fix docs

Author: CarloLucibello

.gitignore

@@ -8,4 +8,5 @@ Manifest.toml
 /docs/build/
 .vscode
 LocalPreferences.toml
-.DS_Store
+.DS_Store
+docs/src/democards/gridtheme.css

GNNGraphs/src/operators.jl

@@ -1,4 +1,9 @@
 # 2 or more args graph operators
+""""
+    intersect(g1::GNNGraph, g2::GNNGraph)
+
+Intersect two graphs by keeping only the common edges.
+"""
 function Base.intersect(g1::GNNGraph, g2::GNNGraph)
     @assert g1.num_nodes == g2.num_nodes
     @assert graph_type_symbol(g1) == graph_type_symbol(g2)

GNNGraphs/src/query.jl

@@ -89,7 +89,17 @@ Graphs.ne(g::GNNGraph) = g.num_edges
 Graphs.has_vertex(g::GNNGraph, i::Int) = 1 <= i <= g.num_nodes
 Graphs.vertices(g::GNNGraph) = 1:(g.num_nodes)
 
-function Graphs.neighbors(g::GNNGraph, i; dir = :out)
+
+"""
+    neighbors(g::GNNGraph, i::Integer; dir=:out)
+
+Return the neighbors of node `i` in the graph `g`.
+If `dir=:out`, return the neighbors through outgoing edges.
+If `dir=:in`, return the neighbors through incoming edges.
+
+See also [`outneighbors`](@ref Graphs.outneighbors), [`inneighbors`](@ref Graphs.inneighbors).
+"""
+function Graphs.neighbors(g::GNNGraph, i::Integer; dir::Symbol = :out)
     @assert dir ∈ (:in, :out)
     if dir == :out
         outneighbors(g, i)
@@ -98,6 +108,13 @@ function Graphs.neighbors(g::GNNGraph, i; dir = :out)
     end
 end
 
+"""
+    outneighbors(g::GNNGraph, i::Integer)
+
+Return the neighbors of node `i` in the graph `g` through outgoing edges.
+
+See also [`neighbors`](@ref Graphs.neighbors) and [`inneighbors`](@ref Graphs.inneighbors).
+"""
 function Graphs.outneighbors(g::GNNGraph{<:COO_T}, i::Integer)
     s, t = edge_index(g)
     return t[s .== i]
@@ -108,6 +125,13 @@ function Graphs.outneighbors(g::GNNGraph{<:ADJMAT_T}, i::Integer)
     return findall(!=(0), A[i, :])
 end
 
+"""
+    inneighbors(g::GNNGraph, i::Integer)
+
+Return the neighbors of node `i` in the graph `g` through incoming edges.
+
+See also [`neighbors`](@ref Graphs.neighbors) and [`outneighbors`](@ref Graphs.outneighbors).
+"""
 function Graphs.inneighbors(g::GNNGraph{<:COO_T}, i::Integer)
     s, t = edge_index(g)
     return s[t .== i]

docs/Project.toml

@@ -1,6 +1,7 @@
 [deps]
 DemoCards = "311a05b2-6137-4a5a-b473-18580a3d38b5"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 GNNGraphs = "aed8fd31-079b-4b5a-b342-a13352159b8c"
 GraphNeuralNetworks = "cffab07f-9bc2-4db1-8861-388f63bf7694"

docs/make.jl

@@ -2,12 +2,19 @@ using Flux, NNlib, GraphNeuralNetworks, Graphs, SparseArrays
 using GNNGraphs
 using Pluto, PlutoStaticHTML # for tutorials
 using Documenter, DemoCards
+using DocumenterInterLinks
 
-# tutorials, tutorials_cb, tutorial_assets = makedemos("tutorials")
+# 
 
+# tutorials, tutorials_cb, tutorial_assets = makedemos("tutorials")
 assets = []
 # isnothing(tutorial_assets) || push!(assets, tutorial_assets)
 
+interlinks = InterLinks(
+    "NNlib" => "https://fluxml.ai/NNlib.jl/stable/",
+    "Graphs" => "https://juliagraphs.org/Graphs.jl/stable/")
+
+
 DocMeta.setdocmeta!(GraphNeuralNetworks, :DocTestSetup,
                     :(using GraphNeuralNetworks, Graphs, SparseArrays, NNlib, Flux);
                     recursive = true)
@@ -19,6 +26,7 @@ makedocs(;
          modules = [GraphNeuralNetworks, GNNGraphs],
          doctest = false,
          clean = true,
+         plugins = [interlinks],
          format = Documenter.HTML(; mathengine, prettyurls, assets = assets),
          sitename = "GraphNeuralNetworks.jl",
          pages = ["Home" => "index.md",

docs/src/api/gnngraph.md

@@ -21,6 +21,7 @@ Pages   = ["gnngraph.md"]
 
 ```@docs
 GNNGraph
+Base.copy
 ```
 
 ## DataStore
@@ -40,8 +41,8 @@ Private = false
 ```
 
 ```@docs
-Graphs.outneighbors
-Graphs.inneighbors
+Graphs.neighbors
+Graphs.has_edge
 ```
 
 ## Transform

docs/src/api/utils.md

@@ -33,11 +33,9 @@ GraphNeuralNetworks.softmax_edge_neighbors
 
 ### NNlib
 
-Primitive functions implemented in NNlib.jl.
+Primitive functions implemented in NNlib.jl:
 
-```@docs
-NNlib.gather!
-NNlib.gather
-NNlib.scatter!
-NNlib.scatter
-```
+- [`gather!`](https://fluxml.ai/NNlib.jl/stable/reference/#NNlib.gather!)
+- [`gather`](https://fluxml.ai/NNlib.jl/stable/reference/#NNlib.gather)
+- [`scatter!`](https://fluxml.ai/NNlib.jl/stable/reference/#NNlib.scatter!)
+- [`scatter`](https://fluxml.ai/NNlib.jl/stable/reference/#NNlib.scatter)