From 837a6e95475e480780ae5686491582101ba499e0 Mon Sep 17 00:00:00 2001
From: Carlo Lucibello <carlo.lucibello@gmail.com>
Date: Fri, 25 Oct 2024 16:52:30 +0200
Subject: [PATCH 1/2] fix vector DataStore (#505)

* remove vector access to datastore

* fix

* deprecations
---
 GNNGraphs/src/GNNGraphs.jl                    |  2 ++
 GNNGraphs/src/datastore.jl                    | 10 +---------
 GNNGraphs/src/deprecations.jl                 | 13 +++++++++++++
 GNNGraphs/test/datastore.jl                   |  8 +++-----
 GraphNeuralNetworks/docs/src/temporalgraph.md | 14 ++++++++------
 5 files changed, 27 insertions(+), 20 deletions(-)
 create mode 100644 GNNGraphs/src/deprecations.jl

diff --git a/GNNGraphs/src/GNNGraphs.jl b/GNNGraphs/src/GNNGraphs.jl
index 055ea2789..cd1848b28 100644
--- a/GNNGraphs/src/GNNGraphs.jl
+++ b/GNNGraphs/src/GNNGraphs.jl
@@ -111,4 +111,6 @@ include("gatherscatter.jl")
 include("mldatasets.jl")
 export mldataset2gnngraph
 
+include("deprecations.jl")
+
 end #module
diff --git a/GNNGraphs/src/datastore.jl b/GNNGraphs/src/datastore.jl
index 2afef8970..9581e266d 100644
--- a/GNNGraphs/src/datastore.jl
+++ b/GNNGraphs/src/datastore.jl
@@ -107,15 +107,7 @@ function Base.getproperty(ds::DataStore, s::Symbol)
     end
 end
 
-function Base.getproperty(vds::Vector{DataStore}, s::Symbol)
-    if s === :_n
-        return [getn(ds) for ds in vds]
-    elseif s === :_data
-        return [getdata(ds) for ds in vds]
-    else
-        return [getdata(ds)[s] for ds in vds]
-    end
-end
+
 
 function Base.setproperty!(ds::DataStore, s::Symbol, x)
     @assert s != :_n "cannot set _n directly"
diff --git a/GNNGraphs/src/deprecations.jl b/GNNGraphs/src/deprecations.jl
new file mode 100644
index 000000000..d6a8e1797
--- /dev/null
+++ b/GNNGraphs/src/deprecations.jl
@@ -0,0 +1,13 @@
+## Deprecated in V0.6
+
+function Base.getproperty(vds::Vector{DataStore}, s::Symbol)
+    if s ∈ (:ref, :size) # these are arrays fields in V0.11
+        return getfield(vds, s)
+    elseif s === :_n
+        return [getn(ds) for ds in vds]
+    elseif s === :_data
+        return [getdata(ds) for ds in vds]
+    else
+        return [getdata(ds)[s] for ds in vds]
+    end
+end
diff --git a/GNNGraphs/test/datastore.jl b/GNNGraphs/test/datastore.jl
index 1c8cfdc1c..404136bdf 100644
--- a/GNNGraphs/test/datastore.jl
+++ b/GNNGraphs/test/datastore.jl
@@ -20,11 +20,9 @@ end
     @test_throws DimensionMismatch ds.z=rand(12)
     ds.z = [1:10;]
     @test ds.z == [1:10;]
-    vec = [DataStore(10, (:x => x,)), DataStore(10, (:x => x, :y => rand(2, 10)))]
-    @test vec.x == [x, x]
-    @test_throws KeyError vec.z 
-    @test vec._n == [10, 10]
-    @test vec._data == [Dict(:x => x), Dict(:x => x, :y => vec[2].y)]
+
+    # issue #504, where vector creation failed
+    @test fill(DataStore(), 3) isa Vector
 end
 
 @testset "setindex!" begin
diff --git a/GraphNeuralNetworks/docs/src/temporalgraph.md b/GraphNeuralNetworks/docs/src/temporalgraph.md
index f8283c766..f90b73ff4 100644
--- a/GraphNeuralNetworks/docs/src/temporalgraph.md
+++ b/GraphNeuralNetworks/docs/src/temporalgraph.md
@@ -91,15 +91,15 @@ GNNGraph:
 ```
 
 ## Data Features
-
-Node, edge, and graph features can be added at construction time or later using:
+A temporal graph can stode global feautre 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
 julia> snapshots = [rand_graph(10,20; ndata = rand(3,10)), rand_graph(10,14; ndata = rand(4,10)), rand_graph(10,22; ndata = rand(5,10))]; # node features at construction time
 
 julia> tg = TemporalSnapshotsGNNGraph(snapshots);
 
-julia> tg.tgdata.y = rand(3,1); # graph features after construction
+julia> tg.tgdata.y = rand(3,1); # add global features after construction
 
 julia> tg
 TemporalSnapshotsGNNGraph:
@@ -109,7 +109,7 @@ TemporalSnapshotsGNNGraph:
   tgdata:
         y = 3×1 Matrix{Float64}
 
-julia> tg.ndata # vector of Datastore for node features
+julia> tg.ndata # vector of DataStore containing node features for each snapshot
 3-element Vector{DataStore}:
  DataStore(10) with 1 element:
   x = 3×10 Matrix{Float64}
@@ -118,8 +118,10 @@ julia> tg.ndata # vector of Datastore for node features
  DataStore(10) with 1 element:
   x = 5×10 Matrix{Float64}
 
-julia> typeof(tg.ndata.x) # vector containing the x feature of each snapshot
-Vector{Matrix{Float64}}
+julia> [ds.x for ds in tg.ndata]; # vector containing the x feature of each snapshot
+
+julia> [g.x for g in tg.snapshots]; # same vector as above, now accessing 
+                                   # the x feature directly from the snapshots
 ```
 
 ## Graph convolutions on TemporalSnapshotsGNNGraph

From 9d9e8d0a99f779d6911ccf95bda01a9a9de89439 Mon Sep 17 00:00:00 2001
From: Carlo Lucibello <carlo.lucibello@gmail.com>
Date: Fri, 25 Oct 2024 16:53:10 +0200
Subject: [PATCH 2/2] Update Project.toml

---
 GNNGraphs/Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/GNNGraphs/Project.toml b/GNNGraphs/Project.toml
index 97dee916c..310b1205e 100644
--- a/GNNGraphs/Project.toml
+++ b/GNNGraphs/Project.toml
@@ -1,7 +1,7 @@
 name = "GNNGraphs"
 uuid = "aed8fd31-079b-4b5a-b342-a13352159b8c"
 authors = ["Carlo Lucibello and contributors"]
-version = "1.2.0"
+version = "1.2.1"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"