SciML · ChrisRackauckas · Jan 24, 2023 · Jan 24, 2023
diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml
@@ -1 +1,2 @@
 style = "sciml"
+format_markdown = true
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,3 +1,3 @@
-- This repository follows the [SciMLStyle](https://github.com/SciML/SciMLStyle) and the SciML [ColPrac](https://github.com/SciML/ColPrac).
-- Please run `using JuliaFormatter, ModelingToolkit; format(joinpath(dirname(pathof(ModelingToolkit)), ".."))` before commiting.
-- Add tests for any new features.
+  - This repository follows the [SciMLStyle](https://github.com/SciML/SciMLStyle) and the SciML [ColPrac](https://github.com/SciML/ColPrac).
+  - Please run `using JuliaFormatter, ModelingToolkit; format(joinpath(dirname(pathof(ModelingToolkit)), ".."))` before commiting.
+  - Add tests for any new features.
diff --git a/LICENSE.md b/LICENSE.md
@@ -2,43 +2,36 @@ The ModelingToolkit.jl package is licensed under the MIT "Expat" License:
 
 > Copyright (c) 2018-22: Yingbo Ma, Christopher Rackauckas, Julia Computing, and
 > contributors
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+> 
 > Permission is hereby granted, free of charge, to any person obtaining a copy
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+> 
 > of this software and associated documentation files (the "Software"), to deal
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+> 
 > in the Software without restriction, including without limitation the rights
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+> 
 > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+> 
 > copies of the Software, and to permit persons to whom the Software is
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+> 
 > furnished to do so, subject to the following conditions:
->
->
->
+> 
 > The above copyright notice and this permission notice shall be included in all
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+> 
 > copies or substantial portions of the Software.
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->
->
+> 
 > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+> 
 > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+> 
 > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+> 
 > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+> 
 > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+> 
 > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+> 
 > SOFTWARE.
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->
 
 The code in `src/structural_transformation/bipartite_tearing/modia_tearing.jl`,
 which is from the [Modia.jl](https://github.com/ModiaSim/Modia.jl) project, is

diff --git a/NEWS.md b/NEWS.md
@@ -1,10 +1,9 @@
 # ModelingToolkit v8 Release Notes
 
-
 ### Upgrade guide
 
-- `connect` should not be overloaded by users anymore. `[connect = Flow]`
-  informs ModelingToolkit that particular variable in a connector ought to sum
-  to zero, and by default, variables are equal in a connection. Please check out
-  [acausal components tutorial](https://docs.sciml.ai/ModelingToolkit/stable/tutorials/acausal_components/)
-  for examples.
+  - `connect` should not be overloaded by users anymore. `[connect = Flow]`
+    informs ModelingToolkit that particular variable in a connector ought to sum
+    to zero, and by default, variables are equal in a connection. Please check out
+    [acausal components tutorial](https://docs.sciml.ai/ModelingToolkit/stable/tutorials/acausal_components/)
+    for examples.
diff --git a/README.md b/README.md
@@ -1,14 +1,13 @@
 # ModelingToolkit.jl
 
-
 [![Join the chat at https://julialang.zulipchat.com #sciml-bridged](https://img.shields.io/static/v1?label=Zulip&message=chat&color=9558b2&labelColor=389826)](https://julialang.zulipchat.com/#narrow/stream/279055-sciml-bridged)
 [![Global Docs](https://img.shields.io/badge/docs-SciML-blue.svg)](https://docs.sciml.ai/ModelingToolkit/stable/)
 
 [![codecov](https://codecov.io/gh/SciML/ModelingToolkit.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/SciML/ModelingToolkit.jl)
 [![Coverage Status](https://coveralls.io/repos/github/SciML/ModelingToolkit.jl/badge.svg?branch=master)](https://coveralls.io/github/SciML/ModelingToolkit.jl?branch=master)
 [![Build Status](https://github.com/SciML/ModelingToolkit.jl/workflows/CI/badge.svg)](https://github.com/SciML/ModelingToolkit.jl/actions?query=workflow%3ACI)
 
-[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
+[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
 [![SciML Code Style](https://img.shields.io/static/v1?label=code%20style&message=SciML&color=9558b2&labelColor=389826)](https://github.com/SciML/SciMLStyle)
 
 ModelingToolkit.jl is a modeling framework for high-performance symbolic-numeric computation
@@ -121,7 +120,9 @@ plot(sol, idxs = (a, lorenz1.x, lorenz2.z))
 ![](https://user-images.githubusercontent.com/17304743/187790221-528046c3-dbdb-4853-b977-799596c147f3.png)
 
 # Citation
+
 If you use ModelingToolkit.jl in your research, please cite [this paper](https://arxiv.org/abs/2103.05244):
+
 ```
 @misc{ma2021modelingtoolkit,
       title={ModelingToolkit: A Composable Graph Transformation System For Equation-Based Modeling},

diff --git a/docs/src/basics/AbstractSystem.md b/docs/src/basics/AbstractSystem.md
@@ -10,28 +10,29 @@ model manipulation and compilation.
 ### Subtypes
 
 There are three immediate subtypes of `AbstractSystem`, classified by how many independent variables each type has:
-* `AbstractTimeIndependentSystem`: has no independent variable (e.g.: `NonlinearSystem`)
-* `AbstractTimeDependentSystem`: has a single independent variable (e.g.: `ODESystem`)
-* `AbstractMultivariateSystem`: may have multiple independent variables (e.g.: `PDESystem`)
+
+  - `AbstractTimeIndependentSystem`: has no independent variable (e.g.: `NonlinearSystem`)
+  - `AbstractTimeDependentSystem`: has a single independent variable (e.g.: `ODESystem`)
+  - `AbstractMultivariateSystem`: may have multiple independent variables (e.g.: `PDESystem`)
 
 ## Constructors and Naming
 
 The `AbstractSystem` interface has a consistent method for constructing systems.
 Generally, it follows the order of:
 
-1. Equations
-2. Independent Variables
-3. Dependent Variables (or States)
-4. Parameters
+ 1. Equations
+ 2. Independent Variables
+ 3. Dependent Variables (or States)
+ 4. Parameters
 
 All other pieces are handled via keyword arguments. `AbstractSystem`s share the
 same keyword arguments, which are:
 
-- `system`: This is used for specifying subsystems for hierarchical modeling with
-  reusable components. For more information, see the [components page](@ref components).
-- Defaults: Keyword arguments like `defaults` are used for specifying default
-  values which are used. If a value is not given at the `SciMLProblem` construction
-  time, its numerical value will be the default.
+  - `system`: This is used for specifying subsystems for hierarchical modeling with
+    reusable components. For more information, see the [components page](@ref components).
+  - Defaults: Keyword arguments like `defaults` are used for specifying default
+    values which are used. If a value is not given at the `SciMLProblem` construction
+    time, its numerical value will be the default.
 
 ## Composition and Accessor Functions
 
@@ -43,32 +44,32 @@ total set, which includes that of all systems held inside.
 
 The values which are common to all `AbstractSystem`s are:
 
-- `equations(sys)`: All equations that define the system and its subsystems.
-- `states(sys)`: All the states in the system and its subsystems.
-- `parameters(sys)`: All parameters of the system and its subsystems.
-- `nameof(sys)`: The name of the current-level system.
-- `get_eqs(sys)`: Equations that define the current-level system.
-- `get_states(sys)`: States that are in the current-level system.
-- `get_ps(sys)`: Parameters that are in the current-level system.
-- `get_systems(sys)`: Subsystems of the current-level system.
+  - `equations(sys)`: All equations that define the system and its subsystems.
+  - `states(sys)`: All the states in the system and its subsystems.
+  - `parameters(sys)`: All parameters of the system and its subsystems.
+  - `nameof(sys)`: The name of the current-level system.
+  - `get_eqs(sys)`: Equations that define the current-level system.
+  - `get_states(sys)`: States that are in the current-level system.
+  - `get_ps(sys)`: Parameters that are in the current-level system.
+  - `get_systems(sys)`: Subsystems of the current-level system.
 
 Optionally, a system could have:
 
-- `observed(sys)`: All observed equations of the system and its subsystems.
-- `get_observed(sys)`: Observed equations of the current-level system.
-- `get_continuous_events(sys)`: `SymbolicContinuousCallback`s of the current-level system.
-- `get_defaults(sys)`: A `Dict` that maps variables into their default values.
-- `independent_variables(sys)`: The independent variables of a system.
-- `get_noiseeqs(sys)`: Noise equations of the current-level system.
-- `get_metadata(sys)`: Any metadata about the system or its origin to be used by downstream packages.
+  - `observed(sys)`: All observed equations of the system and its subsystems.
+  - `get_observed(sys)`: Observed equations of the current-level system.
+  - `get_continuous_events(sys)`: `SymbolicContinuousCallback`s of the current-level system.
+  - `get_defaults(sys)`: A `Dict` that maps variables into their default values.
+  - `independent_variables(sys)`: The independent variables of a system.
+  - `get_noiseeqs(sys)`: Noise equations of the current-level system.
+  - `get_metadata(sys)`: Any metadata about the system or its origin to be used by downstream packages.
 
-Note that if you know a system is an `AbstractTimeDependentSystem` you could use `get_iv` to get the 
+Note that if you know a system is an `AbstractTimeDependentSystem` you could use `get_iv` to get the
 unique independent variable directly, rather than using `independent_variables(sys)[1]`, which is clunky and may cause problems if `sys` is an `AbstractMultivariateSystem` because there may be more than one independent variable. `AbstractTimeIndependentSystem`s do not have a method `get_iv`, and `independent_variables(sys)` will return a size-zero result for such. For an `AbstractMultivariateSystem`, `get_ivs` is equivalent.
 
 A system could also have caches:
 
-- `get_jac(sys)`: The Jacobian of a system.
-- `get_tgrad(sys)`: The gradient with respect to time of a system.
+  - `get_jac(sys)`: The Jacobian of a system.
+  - `get_tgrad(sys)`: The gradient with respect to time of a system.
 
 ## Transformations