Refactoring (#13)

* Soft checks * Modyfied tests * Adding dependencies for DiffEqCallbacks * improoved jacobian build-up * Update README.md Co-authored-by: Jayesh K. Gupta <[email protected]> * Adding compat entry for Documenter * Updated docs/manifest * Update Documentation.yml * Upgraded documentation to Julia 1.6
ThummeTo · Oct 7, 2021 · a0d162d · a0d162d · ThummeTo · Oct 7, 2021
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diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml
@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
         with:
-          version: '1.5'
+          version: '1.6'
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

diff --git a/Manifest.toml b/Manifest.toml
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "FMIFlux"
 uuid = "fabad875-0d53-4e47-9446-963b74cae21f"
 authors = ["TT <[email protected]>", "LM <[email protected]>"]
-version = "0.1.2"
+version = "0.1.3"
 
 [deps]
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
@@ -15,9 +15,9 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 [compat]
 DiffEqCallbacks = "2.16.1"
 DiffEqFlux = "1.36.1"
-FMI = "0.1.4"
+FMI = "0.1.7"
 Flux = "0.12.1"
 OrdinaryDiffEq = "5.53.1"
 Plots = "1.14.0"
-Zygote = "0.6.10"
-julia = "1.5"
+Zygote = "0.6.17"
+julia = "1.6"
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-![FMIFlux.jl Logo](https://github.com/ThummeTo/FMIFlux.jl/blob/main/logo/fmifluxjl_logo_640_320.png "FMIFlux.jl Logo")
+![FMIFlux.jl Logo](https://github.com/ThummeTo/FMIFlux.jl/blob/main/logo/dark/fmifluxjl_logo_640_320.png "FMIFlux.jl Logo")
 # FMIFlux.jl
 
 ## What is FMIFlux.jl?
@@ -15,11 +15,20 @@ FMIFlux.jl is a free-to-use software library for the Julia programming language,
 
 ## What is currently supported in FMIFlux.jl?
 - building and training ME-NeuralFMUs with the default Flux-Front-End
-- building and training CS-NeuralFMUs 
+- building and training CS-NeuralFMUs with the default Flux-Front-End
 - ...
 
 ## What is under development in FMIFlux.jl?
+- performance optimizations
 - different modes for sensitivity estimation
-- documentation
+- improved documentation
 - more examples
 - ...
+
+## What Platforms are supported?
+FMI.jl is tested (and testing) under Julia Version 1.6 on Windows (latest) and Ubuntu (latest). Mac should work, but untested.
+
+## How to cite? Related publications?
+Tobias Thummerer, Lars Mikelsons and Josef Kircher. 2021. **NeuralFMU: towards structural integration of FMUs into neural networks** In Martin Sjölund, Lena Buffoni, Adrian Pop and Lennart Ochel (Ed.). Proceedings of 14th Modelica Conference 2021, Linköping, Sweden, September 20-24, 2021. Linköping University Electronic Press, Linköping (Linköping Electronic Conference Proceedings ; 181), 297-306. [DOI: 10.3384/ecp21181297](https://doi.org/10.3384/ecp21181297)
+
+Tobias Thummerer, Johannes Tintenherr, Lars Mikelsons 2021 **Hybrid modeling of the human cardiovascular system using NeuralFMUs** (10th International Conference on Mathematical Modeling in Physical Sciences, Preprint, Accepted) [arXiv:2109.04880](https://arxiv.org/abs/2109.04880)
diff --git a/docs/Manifest.toml b/docs/Manifest.toml
@@ -1,16 +1,18 @@
 # This file is machine-generated - editing it directly is not advised
 
+[[ArgTools]]
+uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
+
+[[Artifacts]]
+uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[Dates]]
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
-[[Distributed]]
-deps = ["Random", "Serialization", "Sockets"]
-uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
-
 [[DocStringExtensions]]
 deps = ["LibGit2", "Markdown", "Pkg", "Test"]
 git-tree-sha1 = "9d4f64f79012636741cf01133158a54b24924c32"
@@ -23,6 +25,10 @@ git-tree-sha1 = "3ebb967819b284dc1e3c0422229b58a40a255649"
 uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 version = "0.26.3"
 
+[[Downloads]]
+deps = ["ArgTools", "LibCURL", "NetworkOptions"]
+uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+
 [[IOCapture]]
 deps = ["Logging"]
 git-tree-sha1 = "377252859f740c217b936cebcd918a44f9b53b59"
@@ -39,10 +45,22 @@ git-tree-sha1 = "81690084b6198a2e1da36fcfda16eeca9f9f24e4"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 version = "0.21.1"
 
+[[LibCURL]]
+deps = ["LibCURL_jll", "MozillaCACerts_jll"]
+uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
+
+[[LibCURL_jll]]
+deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
+uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
+
 [[LibGit2]]
-deps = ["Printf"]
+deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 
+[[LibSSH2_jll]]
+deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
+uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
+
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
@@ -53,25 +71,35 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
+[[MbedTLS_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
+
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
+[[MozillaCACerts_jll]]
+uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
+
+[[NetworkOptions]]
+uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
+
 [[Parsers]]
 deps = ["Dates"]
 git-tree-sha1 = "c8abc88faa3f7a3950832ac5d6e690881590d6dc"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
 version = "1.1.0"
 
 [[Pkg]]
-deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[Printf]]
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [[REPL]]
-deps = ["InteractiveUtils", "Markdown", "Sockets"]
+deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 
 [[Random]]
@@ -87,8 +115,16 @@ uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 [[Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
+[[TOML]]
+deps = ["Dates"]
+uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+
+[[Tar]]
+deps = ["ArgTools", "SHA"]
+uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
+
 [[Test]]
-deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[UUIDs]]
@@ -97,3 +133,15 @@ uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [[Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+
+[[Zlib_jll]]
+deps = ["Libdl"]
+uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+
+[[nghttp2_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
+
+[[p7zip_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,2 +1,5 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
+[compat]
+julia = "1.6"
diff --git a/example/.gitignore b/example/.gitignore
@@ -1,3 +1,4 @@
 *.svg
 *.pdf
-*.gif
+*.gif
+tmp/