dependency updates (#95)

* dependency updates * reverted changes in notebook * cleared notebook to enable build process for docu * clean up dead references in docu * updated readme * removed dor * adjustments because of dependency changes * check for ReverseDiffAdjoint() * added testing benchmark for different sensitivities * Quadrature Adjoint test * removed dead line * cleaned up tests * more decimals for gradient printing * added different gradient tests * fixed runtest * test fix * test new sensitivity
ThummeTo · Aug 8, 2023 · 52a0294 · 52a0294 · ThummeTo · Aug 8, 2023
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diff --git a/Project.toml b/Project.toml
@@ -1,9 +1,8 @@
 name = "FMIFlux"
 uuid = "fabad875-0d53-4e47-9446-963b74cae21f"
-version = "0.10.5"
+version = "0.10.6"
 
 [deps]
-ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 DifferentiableEigen = "73a20539-4e65-4dcb-a56d-dc20f210a01b"
@@ -18,13 +17,12 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 ThreadPools = "b189fb0b-2eb5-4ed4-bc0c-d34c51242431"
 
 [compat]
-ChainRulesCore = "1.16.0"
 Colors = "0.12.8"
 DiffEqCallbacks = "2.26.0"
 DifferentiableEigen = "0.2.0"
 DifferentialEquations = "7.8.0"
-FMIImport = "0.15.7"
-Flux = "0.13.17"
+FMIImport = "0.15.8"
+Flux = "0.13, 0.14"
 Optim = "1.7.0"
 ProgressMeter = "1.7.0"
 Requires = "1.3.0"

diff --git a/README.md b/README.md
@@ -2,7 +2,12 @@
 # FMIFlux.jl
 
 ## What is FMIFlux.jl?
-[*FMIFlux.jl*](https://github.com/ThummeTo/FMIFlux.jl) is a free-to-use software library for the Julia programming language, which offers the ability to set up NeuralFMUs just like NeuralODEs: You can place FMUs ([fmi-standard.org](http://fmi-standard.org/)) simply inside any feed-forward ANN topology and still keep the resulting hybrid model trainable with a standard (or custom) FluxML training process.
+[*FMIFlux.jl*](https://github.com/ThummeTo/FMIFlux.jl) is a free-to-use software library for the Julia programming language, which offers the ability to simply place your FMU ([fmi-standard.org](http://fmi-standard.org/)) everywhere inside of your ML topologies and still keep the resulting models trainable with a standard (or custom) FluxML training process. This includes for example:
+- NeuralODEs including FMUs, so called *Neural Functional Mock-up Units* (NeuralFMUs): 
+You can place FMUs inside of your ML topology.
+- PINNs including FMUs, so called *Functional Mock-Up Unit informed Neural Networks* (FMUINNs): 
+You can evaluate FMUs inside of your loss function. 
+
 
 [![Dev Docs](https://img.shields.io/badge/docs-dev-blue.svg)](https://ThummeTo.github.io/FMIFlux.jl/dev) 
 [![Test (latest)](https://github.com/ThummeTo/FMIFlux.jl/actions/workflows/TestLatest.yml/badge.svg)](https://github.com/ThummeTo/FMIFlux.jl/actions/workflows/TestLatest.yml)
@@ -12,40 +17,43 @@
 [![Run PkgEval](https://github.com/ThummeTo/FMIFlux.jl/actions/workflows/Eval.yml/badge.svg)](https://github.com/ThummeTo/FMIFlux.jl/actions/workflows/Eval.yml)
 [![Coverage](https://codecov.io/gh/ThummeTo/FMIFlux.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/ThummeTo/FMIFlux.jl)
 [![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)
-
+[![FMIFlux Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/FMIFlux)](https://pkgs.genieframework.com?packages=FMIFlux)
 
 ## How can I use FMIFlux.jl?
 
 1\. Open a Julia-REPL, switch to package mode using `]`, activate your preferred environment.
 
 2\. Install  [*FMIFlux.jl*](https://github.com/ThummeTo/FMIFlux.jl):
 ```julia-repl
-(@v1.x) pkg> add FMIFlux
+(@v1) pkg> add FMIFlux
 ```
 
 3\. If you want to check that everything works correctly, you can run the tests bundled with [*FMIFlux.jl*](https://github.com/ThummeTo/FMIFlux.jl):
 ```julia-repl
-(@v1.x) pkg> test FMIFlux
+(@v1) pkg> test FMIFlux
 ```
 
 4\. Have a look inside the [examples folder](https://github.com/ThummeTo/FMIFlux.jl/tree/examples/examples) in the examples branch or the [examples section](https://thummeto.github.io/FMIFlux.jl/dev/examples/overview/) of the documentation. All examples are available as Julia-Script (*.jl*), Jupyter-Notebook (*.ipynb*) and Markdown (*.md*).
 
 ## What is currently supported in FMIFlux.jl?
-- building and training ME-NeuralFMUs (event-handling is supported) with the default Flux-Front-End
-- building and training CS-NeuralFMUs with the default Flux-Front-End
-- different AD-frameworks: ForwardDiff.jl, ReverseDiff.jl (default setting) and Zygote.jl
+- building and training ME-NeuralFMUs (NeuralODEs) with support for event-handling (*DiffEqCallbacks.jl*) and discontinuous sensitivity analysis (*SciMLSensitivity.jl*)
+- building and training CS-NeuralFMUs 
+- building and training NeuralFMUs consisiting of multiple FMUs
+- building and training FMUINNs (PINNs)
+- different AD-frameworks: ForwardDiff.jl (CI-tested), ReverseDiff.jl (CI-tested, default setting), FiniteDiff.jl (not CI-tested) and Zygote.jl (not CI-tested)
 - ...
 
 ## What is under development in FMIFlux.jl?
 - performance optimizations
 - improved documentation
 - more examples
+- FMI3 integration
 - ...
 
 ## What Platforms are supported?
-[*FMIFlux.jl*](https://github.com/ThummeTo/FMIFlux.jl) is tested (and testing) under Julia versions *1.6* (LTS) and *1.8* (latest) on Windows (latest) and Ubuntu (latest). MacOS should work, but untested.
+[*FMIFlux.jl*](https://github.com/ThummeTo/FMIFlux.jl) is tested (and testing) under Julia versions *v1.6* (LTS) and *v1* (latest) on Windows (latest) and Ubuntu (latest). MacOS should work, but untested.
 [*FMIFlux.jl*](https://github.com/ThummeTo/FMIFlux.jl) currently only works with FMI2-FMUs. 
-All shipped examples are automatically tested under Julia version *1.8* (latest) on Windows (latest).
+All shipped examples are automatically tested under Julia version *v1* (latest) on Windows (latest).
 
 ## What FMI.jl-Library should I use?
 ![FMI.jl Family](https://github.com/ThummeTo/FMI.jl/blob/main/docs/src/assets/FMI_JL_family.png?raw=true "FMI.jl Family")

diff --git a/docs/make.jl b/docs/make.jl
@@ -19,8 +19,9 @@ makedocs(sitename="FMIFlux.jl",
                     "Simple CS-NeuralFMU" => "examples/simple_hybrid_CS.md"
                     "Simple ME-NeuralFMU" => "examples/simple_hybrid_ME.md"
                     "Advanced ME-NeuralFMU" => "examples/advanced_hybrid_ME.md"
+                    "JuliaCon 2023" => "examples/julicon_2023.md"
+                    "MDPI 2022" => "examples/mdpi_2022.md"
                     "Modelica Conference 2021" => "examples/modelica_conference_2021.md"
-                    "Physics-enhanced NeuralODEs in real-world applications" => "examples/mdpi_2022.md"
             ]
             "FAQ" => "faq.md"
             "Library Functions" => "library.md"

diff --git a/docs/src/examples/overview.md b/docs/src/examples/overview.md
@@ -16,3 +16,6 @@ The examples show how to combine FMUs with machine learning ("NeuralFMU") and il
 - [__JuliaCon 2023: Using NeuralODEs in real life applications__](https://thummeto.github.io/FMIFlux.jl/dev/examples/juliacon_2023/): An example for a NeuralODE in a real world engineering scenario.
 - [__MDPI 2022: Physics-enhanced NeuralODEs in real-world applications__](https://thummeto.github.io/FMIFlux.jl/dev/examples/mdpi_2022/): An example for a NeuralODE in a real world modeling scenario (Contribution in *MDPI Electronics 2022*).
 - [__Modelica Conference 2021: NeuralFMUs__](https://thummeto.github.io/FMIFlux.jl/dev/examples/modelica_conference_2021/): Showing basics on how to train a NeuralFMU (Contribution for the *Modelica Conference 2021*).
+
+## Archived
+- ...
diff --git a/examples/src/juliacon_2023.ipynb b/examples/src/juliacon_2023.ipynb
diff --git a/src/batch.jl b/src/batch.jl
@@ -4,34 +4,34 @@
 #
 
 import FMIImport: fmi2Real, fmi2FMUstate, fmi2EventInfo, fmi2ComponentState
-import ChainRulesCore: ignore_derivatives
+import FMIImport.ChainRulesCore: ignore_derivatives
 using DiffEqCallbacks: FunctionCallingCallback
 using FMIImport.ForwardDiff
 import FMIImport: unsense
 
-struct FMU2Loss{T}
+struct FMULoss{T}
     loss::T
     step::Integer 
     time::Real 
 
-    function FMU2Loss{T}(loss::T, step::Integer=0, time::Real=time()) where {T}
+    function FMULoss{T}(loss::T, step::Integer=0, time::Real=time()) where {T}
         inst = new{T}(loss, step, time)
         return inst
     end
 
-    function FMU2Loss(loss, step::Integer=0, time::Real=time())
+    function FMULoss(loss, step::Integer=0, time::Real=time())
         loss = unsense(loss)
         T = typeof(loss)
         inst = new{T}(loss, step, time)
         return inst
     end
 end
 
-function nominalLoss(l::FMU2Loss{T}) where T <: AbstractArray
+function nominalLoss(l::FMULoss{T}) where T <: AbstractArray
     return unsense(sum(l.loss))
 end
 
-function nominalLoss(l::FMU2Loss{T}) where T <: Real
+function nominalLoss(l::FMULoss{T}) where T <: Real
     return unsense(l.loss)
 end
 
@@ -45,7 +45,7 @@ mutable struct FMU2SolutionBatchElement <: FMU2BatchElement
     initialState::Union{fmi2FMUstate, Nothing}
     initialComponentState::fmi2ComponentState
     initialEventInfo::Union{fmi2EventInfo, Nothing}
-    losses::Array{<:FMU2Loss} 
+    losses::Array{<:FMULoss} 
     step::Integer
 
     saveat::Union{AbstractVector{<:Real}, Nothing}
@@ -65,7 +65,7 @@ mutable struct FMU2SolutionBatchElement <: FMU2BatchElement
 
         inst.initialState = nothing
         inst.initialEventInfo = nothing 
-        inst.losses = Array{FMU2Loss,1}()
+        inst.losses = Array{FMULoss,1}()
         inst.step = 0
 
         inst.saveat = nothing
@@ -83,7 +83,7 @@ mutable struct FMU2EvaluationBatchElement <: FMU2BatchElement
     tStart::fmi2Real 
     tStop::fmi2Real 
 
-    losses::Array{<:FMU2Loss} 
+    losses::Array{<:FMULoss} 
     step::Integer
 
     saveat::Union{AbstractVector{<:Real}, Nothing}
@@ -102,7 +102,7 @@ mutable struct FMU2EvaluationBatchElement <: FMU2BatchElement
         inst.tStart = -Inf
         inst.tStop = Inf
 
-        inst.losses = Array{FMU2Loss,1}()
+        inst.losses = Array{FMULoss,1}()
         inst.step = 0
 
         inst.saveat = nothing
@@ -335,7 +335,7 @@ function loss!(batchElement::FMU2SolutionBatchElement, lossFct; logLoss::Bool=tr
 
     ignore_derivatives() do 
         if logLoss
-            push!(batchElement.losses, FMU2Loss(loss, batchElement.step))
+            push!(batchElement.losses, FMULoss(loss, batchElement.step))
         end
     end
 
@@ -370,7 +370,7 @@ function loss!(batchElement::FMU2EvaluationBatchElement, lossFct; logLoss::Bool=
 
     ignore_derivatives() do 
         if logLoss
-            push!(batchElement.losses, FMU2Loss(loss, batchElement.step))
+            push!(batchElement.losses, FMULoss(loss, batchElement.step))
         end
     end
 

diff --git a/src/flux_overload.jl b/src/flux_overload.jl
@@ -4,7 +4,7 @@
 #
 
 import Flux
-import ChainRulesCore
+import FMIImport.ChainRulesCore
 import Flux.Random: AbstractRNG
 import Flux.LinearAlgebra: I