Merge pull request #172 from CarloLucibello/cl/tutorials

add Pluto tutorials

Author: CarloLucibello

Project.toml

@@ -33,6 +33,7 @@ Flux = "0.13"
 Functors = "0.2"
 Graphs = "1.4"
 KrylovKit = "0.5"
+MLDatasets = "0.6, 0.7"
 MLUtils = "0.2.3"
 MacroTools = "0.5"
 NNlib = "0.8"

docs/Project.toml

@@ -3,5 +3,11 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 GraphNeuralNetworks = "cffab07f-9bc2-4db1-8861-388f63bf7694"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MarkdownLiteral = "736d6165-7244-6769-4267-6b50796e6954"
 NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
+Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
+PlutoStaticHTML = "359b1769-a58e-495b-9770-312e911026ad"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

docs/make.jl

@@ -1,19 +1,97 @@
 using Flux, NNlib, GraphNeuralNetworks, Graphs, SparseArrays
 using Documenter
 
+# See this for a template of Pluto+Documenter 
+# https://github.com/rikhuijzer/PlutoStaticHTML.jl/blob/main/docs/make.jl
+using Pluto, PlutoStaticHTML
+using Documenter: MathJax3
+
+tutorial_menu = Array{Pair{String,String},1}()
+
+#
+# Generate Pluto Tutorial HTMLs
+
+# pluto_src_folder = joinpath(@__DIR__, "src", "tutorials")
+# pluto_output_folder = joinpath(@__DIR__, "src", "tutorials")
+# pluto_relative_path = "tutorials/"
+# mkpath(pluto_output_folder)
+
+# """
+#     build()
+# Run all Pluto notebooks (".jl" files) in `NOTEBOOK_DIR`.
+# """
+# function build()
+#     println("Building notebooks")
+#     hopts = HTMLOptions(; append_build_context=true)
+#     output_format = documenter_output
+#     bopts = BuildOptions(pluto_src_folder; output_format)
+#     build_notebooks(bopts, hopts)
+#     return nothing
+# end
+
+# # Build the notebooks; defaults to true.
+# if get(ENV, "BUILD_DOCS_NOTEBOOKS", "true") == "true"
+#     build()
+# end
+
+# # Please do not use the same name as for a(n old) literate Tutorial
+# pluto_files = [
+#     "gnn_intro_pluto",
+#     "graph_classification_pluto",
+# ]
+# pluto_titles = [
+#     "Intro to Graph Neural Networks ",
+#     "Graph Classification",
+# ]
+
+# # build menu and write files myself - tp set edit url correctly.
+# for (title, file) in zip(pluto_titles, pluto_files)
+#     global tutorial_menu
+#     rendered = build_notebooks( #though not really parallel here
+#         BuildOptions(
+#             pluto_src_folder;
+#             output_format=documenter_output,
+#             write_files=false,
+#             use_distributed=false,
+#         ),
+#         ["$(file).jl"],
+#     )
+#     write(
+#         joinpath(pluto_output_folder, file * ".md"),
+#         """
+#         ```@meta
+#         EditURL = "$(joinpath(pluto_src_folder, file * ".jl"))"
+#         ```
+#         $(rendered[1])
+#         """,
+#     )
+#     push!(tutorial_menu, title => joinpath(pluto_relative_path, file * ".md"))
+# end
+
 DocMeta.setdocmeta!(GraphNeuralNetworks, :DocTestSetup, 
     :(using GraphNeuralNetworks, Graphs, SparseArrays, NNlib, Flux); 
     recursive=true)
 
+prettyurls = get(ENV, "CI", nothing) == "true"
+mathengine = MathJax3()
+    
 makedocs(;
-    modules=[GraphNeuralNetworks, NNlib, Flux, Graphs, SparseArrays],
-    doctest=false, clean=true,     
+    modules = [GraphNeuralNetworks, NNlib, Flux, Graphs, SparseArrays],
+    doctest = false, 
+    clean = true,    
+    format= Documenter.HTML(; mathengine, prettyurls),
     sitename = "GraphNeuralNetworks.jl",
     pages = ["Home" => "index.md",
              "Graphs" => "gnngraph.md",
              "Message Passing" => "messagepassing.md",
              "Model Building" => "models.md",
              "Datasets" => "datasets.md",
+            #  "Tutorials" => tutorial_menu,
+            #  "Tutorials" => 
+            #     [
+            #         "Intro to Graph Neural Networks" => "gnn_intro_pluto.md",
+            #         "Graph Classification" => "graph_classification_pluto.md",
+            #     ],
              "API Reference" =>
                [
                 "GNNGraph" => "api/gnngraph.md",

docs/src/datasets.md

@@ -2,8 +2,8 @@
 
 GraphNeuralNetworks.jl doesn't come with its own datasets, but leverages those available in the Julia (and non-Julia) ecosystem. In particular, the [examples in the GraphNeuralNetworks.jl repository](https://github.com/CarloLucibello/GraphNeuralNetworks.jl/tree/master/examples) make use of the [MLDatasets.jl](https://github.com/JuliaML/MLDatasets.jl) package. There you will find common graph datasets such as Cora, PubMed, Citeseer, TUDataset and [many others](https://juliaml.github.io/MLDatasets.jl/dev/datasets/graphs/).
 
-GraphNeuralNetworks.jl provides the [`mldatasets2gnngraph`](@ref) method for interfacing with MLDatasets.jl.
+GraphNeuralNetworks.jl provides the [`mldataset2gnngraph`](@ref) method for interfacing with MLDatasets.jl.
 
 ```@docs
-mldatasets2gnngraph
+mldataset2gnngraph
 ```