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SciML / Catalyst.jl

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
https://docs.sciml.ai/Catalyst/stable/
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link errors in doc builds #941

Closed isaacsas closed 3 months ago

isaacsas commented 3 months ago

Had to set warnonly = true due to the following link errors. These should be fixed and the warnonly restored to the more strict setting

┌ Warning: Cannot resolve @ref for md"[computed using homotopy continuation](@ref homotopy_continuation_basic_example)" in src/steady_state_functionality/dynamical_systems.md.
│ - No docstring found in doc for binding `Main.homotopy_continuation_basic_example`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[parallelise it on CPUs or GPUs](@ref investigating)" in src/model_simulation/ode_simulation_performance.md.
│ - No docstring found in doc for binding `Main.investigating`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[PEtab.jl](@ref petab_parameter_fitting)" in src/inverse_problems/behaviour_optimisation.md.
│ - No docstring found in doc for binding `Main.petab_parameter_fitting`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[When fitting a model's parameters to data](@ref petab_parameter_fitting)" in src/inverse_problems/global_sensitivity_analysis.md.
│ - No docstring found in doc for binding `Main.petab_parameter_fitting`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[previously described](@ref optimization_parameter_fitting_logarithmic_scale)" in src/inverse_problems/global_sensitivity_analysis.md.
│ - No docstring found in doc for binding `Main.optimization_parameter_fitting_logarithmic_scale`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[interpolation of variables](@ref dsl_description_interpolation_of_variables)" in src/model_creation/constraint_equations.md.
│ - No docstring found in doc for binding `Main.dsl_description_interpolation_of_variables`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[`la` plotting option](@ref simulation_plotting_options)" in src/model_simulation/ensemble_simulations.md.
│ - Header with slug 'simulation_plotting_options' is not unique in src/model_simulation/ensemble_simulations.md.
│ - No docstring found in doc for binding `Main.simulation_plotting_options`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[Basic Syntax](@ref basic_examples)" in src/introduction_to_catalyst/introduction_to_catalyst.md.
│ - No docstring found in doc for binding `Main.basic_examples`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[two-state model](@ref rbasic_CRN_library_two_statesef)" in src/model_simulation/simulation_structure_interfacing.md.
│ - No docstring found in doc for binding `Main.rbasic_CRN_library_two_statesef`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[`remake_reactionsystem`](@ref)" in src/model_simulation/simulation_introduction.md.
│ - No docstring found in doc for binding `Main.remake_reactionsystem`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[Interpolation of Julia Variables](@ref dsl_description_interpolation_of_variables)" in src/model_creation/compositional_modeling.md.
│ - No docstring found in doc for binding `Main.dsl_description_interpolation_of_variables`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[Reaction rate laws used in simulations](@ref)" in src/faqs.md.
│ - No docstring found in doc for binding `Base.-`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[Reaction rate laws used in simulations](@ref)" in src/faqs.md.
│ - No docstring found in doc for binding `Base.-`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[here](@ref dsl_description_defaults)" in src/faqs.md.
│ - No docstring found in doc for binding `Main.dsl_description_defaults`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[using `remake`](@ref simulation_structure_interfacing_remake)" in src/inverse_problems/optimization_ode_param_fitting.md.
│ - No docstring found in doc for binding `Main.simulation_structure_interfacing_remake`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[corresponding `EnsembleProblem`](@ref advanced_simulations_ensemble_problems)" in src/inverse_problems/optimization_ode_param_fitting.md.
│ - No docstring found in doc for binding `Main.advanced_simulations_ensemble_problems`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
┌ Warning: Cannot resolve @ref for md"[NonlinearSolve.jl](@ref nonlinear_solve)" in src/steady_state_functionality/steady_state_stability_computation.md.
│ - No docstring found in doc for binding `Main.nonlinear_solve`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:46
[ Info: CheckDocument: running document checks.
isaacsas commented 3 months ago

@TorkelE these are now fixed right?

TorkelE commented 3 months ago

yes