diff --git a/ext/SciMLBaseForwardDiffExt.jl b/ext/SciMLBaseForwardDiffExt.jl index 651f2fe00..d65b05be7 100644 --- a/ext/SciMLBaseForwardDiffExt.jl +++ b/ext/SciMLBaseForwardDiffExt.jl @@ -98,7 +98,7 @@ to be specified at compiled time and thus cannot have a Bool-based opt out, so i may be extended to use a preference system to opt-out with a `UPCONVERT_DUALS`. In the case where upconversion is not done automatically, the user is required to upconvert all initial conditions themselves, for an example of how this can be confusing to a user see -https://discourse.julialang.org/t/typeerror-in-julia-turing-when-sampling-for-a-forced-differential-equation/82937 + """ @generated function anyeltypedual(x, ::Type{Val{counter}}) where {counter} x = x.name === Core.Compiler.typename(Type) ? x.parameters[1] : x diff --git a/ext/SciMLBaseMakieExt.jl b/ext/SciMLBaseMakieExt.jl index 0071ee47c..eedfb1fda 100644 --- a/ext/SciMLBaseMakieExt.jl +++ b/ext/SciMLBaseMakieExt.jl @@ -16,7 +16,7 @@ function ensure_plottrait(PT::Type, arg, desired_plottrait_type::Type) ::$(string(typeof(arg))) Makie needs to convert all plot input arguments to types that can be consumed by the backends (typically Arrays with Float32 elements). - You can define a method for `Makie.convert_arguments` (a type recipe) for these types or their supertypes to make this set of arguments convertible (See http://docs.makie.org/stable/documentation/recipes/index.html). + You can define a method for `Makie.convert_arguments` (a type recipe) for these types or their supertypes to make this set of arguments convertible (See ). Alternatively, you can define `Makie.convert_single_argument` for single arguments which have types that are unknown to Makie but which can be converted to known types and fed back to the conversion pipeline. """) diff --git a/src/alg_traits.jl b/src/alg_traits.jl index e63f142f6..16994c2fb 100644 --- a/src/alg_traits.jl +++ b/src/alg_traits.jl @@ -275,7 +275,7 @@ not converge to the same answer. In the context of a stochastic differential equ on the integral rule that is chosen. This trait describes which interpretation the solver algorithm subscribes to, and thus whether the solution should be interpreted as the solution to the SDE under the Ito or Stratonovich interpretation. -For more information, see https://oatml.cs.ox.ac.uk/blog/2022/03/22/ito-strat.html as a good high-level explanation. +For more information, see as a good high-level explanation. !!! note diff --git a/src/debug.jl b/src/debug.jl index d8c1ae21d..077af3a53 100644 --- a/src/debug.jl +++ b/src/debug.jl @@ -20,7 +20,7 @@ one could perform a domain transformation on the variables so that such an issue definition of `f`. For more information, check out the following FAQ page: -https://docs.sciml.ai/Optimization/stable/API/FAQ/#The-Solver-Seems-to-Violate-Constraints-During-the-Optimization,-Causing-DomainErrors,-What-Can-I-Do-About-That?""" +""" FUNCTIONWRAPPERSWRAPPERS_MSG = """ No appropriate function wrapper found. This means that the auto-despecialization code used for the reduction @@ -36,11 +36,11 @@ if `f` has 3 arguments `(u,p,t)` then it's false, otherwise `f(du,u,p,t)` is tru For more information on the control of specialization options, please see the documentation at: -https://docs.sciml.ai/SciMLBase/stable/interfaces/Problems/#Specialization-Choices + If one wants way more detail than necessary on why the function wrappers exist and what they are doing, see: -https://sciml.ai/news/2022/09/21/compile_time/""" +""" const NO_PARAMETERS_ARITHMETIC_ERROR_MESSAGE = """ diff --git a/src/errors.jl b/src/errors.jl index bc18e54c8..d98ed924f 100644 --- a/src/errors.jl +++ b/src/errors.jl @@ -96,7 +96,7 @@ const KWARGWARN_MESSAGE = """ The only allowed keyword arguments to `solve` are: $allowedkeywords - See https://diffeq.sciml.ai/stable/basics/common_solver_opts/ for more details. + See for more details. Set kwargshandle=KeywordArgError for an error message. Set kwargshandle=KeywordArgSilent to ignore this message. @@ -107,7 +107,7 @@ const KWARGERROR_MESSAGE = """ The only allowed keyword arguments to `solve` are: $allowedkeywords - See https://diffeq.sciml.ai/stable/basics/common_solver_opts/ for more details. + See for more details. """ struct CommonKwargError <: Exception @@ -138,7 +138,7 @@ const INCOMPATIBLE_U0_MESSAGE = """ choice in the problem constructor, i.e. `ODEProblem{false}(f,u0,tspan,p,kwargs...)`. For a longer discussion on mutability vs immutability and in-place vs out-of-place, see: - https://diffeq.sciml.ai/stable/tutorials/faster_ode_example/#Example-Accelerating-a-Non-Stiff-Equation:-The-Lorenz-Equation + """ struct IncompatibleInitialConditionError <: Exception end @@ -153,7 +153,7 @@ const NO_DEFAULT_ALGORITHM_MESSAGE = """ `init(prob, Tsit5())` for an ODE) or import DifferentialEquations directly. - You can find the list of available solvers at https://diffeq.sciml.ai/stable/solvers/ode_solve/ + You can find the list of available solvers at and its associated pages. """ @@ -193,7 +193,7 @@ const NON_SOLVER_MESSAGE = """ Please double check the arguments being sent to the solver. - You can find the list of available solvers at https://diffeq.sciml.ai/stable/solvers/ode_solve/ + You can find the list of available solvers at and its associated pages. """ @@ -281,7 +281,7 @@ const DIRECT_AUTODIFF_INCOMPATABILITY_MESSAGE = """ For more details on automatic differentiation, adjoint, and sensitivity analysis of differential equations, see the documentation page: - https://diffeq.sciml.ai/stable/analysis/sensitivity/ + """ struct DirectAutodiffError <: Exception end @@ -413,7 +413,7 @@ const TUPLE_STATE_ERROR_MESSAGE = """ ``` This will be safer and fast for small ODEs. For more information, see: - https://diffeq.sciml.ai/stable/tutorials/faster_ode_example/#Further-Optimizations-of-Small-Non-Stiff-ODEs-with-StaticArrays + """ struct TupleStateError <: Exception end diff --git a/src/problems/bvp_problems.jl b/src/problems/bvp_problems.jl index fcdbbaa86..fa8ff8a6f 100644 --- a/src/problems/bvp_problems.jl +++ b/src/problems/bvp_problems.jl @@ -11,7 +11,7 @@ struct TwoPointBVProblem{iip} end # The iip is needed to make type stable constr @doc doc""" Defines an BVP problem. -Documentation Page: [https://docs.sciml.ai/DiffEqDocs/stable/types/bvp_types/](https://docs.sciml.ai/DiffEqDocs/stable/types/bvp_types/) +Documentation Page: ## Mathematical Specification of a BVP Problem @@ -253,7 +253,7 @@ struct TwoPointSecondOrderBVProblem{iip} end # The iip is needed to make type st @doc doc""" Defines a second order BVP problem. -Documentation Page: [https://docs.sciml.ai/DiffEqDocs/stable/types/bvp_types/](https://docs.sciml.ai/DiffEqDocs/stable/types/bvp_types/) +Documentation Page: ## Mathematical Specification of a second order BVP Problem diff --git a/src/problems/dae_problems.jl b/src/problems/dae_problems.jl index 999587d95..38af0eec7 100644 --- a/src/problems/dae_problems.jl +++ b/src/problems/dae_problems.jl @@ -2,7 +2,7 @@ Defines an implicit ordinary differential equation (ODE) or differential-algebraic equation (DAE) problem. -Documentation Page: [https://docs.sciml.ai/DiffEqDocs/stable/types/dae_types/](https://docs.sciml.ai/DiffEqDocs/stable/types/dae_types/) +Documentation Page: ## Mathematical Specification of an DAE Problem diff --git a/src/problems/dde_problems.jl b/src/problems/dde_problems.jl index 090a91524..30c0066fd 100644 --- a/src/problems/dde_problems.jl +++ b/src/problems/dde_problems.jl @@ -6,7 +6,7 @@ struct StandardDDEProblem end @doc doc""" Defines a delay differential equation (DDE) problem. -Documentation Page: [https://docs.sciml.ai/DiffEqDocs/stable/types/dde_types/](https://docs.sciml.ai/DiffEqDocs/stable/types/dde_types/) +Documentation Page: ## Mathematical Specification of a DDE Problem diff --git a/src/problems/discrete_problems.jl b/src/problems/discrete_problems.jl index 75c908b22..6c28d2877 100644 --- a/src/problems/discrete_problems.jl +++ b/src/problems/discrete_problems.jl @@ -4,7 +4,7 @@ const DISCRETE_OUTOFPLACE_DEFAULT = DiscreteFunction{false}((u, p, t) -> u) @doc doc""" Defines a discrete dynamical system problem. -Documentation Page: [https://docs.sciml.ai/DiffEqDocs/stable/types/discrete_types/](https://docs.sciml.ai/DiffEqDocs/stable/types/discrete_types/) +Documentation Page: ## Mathematical Specification of a Discrete Problem diff --git a/src/problems/implicit_discrete_problems.jl b/src/problems/implicit_discrete_problems.jl index 515bd48fb..a4593ff87 100644 --- a/src/problems/implicit_discrete_problems.jl +++ b/src/problems/implicit_discrete_problems.jl @@ -1,7 +1,7 @@ @doc doc""" Defines a discrete dynamical system problem. -Documentation Page: [https://docs.sciml.ai/DiffEqDocs/stable/types/discrete_types/](https://docs.sciml.ai/DiffEqDocs/stable/types/discrete_types/) +Documentation Page: ## Mathematical Specification of a ImplicitDiscrete Problem diff --git a/src/problems/integral_problems.jl b/src/problems/integral_problems.jl index 27e1ae9b4..de55dc5f4 100644 --- a/src/problems/integral_problems.jl +++ b/src/problems/integral_problems.jl @@ -1,7 +1,7 @@ @doc doc""" Defines an integral problem. -Documentation Page: [https://docs.sciml.ai/Integrals/stable/](https://docs.sciml.ai/Integrals/stable/) +Documentation Page: ## Mathematical Specification of an Integral Problem @@ -123,7 +123,7 @@ struct QuadratureProblem end @doc doc""" Defines a integral problem over pre-sampled data. -Documentation Page: https://docs.sciml.ai/Integrals/stable/ +Documentation Page: ## Mathematical Specification of a data Integral Problem diff --git a/src/problems/linear_problems.jl b/src/problems/linear_problems.jl index e41f7e0ae..f93337eec 100644 --- a/src/problems/linear_problems.jl +++ b/src/problems/linear_problems.jl @@ -50,7 +50,7 @@ end @doc doc""" Defines a linear system problem. -Documentation Page: [https://docs.sciml.ai/LinearSolve/stable/basics/LinearProblem/](https://docs.sciml.ai/LinearSolve/stable/basics/LinearProblem/) +Documentation Page: ## Mathematical Specification of a Linear Problem diff --git a/src/problems/nonlinear_problems.jl b/src/problems/nonlinear_problems.jl index 4dd5744bd..bddaea13c 100644 --- a/src/problems/nonlinear_problems.jl +++ b/src/problems/nonlinear_problems.jl @@ -6,7 +6,7 @@ struct StandardNonlinearProblem end @doc doc""" Defines an interval nonlinear system problem. -Documentation Page: [https://docs.sciml.ai/NonlinearSolve/stable/basics/nonlinear_problem/](https://docs.sciml.ai/NonlinearSolve/stable/basics/nonlinear_problem/) +Documentation Page: ## Mathematical Specification of an Interval Nonlinear Problem @@ -107,7 +107,7 @@ end @doc doc""" Defines a nonlinear system problem. -Documentation Page: [https://docs.sciml.ai/NonlinearSolve/stable/basics/nonlinear_problem/](https://docs.sciml.ai/NonlinearSolve/stable/basics/nonlinear_problem/) +Documentation Page: ## Mathematical Specification of a Nonlinear Problem diff --git a/src/problems/ode_problems.jl b/src/problems/ode_problems.jl index d0d382821..8e5088190 100644 --- a/src/problems/ode_problems.jl +++ b/src/problems/ode_problems.jl @@ -6,7 +6,7 @@ struct StandardODEProblem end @doc doc""" Defines an ordinary differential equation (ODE) problem. -Documentation Page: [https://docs.sciml.ai/DiffEqDocs/stable/types/ode_types/](https://docs.sciml.ai/DiffEqDocs/stable/types/ode_types/) +Documentation Page: ## Mathematical Specification of an ODE Problem @@ -210,7 +210,7 @@ abstract type AbstractDynamicalODEProblem end @doc doc""" Defines a dynamical ordinary differential equation (ODE) problem. -Documentation Page: https://docs.sciml.ai/DiffEqDocs/stable/types/dynamical_types/ +Documentation Page: Dynamical ordinary differential equations, such as those arising from the definition of a Hamiltonian system or a second order ODE, have a special structure that can be @@ -288,7 +288,7 @@ end @doc doc""" Defines a second order ordinary differential equation (ODE) problem. -Documentation Page: https://docs.sciml.ai/DiffEqDocs/stable/types/dynamical_types/ +Documentation Page: ## Mathematical Specification of a 2nd Order ODE Problem @@ -392,7 +392,7 @@ abstract type AbstractSplitODEProblem end @doc doc""" Defines a split ordinary differential equation (ODE) problem. -Documentation Page: https://docs.sciml.ai/DiffEqDocs/stable/types/split_ode_types/ +Documentation Page: ## Mathematical Specification of a Split ODE Problem diff --git a/src/problems/optimization_problems.jl b/src/problems/optimization_problems.jl index cd3d4436b..ebbacec37 100644 --- a/src/problems/optimization_problems.jl +++ b/src/problems/optimization_problems.jl @@ -3,7 +3,7 @@ @doc doc""" Defines an optimization problem. -Documentation Page: [https://docs.sciml.ai/Optimization/stable/API/optimization_problem/](https://docs.sciml.ai/Optimization/stable/API/optimization_problem/) +Documentation Page: ## Mathematical Specification of an Optimization Problem diff --git a/src/problems/rode_problems.jl b/src/problems/rode_problems.jl index 61e46bb67..cc0a76c8e 100644 --- a/src/problems/rode_problems.jl +++ b/src/problems/rode_problems.jl @@ -1,7 +1,7 @@ @doc doc""" Defines a random ordinary differential equation (RODE) problem. -Documentation Page: [https://docs.sciml.ai/DiffEqDocs/stable/types/rode_types/](https://docs.sciml.ai/DiffEqDocs/stable/types/rode_types/) +Documentation Page: ## Mathematical Specification of a RODE Problem diff --git a/src/problems/sdde_problems.jl b/src/problems/sdde_problems.jl index 5b313326f..d865415c2 100644 --- a/src/problems/sdde_problems.jl +++ b/src/problems/sdde_problems.jl @@ -1,7 +1,7 @@ @doc doc""" Defines a stochastic delay differential equation (SDDE) problem. -Documentation Page: [https://docs.sciml.ai/DiffEqDocs/stable/types/sdde_types/](https://docs.sciml.ai/DiffEqDocs/stable/types/sdde_types/) +Documentation Page: ## Mathematical Specification of a Stochastic Delay Differential Equation (SDDE) Problem diff --git a/src/problems/sde_problems.jl b/src/problems/sde_problems.jl index 622373778..4f4993ace 100644 --- a/src/problems/sde_problems.jl +++ b/src/problems/sde_problems.jl @@ -6,7 +6,7 @@ struct StandardSDEProblem end @doc doc""" Defines an stochastic differential equation (SDE) problem. -Documentation Page: [https://docs.sciml.ai/DiffEqDocs/stable/types/sde_types/](https://docs.sciml.ai/DiffEqDocs/stable/types/sde_types/) +Documentation Page: ## Mathematical Specification of a SDE Problem diff --git a/src/problems/steady_state_problems.jl b/src/problems/steady_state_problems.jl index 52f5bce5b..652dd596e 100644 --- a/src/problems/steady_state_problems.jl +++ b/src/problems/steady_state_problems.jl @@ -1,7 +1,7 @@ @doc doc""" Defines a steady state ODE problem. -Documentation Page: [https://docs.sciml.ai/DiffEqDocs/stable/types/steady_state_types/](https://docs.sciml.ai/DiffEqDocs/stable/types/steady_state_types/) +Documentation Page: ## Mathematical Specification of a Steady State Problem diff --git a/src/solutions/basic_solutions.jl b/src/solutions/basic_solutions.jl index dd2898afd..e6a20ee2a 100644 --- a/src/solutions/basic_solutions.jl +++ b/src/solutions/basic_solutions.jl @@ -17,7 +17,7 @@ Representation of the solution to an linear system Ax=b defined by a LinearProbl - `cache`: the `LinearCache` object containing the solver's internal cached variables. This is given to allow continuation of solver usage, for example, solving `Ax=b` with the same `A` and a new `b` without refactorizing `A`. See the caching interface tutorial for details - on how to use the `cache` effectively: http://docs.sciml.ai/LinearSolve/stable/tutorials/caching_interface/ + on how to use the `cache` effectively: - `stats`: statistics of the solver, such as the number of function evaluations required. """ struct LinearSolution{T, N, uType, R, A, C, S} <: AbstractLinearSolution{T, N} diff --git a/src/solutions/dae_solutions.jl b/src/solutions/dae_solutions.jl index dd3960624..1e4187d74 100644 --- a/src/solutions/dae_solutions.jl +++ b/src/solutions/dae_solutions.jl @@ -8,7 +8,7 @@ Representation of the solution to an differential-algebraic equation defined by For more information on interacting with `DESolution` types, check out the Solution Handling page of the DifferentialEquations.jl documentation. -https://docs.sciml.ai/DiffEqDocs/stable/basics/solution/ + ## Fields diff --git a/src/solutions/ode_solutions.jl b/src/solutions/ode_solutions.jl index 47d375627..0a8124881 100644 --- a/src/solutions/ode_solutions.jl +++ b/src/solutions/ode_solutions.jl @@ -87,7 +87,7 @@ Representation of the solution to an ordinary differential equation defined by a For more information on interacting with `DESolution` types, check out the Solution Handling page of the DifferentialEquations.jl documentation. -https://docs.sciml.ai/DiffEqDocs/stable/basics/solution/ + ## Fields diff --git a/src/solutions/rode_solutions.jl b/src/solutions/rode_solutions.jl index 2e31dabd9..6c1a66dcc 100644 --- a/src/solutions/rode_solutions.jl +++ b/src/solutions/rode_solutions.jl @@ -11,7 +11,7 @@ or of a random ordinary differential equation defined by an RODEProblem. For more information on interacting with `DESolution` types, check out the Solution Handling page of the DifferentialEquations.jl documentation. -https://docs.sciml.ai/DiffEqDocs/stable/basics/solution/ + ## Fields diff --git a/src/solve.jl b/src/solve.jl index fe329c1eb..b00a2ad1f 100644 --- a/src/solve.jl +++ b/src/solve.jl @@ -177,7 +177,7 @@ const OPTIMIZER_MISSING_ERROR_MESSAGE = """ `solve(prob,Optim.BFGS())` requires `using OptimizationOptimJL` and `solve(prob,Adam())` requires `using OptimizationOptimisers`. - For more information, see the Optimization.jl documentation: https://docs.sciml.ai/Optimization/stable/. + For more information, see the Optimization.jl documentation: . """ struct OptimizerMissingError <: Exception @@ -523,7 +523,7 @@ end const ADJOINT_NOT_FOUND_MESSAGE = """ Compatibility with reverse-mode automatic differentiation requires SciMLSensitivity.jl. Please install SciMLSensitivity.jl and do `using SciMLSensitivity`/`import SciMLSensitivity` - for this functionality. For more details, see https://sensitivity.sciml.ai/dev/. + for this functionality. For more details, see . """ struct AdjointNotFoundError <: Exception end @@ -539,7 +539,7 @@ end const FORWARD_SENSITIVITY_NOT_FOUND_MESSAGE = """ Compatibility with forward-mode automatic differentiation requires SciMLSensitivity.jl. Please install SciMLSensitivity.jl and do `using SciMLSensitivity`/`import SciMLSensitivity` - for this functionality. For more details, see https://sensitivity.sciml.ai/dev/. + for this functionality. For more details, see . """ struct ForwardSensitivityNotFoundError <: Exception end