merge-v0.13.0

.github/workflows/Example.yml

@@ -24,20 +24,20 @@ jobs:
         julia-version: ['1.8'] 
         julia-arch: [x64]
         experimental: [false]
-
+        
     steps:
       - name: "Check out repository"
         uses: actions/checkout@v3
-
+        
       - name: "Set up Julia"
         uses: julia-actions/setup-julia@v1
         with:
             version: ${{ matrix.julia-version }}
             arch: ${{ matrix.julia-arch }}
-
+            
       - name: "Install dependencies"
         run: julia --project=examples/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-
+        
       - name: "Install packages"
         run: pip install jupyter nbconvert
 
@@ -48,7 +48,7 @@ jobs:
           jupyter nbconvert --ExecutePreprocessor.kernel_name="julia-1.8" --to notebook --inplace --execute ${{ env.FILE }}
           jupyter nbconvert --to script ${{ env.FILE }}
           jupyter nbconvert --to markdown ${{ env.FILE }}
-
+          
       - name: "Fix GIFs"
         run: |
           echo "starting gif fixing"
@@ -57,7 +57,7 @@ jobs:
           awk '{if($0~/<img src="data:image\/gif;base64,[[:alpha:],[:digit:],\/,+,=]*" \/>/) {sub(/<img src="data:image\/gif;base64,[[:alpha:],[:digit:],\/,+,=]*" \/>/,"![gif](${{ matrix.file-name }}_files\/gif_"++i".gif)")}}1' examples/jupyter-src/${{ matrix.file-name }}.md > examples/jupyter-src/tmp_${{ matrix.file-name }}.md
           mv -Force examples/jupyter-src/tmp_${{ matrix.file-name }}.md examples/jupyter-src/${{ matrix.file-name }}.md
           echo "gifs should be fixed"
-
+          
       - name: Archive examples artifacts (success)
         if: success() && matrix.os == 'windows-latest'
         uses: actions/upload-artifact@v3
@@ -70,30 +70,52 @@ jobs:
     steps:
       - name: "Check out repository"
         uses: actions/checkout@v3
-
+        
       - name: "Set up Julia"
         uses: julia-actions/setup-julia@v1
         with:
             version: '1.10'
-
+            
       - run: julia -e 'using Pkg; Pkg.add("PlutoSliderServer"); Pkg.add("FMIFlux")'
       - run: julia -e 'using PlutoSliderServer; PlutoSliderServer.export_directory("examples/pluto-src")'
-
+      
       - name: Archive examples artifacts (success)
         if: success()
         uses: actions/upload-artifact@v3
         with:
           name: pluto-examples
           path: examples/pluto-src/*
 
-  auto-commit:
+  filecheck: 
     needs: [jypiter, pluto]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download jupyter examples
+        uses: actions/download-artifact@v3
+        with:
+          name: jupyter-examples
+          path: examples/jupyter-src/
+
+      - name: Download pluto examples
+        uses: actions/download-artifact@v3
+        with:
+          name: pluto-examples
+          path: examples/pluto-src/
+
+      - name: Check if the example files generated are valid (if jupyter-examples failed, svgs are missing; jupyter command does not fail even if examples fail)
+        uses: andstor/file-existence-action@v3
+        with: 
+          files: "examples/jupyter-src/*/*.svg"
+          fail: true
+
+  auto-commit:
+    needs: [jypiter, pluto, filecheck]
     if: github.event_name != 'pull_request'
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
         uses: actions/checkout@v3
-
+        
       - name: Download jupyter examples
         uses: actions/download-artifact@v3
         with:
@@ -130,7 +152,7 @@ jobs:
           git add ${{ env.EXAMPLES_PATH }}
           git commit -m "${{ env.CI_COMMIT_MESSAGE }}"
           git push origin examples 
-
+          
   call-docu:
     needs: auto-commit
     if: github.event_name != 'pull_request'

Project.toml

@@ -1,30 +1,33 @@
 name = "FMIFlux"
 uuid = "fabad875-0d53-4e47-9446-963b74cae21f"
-version = "0.12.2"
+version = "0.13.0"
 
 [deps]
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 DifferentiableEigen = "73a20539-4e65-4dcb-a56d-dc20f210a01b"
-DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 FMIImport = "9fcbc62e-52a0-44e9-a616-1359a0008194"
 FMISensitivity = "3e748fe5-cd7f-4615-8419-3159287187d2"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
-ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 ThreadPools = "b189fb0b-2eb5-4ed4-bc0c-d34c51242431"
 
+[weakdeps]
+JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+
+[extensions]
+JLD2Ext = ["JLD2"]
+
 [compat]
-Colors = "0.12.8"
+Colors = "0.12"
 DifferentiableEigen = "0.2.0"
-DifferentialEquations = "7.7.0 - 7.12"
-FMIImport = "0.16.4"
-FMISensitivity = "0.1.4"
-Flux = "0.13.0 - 0.14"
-Optim = "1.7.0"
-ProgressMeter = "1.7.0 - 1.9"
-Requires = "1.3.0"
-ThreadPools = "2.1.1"
+FMIImport = "1.0.0"
+FMISensitivity = "0.2.0"
+Flux = "0.9 - 0.14"
+Optim = "1.6"
+OrdinaryDiffEq = "6.0"
+Statistics = "1"
+ThreadPools = "2.1"
 julia = "1.6"

README.md

@@ -82,10 +82,11 @@ To keep dependencies nice and clean, the original package [*FMI.jl*](https://git
 - [*FMI.jl*](https://github.com/ThummeTo/FMI.jl): High level loading, manipulating, saving or building entire FMUs from scratch
 - [*FMIImport.jl*](https://github.com/ThummeTo/FMIImport.jl): Importing FMUs into Julia
 - [*FMIExport.jl*](https://github.com/ThummeTo/FMIExport.jl): Exporting stand-alone FMUs from Julia Code
+- [*FMIBase.jl*](https://github.com/ThummeTo/FMIBase.jl): Common concepts for import and export of FMUs
 - [*FMICore.jl*](https://github.com/ThummeTo/FMICore.jl): C-code wrapper for the FMI-standard
 - [*FMISensitivity.jl*](https://github.com/ThummeTo/FMISensitivity.jl): Static and dynamic sensitivities over FMUs
 - [*FMIBuild.jl*](https://github.com/ThummeTo/FMIBuild.jl): Compiler/Compilation dependencies for FMIExport.jl
-- [*FMIFlux.jl*](https://github.com/ThummeTo/FMIFlux.jl): Machine Learning with FMUs (differentiation over FMUs)
+- [*FMIFlux.jl*](https://github.com/ThummeTo/FMIFlux.jl): Machine Learning with FMUs
 - [*FMIZoo.jl*](https://github.com/ThummeTo/FMIZoo.jl): A collection of testing and example FMUs
 
 ## How to cite?

src/extensions/JLD2.jl → ext/JLD2Ext.jl

@@ -3,14 +3,18 @@
 # Licensed under the MIT license. See LICENSE file in the project root for details.
 #
 
-function fmiSaveParameters(nfmu::NeuralFMU, path::String; keyword="parameters")
+module JLD2Ext
+
+using FMIFlux, JLD2
+
+function FMIFlux.saveParameters(nfmu::NeuralFMU, path::String; keyword="parameters")
 
     params = Flux.params(nfmu)
 
     JLD2.save(path, Dict(keyword=>params[1]))
 end
 
-function fmiLoadParameters(nfmu::NeuralFMU, path::String; flux_model=nothing, keyword="parameters")
+function FMIFlux.loadParameters(nfmu::NeuralFMU, path::String; flux_model=nothing, keyword="parameters")
 
     paramsLoad = JLD2.load(path, keyword) 
 
@@ -40,4 +44,6 @@ function fmiLoadParameters(nfmu::NeuralFMU, path::String; flux_model=nothing, ke
     end
 
     return nothing
-end
+end
+
+end # JLD2Ext

src/FMIFlux.jl

@@ -17,32 +17,20 @@ if VERSION < v"1.7.0"
     @warn "Training under Julia 1.6 is very slow, please consider using Julia 1.7 or newer." maxlog=1
 end
 
-import FMIImport.FMICore: hasCurrentComponent, getCurrentComponent, unsense
-import FMIImport.FMICore.ChainRulesCore: ignore_derivatives
+import FMIImport.FMIBase: hasCurrentInstance, getCurrentInstance, unsense
+import FMISensitivity.ChainRulesCore: ignore_derivatives
 
-import DifferentialEquations
 import FMIImport
 
-using Requires
 import Flux
 
 using FMIImport
-using FMIImport: fmi2ValueReference, FMU, FMU2, FMU2Component
-using FMIImport: fmi2Struct
-using FMIImport: fmi2SetupExperiment, fmi2EnterInitializationMode, fmi2ExitInitializationMode, fmi2Reset, fmi2Terminate
-using FMIImport: fmi2NewDiscreteStates, fmi2SetContinuousStates, fmi2GetContinuousStates, fmi2GetNominalsOfContinuousStates
-using FMIImport: fmi2SetTime, fmi2CompletedIntegratorStep, fmi2GetEventIndicators, fmi2GetDerivatives, fmi2GetReal
-using FMIImport: fmi2SampleJacobian, fmi2GetDirectionalDerivative, fmi2GetJacobian, fmi2GetJacobian!
-using FMIImport: fmi2True, fmi2False
-
-import FMIImport.FMICore: fmi2ValueReferenceFormat, fmi2Real
 
 include("optimiser.jl")
 include("hotfixes.jl")
 include("convert.jl")
 include("flux_overload.jl")
 include("neural.jl")
-#include("chain_rules.jl")
 include("misc.jl")
 include("layers.jl")
 include("deprecated.jl")
@@ -51,46 +39,17 @@ include("losses.jl")
 include("scheduler.jl")
 include("compatibility_check.jl")
 
-# from Plots.jl 
-# No export here, Plots.plot is extended if available.
-
-# from FMI.jl 
-function fmiPlot(nfmu::NeuralFMU; kwargs...)
-    @assert false "fmiPlot(...) needs `Plots` package. Please install `Plots` and do `using Plots` or `import Plots`."
-end
-function fmiPlot!(fig, nfmu::NeuralFMU; kwargs...)
-    @assert false "fmiPlot!(...) needs `Plots` package. Please install `Plots` and do `using Plots` or `import Plots`."
-end
-# No export here, FMI.fmiPlot is extended.
-
-# from JLD2.jl
-function fmiSaveParameters(nfmu::NeuralFMU, path::String; keyword="parameters")
-    @assert false "fmiSaveParameters(...) needs `JLD2` package. Please install `JLD2` and do `using JLD2` or `import JLD2`."
-end
-function fmiLoadParameters(nfmu::NeuralFMU, path::String; flux_model=nothing, keyword="parameters")
-    @assert false "fmiLoadParameters(...) needs `JLD2` package. Please install `JLD2` and do `using JLD2` or `import JLD2`."
-end
-export fmiSaveParameters, fmiLoadParameters
-
+# optional extensions
+using FMIImport.FMIBase.Requires
+using FMIImport.FMIBase.PackageExtensionCompat
 function __init__()
-    @require Plots="91a5bcdd-55d7-5caf-9e0b-520d859cae80" begin 
-        import .Plots
-        include("extensions/Plots.jl")
-    end
-
-    @require FMI="14a09403-18e3-468f-ad8a-74f8dda2d9ac" begin 
-        @require Plots="91a5bcdd-55d7-5caf-9e0b-520d859cae80" begin 
-            import .FMI 
-            include("extensions/FMI.jl")
-        end
-    end
-
-    @require JLD2="033835bb-8acc-5ee8-8aae-3f567f8a3819" begin
-        import .JLD2
-        include("extensions/JLD2.jl")
-    end
+    @require_extensions
 end
 
+# JLD2.jl
+function saveParameters end
+function loadParameters end
+
 # FMI_neural.jl
 export ME_NeuralFMU, CS_NeuralFMU, NeuralFMU
 

src/batch.jl

@@ -3,9 +3,9 @@
 # Licensed under the MIT license. See LICENSE file in the project root for details.
 #
 
-import FMIImport.FMICore: FMUSnapshot
+import FMIImport.FMIBase: FMUSnapshot
 import FMIImport: fmi2Real, fmi2FMUstate, fmi2EventInfo, fmi2ComponentState
-using DifferentialEquations.DiffEqCallbacks: FunctionCallingCallback
+using FMIImport.FMIBase.DiffEqCallbacks: FunctionCallingCallback
 
 abstract type FMU2BatchElement end
 
@@ -66,7 +66,7 @@ mutable struct FMU2SolutionBatchElement{D} <: FMU2BatchElement
 
     indicesModel
 
-    solution::FMU2Solution
+    solution::FMUSolution
 
     scalarLoss::Bool
     # canGetSetState::Bool
@@ -309,10 +309,10 @@ function loss!(batchElement::FMU2SolutionBatchElement, lossFct; logLoss::Bool=fa
 
     loss = 0.0 # will be incremented
 
-    if hasmethod(lossFct, Tuple{FMU2Solution})
+    if hasmethod(lossFct, Tuple{FMUSolution})
         loss = lossFct(batchElement.solution)
 
-    elseif hasmethod(lossFct, Tuple{FMU2Solution, Union{}})
+    elseif hasmethod(lossFct, Tuple{FMUSolution, Union{}})
         loss = lossFct(batchElement.solution, batchElement.targets)
 
     else # hasmethod(lossFct, Tuple{Union{}, Union{}})

src/deprecated.jl

@@ -3,6 +3,8 @@
 # Licensed under the MIT license. See LICENSE file in the project root for details.
 #
 
+using FMIImport.FMIBase: FMI2Struct
+
 """
 DEPRECATED:
 
@@ -46,7 +48,7 @@ DEPRECATED:
 
 Wrapper. Call ```fmi2EvaluateME``` for more information.
 """
-function fmiEvaluateME(str::fmi2Struct, 
+function fmiEvaluateME(str::FMI2Struct, 
                      x::Array{<:Real}, 
                      t::Real = (typeof(str) == FMU2 ? str.components[end].t : str.t),
                      setValueReferences::Union{Array{fmi2ValueReference}, Nothing} = nothing, 
@@ -64,7 +66,7 @@ DEPRECATED:
 
 Wrapper. Call ```fmi2DoStepCS``` for more information.
 """
-function fmiDoStepCS(str::fmi2Struct, 
+function fmiDoStepCS(str::FMI2Struct, 
                      dt::Real,
                      setValueReferences::Array{fmi2ValueReference} = zeros(fmi2ValueReference, 0), 
                      setValues::Array{<:Real} = zeros(Real, 0),
@@ -78,7 +80,7 @@ DEPRECATED:
 
 Wrapper. Call ```fmi2InputDoStepCSOutput``` for more information.
 """
-function fmiInputDoStepCSOutput(str::fmi2Struct, 
+function fmiInputDoStepCSOutput(str::FMI2Struct, 
                                 dt::Real, 
                                 u::Array{<:Real})
     fmi2InputDoStepCSOutput(str, dt, u)