try to add docs

.github/workflows/doc.yml

@@ -0,0 +1,22 @@
+name: Doc
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  docs:
+    name: Doc
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: Run tests
+name: Test
 
 on:
   push:

Manifest.toml

@@ -2,7 +2,12 @@
 
 julia_version = "1.10.2"
 manifest_format = "2.0"
-project_hash = "de4af1fb3390e68a97ccc9215147284c1486a39a"
+project_hash = "851282b9d4540d4f1d1d921b1dd41c97e2e71062"
+
+[[deps.ANSIColoredPrinters]]
+git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"
+uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"
+version = "0.0.1"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
@@ -363,6 +368,12 @@ git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d"
 uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 version = "0.9.3"
 
+[[deps.Documenter]]
+deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "CodecZlib", "Dates", "DocStringExtensions", "Downloads", "Git", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "MarkdownAST", "Pkg", "PrecompileTools", "REPL", "RegistryInstances", "SHA", "TOML", "Test", "Unicode"]
+git-tree-sha1 = "5a1ee886566f2fa9318df1273d8b778b9d42712d"
+uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+version = "1.7.0"
+
 [[deps.Downloads]]
 deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
@@ -572,6 +583,18 @@ git-tree-sha1 = "43ba3d3c82c18d88471cfd2924931658838c9d8f"
 uuid = "61579ee1-b43e-5ca0-a5da-69d92c66a64b"
 version = "9.55.0+4"
 
+[[deps.Git]]
+deps = ["Git_jll"]
+git-tree-sha1 = "04eff47b1354d702c3a85e8ab23d539bb7d5957e"
+uuid = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2"
+version = "1.3.1"
+
+[[deps.Git_jll]]
+deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"]
+git-tree-sha1 = "ea372033d09e4552a04fd38361cd019f9003f4f4"
+uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb"
+version = "2.46.2+0"
+
 [[deps.Glib_jll]]
 deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
 git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba"
@@ -631,6 +654,12 @@ git-tree-sha1 = "20b6765a3016e1fca0c9c93c80d50061b94218b7"
 uuid = "a51ab1cf-af8e-5615-a023-bc2c838bba6b"
 version = "69.1.0+0"
 
+[[deps.IOCapture]]
+deps = ["Logging", "Random"]
+git-tree-sha1 = "b6d6bfdd7ce25b0f9b2f6b3dd56b2673a66c8770"
+uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89"
+version = "0.2.5"
+
 [[deps.ImageAxes]]
 deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"]
 git-tree-sha1 = "2e4520d67b0cef90865b3ef727594d2a58e0e1f8"
@@ -830,6 +859,11 @@ git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec"
 uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 version = "1.3.1"
 
+[[deps.LazilyInitializedFields]]
+git-tree-sha1 = "8f7f3cabab0fd1800699663533b6d5cb3fc0e612"
+uuid = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf"
+version = "1.2.2"
+
 [[deps.LazyArtifacts]]
 deps = ["Artifacts", "Pkg"]
 uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
@@ -1000,6 +1034,12 @@ version = "0.4.2"
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
+[[deps.MarkdownAST]]
+deps = ["AbstractTrees", "Markdown"]
+git-tree-sha1 = "465a70f0fc7d443a00dcdc3267a497397b8a3899"
+uuid = "d0879d2d-cac2-40c8-9cee-1863dc0c7391"
+version = "0.1.2"
+
 [[deps.MathTeXEngine]]
 deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "UnicodeFun"]
 git-tree-sha1 = "96ca8a313eb6437db5ffe946c457a401bbb8ce1d"
@@ -1406,6 +1446,12 @@ git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
 uuid = "189a3867-3050-52da-a836-e630ba90ab69"
 version = "1.2.2"
 
+[[deps.RegistryInstances]]
+deps = ["LazilyInitializedFields", "Pkg", "TOML", "Tar"]
+git-tree-sha1 = "ffd19052caf598b8653b99404058fce14828be51"
+uuid = "2792f1a3-b283-48e8-9a74-f99dce5104f3"
+version = "0.1.0"
+
 [[deps.RelocatableFolders]]
 deps = ["SHA", "Scratch"]
 git-tree-sha1 = "ffdaf70d81cf6ff22c2b6e733c900c3321cab864"

Project.toml

@@ -7,6 +7,7 @@ version = "0.1.0"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 Gridap = "56d4f2e9-7ea1-5844-9cf6-b9c51ca7ce8e"
 LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255"

README.md

@@ -6,12 +6,14 @@
 <img src="https://github.com/lamBOOO/GenMatFlow.jl/actions/workflows/test.yml/badge.svg" alt="Testing workflow badge"/>
 </div>
 
-# GenMatFlow.jl
+# GenMatFlow.jl: A Navier-Stokes-Fourier Solver for generalized material laws
 
-- Navier-Stokes-Fourier Solver for generalized material laws, including:
+- Different material laws, including:
   - Newtonian fluids: $\boldsymbol{\sigma} = \boldsymbol{D}(\boldsymbol{u}) = \frac12 (\boldsymbol{\nabla} \boldsymbol{u} + \boldsymbol{\nabla} \boldsymbol{u}^T)$
   - Non-Newtonian fluids with power-law: $\boldsymbol{\sigma} = K {\left(2 \boldsymbol{D} \boldsymbol{\colon}  \boldsymbol{D} \right)}^{\frac{1-n}{2}} \boldsymbol{D}(\boldsymbol{u})$
 - Discretization using Finite Elements in [Gridap.jl](https://github.com/gridap/Gridap.jl)
+- Solve nonlinear systems using Newtons method
+
 
 ## Installation
 
@@ -28,5 +30,6 @@ julia --project -e 'import Pkg; Pkg.instantiate()'
 
 - Run examples by navigating to the folder and execute the examples from the shell:
 ```bash
-cd TODO
+cd examples/validation-basak
+include("basak.jl")
 ```

docs/.gitignore

@@ -0,0 +1 @@
+build/**

docs/make.jl

@@ -0,0 +1,19 @@
+push!(LOAD_PATH,"../src/")
+push!(LOAD_PATH,"src/")
+
+using GenMatFlow
+using Documenter
+
+makedocs(
+  sitename="GenMatFlow.jl",
+  remotes = nothing,
+  pages = Any[
+        "Home" => "index.md",
+        "API" => "api.md",
+    ]
+)
+
+# optionally deploy docs to github pages
+deploydocs(
+    repo = "github.com/lamBOOO/GenMatFlow.jl.git",
+)

docs/src/api.md

@@ -0,0 +1,14 @@
+# Developer Documentation
+
+## API
+
+```@autodocs
+Modules = [GenMatFlow]
+Private = true
+Order   = [:function, :type]
+```
+
+## Index
+
+```@index
+```

docs/src/index.md

@@ -0,0 +1,26 @@
+```@eval
+using Markdown
+# Read the README.md file as a string
+readme = read("../../README.md", String)
+
+# Find the position of the first '#' character (first headline)
+pos = findfirst(r"#", readme)[1]
+
+# Check if a '#' was found
+if isnothing(pos)
+    error("No '#' found in README.md")
+end
+
+print(readme)
+print(pos)
+
+# Extract the content from the first headline onward
+readme_content = readme[pos:end]
+
+# Parse the extracted content as Markdown and include it
+Markdown.parse(readme_content)
+```
+
+## API
+
+- See [API reference](./api.md)

src/Solver.jl

@@ -8,6 +8,44 @@ using LineSearches: BackTracking, StrongWolfe
 using Random
 Random.seed!(1234)
 
+export simulate
+
+"""
+    simulate(;name="sim",Pr=1.0,Ra=1.0,n=1.0,n_elems=20,nlsolver_opts=(;show_trace=true,method=:newton,linesearch=BackTracking(),ftol=1E-8,xtol=1E-10),levels=(;T=5,psi=5,Sth=5,Sfl=5),T_diri_tags=["leftline","rightline","botleftpoint","botrightpoint","topleftpoint","toprightpoint"],T_diri_expressions=[0.0,1.0,0.0,1.0,0.0,1.0])
+
+Simulate the flow in a square cavity with a moving lid and a temperature gradient.
+
+# Arguments
+- `name::String`: Name of the simulation.
+- `Pr::Float64`: Prandtl number.
+- `Ra::Float64`: Rayleigh number.
+- `n::Float64`: Power of the viscosity.
+- `n_elems::Int`: Number of elements in each direction.
+- `nlsolver_opts::Dict`: Options for the nonlinear solver.
+- `levels::Dict`: Levels for the contour plots.
+- `T_diri_tags::Array{String}`: Tags for the Dirichlet boundary conditions for the temperature.
+- `T_diri_expressions::Array{Float64}`: Expressions for the Dirichlet boundary conditions for the temperature.
+
+# Returns
+- `uh::FEFunction`: Velocity field.
+- `ph::FEFunction`: Pressure field.
+- `Th::FEFunction`: Temperature field.
+- `psih::FEFunction`: Stream function.
+- `Nu::Interpolable`: Nusselt number.
+- `Sth::FEFunction`: Local heat entropy.
+- `Sfl::FEFunction`: Local fluid entropy.
+- `btrian::BoundaryTriangulation`: Boundary triangulation.
+- `model::CartesianDiscreteModel`: Model.
+- `Ωₕ::Triangulation`: Triangulation.
+- `Pr::Float64`: Prandtl number.
+- `Ra::Float64`: Rayleigh number.
+
+# Example
+```julia
+simulate(;name="sim",Pr=1.0,Ra=1.0,n=1.0,n_elems=20,nlsolver_opts=(;show_trace=true,method=:newton,linesearch=BackTracking(),ftol=1E-8,xtol=1E-10),levels=(;T=5,psi=5,Sth=5,Sfl=5),T_diri_tags=["leftline","rightline","botleftpoint","botrightpoint","topleftpoint","toprightpoint"],T_diri_expressions=[0.0,1.0,0.0,1.0,0.0,1.0])
+```
+
+"""
 function simulate(;
   name="sim",
   Pr=1.0,