Merge pull request #34 from CarloLucibello/cl/docs

doc update

Author: CarloLucibello

README.md

@@ -19,8 +19,6 @@ GraphNeuralNetworks.jl is a registered julia package.
 You can easily install it through the package manager:
 
 ```julia
-julia> ]
-
 pkg> add GraphNeuralNetworks
 ```
 

docs/src/api/basic.md

@@ -1,11 +1,19 @@
+```@meta
+CurrentModule = GraphNeuralNetworks
+```
+
 # Basic Layers
 
+## Index
+
 ```@index
 Order = [:type, :function]
-Modules = [GraphNeuralNetworks, LightGraphs, Flux, NNlib]
+Modules = [GraphNeuralNetworks]
 Pages = ["api/basics.md"]
 ```
 
+## Docs
+
 ```@docs
 GNNLayer
 GNNChain

docs/src/api/conv.md

@@ -1,10 +1,18 @@
+```@meta
+CurrentModule = GraphNeuralNetworks
+```
+
 # Convolutional Layers
 
+## Index 
+
 ```@index
 Order = [:type, :function]
-Pages   = ["api/conv.md"]
+Pages   = ["conv.md"]
 ```
 
+## Docs
+
 ```@autodocs
 Modules = [GraphNeuralNetworks]
 Pages   = ["layers/conv.jl"]

docs/src/api/gnngraph.md

@@ -1,15 +1,26 @@
-# Graphs
+```@meta
+CurrentModule = GraphNeuralNetworks
+```
+
+# GNNGraph
+
+Documentation page for the graph type `GNNGraph` provided GraphNeuralNetworks.jl and its related methods. 
+
+## Index 
 
 ```@index
 Order = [:type, :function]
-Pages   = ["api/graphs.md"]
+Pages   = ["graphs.md"]
 ```
 
+## Docs
+
 ```@autodocs
 Modules = [GraphNeuralNetworks]
 Pages   = ["gnngraph.jl"]
 Private = false
 ```
+
 ```@docs
 Flux.batch
 SparseArrays.blockdiag

docs/src/api/messagepassing.md

@@ -1,7 +1,21 @@
+```@meta
+CurrentModule = GraphNeuralNetworks
+```
+
 # Message Passing
 
+## Index
+
+```@index
+Order = [:type, :function]
+Pages   = ["messagepassing.md"]
+```
+
+## Docs
+
 ```@docs
-GraphNeuralNetworks.compute_message
-GraphNeuralNetworks.update_node
-GraphNeuralNetworks.propagate
+compute_message
+update_node
+update_edge
+propagate
 ```

docs/src/api/nnlib.md

@@ -1,7 +1,20 @@
+```@meta
+CurrentModule = GraphNeuralNetworks
+```
+
 # NNlib
 
 Primitive functions implemented in NNlib.jl.
 
+## Index
+
+```@index
+Order = [:type, :function]
+Pages   = ["nnlib.md"]
+```
+
+## Docs
+
 ```@docs
 NNlib.gather!
 NNlib.gather

docs/src/api/pool.md

@@ -1,10 +1,18 @@
+```@meta
+CurrentModule = GraphNeuralNetworks
+```
+
 # Pooling Layers
 
+## Index
+
 ```@index
 Order = [:type, :function]
-Pages   = ["api/pool.md"]
+Pages   = ["pool.md"]
 ```
 
+## Docs
+
 ```@autodocs
 Modules = [GraphNeuralNetworks]
 Pages   = ["layers/pool.jl"]

docs/src/messagepassing.md

@@ -4,7 +4,6 @@ The message passing is initiated by [`propagate`](@ref)
 and can be customized for a specific layer by overloading the methods
 [`compute_message`](@ref), [`update_node`](@ref), and [`update_edge`](@ref).
 
-
 The message passing corresponds to the following operations 
 
 ```math
@@ -26,7 +25,7 @@ The convolution reads
 ```math
 \mathbf{x}'_i = \sum_{j \in N(i)} \frac{1}{c_{ij}} W \mathbf{x}_j
 ```
-where ``c_{ij} = \sqrt{(|N(i)|)(|N(j)|)}``. We will also add a bias and an activation function.
+where ``c_{ij} = \sqrt{|N(i)||N(j)|}``. We will also add a bias and an activation function.
 
 ```julia
 using Flux, LightGraphs, GraphNeuralNetworks
@@ -60,5 +59,3 @@ end
 ```
 
 See the [`GATConv`](@ref) implementation [here](https://github.com/CarloLucibello/GraphNeuralNetworks.jl/blob/master/src/layers/conv.jl) for a more complex example.
-
-

src/GraphNeuralNetworks.jl

@@ -31,7 +31,7 @@ export
     sprand, sparse, 
 
     # msgpass
-    # update_node, update_edge, compute_message, propagate,
+    update_node, update_edge, compute_message, propagate,
 
     # layers/basic
     GNNLayer,

src/gnngraph.jl

@@ -240,6 +240,17 @@ end
 LightGraphs.is_directed(::GNNGraph) = true
 LightGraphs.is_directed(::Type{GNNGraph}) = true
 
+"""
+    adjacency_list(g; dir=:out)
+
+Return the adjacency list representation (a vector of vectors)
+of the graph `g`.
+
+Calling `a` the adjacency list, if `dir=:out`
+`a[i]` will contain the neighbors of node `i` through
+outgoing edges. If `dir=:in`, it will contain neighbors from
+incoming edges instead.
+"""
 function adjacency_list(g::GNNGraph; dir=:out)
     @assert dir ∈ [:out, :in]
     fneighs = dir == :out ? outneighbors : inneighbors