manual canonical

docs/src/manual/API.md

@@ -15,18 +15,21 @@ DifferentialEquation
 HarmonicVariable
 HarmonicEquation
 ```
-```@docs; canonical=false
+
+```@docs
 rearrange_standard
 rearrange_standard!
 first_order_transform!
 is_rearranged_standard
 get_equations
 ```
+
 ```@docs
 get_harmonic_equations
 get_krylov_equations
 add_harmonic!
 ```
+
 ```@docs
 get_independent_variables
 get_variables
@@ -39,19 +42,22 @@ get_steady_states
 ```
 
 ### Methods
+
 ```@docs
 WarmUp
 TotalDegree
 Polyhedral
 ```
 
 ### Access solutions
+
 ```@docs
 get_single_solution
 transform_solutions
 ```
 
 ### Classify
+
 ```@docs
 classify_solutions!
 get_class
@@ -66,6 +72,7 @@ plot_spaghetti
 ```
 
 ## Limit cycles
+
 ```@docs
 get_limit_cycles
 get_cycle_variables
@@ -84,20 +91,23 @@ plot_linear_response
 plot_rotframe_jacobian_response
 ```
 
-## Extentsions
+## Extensions
 
 ### OrdinaryDiffEq
+
 ```@docs
 AdiabaticSweep
 follow_branch
 plot_1D_solutions_branch
 ```
 
 ### SteadyStateSweep
+
 ```@docs
 steady_state_sweep
 ```
 
 ### ModelingToolkit
+
 ```@docs
 ```

docs/src/manual/entering_eom.md

@@ -2,7 +2,7 @@
 
 The struct `DifferentialEquation` is the primary input method; it holds an ODE or a coupled system of ODEs composed of terms with harmonic time-dependence
 The dependent variables are specified during input, any other symbols
-are identified as parameters. Information on which variable is to be expanded in which harmonic is specified using `add_harmonic!`. 
+are identified as parameters. Information on which variable is to be expanded in which harmonic is specified using `add_harmonic!`.
 
 `DifferentialEquation.equations` stores a dictionary assigning variables to equations. This information is necessary because the harmonics belonging to a variable are later used to Fourier-transform its corresponding ODE.
 
@@ -11,4 +11,4 @@ DifferentialEquation
 add_harmonic!
 get_variables(::DifferentialEquation)
 get_independent_variables(::DifferentialEquation)
-```
+```

docs/src/manual/extracting_harmonics.md

@@ -22,10 +22,10 @@ The equations governing the harmonics are stored using the two following structs
 HarmonicVariable
 ```
 
-When the full set of equations of motion is expanded using the harmonic ansatz, the result is stored as a `HarmonicEquation`. For an initial equation of motion consisting of $M$ variables, each expanded in $N$ harmonics, the resulting `HarmonicEquation` holds $2NM$ equations of $2NM$ variables. Each symbol not corresponding to a variable is identified as a parameter. 
+When the full set of equations of motion is expanded using the harmonic ansatz, the result is stored as a `HarmonicEquation`. For an initial equation of motion consisting of $M$ variables, each expanded in $N$ harmonics, the resulting `HarmonicEquation` holds $2NM$ equations of $2NM$ variables. Each symbol not corresponding to a variable is identified as a parameter.
 
 A `HarmonicEquation` can be either parsed into a steady-state `Problem` or solved using a dynamical ODE solver.
 
 ```@docs; canonical=false
 HarmonicEquation
-```
+```\

docs/src/manual/linear_response.md

@@ -27,7 +27,7 @@ The simplest way to extract the linear response of a steady state is to evaluate
 The advantage of this method is that for a given parameter set, only one matrix diagonalization is needed to fully describe the response spectrum. However, the method is inaccurate for response frequencies far from the frequencies used in the harmonic ansatz (it relies on the response oscillating slowly in the rotating frame). 
 
 Behind the scenes, the spectra are stored using the dedicated structs `Lorentzian` and `JacobianSpectrum`.
-```@docs
+```@docs; canonical=false
 HarmonicBalance.LinearResponse.JacobianSpectrum
 HarmonicBalance.LinearResponse.Lorentzian
 ```
@@ -36,7 +36,7 @@ HarmonicBalance.LinearResponse.Lorentzian
 
 Setting `order > 1` increases the accuracy of the response spectra. However, unlike for the Jacobian, here we must perform a matrix inversion for each response frequency.  
 
-```@docs
+```@docs; canonical=false
 HarmonicBalance.LinearResponse.ResponseMatrix
 HarmonicBalance.get_response
 HarmonicBalance.LinearResponse.get_response_matrix

docs/src/manual/methods.md

@@ -3,16 +3,19 @@
 We offer several methods for solving the nonlinear algebraic equations that arise from the harmonic balance procedure. Each method has different tradeoffs between speed, robustness, and completeness.
 
 ## Total Degree Method
+
 ```@docs; canonical=false
 TotalDegree
 ```
 
 ## Polyhedral Method
+
 ```@docs; canonical=false
 Polyhedral
 ```
 
 ## Warm Up Method
+
 ```@docs; canonical=false
 WarmUp
 ```

docs/src/manual/saving.md

@@ -4,7 +4,7 @@ All of the types native to `HarmonicBalance.jl` can be saved into a `.jld2` file
 
 The function `export_csv` saves a .csv file which can be plot elsewhere.
 
-```@docs
+```@docs; canonical=false
 HarmonicBalance.save
 HarmonicBalance.load
 HarmonicBalance.export_csv

docs/src/manual/solving_harmonics.md

@@ -19,7 +19,7 @@ The solutions in `Result` are accompanied by similarly-sized boolean arrays stor
 
 By default, classes "physical", "stable" and "binary\_labels" are created. User-defined classification is possible with `classify_solutions!`.
 
-```@docs
+```@docs; canonical=false
 HarmonicBalance.classify_solutions!
 ```
 
@@ -35,6 +35,6 @@ The function `sort_solutions` goes over the the raw output of `get_steady_states
 
 Currently, `sort_solutions` is compatible with 1D and 2D arrays of solution sets.
 
-```@docs
+```@docs; canonical=false
 HarmonicBalance.sort_solutions
 ```

docs/src/manual/time_dependent.md

@@ -17,6 +17,6 @@ HarmonicBalance.plot(::OrdinaryDiffEqTsit5.ODESolution, ::Any, ::HarmonicEquatio
 ## Miscellaneous
 Using a time-dependent simulation can verify solution stability in cases where the Jacobian is too expensive to compute.
 
-```@docs
+```@docs; canonical=false
 HarmonicBalance.is_stable
 ```