Interface with MTK and allow using symbolic variables in get/set para…

…m and get state (#190) * fix the successful step function not having nan * mtk integration works * improve docs * get state also works with symbolics! * add changelog * add MTK to test deps * mention MTK interfacing in CoupledODEs * rename current_state to observe_State * MTK works woth stroboscopic * ProjectedDS works as well * remove unecessary set_parameter extensions * finish MTK integration * export the function referrencing the system * use getu/setu directly on numeric containers Requires SciML/SymbolicIndexingInterface.jl#33 to be merged! * make sure tests pass * simplify referrenced sys function: we only need sys now * all tests pass! * finish changelog * better/clearer handling of observation index * use the referrenced SciML Problem instead of System! * correct retrieval of referrenced system * allow `set_u` to set a specific component of the system! with symbolic! * make sure function is only used with core systems * Throw error if no referrenced MTK * simplify set_state!@ * fix set state for parallel systems * request merged and tagged functionality * trigger tests * fix tests * update docs * finish changelog * correct set_paramters! * remove examples from index * fix stroboscopic tests * fix successful step tests * fix docs!
JuliaDynamics · Jan 25, 2024 · ea3f650 · ea3f650
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,31 @@
+# v3.5.0
+
+Dynamical systems that have been constructed from `DEProblem`s that themselves
+have been constructed from ModelingToolkit.jl keep a reference to the symbolic
+model and all symbolic variables. Accessing a `DynamicalSystem` using symbolic variables
+is possible via the functions [`observe_state`](@ref), [`set_state!`](@ref),
+[`current_parameter`](@ref) and [`set_parameter!`](@ref).
+The referenced MTK model corresponding to the dynamical system can be obtained with
+`model = referrenced_sciml_model(ds::DynamicalSystem)`.
+
+See also the online overarching tutorial for an example.
+
+At the moment this is only possible for `CoupledODEs` and its derivative systems, as these are the only systems that can be made by a `DEProblem`, however it should be easy to allow e.g., `DeterministicIterated` to be created by a `DiscreteProblem`.
+
+The integration is supported by the functions `current_parameter`, `set_parameter!` where a symbolic MTK parameter can be given as an index. In `observe_state`, a state variable or observed variable symbol can be given.
+
+Also:
+
+- Crucial bugfix for `successful_step` that was not working properly for discrete time systems.
+
+# v3.4.0
+
+Better error handling for `diffeq` and `CoupledODEs`: passing a keyword was possible but should not have been.
+
+# v3.3.0
+
+Sorry, I forgot what goes here!
+
 # v3.2.0
 The keyword `Dt` can now be used instead of `Δt` in `trajectory` if access to unicode isn't available.
 

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "DynamicalSystemsBase"
 uuid = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
 repo = "https://github.com/JuliaDynamics/DynamicalSystemsBase.jl.git"
-version = "3.4.3"
+version = "3.5.0"
 
 [deps]
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
@@ -13,6 +13,7 @@ SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StateSpaceSets = "40b095a5-5852-4c12-98c7-d43bf788e795"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
 
 [compat]
 ForwardDiff = "0.10"
@@ -22,4 +23,5 @@ Roots = "1, 2"
 SciMLBase = "1.19.5, 2"
 StateSpaceSets = "1"
 Statistics = "1"
+SymbolicIndexingInterface = "0.3.4"
 julia = "1.9"
diff --git a/docs/juliadynamics-dark.scss b/docs/juliadynamics-dark.scss
@@ -4,7 +4,6 @@
 // under documenter/_variables or documenter/_overrides. But some stuff are Bulma defaults
 // as well, so you may need to look them up too: https://bulma.io/documentation/customize/variables/
 
-
 ////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////
 // Thse define the JuliaDynamics template:
@@ -87,6 +86,8 @@ $input-focus-border-color: $mainwhite;
 
 $documenter-docstring-shadow: 3px 3px 4px invert($shadow-color);
 
+
+
 // Admonition stuff
 $admbg: lighten-color($body-background-color, 0.5);
 $admonition-background: (
@@ -97,16 +98,23 @@ $admonition-header-background: (
   'default': #ba3f1f, 'warning': #a88b17, 'danger': #c7524c,
   'success': #42ac68, 'info': #28c);
 
+// Deprecations
+$admonition-body-color: null;
+$admonition-body-color: null;
+$admonition-header-color: null;
+
 // All secondary themes have to be nested in a theme--$(themename) class. When Documenter
 // switches themes, it applies this class to <html> and then disables the primary
 // stylesheet.
 @import "documenter/utilities";
 @import "documenter/variables";
 @import "bulma/utilities/all";
 @import "bulma/base/minireset.sass";
-@import "bulma/base/helpers.sass";
+@import "bulma/helpers/_all.sass";
 
 html.theme--#{$themename} {
+  @extend .is-size-7 !optional;
+
   @import "bulma/base/generic.sass";
 
   @import "documenter/overrides";
@@ -127,7 +135,7 @@ html.theme--#{$themename} {
   @import "documenter/theme_overrides";
 
   // $shadow-color: #202224;
-
+  
   #documenter .docs-sidebar { // This makes sidebar have shadow at all displays
     border-right: none;
     box-shadow: 1.2*$shadow-size 0rem 1*$shadow-blur invert($shadow-color);

diff --git a/docs/juliadynamics-darkdefs.scss b/docs/juliadynamics-darkdefs.scss
@@ -40,6 +40,8 @@ $input-focus-border-color: $mainwhite;
 
 $documenter-docstring-shadow: 3px 3px 4px invert($shadow-color);
 
+
+
 // Admonition stuff
 $admbg: lighten-color($body-background-color, 0.5);
 $admonition-background: (
@@ -50,16 +52,23 @@ $admonition-header-background: (
   'default': #ba3f1f, 'warning': #a88b17, 'danger': #c7524c,
   'success': #42ac68, 'info': #28c);
 
+// Deprecations
+$admonition-body-color: null;
+$admonition-body-color: null;
+$admonition-header-color: null;
+
 // All secondary themes have to be nested in a theme--$(themename) class. When Documenter
 // switches themes, it applies this class to <html> and then disables the primary
 // stylesheet.
 @import "documenter/utilities";
 @import "documenter/variables";
 @import "bulma/utilities/all";
 @import "bulma/base/minireset.sass";
-@import "bulma/base/helpers.sass";
+@import "bulma/helpers/_all.sass";
 
 html.theme--#{$themename} {
+  @extend .is-size-7 !optional;
+
   @import "bulma/base/generic.sass";
 
   @import "documenter/overrides";
@@ -80,7 +89,7 @@ html.theme--#{$themename} {
   @import "documenter/theme_overrides";
 
   // $shadow-color: #202224;
-
+  
   #documenter .docs-sidebar { // This makes sidebar have shadow at all displays
     border-right: none;
     box-shadow: 1.2*$shadow-size 0rem 1*$shadow-blur invert($shadow-color);

diff --git a/docs/juliadynamics-light.scss b/docs/juliadynamics-light.scss
@@ -4,7 +4,6 @@
 // under documenter/_variables or documenter/_overrides. But some stuff are Bulma defaults
 // as well, so you may need to look them up too: https://bulma.io/documentation/customize/variables/
 
-
 ////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////
 // Thse define the JuliaDynamics template:
@@ -93,10 +92,6 @@ $documenter-sidebar-size: 1.0em; // the default is 1.0 as well
 $input-hover-border-color: $secondcolor;
 $input-focus-border-color: $mainwhite;
 
-// Include the original theme which will now use the updated variables.
-// This should be the last thing in the SCSS file.
-@import "documenter-light";
-
 #documenter .docs-sidebar { // This makes sidebar have shadow at all displays
   border-right: none;
   box-shadow: 1.2*$shadow-size 0rem 1*$shadow-blur $shadow-color;
@@ -112,3 +107,7 @@ $input-focus-border-color: $mainwhite;
     }
   }
 }
+
+// Include the original theme which will now use the updated variables.
+// This should be the last thing in the SCSS file.
+@import "documenter-light";
diff --git a/docs/juliadynamics-lightdefs.scss b/docs/juliadynamics-lightdefs.scss
@@ -46,10 +46,6 @@ $documenter-sidebar-size: 1.0em; // the default is 1.0 as well
 $input-hover-border-color: $secondcolor;
 $input-focus-border-color: $mainwhite;
 
-// Include the original theme which will now use the updated variables.
-// This should be the last thing in the SCSS file.
-@import "documenter-light";
-
 #documenter .docs-sidebar { // This makes sidebar have shadow at all displays
   border-right: none;
   box-shadow: 1.2*$shadow-size 0rem 1*$shadow-blur $shadow-color;
@@ -65,3 +61,7 @@ $input-focus-border-color: $mainwhite;
     }
   }
 }
+
+// Include the original theme which will now use the updated variables.
+// This should be the last thing in the SCSS file.
+@import "documenter-light";
diff --git a/docs/juliadynamics-style.scss b/docs/juliadynamics-style.scss
@@ -4,7 +4,6 @@
 // under documenter/_variables or documenter/_overrides. But some stuff are Bulma defaults
 // as well, so you may need to look them up too: https://bulma.io/documentation/customize/variables/
 
-
 ////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////
 // Thse define the JuliaDynamics template:

diff --git a/docs/make.jl b/docs/make.jl
@@ -1,38 +1,19 @@
 cd(@__DIR__)
 
-import Downloads
-Downloads.download(
-    "https://raw.githubusercontent.com/JuliaDynamics/doctheme/master/apply_style.jl",
-    joinpath(@__DIR__, "apply_style.jl")
-)
-include("apply_style.jl")
-
 using DynamicalSystemsBase
 
-DYNAMICALSYSTEMSBASE_PAGES = [
+pages = [
     "index.md",
 ]
 using DynamicalSystemsBase.SciMLBase
 
-makedocs(
-    modules = [DynamicalSystemsBase, SciMLBase, StateSpaceSets],
-    format = Documenter.HTML(
-        prettyurls = CI,
-        assets = [
-            asset("https://fonts.googleapis.com/css?family=Montserrat|Source+Code+Pro&display=swap", class=:css),
-        ],
-    ),
-    sitename = "DynamicalSystemsBase.jl",
-    authors = "George Datseris",
-    pages = DYNAMICALSYSTEMSBASE_PAGES,
-    doctest = false,
-    draft = false,
+import Downloads
+Downloads.download(
+    "https://raw.githubusercontent.com/JuliaDynamics/doctheme/master/build_docs_with_style.jl",
+    joinpath(@__DIR__, "build_docs_with_style.jl")
 )
+include("build_docs_with_style.jl")
 
-if CI
-    deploydocs(
-        repo = "github.com/JuliaDynamics/DynamicalSystemsBase.jl.git",
-        target = "build",
-        push_preview = true
-    )
-end
+build_docs_with_style(pages,
+    DynamicalSystemsBase, SciMLBase, StateSpaceSets;
+)