fix docs

docs/make.jl

@@ -1,7 +1,9 @@
 using Flux, NNlib, GraphNeuralNetworks, Graphs, SparseArrays
 using Documenter
 
-DocMeta.setdocmeta!(GraphNeuralNetworks, :DocTestSetup, :(using GraphNeuralNetworks); recursive=true)
+DocMeta.setdocmeta!(GraphNeuralNetworks, :DocTestSetup, 
+    :(using GraphNeuralNetworks, Graphs, SparseArrays, NNlib, Flux); 
+    recursive=true)
 
 makedocs(;
     modules=[GraphNeuralNetworks, NNlib, Flux, Graphs, SparseArrays],

docs/src/api/gnngraph.md

@@ -4,7 +4,12 @@ CurrentModule = GraphNeuralNetworks
 
 # GNNGraph
 
-Documentation page for the graph type `GNNGraph` provided GraphNeuralNetworks.jl and its related methods. 
+Documentation page for the graph type `GNNGraph` provided by GraphNeuralNetworks.jl and related methods. 
+
+```@contents
+Pages = ["gnngraph.md"]
+Depth = 5
+```
 
 Besides the methods documented here, one can rely on the large set of functionalities
 given by [Graphs.jl](https://github.com/JuliaGraphs/Graphs.jl)
@@ -17,21 +22,19 @@ Order = [:type, :function]
 Pages   = ["gnngraph.md"]
 ```
 
-## Docs
-
-### GNNGraph
+## GNNGraph type
 
 ```@autodocs
-Modules = [GraphNeuralNetworks]
-Pages   = ["GNNGraphs/gnngraph.jl"]
+Modules = [GraphNeuralNetworks.GNNGraphs]
+Pages   = ["gnngraph.jl"]
 Private = false
 ```
 
-### Query
+## Query
 
 ```@autodocs
-Modules = [GraphNeuralNetworks]
-Pages   = ["GNNGraphs/query.jl"]
+Modules = [GraphNeuralNetworks.GNNGraphs]
+Pages   = ["query.jl"]
 Private = false
 ```
 
@@ -42,29 +45,18 @@ Graphs.outneighbors
 Graphs.inneighbors
 ```
 
-### Transform
+## Transform
 
 ```@autodocs
-Modules = [GraphNeuralNetworks]
-Pages   = ["GNNGraphs/transform.jl"]
+Modules = [GraphNeuralNetworks.GNNGraphs]
+Pages   = ["transform.jl"]
 Private = false
 ```
 
-```@docs
-Flux.batch
-SparseArrays.blockdiag
-```
-
-### Generate
+## Generate
 
 ```@autodocs
-Modules = [GraphNeuralNetworks]
-Pages   = ["GNNGraphs/generate.jl"]
+Modules = [GraphNeuralNetworks.GNNGraphs]
+Pages   = ["generate.jl"]
 Private = false
 ```
-
-### Related methods
-
-```@docs
-SparseArrays.sparse
-```

docs/src/gnngraph.md

@@ -36,7 +36,7 @@ target = [2,3,1,3,1,2,4,3]
 g = GNNGraph(source, target)
 ```
 
-See also the related methods [`adjacency_matrix`](@ref), [`edge_index`](@ref), and [`adjacency_list`](@ref).
+See also the related methods [`Graphs.adjacency_matrix`](@ref), [`edge_index`](@ref), and [`adjacency_list`](@ref).
 
 ## Basic Queries
 

src/GraphNeuralNetworks.jl

@@ -12,6 +12,8 @@ using NNlib: scatter, gather
 using ChainRulesCore
 using Reexport
 
+using SparseArrays, Graphs # not needed but if removed Documenter will complain
+
 include("GNNGraphs/GNNGraphs.jl")
 @reexport using .GNNGraphs
 using .GNNGraphs: COO_T, ADJMAT_T, SPARSE_T,

src/utils.jl

@@ -121,7 +121,7 @@ Softmax over each node's neighborhood of the edge features `e`.
 
 ```math
 \mathbf{e}'_{j\to i} = \frac{e^{\mathbf{e}_{j\to i}}}
-                    {\sum_{j'\in N(i)} e^{\mathbf{e}_{j\to i}}}.
+                    {\sum_{j'\in N(i)} e^{\mathbf{e}_{j'\to i}}}.
 ```
 """
 function softmax_edge_neighbors(g::GNNGraph, e)