Merge remote-tracking branch 'origin/master' into sm/symutils3

Author: shashi

.github/workflows/CompatHelper.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: [1.2.0]
+        julia-version: [1.5.0]
         julia-arch: [x86]
         os: [ubuntu-latest]
     steps:

Project.toml

@@ -1,7 +1,7 @@
 name = "ModelingToolkit"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
 authors = ["Chris Rackauckas <[email protected]>"]
-version = "3.13.0"
+version = "3.20.0"
 
 [deps]
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
@@ -12,8 +12,10 @@ DiffRules = "b552c78f-8df3-52c6-915a-8e097449b14b"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 GeneralizedGenerated = "6b9d7cbe-bcb9-11e9-073f-15a7a543e2eb"
+IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
+Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
@@ -31,14 +33,15 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
 ArrayInterface = "2.8"
-DataStructures = "0.17"
+DataStructures = "0.17, 0.18"
 DiffEqBase = "6.38"
 DiffEqJump = "6.7.5"
 DiffRules = "0.1, 1.0"
 DocStringExtensions = "0.7, 0.8"
 GeneralizedGenerated = "0.1.4, 0.2"
+IfElse = "0.1"
 LabelledArrays = "1.3"
-Latexify = "0.11, 0.12, 0.13"
+Latexify = "0.11, 0.12, 0.13, 0.14"
 LightGraphs = "1.3"
 MacroTools = "0.5"
 NaNMath = "0.3"
@@ -47,7 +50,7 @@ Requires = "1.0"
 SafeTestsets = "0.0.1"
 SpecialFunctions = "0.7, 0.8, 0.9, 0.10"
 StaticArrays = "0.10, 0.11, 0.12"
-SymbolicUtils = "0.4.3"
+SymbolicUtils = "0.5"
 TreeViews = "0.3"
 UnPack = "0.1, 1.0"
 Unitful = "1.1"

docs/make.jl

@@ -16,7 +16,8 @@ makedocs(
             "tutorials/higher_order.md",
             "tutorials/nonlinear.md",
             "tutorials/modelingtoolkitize.md",
-            "tutorials/auto_parallel.md"
+            "tutorials/auto_parallel.md",
+            "tutorials/converting_to_C.md"
         ],
         "Systems" => Any[
             "systems/AbstractSystem.md",
@@ -25,12 +26,14 @@ makedocs(
             "systems/JumpSystem.md",
             "systems/NonlinearSystem.md",
             "systems/OptimizationSystem.md",
+            "systems/ControlSystem.md",
             "systems/ReactionSystem.md",
             "systems/PDESystem.md",
             "systems/DependencyGraphs.md"
         ],
         "Comparison Against SymPy" => "comparison.md",
         "highlevel.md",
+        "build_function.md",
         "IR.md"
     ]
 )

docs/src/IR.md

@@ -111,18 +111,3 @@ rename
 get_variables
 substitute_expr!
 ```
-
-### Expression Generation and `build_function`
-
-At any time, Julia expressions can be generated from ModelingToolkit IR by using
-`convert(Expr,x)`. This performs some cleaning to return an expression without
-extraneous pieces that commonly matches expressions one would write in functions
-like those for differential equation solvers and optimization libraries.
-
-Additionally, the core compilation process of ModelingToolkit IR is `build_function`.
-`build_function` takes an operation or an `AbstractArray` of operations and
-generates a compilable version of the model for numerical solvers.
-
-```@docs
-build_function
-```

docs/src/build_function.md

@@ -0,0 +1,32 @@
+# Function Building and Compilation (build_function)
+
+At any time, callable functions can be generated from ModelingToolkit IR by using
+`convert(Expr,x)`. This performs some cleaning to return an expression without
+extraneous pieces that commonly matches expressions one would write in functions
+like those for differential equation solvers and optimization libraries. These
+functions can be automatically parallelize and specialize on Julia types like
+static arrays and sparse matrices.
+
+The core compilation process of ModelingToolkit IR is `build_function`.
+`build_function` takes an operation or an `AbstractArray` of operations and
+generates a compilable version of the model for numerical solvers. The form of
+this output is dependent on the `target`. By default, the target outputs
+Julia code, but other formats, such as C, Stan, and MATLAB are available.
+These can be generated as expressions which can then be evaluated into a callable
+function, or the compilers for the respective targets can be invoked to directly
+give back the function handle.
+
+## build_function
+
+```@docs
+build_function
+```
+
+## Target-Specific Definitions
+
+```@docs
+_build_function(target::JuliaTarget,args...;kwargs...)
+_build_function(target::CTarget,args...;kwargs...)
+_build_function(target::StanTarget,args...;kwargs...)
+_build_function(target::MATLABTarget,args...;kwargs...)
+```

docs/src/systems/AbstractSystem.md

@@ -56,6 +56,10 @@ generate_factorized_W
 generate_hessian
 ```
 
+Additionally, `jacobian_sparsity(sys)` and `hessian_sparsity(sys)`
+exist on the appropriate systems for fast generation of the sparsity
+patterns via an abstract interpretation without requiring differentiation.
+
 ## Problem Constructors
 
 At the end, the system types have `DEProblem` constructors, like `ODEProblem`,

docs/src/systems/ControlSystem.md

@@ -0,0 +1,20 @@
+# ControlSystem
+
+## System Constructors
+
+```@docs
+ControlSystem
+```
+
+## Composition and Accessor Functions
+
+- `sys.eqs` or `equations(sys)`: The equations that define the system.
+- `sys.states` or `states(sys)`: The set of states in the system.
+- `sys.parameters` or `parameters(sys)`: The parameters of the system.
+- `sys.controls` or `controls(sys)`: The control variables of the system
+
+## Transformations
+
+```@docs
+runge_kutta_discretize
+```

docs/src/systems/NonlinearSystem.md

@@ -19,6 +19,7 @@ NonlinearSystem
 ```julia
 calculate_jacobian
 generate_jacobian
+jacobian_sparsity
 ```
 
 ## Problem Constructors

docs/src/systems/ODESystem.md

@@ -28,6 +28,7 @@ calculate_factorized_W
 generate_jacobian
 generate_tgrad
 generate_factorized_W
+jacobian_sparsity
 ```
 
 ## Problem Constructors

docs/src/systems/OptimizationSystem.md

@@ -21,6 +21,7 @@ calculate_gradient
 calculate_hessian
 generate_gradient
 generate_hessian
+hessian_sparsity
 ```
 
 ## Problem Constructors