Documentation with MultiDocumenter.jl (#508)

* New docs * Update * Actions * Fix branch * Fix * Change path * Tentative * Fix * Some checks * Add Graphs interlink * FIx * ok * fix? * update julia version * Change a bit * dev GNNGraphs * Fix path * Test * Add envs * Rewrite GraphNeuralNetwork part * Fix typo * Remove old docs * Test branch docs * Other test * Another test * Test * New test * Back to prevous path * Back to git error * As Datatoolkit * Change name * remove * Locally works * Test push in branch * Add check * Change repo * Test GNNGraphs deploy * Fix spaces * Fix workflows * Remove https from repo paths * Fix datasets * Fixes * Remove git ignore * Test url * Back to previous urls and update yml * Fix * test yml * Later * Fix L * Test as multi * Update gitignore * Test orphan branch * Add git config * Add checks * Stash * drop stash useless * Force checkout * Add restore * Check what is deleting * Other check to understand * It was deleting docs * Fix typo * Fix name * Cleaner * Clean to be merge in master * Fix branch switch to master
JuliaGraphs · Nov 4, 2024 · 9d982be · 9d982be
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
diff --git a/.github/workflows/multidocs.yml b/.github/workflows/multidocs.yml
@@ -0,0 +1,113 @@
+name: MultiDocumentation
+
+on:
+  push:
+    branches:
+      - master
+    tags: '*'
+  pull_request:
+
+jobs:
+  build_multidocs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1.10.5'
+      - uses: julia-actions/cache@v2
+
+      - name: Set up
+        run: git config --global init.defaultBranch master
+
+      # Build GNNGraphs docs
+      - name: Install dependencies for GNNGraphs
+        run: 
+          julia --project=GNNGraphs/docs/ -e '
+          using Pkg;
+          Pkg.develop(PackageSpec(path=joinpath(pwd(), "GNNGraphs")));
+          Pkg.instantiate();'
+      - name: Build GNNGraphs docs
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia --project=GNNGraphs/docs/ GNNGraphs/docs/make.jl
+
+      # Build GNNlib docs
+      - name: Install dependencies for GNNlib
+        run: julia --project=GNNlib/docs/ -e 'using Pkg; Pkg.instantiate();'
+      - name: Build GNNlib docs
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia --project=GNNlib/docs/ GNNlib/docs/make.jl
+
+      # Build GNNLux docs
+      - name: Install dependencies for GNNLux
+        run: julia --project=GNNLux/docs/ -e '
+            using Pkg;
+            Pkg.develop(PackageSpec(path=joinpath(pwd(), "GNNLux"))); 
+            Pkg.instantiate();'
+      - name: Build GNNLux docs
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia --project=GNNLux/docs/ GNNLux/docs/make.jl
+
+      # Build GraphNeuralNetworks docs
+      - name: Install dependencies for GraphNeuralNetworks
+        run: julia --project=GraphNeuralNetworks/docs/ -e '
+            using Pkg;
+            Pkg.develop(PackageSpec(path=joinpath(pwd(), "GraphNeuralNetworks"))); 
+            Pkg.instantiate();'
+      - name: Build GraphNeuralNetworks docs
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia --project=GraphNeuralNetworks/docs/ GraphNeuralNetworks/docs/make.jl
+
+      # Build  multidocs
+      - name: Install dependencies for main docs
+        run: julia --project=GraphNeuralNetworks/docs/ -e ' 
+            using Pkg;
+            Pkg.develop(PackageSpec(path=joinpath(pwd(), "GraphNeuralNetworks"))); 
+            Pkg.instantiate();'
+      - name: Build main docs
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia --project=GraphNeuralNetworks/docs/make.jl
+
+      # Build tutorials
+      - name: Install dependencies for tutorials
+        run: julia --project=tutorials/docs/ -e 'using Pkg; Pkg.instantiate();'
+      - name: Build tutorials
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia --project=tutorials/docs/ tutorials/docs/make.jl
+
+      # Build and deploy multidocs
+      - name: Install dependencies for multidocs
+        run: julia --project=docs/ -e '
+          using Pkg;
+          Pkg.develop([PackageSpec(path=joinpath(pwd(), "GraphNeuralNetworks")),
+                      PackageSpec(path=joinpath(pwd(), "GNNGraphs")),
+                      PackageSpec(path=joinpath(pwd(), "GNNlib")),
+                      PackageSpec(path=joinpath(pwd(), "GNNLux"))]);
+          Pkg.instantiate();'
+      - name: Check if objects.inv exists for GraphNeuralNetworks
+        run: |
+          if [ -f GraphNeuralNetworks/docs/build/objects.inv ]; then
+            echo "GraphNeuralNetworks: objects.inv exists."
+          else
+            echo "GraphNeuralNetworks: objects.inv does not exist!" && exit 1
+          fi
+      - name: Build and deploy multidocs
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+        run: |
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+          julia --project=docs/ docs/make-multi.jl 
diff --git a/.gitignore b/.gitignore
@@ -5,9 +5,14 @@
 *.swp
 *.swo
 Manifest.toml
-/docs/build/
 .vscode
 LocalPreferences.toml
 .DS_Store
 docs/src/democards/gridtheme.css
-test.jl
+test.jl
+docs/build
+GNNGraphs/docs/build
+GNNlib/docs/build
+GNNLux/docs/build
+GraphNeuralNetworks/docs/build
+tutorials/docs/build
diff --git a/GNNGraphs/docs/Project.toml b/GNNGraphs/docs/Project.toml
@@ -0,0 +1,6 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
+GNNGraphs = "aed8fd31-079b-4b5a-b342-a13352159b8c"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
diff --git a/GNNGraphs/docs/make.jl b/GNNGraphs/docs/make.jl
@@ -0,0 +1,32 @@
+using Documenter
+using DocumenterInterLinks
+using GNNGraphs
+import Graphs
+using Graphs: induced_subgraph
+
+assets=[]
+prettyurls = get(ENV, "CI", nothing) == "true"
+mathengine = MathJax3()
+
+
+makedocs(;
+         modules = [GNNGraphs],
+         doctest = false,
+         clean = true,
+         format = Documenter.HTML(; mathengine, prettyurls, assets = assets, size_threshold=nothing),
+         sitename = "GNNGraphs.jl",
+         pages = ["Home" => "index.md",
+            "Graphs" => ["gnngraph.md", "heterograph.md", "temporalgraph.md"],
+            "Datasets" => "datasets.md",
+            "API Reference" => [
+                 "GNNGraph" => "api/gnngraph.md",
+                 "GNNHeteroGraph" => "api/heterograph.md",
+                 "TemporalSnapshotsGNNGraph" => "api/temporalgraph.md",
+              ],      
+         ]
+         )
+
+deploydocs(;repo = "github.com/JuliaGraphs/GraphNeuralNetworks.jl.git",
+devbranch = "master",
+push_preview = true,
+dirname = "GNNGraphs")
diff --git a/GraphNeuralNetworks/docs/src/api/gnngraph.md → GNNGraphs/docs/src/api/gnngraph.md b/GraphNeuralNetworks/docs/src/api/gnngraph.md → GNNGraphs/docs/src/api/gnngraph.md
@@ -4,7 +4,7 @@ CurrentModule = GNNGraphs
 
 # GNNGraph
 
-Documentation page for the graph type `GNNGraph` provided by GraphNeuralNetworks.jl and related methods. 
+Documentation page for the graph type `GNNGraph` provided by GNNGraphs.jl and related methods. 
 
 Besides the methods documented here, one can rely on the large set of functionalities
 given by [Graphs.jl](https://github.com/JuliaGraphs/Graphs.jl) thanks to the fact

diff --git a/GNNGraphs/docs/src/api/heterograph.md b/GNNGraphs/docs/src/api/heterograph.md
@@ -0,0 +1,17 @@
+# Heterogeneous Graphs
+
+
+## GNNHeteroGraph
+Documentation page for the type `GNNHeteroGraph` representing heterogeneous graphs, where  nodes and edges can have different types.
+
+
+```@autodocs
+Modules = [GNNGraphs]
+Pages   = ["gnnheterograph.jl"]
+Private = false
+```
+
+```@docs
+Graphs.has_edge(::GNNHeteroGraph, ::Tuple{Symbol, Symbol, Symbol}, ::Integer, ::Integer)
+```
+
diff --git a/...ralNetworks/docs/src/api/temporalgraph.md → GNNGraphs/docs/src/api/temporalgraph.md b/...ralNetworks/docs/src/api/temporalgraph.md → GNNGraphs/docs/src/api/temporalgraph.md
diff --git a/GNNGraphs/docs/src/datasets.md b/GNNGraphs/docs/src/datasets.md
@@ -0,0 +1,10 @@
+# Datasets
+
+GNNGraphs.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/JuliaGraphs/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/).
+For graphs with static structures and temporal features, datasets such as METRLA, PEMSBAY, ChickenPox, and WindMillEnergy are available. For graphs featuring both temporal structures and temporal features, the TemporalBrains dataset is suitable.
+
+GraphNeuralNetworks.jl provides the [`mldataset2gnngraph`](@ref) method for interfacing with MLDatasets.jl.
+
+```@docs
+mldataset2gnngraph
+```
diff --git a/GraphNeuralNetworks/docs/src/gnngraph.md → GNNGraphs/docs/src/gnngraph.md b/GraphNeuralNetworks/docs/src/gnngraph.md → GNNGraphs/docs/src/gnngraph.md
@@ -1,6 +1,6 @@
-# Working with GNNGraph 
+# Static Graphs 
 
-The fundamental graph type in GraphNeuralNetworks.jl is the [`GNNGraph`](@ref).
+The fundamental graph type in GNNGraphs.jl is the [`GNNGraph`](@ref).
 A GNNGraph `g` is a directed graph with nodes labeled from 1 to `g.num_nodes`.
 The underlying implementation allows for efficient application of graph neural network
 operators, gpu movement, and storage of node/edge/graph related feature arrays.
@@ -12,7 +12,7 @@ therefore it supports most functionality from that library.
 A GNNGraph can be created from several different data sources encoding the graph topology:
 
 ```julia
-using GraphNeuralNetworks, Graphs, SparseArrays
+using GNNGraphs, Graphs, SparseArrays
 
 
 # Construct a GNNGraph from from a Graphs.jl's graph
@@ -124,7 +124,7 @@ g′.e
 ## Edge weights
 
 It is common to denote scalar edge features as edge weights. The `GNNGraph` has specific support
-for edge weights: they can be stored as part of internal representations of the graph (COO or adjacency matrix). Some graph convolutional layers, most notably the [`GCNConv`](@ref), can use the edge weights to perform weighted sums over the nodes' neighborhoods.
+for edge weights: they can be stored as part of internal representations of the graph (COO or adjacency matrix). Some graph convolutional layers, most notably the `GCNConv`, can use the edge weights to perform weighted sums over the nodes' neighborhoods.
 
 ```julia
 julia> source = [1, 1, 2, 2, 3, 3];
@@ -233,7 +233,7 @@ Moreover, a `GNNGraph` can be easily constructed from a `Graphs.Graph` or a `Gra
 ```julia
 julia> import Graphs
 
-julia> using GraphNeuralNetworks
+julia> using GNNGraphs
 
 # A Graphs.jl undirected graph
 julia> gu = Graphs.erdos_renyi(10, 20)    

diff --git a/GraphNeuralNetworks/docs/src/heterograph.md → GNNGraphs/docs/src/heterograph.md b/GraphNeuralNetworks/docs/src/heterograph.md → GNNGraphs/docs/src/heterograph.md
@@ -6,7 +6,7 @@ Relations such as `:rate` or `:like` can connect nodes of different types. We ca
 
 Different node/edge types can store different groups of features
 and this makes heterographs a very flexible modeling tools 
-and data containers. In GraphNeuralNetworks.jl heterographs are implemented in 
+and data containers. In GNNGraphs.jl heterographs are implemented in 
 the type [`GNNHeteroGraph`](@ref).
 
 
@@ -137,4 +137,4 @@ end
 
 ## Graph convolutions on heterographs
 
-See [`HeteroGraphConv`](@ref) for how to perform convolutions on heterogeneous graphs.
+See `HeteroGraphConv` for how to perform convolutions on heterogeneous graphs.
diff --git a/GNNGraphs/docs/src/index.md b/GNNGraphs/docs/src/index.md
@@ -0,0 +1,15 @@
+# GNNGraphs.jl
+
+GNNGraphs.jl is a package that provides graph data structures and helper functions specifically designed for working with graph neural networks. This package allows to store not only the graph structure, but also features associated with nodes, edges, and the graph itself. It is the core foundation for the GNNlib, GraphNeuralNetworks, and GNNLux packages.
+
+It supports three types of graphs: 
+
+- **Static graph** is the basic graph type represented by [`GNNGraph`](@ref), where each node and edge can have associated features. This type of graph is used in typical graph neural network applications, where neural networks operate on both the structure of the graph and the features stored in it. It can be used to represent a graph where the structure does not change over time, but the features of the nodes and edges can change over time.
+
+- **Heterogeneous graph** is a graph that supports multiple types of nodes and edges, and is represented by [`GNNHeteroGraph`](@ref). Each type can have its own properties and relationships. This is useful in scenarios with different entities and interactions, such as in citation graphs or multi-relational data.
+
+- **Temporal graph** is a graph that changes over time, and is represented by [`TemporalSnapshotsGNNGraph`](@ref). Edges and features can change dynamically. This type of graph is useful for applications that involve tracking time-dependent relationships, such as social networks.
+
+
+
+This package depends on the package [Graphs.jl] (https://github.com/JuliaGraphs/Graphs.jl).
diff --git a/...hNeuralNetworks/docs/src/temporalgraph.md → GNNGraphs/docs/src/temporalgraph.md b/...hNeuralNetworks/docs/src/temporalgraph.md → GNNGraphs/docs/src/temporalgraph.md
@@ -1,6 +1,6 @@
 # Temporal Graphs
 
-Temporal Graphs are graphs with time varying topologies and node features. In GraphNeuralNetworks.jl temporal graphs with fixed number of nodes over time are supported by the [`TemporalSnapshotsGNNGraph`](@ref) type.
+Temporal Graphs are graphs with time varying topologies and  features. In GNNGraphs.jl, temporal graphs with fixed number of nodes over time are supported by the [`TemporalSnapshotsGNNGraph`](@ref) type.
 
 ## Creating a TemporalSnapshotsGNNGraph
 
@@ -91,7 +91,7 @@ GNNGraph:
 ```
 
 ## Data Features
-A temporal graph can stode global feautre for the entire time series in the `tgdata` filed.
+A temporal graph can store global feature for the entire time series in the `tgdata` filed.
 Also, each snapshot can store node, edge, and graph features in the `ndata`, `edata`, and `gdata` fields, respectively. 
 
 ```jldoctest
@@ -126,10 +126,10 @@ julia> [g.x for g in tg.snapshots]; # same vector as above, now accessing
 
 ## Graph convolutions on TemporalSnapshotsGNNGraph
 
-A graph convolutional layer can be applied to each snapshot independently, in the next example we apply a `GINConv` layer to each snapshot of a `TemporalSnapshotsGNNGraph`. The list of compatible graph convolution layers can be found [here](api/conv.md). 
+A graph convolutional layer can be applied to each snapshot independently, in the next example we apply a `GINConv` layer to each snapshot of a `TemporalSnapshotsGNNGraph`.  
 
 ```jldoctest
-julia> using GraphNeuralNetworks, Flux
+julia> using GNNGraphs, Flux
 
 julia> snapshots = [rand_graph(10, 20; ndata = rand(3, 10)), rand_graph(10, 14; ndata = rand(3, 10))];
 

diff --git a/GNNLux/docs/Project.toml b/GNNLux/docs/Project.toml
@@ -0,0 +1,5 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+GNNLux = "e8545f4d-a905-48ac-a8c4-ca114b98986d"
+GNNlib = "a6a84749-d869-43f8-aacc-be26a1996e48"
+LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
diff --git a/GNNLux/docs/make.jl b/GNNLux/docs/make.jl
@@ -0,0 +1,28 @@
+using Documenter
+using GNNlib
+using GNNLux
+
+
+
+assets=[]
+prettyurls = get(ENV, "CI", nothing) == "true"
+mathengine = MathJax3()
+
+
+makedocs(;
+         modules = [GNNLux],
+         doctest = false,
+         clean = true,
+         format = Documenter.HTML(; mathengine, prettyurls, assets = assets, size_threshold=nothing),
+         sitename = "GNNLux.jl",
+         pages = ["Home" => "index.md",
+         "Basic" => "api/basic.md"],
+         )
+
+
+
+
+deploydocs(;repo = "github.com/JuliaGraphs/GraphNeuralNetworks.jl.git",
+devbranch = "master",
+push_preview = true,
+dirname = "GNNLux")
diff --git a/GNNLux/docs/src/api/basic.md b/GNNLux/docs/src/api/basic.md
@@ -0,0 +1,8 @@
+```@meta
+CurrentModule = GNNLux
+```
+
+## GNNLayer
+```@docs
+GNNLux.GNNLayer
+```
diff --git a/GNNLux/docs/src/index.md b/GNNLux/docs/src/index.md
@@ -0,0 +1,5 @@
+# GNNLux.jl 
+
+GNNLux.jl is a work-in-progress package that implements stateless graph convolutional layers, fully compatible with the [Lux.jl](https://lux.csail.mit.edu/stable/) machine learning framework. It is built on top of the GNNGraphs.jl, GNNlib.jl, and Lux.jl packages.
+
+The full documentation will be available soon.