docs and testing handled by ExampleJuggler.jl (#13)

* docs and testing handle by ExampleJuggler pkg * replace fieldtype jac * add repo link * bump v1.0.0 (breaking change): Params is now given as a struct, params fields can also be given as kwargs in pdepe function
gregoirepourtier · Nov 27, 2023 · b64d8cf · b64d8cf · gregoirepourtier · Nov 27, 2023
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diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "SkeelBerzins"
 uuid = "15eb0f9a-d441-4223-9ae5-4829ae804a45"
 authors = ["gregoirepourtier <gpourtier@icloud.com>"]
-version = "0.1.6"
+version = "1.0.0"
 
 [deps]
 BandedMatrices = "aae01518-5342-5314-be14-df237901396f"
@@ -37,6 +37,7 @@ julia = "1.6"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 DoubleFloats = "497a8b3b-efae-58df-a0af-a86822472b78"
+ExampleJuggler = "3bbe58f8-ed81-4c4e-a134-03e85fcf4a1a"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
@@ -46,4 +47,4 @@ SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "SpecialFunctions", "SciMLSensitivity", "OptimizationPolyalgorithms", "OptimizationOptimJL", "Optimization", "LinearAlgebra", "DifferentialEquations", "DelimitedFiles", "DoubleFloats"]
+test = ["Test", "SpecialFunctions", "SciMLSensitivity", "OptimizationPolyalgorithms", "OptimizationOptimJL", "Optimization", "LinearAlgebra", "DifferentialEquations", "DelimitedFiles", "DoubleFloats", "ExampleJuggler"]
diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 
 Solver for one-dimensional parabolic and elliptic nonlinear partial differential equations.
 
-This package is based on the spatial discretization for the method of lines introduced by Skeel and Berzins in [[1]](#Reference) and MATLAB's [pdepe](https://de.mathworks.com/help/matlab/ref/pdepe.html) API. For transient problems, the time discretization is performed either by the implicit Euler method (internal method) or by using an ODE/DAE solver from the [DifferentialEquations.jl](https://github.com/SciML/DifferentialEquations.jl) package.
+This package is based on the spatial discretization for the method of lines introduced by Skeel and Berzins in [[1]](#Reference) and provides an API similar to MATLAB's [pdepe](https://de.mathworks.com/help/matlab/ref/pdepe.html). For transient problems, the time discretization is performed either by the implicit Euler method (internal method) or by using an ODE/DAE solver from the [DifferentialEquations.jl](https://github.com/SciML/DifferentialEquations.jl) package.
 
 # Prerequisite
 

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,5 +1,12 @@
 [deps]
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DoubleFloats = "497a8b3b-efae-58df-a0af-a86822472b78"
+ExampleJuggler = "3bbe58f8-ed81-4c4e-a134-03e85fcf4a1a"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
+Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
+OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
+OptimizationPolyalgorithms = "500b13db-7e66-49ce-bda4-eed966be6282"
+SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1"
 SkeelBerzins = "15eb0f9a-d441-4223-9ae5-4829ae804a45"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,32 +1,55 @@
 using Documenter
 using SkeelBerzins, DifferentialEquations
+using ExampleJuggler
 
-makedocs(
-    modules = [SkeelBerzins, Base.get_extension(SkeelBerzins, :SkeelBerzinsDiffEq)],
-    sitename = "SkeelBerzins.jl",
-    doctest = false, clean = true,
-    warnonly = true,
-    format = Documenter.HTML(),
-    authors = "Grégoire Pourtier",
-    pages = ["Home" => "index.md",
-             "Manual" => ["Problem Definition" => "problem_definition.md",
-                          "Solvers" => "solvers.md",
-                          "Achieve performance" => "performance.md",
-                          "Public and Private APIs" => "public_private_APIs.md"
-                         ],
-             "Examples" => ["101: Linear Diffusion equation" =>"examples/example101.md",
-                            "102: Nonlinear Diffusion equation" =>"examples/example102.md",
-                            "103: Linear Diffusion equation in cylindrical coordinates" =>"examples/example103.md",
-                            "104: Poisson equation" =>"examples/example104.md",
-                            "105: Stationary nonlinear diffusion equation" =>"examples/example105.md",
-                            "106: System of Reaction-Diffusion equations" =>"examples/example106.md",
-                            "107: Linear Diffusion equation in spherical coordinates" =>"examples/example107.md",
-                            "201: Interpolation of Partial Derivatives" =>"examples/example201.md",
-                            "301: PDE Constrained Optimization" =>"examples/example301.md"
-                            ]
-            ]
-)
-
-deploydocs(
-    repo = "github.com/gregoirepourtier/SkeelBerzins.jl.git"
-)
+
+function create_doc()
+    ExampleJuggler.verbose!(true)
+
+    cleanexamples()
+
+    exampledir = joinpath(@__DIR__, "..", "examples")
+
+    modules = filter(ex -> splitext(ex)[2] == ".jl", basename.(readdir(exampledir)))
+    module_examples = @docmodules(exampledir, modules)
+
+    module_examples_reformated = Array{Pair{String,String}}(undef, length(module_examples))
+    for i in eachindex(module_examples)
+        mod = module_examples[i]
+        tmp_new = tmp = replace(replace(first(mod), "_" => ": " ; count=1), "Example" => "")
+        cpt_spaces = 0
+        for i in 2:length(tmp[2:end-1])
+            if isuppercase(tmp[i]) && islowercase(tmp[i+1])
+                tmp_new = tmp_new[1:i-1+cpt_spaces]*" "*tmp[i:end]
+                cpt_spaces += 1
+            end
+        end
+        module_examples_reformated[i] = Pair(tmp_new, mod[2]) 
+    end
+
+    makedocs(; modules = [SkeelBerzins, Base.get_extension(SkeelBerzins, :SkeelBerzinsDiffEq)],
+             sitename = "SkeelBerzins.jl",
+             checkdocs = :all,
+             doctest = false, clean = false,
+             warnonly = true,
+             format = Documenter.HTML(; mathengine = MathJax3(), repolink = "https://github.com/gregoirepourtier/SkeelBerzins.jl"),
+             authors = "G. Pourtier",
+             repo = "https://github.com/gregoirepourtier/SkeelBerzins.jl",
+             pages = ["Home" => "index.md",
+                      "Manual" => ["Problem Definition" => "problem_definition.md",
+                                   "Solvers" => "solvers.md",
+                                   "Achieve performance" => "performance.md",
+                                   "Public and Private APIs" => "public_private_APIs.md"
+                                  ],
+                      "Examples" => module_examples_reformated
+                    ])
+
+    cleanexamples()
+
+    deploydocs(
+        repo = "github.com/gregoirepourtier/SkeelBerzins.jl.git"
+    )
+
+end
+
+create_doc()
diff --git a/docs/src/examples/example101.md b/docs/src/examples/example101.md
diff --git a/docs/src/examples/example102.md b/docs/src/examples/example102.md