interactive_brusselator_simulation.md"
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]
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],
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"Network Analysis" => Any[
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"network_analysis/odes.md",
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"network_analysis/crn_theory.md",
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"network_analysis/network_properties.md"
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],
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"Steady state analysis" => Any[
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"steady_state_functionality/homotopy_continuation.md",
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"steady_state_functionality/nonlinear_solve.md",
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"steady_state_functionality/steady_state_stability_computation.md",
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"steady_state_functionality/bifurcation_diagrams.md",
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"steady_state_functionality/dynamical_systems.md",
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"Examples" => Any[
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"steady_state_functionality/examples/nullcline_plotting.md",
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"steady_state_functionality/examples/bifurcationkit_periodic_orbits.md",
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"steady_state_functionality/examples/bifurcationkit_codim2.md"
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]
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],
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"Inverse problems" => Any[
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"inverse_problems/petab_ode_param_fitting.md",
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"inverse_problems/optimization_ode_param_fitting.md",
63-
"inverse_problems/behaviour_optimisation.md",
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"inverse_problems/structural_identifiability.md",
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"inverse_problems/global_sensitivity_analysis.md",
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#"Examples" => Any[
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# "inverse_problems/examples/ode_fitting_oscillation.md"
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#]
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],
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"Spatial modelling" => Any[
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"spatial_modelling/lattice_reaction_systems.md",
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"spatial_modelling/lattice_simulation_structure_ interaction.md",
73-
"spatial_modelling/lattice_simulation_plotting.md",
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"spatial_modelling/spatial_ode_simulations.md",
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"spatial_modelling/spatial_jump_simulations.md"
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],
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"FAQs" => "faqs.md",
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"API" => Any[
79-
"api/core_api.md",
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"api/network_analysis_api.md"
81-
],
82-
"Developer Documentation" => "devdocs/dev_guide.md"
2+
"Home" => "index.md",
3+
"Introduction to Catalyst" => Any[
4+
"introduction_to_catalyst/catalyst_for_new_julia_users.md",
5+
"introduction_to_catalyst/introduction_to_catalyst.md",
6+
"introduction_to_catalyst/math_models_intro.md"
7+
],
8+
"Model creation and properties" => Any[
9+
"model_creation/dsl_basics.md",
10+
"model_creation/dsl_advanced.md",
11+
"model_creation/programmatic_CRN_construction.md",
12+
"model_creation/compositional_modeling.md",
13+
"model_creation/constraint_equations.md",
14+
"model_creation/conservation_laws.md",
15+
"model_creation/parametric_stoichiometry.md",
16+
"model_creation/functional_parameters.md",
17+
"model_creation/model_file_loading_and_export.md",
18+
"model_creation/model_visualisation.md",
19+
"model_creation/reactionsystem_content_accessing.md",
20+
"model_creation/chemistry_related_functionality.md",
21+
"Examples" => Any[
22+
"model_creation/examples/basic_CRN_library.md",
23+
"model_creation/examples/programmatic_generative_linear_pathway.md",
24+
"model_creation/examples/hodgkin_huxley_equation.md",
25+
"model_creation/examples/smoluchowski_coagulation_equation.md",
26+
"model_creation/examples/noise_modelling_approaches.md"
27+
]
28+
],
29+
"Model simulation and visualization" => Any[
30+
"model_simulation/simulation_introduction.md",
31+
"model_simulation/simulation_plotting.md",
32+
"model_simulation/simulation_structure_interfacing.md",
33+
"model_simulation/ensemble_simulations.md",
34+
"model_simulation/ode_simulation_performance.md",
35+
"model_simulation/sde_simulation_performance.md",
36+
"model_simulation/finite_state_projection_simulation.md",
37+
"Examples" => Any[
38+
"model_simulation/examples/periodic_events_simulation.md",
39+
"model_simulation/examples/activation_time_distribution_measurement.md",
40+
"model_simulation/examples/interactive_brusselator_simulation.md"
41+
]
42+
],
43+
"Network Analysis" => Any[
44+
"network_analysis/odes.md",
45+
"network_analysis/crn_theory.md",
46+
"network_analysis/network_properties.md"
47+
],
48+
"Steady state analysis" => Any[
49+
"steady_state_functionality/homotopy_continuation.md",
50+
"steady_state_functionality/nonlinear_solve.md",
51+
"steady_state_functionality/steady_state_stability_computation.md",
52+
"steady_state_functionality/bifurcation_diagrams.md",
53+
"steady_state_functionality/dynamical_systems.md",
54+
"Examples" => Any[
55+
"steady_state_functionality/examples/nullcline_plotting.md",
56+
"steady_state_functionality/examples/bifurcationkit_periodic_orbits.md",
57+
"steady_state_functionality/examples/bifurcationkit_codim2.md"
58+
]
59+
],
60+
"Inverse problems" => Any[
61+
"inverse_problems/petab_ode_param_fitting.md",
62+
"inverse_problems/optimization_ode_param_fitting.md",
63+
"inverse_problems/behaviour_optimisation.md",
64+
"inverse_problems/structural_identifiability.md",
65+
"inverse_problems/global_sensitivity_analysis.md" #"Examples" => Any[ # "inverse_problems/examples/ode_fitting_oscillation.md" #]
66+
],
67+
"Spatial modelling" => Any[
68+
"spatial_modelling/lattice_reaction_systems.md",
69+
"spatial_modelling/lattice_simulation_structure_ interaction.md",
70+
"spatial_modelling/lattice_simulation_plotting.md",
71+
"spatial_modelling/spatial_ode_simulations.md",
72+
"spatial_modelling/spatial_jump_simulations.md"
73+
],
74+
"FAQs" => "faqs.md",
75+
"API" => Any[
76+
"api/core_api.md",
77+
"api/network_analysis_api.md"
78+
],
79+
"Developer Documentation" => "devdocs/dev_guide.md"
8380
]

‎ext/CatalystBifurcationKitExtension/bifurcation_kit_extension.jl

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -37,6 +37,7 @@ function bkext_make_nsys(rs, u0)
3737
cons_default = [cons_eq.rhs for cons_eq in cons_eqs]
3838
cons_default = Catalyst.get_networkproperties(rs).conservedconst => cons_default
3939
defaults = Dict([u0; cons_default])
40-
nsys = convert(NonlinearSystem, rs; defaults, remove_conserved = true, conseqs_remake_warn = false)
40+
nsys = convert(
41+
NonlinearSystem, rs; defaults, remove_conserved = true, conseqs_remake_warn = false)
4142
return complete(nsys)
4243
end

‎ext/CatalystCairoMakieExtension/cairo_makie_extension_spatial_modelling.jl

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,8 @@ function lattice_animation(
2424
vals, plot_min, plot_max = Catalyst.extract_vals(sol, sp, lrs, plot_min, plot_max, t)
2525

2626
# Creates the base figure (which is modified in the animation).
27-
fig, ax, plt = scatterlines(vals[1];
27+
fig, ax,
28+
plt = scatterlines(vals[1];
2829
axis = (xlabel = "Compartment", ylabel = "$(sp)",
2930
limits = (nothing, nothing, plot_min, plot_max)),
3031
markersize = markersize, kwargs...)
@@ -100,8 +101,10 @@ function lattice_animation(
100101
x_vals, y_vals = Catalyst.extract_grid_axes(lrs)
101102

102103
# Creates the base figure (which is modified in the animation).
103-
fig, ax, hm = heatmap(x_vals, y_vals, vals[1];
104-
axis = (xgridvisible = false, ygridvisible = false, xlabel = "Compartment", ylabel = "Compartment"),
104+
fig, ax,
105+
hm = heatmap(x_vals, y_vals, vals[1];
106+
axis = (xgridvisible = false, ygridvisible = false,
107+
xlabel = "Compartment", ylabel = "Compartment"),
105108
colormap, colorrange = (plot_min, plot_max),
106109
kwargs...)
107110
ttitle && (ax.title = "Time: $(round(t[1]; sigdigits = 3))")

‎ext/CatalystGraphMakieExtension/graph_makie_extension_spatial_modelling.jl

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -27,7 +27,8 @@ function lattice_animation(
2727
vals, plot_min, plot_max = Catalyst.extract_vals(sol, sp, lrs, plot_min, plot_max, t)
2828

2929
# Creates the base figure (which is modified in the animation).
30-
fig, ax, plt = graphplot(plot_graph; node_color = vals[1],
30+
fig, ax,
31+
plt = graphplot(plot_graph; node_color = vals[1],
3132
node_attr = (colorrange = (plot_min, plot_max), colormap), node_size, kwargs...
3233
)
3334
ttitle && (ax.title = "Time: $(round(t[1]; sigdigits = 3))")

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