Merge pull request #37 from SINTEF/dev

ready for 0.5

Author: ThomasSauder

.github/workflows/ci.yml

@@ -1,32 +1,36 @@
-name: CI
+name: Running tests on all platforms
 on:
-  - pull_request
+  push: 
+    branches:
+      - main
+      - dev
+    tags: '*'
+    pull_request:  
 env:
   JULIA_NUM_THREADS: 2
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         version:
-          - '1.9'
-          - '^1.9'
+          - '1.10'
+          - '^1.10'
         os:
           - ubuntu-latest
           - macOS-latest
           - windows-latest
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-          include-all-prereleases: true
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:
@@ -39,30 +43,7 @@ jobs:
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
-  docs:
-    name: Documentation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: '1'
-      - run: |
-          julia --project=docs -e '
-            import Pkg; Pkg.add("Documenter")
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()'
-      - run: |
-          julia --project=docs -e '
-            import Pkg; Pkg.add("Documenter")
-            using Documenter: doctest
-            using Muscade
-            doctest(Muscade)'
-      - run: julia --project=docs docs/make.jl
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/documentation.yml

@@ -1,28 +1,46 @@
-name: Documentation
-# See https://documenter.juliadocs.org/stable/man/hosting/ 
+name: Documentation build and deploy
+# See  https://documenter.juliadocs.org/stable/man/hosting/ 
 # Should host doc at https://sintef.github.io/Muscade.jl/dev 
 # or                 https://sintef.github.io/Muscade.jl/stable 
 on:
   push:
     branches:
       - main
+      - dev
     tags: '*'
   pull_request:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
 
 jobs:
-  build:
-    permissions:
-      contents: write
+  build-and-deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
+      - name: Install binary dependencies
+        run: >
+          sudo apt-get update && 
+          sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev xsettingsd x11-xserver-utils
+      - name: Install Julia dependencies
+        run: > 
+          DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24'
+          julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy docs
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
-        #  DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
-        run: julia --project=docs/ docs/make.jl
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 
+        run: >
+          cd docs;
+          DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24'
+          julia --color=yes make.jl
+      - name: Upload site as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: Docs build
+          path: ./docs/build

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2022-2024 SINTEF Ocean
+Copyright (c) 2022-2025 SINTEF Ocean
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Project.toml

@@ -1,19 +1,21 @@
 name = "Muscade"
 uuid = "93488820-1883-11ed-0c34-05177b029e4d"
 authors = ["Philippe Maincon <philippe.maincon@sintef.no>"]
-version = "0.4.0"
+version = "0.5.0"
 
 [deps]
+KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [compat]
 MacroTools = "0.5"
+SparseArrays = "1"
 SpecialFunctions = "2"
 StaticArrays = "1"
-SparseArrays = "1"
 julia = "1.10,1.11"

docs/Project.toml

@@ -6,11 +6,3 @@ Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Muscade = "93488820-1883-11ed-0c34-05177b029e4d"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
-
-[compat]
-Documenter = "1"
-DocumenterCitations = "1"
-GLMakie = "0.10"
-Interpolations = "0.15"
-Literate = "2"
-StaticArrays = "1"

docs/build/SharedAnchor.jpg

@@ -1,10 +1,16 @@
-nodocstr(str) =  replace(str, r"(*ANYCRLF)^\"\"\"$.*?^\"\"\"$"ms => "")
 
 #Assumes that pwd() is docs
-docs    = @__DIR__
-muscade = normpath(joinpath(docs,".."))
-docsrc  = joinpath(docs,"src")
-examplessrc = normpath(joinpath(docs,"..","examples"))
+docs        = @__DIR__
+muscade     = normpath(joinpath(docs,".."))
+docsrc      = joinpath(docs,"src")
+examplesrc(ex) = normpath(joinpath(docs,"..","examples",ex))
+examples    = ["BeamElements","StaticBeamAnalysis","DynamicBeamAnalysis","DecayAnalysis","DryFriction"]
+
+requiredIncludeFiles = ["BeamElements.jl","Rotations.jl"]
+ for includeFile ∈ requiredIncludeFiles
+        cp(joinpath(muscade,"examples",includeFile),joinpath(muscade,"docs","src",includeFile),force=true)             
+ end
+
 
 using Pkg
 Pkg.activate(docs) 
@@ -16,37 +22,23 @@ cp(joinpath(muscade,"LICENSE.md"),joinpath(docsrc,"LICENSE.md"),force=true)
 
 ## Literate
 
-examples = ["StaticBeamAnalysis","DecayAnalysis","DryFriction"]
-
-function replace_includes(str)
-        included = ["BeamElements.jl","Rotations.jl"] # in this order
-        path = "examples/"
-        for ex in included
-                content = read(path*ex, String)
-                str     = replace(str, "include(\"$(ex)\")" => content)
-        end
-        return nodocstr(str)
-end
+nodocstr(str) =  replace(str, r"(*ANYCRLF)^\"\"\"$.*?^\"\"\"$"ms => "") # Take """ somedocstring """ out of str
 
+@printf "\nLiterate.markdown: *.jl → *.md\n\n"
 for ex ∈ examples
-        Literate.markdown(joinpath(examplessrc,@sprintf("%s.jl",ex)),docsrc, preprocess = replace_includes)
+        Literate.markdown(examplesrc(@sprintf("%s.jl",ex)), docsrc, preprocess = nodocstr)
 end
 
-# els = ["DryFriction","BeamElements"]
-# for el ∈ els
-#         Literate.markdown(joinpath(muscade,"examples",@sprintf("%s.jl",el)),docsrc,
-#                        execute=false,codefence= "````julia" => "````", # prevent execution of the code by Literate and Documenter
-#                        preprocess = replace_includes) 
-# end
-
 ## DocumenterCitations
 
 bib = CitationBibliography(joinpath(docsrc, "ref.bib"); style=:authoryear) #:numeric
 
 ## Documenter
 
+@printf "\nDocumenter.makedocs: *.md → *.html\n\n"
 makedocs(sitename ="Muscade.jl",
         modules   = [Muscade],
+        doctest   = false, # we do not use doctest, we run Literate.jl on mydemo.jl files that are also included in unit test files
         format    = Documenter.HTML(    prettyurls          = false,
                                         sidebar_sitename    = false,
                                         size_threshold_warn = 256*1024,
@@ -70,9 +62,9 @@ makedocs(sitename ="Muscade.jl",
                         build   = "build"                 
         )
 
-#deploydocs(muscade = "github.com/SINTEF/Muscade.jl.git",target="build",devbranch="dev")
 
-# https://sintef.github.io/Muscade.jl/v0.3.6/index.html
-# https://sintef.github.io/Muscade.jl/stable/index.html
+deploydocs(repo = "github.com/SINTEF/Muscade.jl.git",devbranch="dev",   devurl="dev",   versions = ["stable" => "stable", "dev" => "dev"])
+deploydocs(repo = "github.com/SINTEF/Muscade.jl.git",devbranch="main",  devurl="stable",versions = ["stable" => "stable", "dev" => "dev"])
 
-Pkg.activate(muscade)
+# https://sintef.github.io/Muscade.jl/dev
+# https://sintef.github.io/Muscade.jl/stable

docs/build/decaysmall.png

@@ -1,8 +1,12 @@
 # Automatic differentiation
 
-`Muscade` has its own implementation of forward automatic differentiation for historical reasons: Prototypes automaticdifferentiation of `Muscade` where developed in parallel with [`ForwardDiff.jl`](https://juliadiff.org/ForwardDiff.jl/stable/).  While the inner workings of [`ForwardDiff.jl`](https://juliadiff.org/ForwardDiff.jl/stable/) and `Muscade`'s version are similar ( with `ForwardDiff.jl` probably having better performance), the API are quite different.
+## History
 
-`Muscade` evaluates second derivative of the Lagrangian, using dneste *forward* differentiation, which is far from optimal.  An ambition is to make use of reverse differentiation (using [`Zygote.jl`](https://fluxml.ai/Zygote.jl/latest/), [`Enzyme.jl`](https://docs.sciml.ai/Enzyme/stable/) or similar).
+`Muscade` has its own implementation of forward automatic differentiation for historical reasons: Prototypes automatic differentiation of `Muscade` where developed in parallel with [`ForwardDiff.jl`](https://juliadiff.org/ForwardDiff.jl/stable/).  While the inner workings of [`ForwardDiff.jl`](https://juliadiff.org/ForwardDiff.jl/stable/) and `Muscade`'s version are similar ( with `ForwardDiff.jl` probably having better performance), the API are quite different.
+
+`Muscade` evaluates second derivative of the Lagrangian, using nested *forward* differentiation, which is far from optimal.  An ambition is to make use of reverse differentiation (using [`Zygote.jl`](https://fluxml.ai/Zygote.jl/latest/), [`Enzyme.jl`](https://docs.sciml.ai/Enzyme/stable/) or similar).
+
+## Usage
 
 `Muscade`s automatic differentiation is used as follows:
 
@@ -45,3 +49,6 @@ y   = value{P}(y1)
 yₓ  = ∂{P,N}(y2)
 ```
 
+## Taylor expansions
+
+One way to accelerate automatic differentiation of complicated functions can be to compose the differentiation of simpler functions, in particular function with smaller inputs.  Use [`fast`](@ref) for basic applications, and [`revariate`](@ref) and [`compose`](@ref) for advanced usage.