From b8d6119664552c3fadd1157e69c1610904332f5b Mon Sep 17 00:00:00 2001 From: Carlo Lucibello Date: Wed, 14 Jun 2023 08:09:41 +0200 Subject: [PATCH 1/4] update to explicit gradient --- docs/src/index.md | 11 +- docs/src/messagepassing.md | 2 +- docs/src/models.md | 2 +- .../introductory_tutorials/gnn_intro_pluto.jl | 7 +- .../graph_classification_pluto.jl | 7 +- .../node_classification_pluto.jl | 22 ++- examples/neural_ode_cora.jl | 9 +- examples/neurosat.jl | 148 ------------------ examples/node_classification_cora.jl | 7 +- src/layers/basic.jl | 4 +- test/examples/node_classification_cora.jl | 3 +- 11 files changed, 32 insertions(+), 190 deletions(-) delete mode 100644 examples/neurosat.jl diff --git a/docs/src/index.md b/docs/src/index.md index fbbd61cd0..703fc9e73 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -53,8 +53,7 @@ model = GNNChain(GCNConv(16 => 64), GlobalPool(mean), # aggregate node-wise features into graph-wise features Dense(64, 1)) |> device -ps = Flux.params(model) -opt = Adam(1f-4) +opt = Flux.setup(Adam(1f-4), model) ``` ### Training @@ -72,15 +71,15 @@ train_loader = DataLoader(train_graphs, test_loader = DataLoader(test_graphs, batchsize=32, shuffle=false, collate=true) -loss(g::GNNGraph) = mean((vec(model(g, g.x)) - g.y).^2) +loss(model, g::GNNGraph) = mean((vec(model(g, g.x)) - g.y).^2) -loss(loader) = mean(loss(g |> device) for g in loader) +loss(model, loader) = mean(loss(model, g |> device) for g in loader) for epoch in 1:100 for g in train_loader g = g |> device - grad = gradient(() -> loss(g), ps) - Flux.Optimise.update!(opt, ps, grad) + grad = gradient(model -> loss(model, g), model) + Flux.update!(opt, model, grad[1]) end @info (; epoch, train_loss=loss(train_loader), test_loss=loss(test_loader)) diff --git a/docs/src/messagepassing.md b/docs/src/messagepassing.md index c0c891dda..9db0062e6 100644 --- a/docs/src/messagepassing.md +++ b/docs/src/messagepassing.md @@ -109,7 +109,7 @@ struct GCN{A<:AbstractMatrix, B, F} <: GNNLayer σ::F end -Flux.@functor GCN # allow collecting params, gpu movement, etc... +Flux.@functor GCN # allow gpu movement, select trainable params etc... function GCN(ch::Pair{Int,Int}, σ=identity) in, out = ch diff --git a/docs/src/models.md b/docs/src/models.md index b105cc22b..d0265964e 100644 --- a/docs/src/models.md +++ b/docs/src/models.md @@ -56,7 +56,7 @@ g = rand_graph(10, 30) X = randn(Float32, din, 10) y = model(g, X) # output size: (dout, g.num_nodes) -gs = gradient(() -> sum(model(g, X)), Flux.params(model)) +grad = gradient(model -> sum(model(g, X)), model) ``` ## Implicit modeling with GNNChains diff --git a/docs/tutorials/introductory_tutorials/gnn_intro_pluto.jl b/docs/tutorials/introductory_tutorials/gnn_intro_pluto.jl index ae1bb283f..df1ea058c 100644 --- a/docs/tutorials/introductory_tutorials/gnn_intro_pluto.jl +++ b/docs/tutorials/introductory_tutorials/gnn_intro_pluto.jl @@ -275,8 +275,7 @@ Let us now start training and see how our node embeddings evolve over time (best # ╔═╡ 912560a1-9c72-47bd-9fce-9702b346b603 begin model = GCN(num_features, num_classes) - ps = Flux.params(model) - opt = Adam(1e-2) + opt = Flux.setup(Adam(1e-2), model) epochs = 2000 emb = h @@ -287,12 +286,12 @@ begin report(0, 10.0, emb) for epoch in 1:epochs - loss, gs = Flux.withgradient(ps) do + loss, grad = Flux.withgradient(model) do model ŷ, emb = model(g, g.ndata.x) logitcrossentropy(ŷ[:, train_mask], y[:, train_mask]) end - Flux.Optimise.update!(opt, ps, gs) + Flux.update!(opt, model, grad[1]) if epoch % 200 == 0 report(epoch, loss, emb) end diff --git a/docs/tutorials/introductory_tutorials/graph_classification_pluto.jl b/docs/tutorials/introductory_tutorials/graph_classification_pluto.jl index dc149434b..f8241044a 100644 --- a/docs/tutorials/introductory_tutorials/graph_classification_pluto.jl +++ b/docs/tutorials/introductory_tutorials/graph_classification_pluto.jl @@ -193,8 +193,7 @@ function train!(model; epochs = 200, η = 1e-2, infotime = 10) # device = Flux.gpu # uncomment this for GPU training device = Flux.cpu model = model |> device - ps = Flux.params(model) - opt = Adam(1e-3) + opt = Flux.setup(Adam(1e-3), model) function report(epoch) train = eval_loss_accuracy(model, train_loader, device) @@ -206,11 +205,11 @@ function train!(model; epochs = 200, η = 1e-2, infotime = 10) for epoch in 1:epochs for (g, y) in train_loader g, y = MLUtils.batch(g) |> device, y |> device - gs = Flux.gradient(ps) do + grad = Flux.gradient(model) do model ŷ = model(g, g.ndata.x) logitcrossentropy(ŷ, y) end - Flux.Optimise.update!(opt, ps, gs) + Flux.update!(opt, model, grad[1]) end epoch % infotime == 0 && report(epoch) end diff --git a/docs/tutorials/introductory_tutorials/node_classification_pluto.jl b/docs/tutorials/introductory_tutorials/node_classification_pluto.jl index cb602f65c..2e88ba08f 100644 --- a/docs/tutorials/introductory_tutorials/node_classification_pluto.jl +++ b/docs/tutorials/introductory_tutorials/node_classification_pluto.jl @@ -172,16 +172,16 @@ This time, we also define a **`accuracy` function** to evaluate how well our fin """ # ╔═╡ 05979cfe-439c-4abc-90cd-6ca2a05f6e0f -function train(model::MLP, data::AbstractMatrix, epochs::Int, opt, ps) +function train(model::MLP, data::AbstractMatrix, epochs::Int, opt) Flux.trainmode!(model) for epoch in 1:epochs - loss, gs = Flux.withgradient(ps) do + loss, grad = Flux.withgradient(model) do model ŷ = model(data) logitcrossentropy(ŷ[:, train_mask], y[:, train_mask]) end - Flux.Optimise.update!(opt, ps, gs) + Flux.update!(opt, model, grad[1]) if epoch % 200 == 0 @show epoch, loss end @@ -276,16 +276,16 @@ The training and testing procedure is once again the same, but this time we make """ # ╔═╡ 901d9478-9a12-4122-905d-6cfc6d80e84c -function train(model::GCN, g::GNNGraph, x::AbstractMatrix, epochs::Int, ps, opt) +function train(model::GCN, g::GNNGraph, x::AbstractMatrix, epochs::Int, opt) Flux.trainmode!(model) for epoch in 1:epochs - loss, gs = Flux.withgradient(ps) do + loss, grad[1] = Flux.withgradient(model) do model ŷ = model(g, x) logitcrossentropy(ŷ[:, train_mask], y[:, train_mask]) end - Flux.Optimise.update!(opt, ps, gs) + Flux.update!(opt, model, grad) if epoch % 200 == 0 @show epoch, loss end @@ -296,10 +296,9 @@ end # ╠═╡ show_logs = false begin mlp = MLP(num_features, num_classes, hidden_channels) - ps_mlp = Flux.params(mlp) - opt_mlp = Adam(1e-3) + opt_mlp = Flux.setup(Adam(1e-3), mlp) epochs = 2000 - train(mlp, g.ndata.features, epochs, opt_mlp, ps_mlp) + train(mlp, g.ndata.features, epochs, opt_mlp) end # ╔═╡ 65d9fd3d-1649-4b95-a106-f26fa4ab9bce @@ -315,9 +314,8 @@ accuracy(mlp, g.ndata.features, y, .!train_mask) # ╔═╡ 20be52b1-1c33-4f54-b5c0-fecc4e24fbb5 # ╠═╡ show_logs = false begin - ps_gcn = Flux.params(gcn) - opt_gcn = Adam(1e-2) - train(gcn, g, x, epochs, ps_gcn, opt_gcn) + opt_gcn = Flux.setup(Adam(1e-2), gcn) + train(gcn, g, x, epochs, opt_gcn) end # ╔═╡ 5aa99aff-b5ed-40ec-a7ec-0ba53385e6bd diff --git a/examples/neural_ode_cora.jl b/examples/neural_ode_cora.jl index df4ff9199..12522b9bf 100644 --- a/examples/neural_ode_cora.jl +++ b/examples/neural_ode_cora.jl @@ -42,11 +42,8 @@ model = GNNChain(GCNConv(nin => nhidden, relu), Dense(nhidden, nout)) |> device # # Training -# ## Model Parameters -ps = Flux.params(model); -# ## Optimizer -opt = Adam(0.01) +opt = Flux.setup(Adam(0.01), model) function eval_loss_accuracy(X, y, mask) ŷ = model(g, X) @@ -57,10 +54,10 @@ end # ## Training Loop for epoch in 1:epochs - gs = gradient(ps) do + grad = gradient(model) do model ŷ = model(g, X) logitcrossentropy(ŷ[:, train_mask], ytrain) end - Flux.Optimise.update!(opt, ps, gs) + Flux.update!(opt, model, grad[1]) @show eval_loss_accuracy(X, y, train_mask) end diff --git a/examples/neurosat.jl b/examples/neurosat.jl deleted file mode 100644 index 2776758ec..000000000 --- a/examples/neurosat.jl +++ /dev/null @@ -1,148 +0,0 @@ -using GraphNeuralNetworks -using Flux -using Random, Statistics, LinearAlgebra -using SparseArrays - -""" -A type representing a conjunctive normal form. -""" -struct CNF - N::Int # num variables - M::Int # num factors - clauses::Vector{Vector{Int}} -end - -function CNF(clauses::Vector{Vector{Int}}) - M = length(clauses) - N = maximum(maximum(abs.(c)) for c in clauses) - return CNF(N, M, clauses) -end - -""" - randomcnf(; N=100, k=3, α=0.1, seed=-1, planted = Vector{Vector{Int}}()) - -Generates a random instance of the k-SAT problem, with `N` variables and `αN` clauses. -Any configuration in `planted` is guaranteed to be a solution of the problem. -""" -function randomcnf(; N::Int = 100, k::Int = 3, α::Float64 = 0.1, seed::Int=-1, - planted = Vector{Vector{Int}}()) - seed > 0 && Random.seed!(seed) - M = round(Int, N*α) - clauses = Vector{Vector{Int}}() - for p in planted - @assert length(p) == N "Wrong size for planted configurations ($N != $(lenght(p)) )" - end - for a=1:M - while true - c = rand(1:N, k) - length(union(c)) != k && continue - c = c .* rand([-1,1], k) - - # reject if not satisfies the planted solutions - sat = Bool[any(i -> i>0, sol[abs.(c)] .* c) for sol in planted] - !all(sat) && continue - - push!(clauses, c) - break - end - end - return CNF(N, M, clauses) -end - - -function to_edge_index(cnf::CNF) - N = cnf.N - srcV, dstF = Vector{Int}(), Vector{Int}() - srcF, dstV = Vector{Int}(), Vector{Int}() - for (a, c) in enumerate(cnf.clauses) - for v in c - negated = v < 0 - push!(srcV, abs(v) + N*negated) - push!(dstF, a) - push!(srcF, a) - push!(dstV, abs(v) + N*negated) - end - end - return srcV, dstF,srcV, dstF -end - -function to_adjacency_matrix(cnf::CNF) - M, N = cnf.M, cnf.N - A = spzeros(Int, M, 2*N) - for (a, c) in enumerate(cnf.clauses) - for v in c - negated = v < 0 - A[a, abs(v) + N*negated] = 1 - end - end - return A -end - -function flip_literals(X::AbstractMatrix) - n = size(X, 2) ÷ 2 - return hcat(X[:,n+1:2n], X[:,1:n]) -end - -## Layer -struct NeuroSAT - Xv0 - Xf0 - MLPv - MLPf - MLPout - LSTMv - LSTMf -end - -# A # rectangular adjacency matrix -Flux.@functor NeuroSAT - -# Optimisers.trainable(m::NeuroSAT) = (; m.MLPv, m.MLPf, m.MLPout, m.LSTMv, m.LSTMf) - -function NeuroSAT(D::Int) - Xv0 = randn(Float32, D) - Xf0 = randn(Float32, D) - MLPv = Chain(Dense(D => 4D, relu), Dense(4D => D)) - MLPf = Chain(Dense(D => 4D, relu), Dense(4D => D)) - MLPout = Chain(Dense(D => 4D, relu), Dense(4D => 1)) - LSTMv = LSTM(2D => D) - LSTMf = LSTM(D => D) - return NeuroSAT(Xv0, Xf0, MLPv, MLPf, MLPout, LSTMv, LSTMf) -end - -function (m::NeuroSAT)(A::AbstractArray, Tmax) - Xv = repeat(m.Xv0, 1, size(A, 2)) - # Xf = repeat(m.Xf0, 1, size(A, 1)) - - for t = 1:Tmax - Xv = m.MLPv(Xv) - Mf = Xv * A' - Xf = m.MLPf(m.LSTMf(Mf)) - Mv = Xf * A - Xv = m.LSTMv(vcat(Mv, flip_literals(Xv))) - end - return mean(m.MLPout(Xv)) -end - -# function Base.show(io, m::NeuroSAT) -# D = size(m.Xv0, 1) -# print(io, "NeuroSAT($(D))") -# end - -N = 100 -cnf = randomcnf(; N, k=3, α=1.5, seed=-1) -M = cnf.M -D = 32 # 128 nel paper -Xv = randn(Float32, D, 2*N) -Xf = randn(Float32, D, M) - -srcV, dstF, srcF, dstV = to_edge_index(cnf) -A = to_adjacency_matrix(cnf) - - -model = NeuroSAT(D) - -m_vtof = GNNGraphs._gather(Xv, srcV) -m_ftov = GNNGraphs._gather(Xf, srcF) - - diff --git a/examples/node_classification_cora.jl b/examples/node_classification_cora.jl index 084c7616c..1eb06d86d 100644 --- a/examples/node_classification_cora.jl +++ b/examples/node_classification_cora.jl @@ -55,8 +55,7 @@ function train(; kws...) GCNConv(nhidden => nhidden, relu), Dense(nhidden, nout)) |> device - ps = Flux.params(model) - opt = Adam(args.η) + opt = Flux.setup(Adam(args.η), model) display(g) @@ -70,12 +69,12 @@ function train(; kws...) ## TRAINING report(0) for epoch in 1:(args.epochs) - gs = Flux.gradient(ps) do + grad = Flux.gradient(model) do model ŷ = model(g, X) logitcrossentropy(ŷ[:, g.train_mask], ytrain) end - Flux.Optimise.update!(opt, ps, gs) + Flux.update!(opt, model, grad[1]) epoch % args.infotime == 0 && report(epoch) end diff --git a/src/layers/basic.jl b/src/layers/basic.jl index ada119737..102313772 100644 --- a/src/layers/basic.jl +++ b/src/layers/basic.jl @@ -24,8 +24,8 @@ A type wrapping the `model` and tying it to the graph `g`. In the forward pass, can only take feature arrays as inputs, returning `model(g, x...; kws...)`. -If `traingraph=false`, the graph's parameters, won't be collected -when calling `Flux.params` on a `WithGraph` object. +If `traingraph=false`, the graph's parameters won't be part of +the `trainable` parameters in the gradient updates. # Examples diff --git a/test/examples/node_classification_cora.jl b/test/examples/node_classification_cora.jl index 32cb2fa47..e0a8d03ef 100644 --- a/test/examples/node_classification_cora.jl +++ b/test/examples/node_classification_cora.jl @@ -52,8 +52,7 @@ function train(Layer; verbose = false, kws...) Layer(nhidden, nhidden), Dense(nhidden, nout)) |> device - ps = Flux.params(model) - opt = Adam(args.η) + opt = Flux.setup(Adam(args.η), model) ## TRAINING function report(epoch) From 108fb9b24d9918e93b31f1241e0bb6a55b3aebde Mon Sep 17 00:00:00 2001 From: Carlo Lucibello Date: Wed, 14 Jun 2023 08:17:07 +0200 Subject: [PATCH 2/4] update DiffEqFlux --- README.md | 3 ++- examples/Project.toml | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a6ee527cc..434e4cd46 100644 --- a/README.md +++ b/README.md @@ -19,6 +19,7 @@ Among its features: * CUDA support. * Integration with [Graphs.jl](https://github.com/JuliaGraphs/Graphs.jl). * [Examples](https://github.com/CarloLucibello/GraphNeuralNetworks.jl/tree/master/examples) of node, edge, and graph level machine learning tasks. +* Heterogeneous and temporal graphs. ## Installation @@ -30,7 +31,7 @@ pkg> add GraphNeuralNetworks ## Usage -Usage examples can be found in the [examples](https://github.com/CarloLucibello/GraphNeuralNetworks.jl/tree/master/examples) and in the [notebooks](https://github.com/CarloLucibello/GraphNeuralNetworks.jl/tree/master/notebooks) folder. Also, make sure to read the [documentation](https://CarloLucibello.github.io/GraphNeuralNetworks.jl/dev) for a comprehensive introduction to the library. +Usage examples can be found in the [examples](https://github.com/CarloLucibello/GraphNeuralNetworks.jl/tree/master/examples) and in the [notebooks](https://github.com/CarloLucibello/GraphNeuralNetworks.jl/tree/master/notebooks) folder. Also, make sure to read the [documentation](https://CarloLucibello.github.io/GraphNeuralNetworks.jl/dev) for a comprehensive introduction to the library. ## Citing diff --git a/examples/Project.toml b/examples/Project.toml index 27a51b5f2..2e56578bd 100644 --- a/examples/Project.toml +++ b/examples/Project.toml @@ -11,7 +11,7 @@ NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" NNlibCUDA = "a00861dc-f156-4864-bf3c-e6376f28a68d" [compat] -DiffEqFlux = "1.45" +DiffEqFlux = "2" Flux = "0.13" GraphNeuralNetworks = "0.6" Graphs = "1" From 50212d0dd5ca6ff01e1717b9571a705869909fd7 Mon Sep 17 00:00:00 2001 From: Carlo Lucibello Date: Wed, 14 Jun 2023 12:30:24 +0200 Subject: [PATCH 3/4] regenerate pluto output --- docs/Project.toml | 5 +- docs/make.jl | 1 + docs/pluto_output/gnn_intro_pluto.md | 39 +- .../graph_classification_pluto.md | 35 +- .../pluto_output/node_classification_pluto.md | 76 +- docs/src/dev.md | 2 +- .../introductory_tutorials/gnn_intro_pluto.jl | 830 +++++++++++------- .../graph_classification_pluto.jl | 665 +++++++++----- .../node_classification_pluto.jl | 761 ++++++++++------ 9 files changed, 1486 insertions(+), 928 deletions(-) diff --git a/docs/Project.toml b/docs/Project.toml index 45a8cb4ff..894cae1ba 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -7,10 +7,11 @@ Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" MarkdownLiteral = "736d6165-7244-6769-4267-6b50796e6954" NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" +Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781" +PlutoStaticHTML = "359b1769-a58e-495b-9770-312e911026ad" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" - [compat] -DemoCards = "^0.4.11" +DemoCards = "0.5.0" diff --git a/docs/make.jl b/docs/make.jl index b103e2e18..818a7191e 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,4 +1,5 @@ using Flux, NNlib, GraphNeuralNetworks, Graphs, SparseArrays +using Pluto, PlutoStaticHTML # for tutorials using Documenter, DemoCards tutorials, tutorials_cb, tutorial_assets = makedemos("tutorials") diff --git a/docs/pluto_output/gnn_intro_pluto.md b/docs/pluto_output/gnn_intro_pluto.md index 1a5786617..4680965bd 100644 --- a/docs/pluto_output/gnn_intro_pluto.md +++ b/docs/pluto_output/gnn_intro_pluto.md @@ -25,11 +25,11 @@ -

This Pluto notebook is a julia adaptation of the Pytorch Geometric tutorials that can be found here.

Recently, deep learning on graphs has emerged to one of the hottest research fields in the deep learning community. Here, Graph Neural Networks (GNNs) aim to generalize classical deep learning concepts to irregular structured data (in contrast to images or texts) and to enable neural networks to reason about objects and their relations.

This is done by following a simple neural message passing scheme, where node features $\mathbf{x}_i^{(\ell)}$ of all nodes $i \in \mathcal{V}$ in a graph $\mathcal{G} = (\mathcal{V}, \mathcal{E})$ are iteratively updated by aggregating localized information from their neighbors $\mathcal{N}(i)$:

$$\mathbf{x}_i^{(\ell + 1)} = f^{(\ell + 1)}_{\theta} \left( \mathbf{x}_i^{(\ell)}, \left\{ \mathbf{x}_j^{(\ell)} : j \in \mathcal{N}(i) \right\} \right)$$

This tutorial will introduce you to some fundamental concepts regarding deep learning on graphs via Graph Neural Networks based on the GraphNeuralNetworks.jl library. GraphNeuralNetworks.jl is an extension library to the popular deep learning framework Flux.jl, and consists of various methods and utilities to ease the implementation of Graph Neural Networks.

Let's first import the packages we need:

+

This Pluto notebook is a Julia adaptation of the Pytorch Geometric tutorials that can be found here.

Recently, deep learning on graphs has emerged to one of the hottest research fields in the deep learning community. Here, Graph Neural Networks (GNNs) aim to generalize classical deep learning concepts to irregular structured data (in contrast to images or texts) and to enable neural networks to reason about objects and their relations.

This is done by following a simple neural message passing scheme, where node features $\mathbf{x}_i^{(\ell)}$ of all nodes $i \in \mathcal{V}$ in a graph $\mathcal{G} = (\mathcal{V}, \mathcal{E})$ are iteratively updated by aggregating localized information from their neighbors $\mathcal{N}(i)$:

$$\mathbf{x}_i^{(\ell + 1)} = f^{(\ell + 1)}_{\theta} \left( \mathbf{x}_i^{(\ell)}, \left\{ \mathbf{x}_j^{(\ell)} : j \in \mathcal{N}(i) \right\} \right)$$

This tutorial will introduce you to some fundamental concepts regarding deep learning on graphs via Graph Neural Networks based on the GraphNeuralNetworks.jl library. GraphNeuralNetworks.jl is an extension library to the popular deep learning framework Flux.jl, and consists of various methods and utilities to ease the implementation of Graph Neural Networks.

Let's first import the packages we need:

begin
     using Flux
@@ -107,12 +107,12 @@ end;
g = GNNGraph(g, ndata = (; x, y, train_mask)) end 
GNNGraph:
-    num_nodes = 34
-    num_edges = 156
-    ndata:
-        x => 34×34 Matrix{Float32}
-        y => 4×34 OneHotMatrix(::Vector{UInt32}) with eltype Bool
-        train_mask => 34-element Vector{Bool}
+ num_nodes: 34 + num_edges: 156 + ndata: + y = 4×34 OneHotMatrix(::Vector{UInt32}) with eltype Bool + train_mask = 34-element Vector{Bool} + x = 34×34 Matrix{Float32}

Let's now look at the underlying graph in more detail:

@@ -138,7 +138,7 @@ Is undirected: true -

Each graph in GraphNeuralNetworks.jl is represented by a GNNGraph object, which holds all the information to describe its graph representation. We can print the data object anytime via print(g) to receive a short summary about its attributes and their shapes.

The g object holds 3 attributes:

  • g.ndata contains node related information;

  • g.edata holds edge-related information;

  • g.gdata: this stores the global data, therefore neither node nor edge specific features.

These attributes are NamedTuples that can store multiple feature arrays: we can access a specific set of features e.g. x, with g.ndata.x.

In our task, g.ndata.train_mask describes for which nodes we already know their community assignments. In total, we are only aware of the ground-truth labels of 4 nodes (one for each community), and the task is to infer the community assignment for the remaining nodes.

The g object also provides some utility functions to infer some basic properties of the underlying graph. For example, we can easily infer whether there exists isolated nodes in the graph (i.e. there exists no edge to any node), whether the graph contains self-loops (i.e., $(v, v) \in \mathcal{E}$), or whether the graph is bidirected (i.e., for each edge $(v, w) \in \mathcal{E}$ there also exists the edge $(w, v) \in \mathcal{E}$).

Let us now inspect the edge_index method:

+

Each graph in GraphNeuralNetworks.jl is represented by a GNNGraph object, which holds all the information to describe its graph representation. We can print the data object anytime via print(g) to receive a short summary about its attributes and their shapes.

The g object holds 3 attributes:

  • g.ndata: contains node-related information.

  • g.edata: holds edge-related information.

  • g.gdata: this stores the global data, therefore neither node nor edge-specific features.

These attributes are NamedTuples that can store multiple feature arrays: we can access a specific set of features e.g. x, with g.ndata.x.

In our task, g.ndata.train_mask describes for which nodes we already know their community assignments. In total, we are only aware of the ground-truth labels of 4 nodes (one for each community), and the task is to infer the community assignment for the remaining nodes.

The g object also provides some utility functions to infer some basic properties of the underlying graph. For example, we can easily infer whether there exist isolated nodes in the graph (i.e. there exists no edge to any node), whether the graph contains self-loops (i.e., $(v, v) \in \mathcal{E}$), or whether the graph is bidirected (i.e., for each edge $(v, w) \in \mathcal{E}$ there also exists the edge $(w, v) \in \mathcal{E}$).

Let us now inspect the edge_index method:

edge_index(g)
([1, 1, 1, 1, 1, 1, 1, 1, 1, 1  …  34, 34, 34, 34, 34, 34, 34, 34, 34, 34], [2, 3, 4, 5, 6, 7, 8, 9, 11, 12  …  21, 23, 24, 27, 28, 29, 30, 31, 32, 33])
@@ -198,7 +198,7 @@ end 
GCN((conv1 = GCNConv(34 => 4), conv2 = GCNConv(4 => 4), conv3 = GCNConv(4 => 2), classifier = Dense(2 => 4)))
_, h = gcn(g, g.ndata.x)
-
(Float32[-0.0309585 0.00945922 … -0.16325654 -0.16372235; 0.0029724604 0.005891501 … -0.102138 -0.1026775; 0.0194636 -0.0015970899 … 0.027272016 0.027191132; 0.0026649572 -0.0063592414 … 0.11012645 0.11064298], Float32[0.020249235 -0.0008903823 … 0.015011376 0.014860965; -0.02326259 0.011758871 … -0.20325856 -0.2040082])
+
(Float32[0.12078241 0.10647664 … 0.078505844 0.09433363; 0.05597087 0.059971973 … 0.034847457 0.033327967; 0.06764817 0.044030245 … 0.046219267 0.06808202; -0.14550589 -0.12921461 … -0.09443963 -0.112721995], Float32[0.10848574 0.119858325 … 0.06702177 0.06106364; -0.21592957 -0.18892974 … -0.1405547 -0.17003746])
function visualize_embeddings(h; colors = nothing)
     xs = h[1, :] |> vec
@@ -208,15 +208,14 @@ end
visualize_embeddings (generic function with 1 method)
visualize_embeddings(h, colors = labels)
- + -

Remarkably, even before training the weights of our model, the model produces an embedding of nodes that closely resembles the community-structure of the graph. Nodes of the same color (community) are already closely clustered together in the embedding space, although the weights of our model are initialized completely at random and we have not yet performed any training so far! This leads to the conclusion that GNNs introduce a strong inductive bias, leading to similar embeddings for nodes that are close to each other in the input graph.

Training on the Karate Club Network

But can we do better? Let's look at an example on how to train our network parameters based on the knowledge of the community assignments of 4 nodes in the graph (one for each community).

Since everything in our model is differentiable and parameterized, we can add some labels, train the model and observe how the embeddings react. Here, we make use of a semi-supervised or transductive learning procedure: we simply train against one node per class, but are allowed to make use of the complete input graph data.

Training our model is very similar to any other Flux model. In addition to defining our network architecture, we define a loss criterion (here, logitcrossentropy and initialize a stochastic gradient optimizer (here, Adam). After that, we perform multiple rounds of optimization, where each round consists of a forward and backward pass to compute the gradients of our model parameters w.r.t. to the loss derived from the forward pass. If you are not new to Flux, this scheme should appear familiar to you.

Note that our semi-supervised learning scenario is achieved by the following line:

loss = logitcrossentropy(ŷ[:,train_mask], y[:,train_mask])

While we compute node embeddings for all of our nodes, we only make use of the training nodes for computing the loss. Here, this is implemented by filtering the output of the classifier out and ground-truth labels data.y to only contain the nodes in the train_mask.

Let us now start training and see how our node embeddings evolve over time (best experienced by explicitly running the code):

+

Remarkably, even before training the weights of our model, the model produces an embedding of nodes that closely resembles the community-structure of the graph. Nodes of the same color (community) are already closely clustered together in the embedding space, although the weights of our model are initialized completely at random and we have not yet performed any training so far! This leads to the conclusion that GNNs introduce a strong inductive bias, leading to similar embeddings for nodes that are close to each other in the input graph.

Training on the Karate Club Network

But can we do better? Let's look at an example on how to train our network parameters based on the knowledge of the community assignments of 4 nodes in the graph (one for each community).

Since everything in our model is differentiable and parameterized, we can add some labels, train the model and observe how the embeddings react. Here, we make use of a semi-supervised or transductive learning procedure: we simply train against one node per class, but are allowed to make use of the complete input graph data.

Training our model is very similar to any other Flux model. In addition to defining our network architecture, we define a loss criterion (here, logitcrossentropy), and initialize a stochastic gradient optimizer (here, Adam). After that, we perform multiple rounds of optimization, where each round consists of a forward and backward pass to compute the gradients of our model parameters w.r.t. to the loss derived from the forward pass. If you are not new to Flux, this scheme should appear familiar to you.

Note that our semi-supervised learning scenario is achieved by the following line:

loss = logitcrossentropy(ŷ[:,train_mask], y[:,train_mask])

While we compute node embeddings for all of our nodes, we only make use of the training nodes for computing the loss. Here, this is implemented by filtering the output of the classifier out and ground-truth labels data.y to only contain the nodes in the train_mask.

Let us now start training and see how our node embeddings evolve over time (best experienced by explicitly running the code):

begin
     model = GCN(num_features, num_classes)
-    ps = Flux.params(model)
-    opt = Adam(1e-2)
+    opt = Flux.setup(Adam(1e-2), model)
     epochs = 2000
 
     emb = h
@@ -227,12 +226,12 @@ end
report(0, 10.0, emb) for epoch in 1:epochs - loss, gs = Flux.withgradient(ps) do + loss, grad = Flux.withgradient(model) do model ŷ, emb = model(g, g.ndata.x) logitcrossentropy(ŷ[:, train_mask], y[:, train_mask]) end - Flux.Optimise.update!(opt, ps, gs) + Flux.update!(opt, model, grad[1]) if epoch % 200 == 0 report(epoch, loss, emb) end @@ -241,7 +240,7 @@ end 
ŷ, emb_final = model(g, g.ndata.x)
-
(Float32[-0.91217184 -0.39988565 … 6.9576254 6.9580946; 7.018002 6.518844 … -0.7402323 -0.73952585; -8.740045 -8.172279 … 0.0855175 0.08470068; -0.11511713 -0.45739585 … -5.346242 -5.3469048], Float32[0.9989928 0.99999094 … 0.9997774 0.9999662; -0.9991084 -0.8695722 … 0.9999995 0.9999999])
+
(Float32[1.6581383 10.223198 … 9.9329815 9.888992; 6.214694 5.664531 … 5.449857 5.4190893; -1.1629901 1.242935 … 1.450836 1.4801507; 1.6831793 -7.9417863 … -8.047817 -8.060606], Float32[0.0006826519 -0.99821377 … -0.99999994 -1.0; 0.9999991 0.99999326 … 0.93681836 0.92772233])
# train accuracy
 mean(onecold(ŷ[:, train_mask]) .== onecold(y[:, train_mask]))
@@ -249,10 +248,10 @@ mean(onecold(ŷ[:, train_mask]) .== onecold(y[:, train_mask])) 
# test accuracy
 mean(onecold(ŷ[:, .!train_mask]) .== onecold(y[:, .!train_mask]))
-
0.8
+
0.5666666666666667
visualize_embeddings(emb_final, colors = labels)
- +

As one can see, our 3-layer GCN model manages to linearly separating the communities and classifying most of the nodes correctly.

Furthermore, we did this all with a few lines of code, thanks to the GraphNeuralNetworks.jl which helped us out with data handling and GNN implementations.

diff --git a/docs/pluto_output/graph_classification_pluto.md b/docs/pluto_output/graph_classification_pluto.md index cb6fad044..1a451591c 100644 --- a/docs/pluto_output/graph_classification_pluto.md +++ b/docs/pluto_output/graph_classification_pluto.md @@ -25,8 +25,8 @@ 
begin
     using Flux
@@ -102,18 +102,18 @@ end

We have some useful utilities for working with graph datasets, e.g., we can shuffle the dataset and use the first 150 graphs as training graphs, while using the remaining ones for testing:

train_data, test_data = splitobs((graphs, y), at = 150, shuffle = true) |> getobs
-
((GraphNeuralNetworks.GNNGraphs.GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}[GNNGraph(16, 34), GNNGraph(15, 32), GNNGraph(19, 44), GNNGraph(20, 44), GNNGraph(20, 46), GNNGraph(15, 34), GNNGraph(18, 40), GNNGraph(16, 36), GNNGraph(13, 28), GNNGraph(16, 34)  …  GNNGraph(23, 48), GNNGraph(20, 44), GNNGraph(28, 66), GNNGraph(25, 56), GNNGraph(13, 28), GNNGraph(16, 36), GNNGraph(12, 24), GNNGraph(22, 50), GNNGraph(25, 58), GNNGraph(19, 42)], Bool[1 1 … 0 0; 0 0 … 1 1]), (GraphNeuralNetworks.GNNGraphs.GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}[GNNGraph(12, 24), GNNGraph(11, 22), GNNGraph(15, 34), GNNGraph(19, 44), GNNGraph(22, 50), GNNGraph(17, 38), GNNGraph(17, 38), GNNGraph(17, 38), GNNGraph(19, 42), GNNGraph(13, 28)  …  GNNGraph(19, 40), GNNGraph(13, 28), GNNGraph(22, 50), GNNGraph(14, 28), GNNGraph(23, 54), GNNGraph(20, 46), GNNGraph(13, 28), GNNGraph(26, 60), GNNGraph(17, 38), GNNGraph(12, 26)], Bool[1 1 … 0 0; 0 0 … 1 1]))
+
((GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}[GNNGraph(12, 24) with x: 7×12 data, GNNGraph(22, 50) with x: 7×22 data, GNNGraph(23, 54) with x: 7×23 data, GNNGraph(25, 56) with x: 7×25 data, GNNGraph(16, 36) with x: 7×16 data, GNNGraph(11, 22) with x: 7×11 data, GNNGraph(18, 38) with x: 7×18 data, GNNGraph(23, 52) with x: 7×23 data, GNNGraph(22, 50) with x: 7×22 data, GNNGraph(20, 46) with x: 7×20 data  …  GNNGraph(16, 34) with x: 7×16 data, GNNGraph(13, 28) with x: 7×13 data, GNNGraph(21, 44) with x: 7×21 data, GNNGraph(17, 38) with x: 7×17 data, GNNGraph(23, 54) with x: 7×23 data, GNNGraph(12, 24) with x: 7×12 data, GNNGraph(22, 50) with x: 7×22 data, GNNGraph(19, 42) with x: 7×19 data, GNNGraph(16, 34) with x: 7×16 data, GNNGraph(16, 36) with x: 7×16 data], Bool[1 0 … 1 0; 0 1 … 0 1]), (GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}[GNNGraph(21, 44) with x: 7×21 data, GNNGraph(22, 50) with x: 7×22 data, GNNGraph(16, 34) with x: 7×16 data, GNNGraph(27, 66) with x: 7×27 data, GNNGraph(13, 26) with x: 7×13 data, GNNGraph(20, 44) with x: 7×20 data, GNNGraph(19, 44) with x: 7×19 data, GNNGraph(20, 46) with x: 7×20 data, GNNGraph(16, 34) with x: 7×16 data, GNNGraph(13, 28) with x: 7×13 data  …  GNNGraph(11, 22) with x: 7×11 data, GNNGraph(20, 46) with x: 7×20 data, GNNGraph(16, 34) with x: 7×16 data, GNNGraph(18, 40) with x: 7×18 data, GNNGraph(13, 28) with x: 7×13 data, GNNGraph(20, 44) with x: 7×20 data, GNNGraph(14, 30) with x: 7×14 data, GNNGraph(13, 26) with x: 7×13 data, GNNGraph(21, 44) with x: 7×21 data, GNNGraph(22, 50) with x: 7×22 data], Bool[0 0 … 0 0; 1 1 … 1 1]))
begin
-    train_loader = DataLoader(train_data, batchsize = 64, shuffle = true)
-    test_loader = DataLoader(test_data, batchsize = 64, shuffle = false)
+    train_loader = DataLoader(train_data, batchsize = 32, shuffle = true)
+    test_loader = DataLoader(test_data, batchsize = 32, shuffle = false)
 end
-
1-element DataLoader(::Tuple{Vector{GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}}, OneHotArrays.OneHotMatrix{UInt32, Vector{UInt32}}}, batchsize=64)
+
2-element DataLoader(::Tuple{Vector{GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}}, OneHotArrays.OneHotMatrix{UInt32, Vector{UInt32}}}, batchsize=32)
   with first element:
-  (38-element Vector{GraphNeuralNetworks.GNNGraphs.GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}}, 2×38 OneHotMatrix(::Vector{UInt32}) with eltype Bool,)

+  (32-element Vector{GraphNeuralNetworks.GNNGraphs.GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}}, 2×32 OneHotMatrix(::Vector{UInt32}) with eltype Bool,)
-

Here, we opt for a batch_size of 64, leading to 3 (randomly shuffled) mini-batches, containing all $2 \cdot 64+22 = 150$ graphs.

+

Here, we opt for a batch_size of 32, leading to 5 (randomly shuffled) mini-batches, containing all $4 \cdot 32+22 = 150$ graphs.

``` @@ -123,15 +123,15 @@ end

Since graphs in graph classification datasets are usually small, a good idea is to batch the graphs before inputting them into a Graph Neural Network to guarantee full GPU utilization. In the image or language domain, this procedure is typically achieved by rescaling or padding each example into a set of equally-sized shapes, and examples are then grouped in an additional dimension. The length of this dimension is then equal to the number of examples grouped in a mini-batch and is typically referred to as the batchsize.

However, for GNNs the two approaches described above are either not feasible or may result in a lot of unnecessary memory consumption. Therefore, GraphNeuralNetworks.jl opts for another approach to achieve parallelization across a number of examples. Here, adjacency matrices are stacked in a diagonal fashion (creating a giant graph that holds multiple isolated subgraphs), and node and target features are simply concatenated in the node dimension (the last dimension).

This procedure has some crucial advantages over other batching procedures:

  1. GNN operators that rely on a message passing scheme do not need to be modified since messages are not exchanged between two nodes that belong to different graphs.

  2. There is no computational or memory overhead since adjacency matrices are saved in a sparse fashion holding only non-zero entries, i.e., the edges.

GraphNeuralNetworks.jl can batch multiple graphs into a single giant graph:

vec_gs, _ = first(train_loader)
-
(GraphNeuralNetworks.GNNGraphs.GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}[GNNGraph(11, 22), GNNGraph(16, 36), GNNGraph(16, 34), GNNGraph(22, 50), GNNGraph(18, 40), GNNGraph(19, 40), GNNGraph(24, 50), GNNGraph(23, 54), GNNGraph(24, 50), GNNGraph(12, 26)  …  GNNGraph(20, 44), GNNGraph(11, 22), GNNGraph(22, 50), GNNGraph(13, 26), GNNGraph(16, 34), GNNGraph(10, 20), GNNGraph(28, 66), GNNGraph(19, 44), GNNGraph(14, 30), GNNGraph(18, 38)], Bool[1 0 … 1 0; 0 1 … 0 1])
+
(GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}[GNNGraph(17, 38) with x: 7×17 data, GNNGraph(19, 42) with x: 7×19 data, GNNGraph(13, 28) with x: 7×13 data, GNNGraph(14, 30) with x: 7×14 data, GNNGraph(13, 28) with x: 7×13 data, GNNGraph(23, 54) with x: 7×23 data, GNNGraph(16, 36) with x: 7×16 data, GNNGraph(24, 50) with x: 7×24 data, GNNGraph(23, 54) with x: 7×23 data, GNNGraph(15, 34) with x: 7×15 data  …  GNNGraph(16, 34) with x: 7×16 data, GNNGraph(16, 34) with x: 7×16 data, GNNGraph(23, 54) with x: 7×23 data, GNNGraph(12, 26) with x: 7×12 data, GNNGraph(17, 38) with x: 7×17 data, GNNGraph(20, 44) with x: 7×20 data, GNNGraph(13, 28) with x: 7×13 data, GNNGraph(26, 60) with x: 7×26 data, GNNGraph(23, 54) with x: 7×23 data, GNNGraph(24, 50) with x: 7×24 data], Bool[0 0 … 0 0; 1 1 … 1 1])
MLUtils.batch(vec_gs)
GNNGraph:
-    num_nodes = 1191
-    num_edges = 2618
-    num_graphs = 64
-    ndata:
-        x => 7×1191 Matrix{Float32}
+ num_nodes: 585 + num_edges: 1292 + num_graphs: 32 + ndata: + x = 7×585 Matrix{Float32}

Each batched graph object is equipped with a graph_indicator vector, which maps each node to its respective graph in the batch:

$$\textrm{graph\_indicator} = [1, \ldots, 1, 2, \ldots, 2, 3, \ldots ]$$

@@ -177,8 +177,7 @@ end # device = Flux.gpu # uncomment this for GPU training device = Flux.cpu model = model |> device - ps = Flux.params(model) - opt = Adam(1e-3) + opt = Flux.setup(Adam(1e-3), model) function report(epoch) train = eval_loss_accuracy(model, train_loader, device) @@ -190,11 +189,11 @@ end for epoch in 1:epochs for (g, y) in train_loader g, y = MLUtils.batch(g) |> device, y |> device - gs = Flux.gradient(ps) do + grad = Flux.gradient(model) do model ŷ = model(g, g.ndata.x) logitcrossentropy(ŷ, y) end - Flux.Optimise.update!(opt, ps, gs) + Flux.update!(opt, model, grad[1]) end epoch % infotime == 0 && report(epoch) end diff --git a/docs/pluto_output/node_classification_pluto.md b/docs/pluto_output/node_classification_pluto.md index 63abb41be..68bd2fef5 100644 --- a/docs/pluto_output/node_classification_pluto.md +++ b/docs/pluto_output/node_classification_pluto.md @@ -25,11 +25,11 @@ -

Following our previous tutorial in GNNs, we covered how to create graph neural networks.

In this tutorial, we will be learning how to use Graph Neural Networks (GNNs) for node classification. Given the ground-truth labels of only a small subset of nodes, and want to infer the labels for all the remaining nodes (transductive learning).

+

In this tutorial, we will be learning how to use Graph Neural Networks (GNNs) for node classification. Given the ground-truth labels of only a small subset of nodes, and want to infer the labels for all the remaining nodes (transductive learning).

``` @@ -51,15 +51,15 @@ ENV["DATADEPS_ALWAYS_ACCEPT"] = "true" Random.seed!(17) # for reproducibility -end -
TaskLocalRNG()
+end; + ``` ## Visualize ```@raw html
-

We want to visualize the the outputs of the resutls using t-distributed stochastic neighbor embedding (tsne) to embed our output embeddings onto a 2D plane.

+

We want to visualize the the outputs of the results using t-distributed stochastic neighbor embedding (tsne) to embed our output embeddings onto a 2D plane.

function visualize_tsne(out, targets)
     z = tsne(out, 2)
@@ -72,7 +72,7 @@ end
## Dataset: Cora ```@raw html
-

For our tutorial, we will be using the Cora dataset. Cora is a citaton network of 2708 documents classified into one of seven classes and 5429 links. Each node represent articles/documents and the edges between these nodes if one of them cite each other.

Each publication in the dataset is described by a 0/1-valued word vector indicating the absence/presence of the corresponding word from the dictionary. The dictionary consists of 1433 unique words.

This dataset was first introduced by Yang et al. (2016) as one of the datasets of the Planetoid benchmark suite. We will be using MLDatasets.jl for an easy accss to this dataset.

+

For our tutorial, we will be using the Cora dataset. Cora is a citation network of 2708 documents classified into one of seven classes and 5429 links. Each node represent articles/documents and the edges between these nodes if one of them cite each other.

Each publication in the dataset is described by a 0/1-valued word vector indicating the absence/presence of the corresponding word from the dictionary. The dictionary consists of 1433 unique words.

This dataset was first introduced by Yang et al. (2016) as one of the datasets of the Planetoid benchmark suite. We will be using MLDatasets.jl for an easy access to this dataset.

dataset = Cora()
dataset Cora:
@@ -89,25 +89,25 @@ end
"num_classes" => 7 -

The graphs variable GraphDataset contains the graph. The Cora dataaset contains only 1 graph.

+

The graphs variable GraphDataset contains the graph. The Cora dataset contains only 1 graph.

dataset.graphs
1-element Vector{MLDatasets.Graph}:
  Graph(2708, 10556)
-

There is only one graph of the dataset. The node_data contians features indicating if certain words are present or not and targets indicating the class for each document. We convert the single-graph dataset to a GNNGraph.

+

There is only one graph of the dataset. The node_data contains features indicating if certain words are present or not and targets indicating the class for each document. We convert the single-graph dataset to a GNNGraph.

g = mldataset2gnngraph(dataset)
GNNGraph:
-    num_nodes = 2708
-    num_edges = 10556
-    ndata:
-        features => 1433×2708 Matrix{Float32}
-        targets => 2708-element Vector{Int64}
-        train_mask => 2708-element BitVector
-        val_mask => 2708-element BitVector
-        test_mask => 2708-element BitVector
+ num_nodes: 2708 + num_edges: 10556 + ndata: + val_mask = 2708-element BitVector + targets = 2708-element Vector{Int64} + test_mask = 2708-element BitVector + features = 1433×2708 Matrix{Float32} + train_mask = 2708-element BitVector 
with_terminal() do
     # Gather some statistics about the graph.
@@ -140,8 +140,8 @@ Is undirected: true
     num_features = size(x)[1]
     hidden_channels = 16
     num_classes = dataset.metadata["num_classes"]
-end
-
7
+end; + ``` @@ -176,18 +176,18 @@ end -

Training a Multilayer Perceptron

Our MLP is defined by two linear layers and enhanced by ReLU non-linearity and Dropout. Here, we first reduce the 1433-dimensional feature vector to a low-dimensional embedding (hidden_channels=16), while the second linear layer acts as a classifier that should map each low-dimensional node embedding to one of the 7 classes.

Let's train our simple MLP by following a similar procedure as described in the first part of this tutorial. We again make use of the cross entropy loss and Adam optimizer. This time, we also define a accuracy function to evaluate how well our final model performs on the test node set (which labels have not been observed during training).

+

Training a Multilayer Perceptron

Our MLP is defined by two linear layers and enhanced by ReLU non-linearity and Dropout. Here, we first reduce the 1433-dimensional feature vector to a low-dimensional embedding (hidden_channels=16), while the second linear layer acts as a classifier that should map each low-dimensional node embedding to one of the 7 classes.

Let's train our simple MLP by following a similar procedure as described in the first part of this tutorial. We again make use of the cross entropy loss and Adam optimizer. This time, we also define a accuracy function to evaluate how well our final model performs on the test node set (which labels have not been observed during training).

-
function train(model::MLP, data::AbstractMatrix, epochs::Int, opt, ps)
+
function train(model::MLP, data::AbstractMatrix, epochs::Int, opt)
     Flux.trainmode!(model)
 
     for epoch in 1:epochs
-        loss, gs = Flux.withgradient(ps) do
+        loss, grad = Flux.withgradient(model) do model
             ŷ = model(data)
             logitcrossentropy(ŷ[:, train_mask], y[:, train_mask])
         end
 
-        Flux.Optimise.update!(opt, ps, gs)
+        Flux.update!(opt, model, grad[1])
         if epoch % 200 == 0
             @show epoch, loss
         end
@@ -203,10 +203,9 @@ end

 
 
begin
     mlp = MLP(num_features, num_classes, hidden_channels)
-    ps_mlp = Flux.params(mlp)
-    opt_mlp = Adam(1e-3)
+    opt_mlp = Flux.setup(Adam(1e-3), mlp)
     epochs = 2000
-    train(mlp, g.ndata.features, epochs, opt_mlp, ps_mlp)
+    train(mlp, g.ndata.features, epochs, opt_mlp)
 end

 
 
@@ -214,7 +213,7 @@ end

After training the model, we can call the accuracy function to see how well our model performs on unseen labels. Here, we are interested in the accuracy of the model, i.e., the ratio of correctly classified nodes:

accuracy(mlp, g.ndata.features, y, .!train_mask)
-
0.5377725856697819
+
0.4824766355140187

As one can see, our MLP performs rather bad with only about 47% test accuracy. But why does the MLP do not perform better? The main reason for that is that this model suffers from heavy overfitting due to only having access to a small amount of training nodes, and therefore generalizes poorly to unseen node representations.

It also fails to incorporate an important bias into the model: Cited papers are very likely related to the category of a document. That is exactly where Graph Neural Networks come into play and can help to boost the performance of our model.

@@ -224,7 +223,7 @@ end ## Training a Graph Convolutional Neural Network (GNN) ```@raw html
-

We can easily convert our MLP to a GNN by swapping the torch.nn.Linear layers with PyG's GNN operators.

Following-up on the first part of this tutorial, we replace the linear layers by the GCNConv module. To recap, the GCN layer (Kipf et al. (2017)) is defined as

$$\mathbf{x}_v^{(\ell + 1)} = \mathbf{W}^{(\ell + 1)} \sum_{w \in \mathcal{N}(v) \, \cup \, \{ v \}} \frac{1}{c_{w,v}} \cdot \mathbf{x}_w^{(\ell)}$$

where $\mathbf{W}^{(\ell + 1)}$ denotes a trainable weight matrix of shape [num_output_features, num_input_features] and $c_{w,v}$ refers to a fixed normalization coefficient for each edge. In contrast, a single Linear layer is defined as

$$\mathbf{x}_v^{(\ell + 1)} = \mathbf{W}^{(\ell + 1)} \mathbf{x}_v^{(\ell)}$$

which does not make use of neighboring node information.

+

Following-up on the first part of this tutorial, we replace the Dense linear layers by the GCNConv module. To recap, the GCN layer (Kipf et al. (2017)) is defined as

$$\mathbf{x}_v^{(\ell + 1)} = \mathbf{W}^{(\ell + 1)} \sum_{w \in \mathcal{N}(v) \, \cup \, \{ v \}} \frac{1}{c_{w,v}} \cdot \mathbf{x}_w^{(\ell)}$$

where $\mathbf{W}^{(\ell + 1)}$ denotes a trainable weight matrix of shape [num_output_features, num_input_features] and $c_{w,v}$ refers to a fixed normalization coefficient for each edge. In contrast, a single Linear layer is defined as

$$\mathbf{x}_v^{(\ell + 1)} = \mathbf{W}^{(\ell + 1)} \mathbf{x}_v^{(\ell)}$$

which does not make use of neighboring node information.

begin
     struct GCN
@@ -259,21 +258,21 @@ end
h_untrained = gcn(g, x) |> transpose visualize_tsne(h_untrained, g.ndata.targets) end - +

We certainly can do better by training our model. The training and testing procedure is once again the same, but this time we make use of the node features xand the graph g as input to our GCN model.

-
function train(model::GCN, g::GNNGraph, x::AbstractMatrix, epochs::Int, ps, opt)
+
function train(model::GCN, g::GNNGraph, x::AbstractMatrix, epochs::Int, opt)
     Flux.trainmode!(model)
 
     for epoch in 1:epochs
-        loss, gs = Flux.withgradient(ps) do
+        loss, grad = Flux.withgradient(model) do model
             ŷ = model(g, x)
             logitcrossentropy(ŷ[:, train_mask], y[:, train_mask])
         end
 
-        Flux.Optimise.update!(opt, ps, gs)
+        Flux.update!(opt, model, grad[1])
         if epoch % 200 == 0
             @show epoch, loss
         end
@@ -289,9 +288,8 @@ end

 
accuracy (generic function with 2 methods)

 
 
begin
-    ps_gcn = Flux.params(gcn)
-    opt_gcn = Adam(1e-2)
-    train(gcn, g, x, epochs, ps_gcn, opt_gcn)
+    opt_gcn = Flux.setup(Adam(1e-2), gcn)
+    train(gcn, g, x, epochs, opt_gcn)
 end

 
 
@@ -306,7 +304,7 @@ end
println("Test accuracy: $(test_accuracy)") end 
Train accuracy: 1.0
-Test accuracy: 0.7484423676012462
+Test accuracy: 0.7457165109034268
@@ -318,21 +316,21 @@ Test accuracy: 0.7484423676012462 out_trained = gcn(g, x) |> transpose visualize_tsne(out_trained, g.ndata.targets) end - + ``` ## (Optional) Exercises ```@raw html
-

  1. To achieve better model performance and to avoid overfitting, it is usually a good idea to select the best model based on an additional validation set.

The Cora dataset provides a validation node set as g.ndata.val_mask, but we haven't used it yet. Can you modify the code to select and test the model with the highest validation performance? This should bring test performance to 82% accuracy.

  1. How does GCN behave when increasing the hidden feature dimensionality or the number of layers?

Does increasing the number of layers help at all?

  1. You can try to use different GNN layers to see how model performance changes. What happens if you swap out all GCNConv instances with GATConv layers that make use of attention? Try to write a 2-layer GAT model that makes use of 8 attention heads in the first layer and 1 attention head in the second layer, uses a dropout ratio of 0.6 inside and outside each GATConv call, and uses a hidden_channels dimensions of 8 per head.

+

  1. To achieve better model performance and to avoid overfitting, it is usually a good idea to select the best model based on an additional validation set. The Cora dataset provides a validation node set as g.ndata.val_mask, but we haven't used it yet. Can you modify the code to select and test the model with the highest validation performance? This should bring test performance to 82% accuracy.

  2. How does GCN behave when increasing the hidden feature dimensionality or the number of layers? Does increasing the number of layers help at all?

  3. You can try to use different GNN layers to see how model performance changes. What happens if you swap out all GCNConv instances with GATConv layers that make use of attention? Try to write a 2-layer GAT model that makes use of 8 attention heads in the first layer and 1 attention head in the second layer, uses a dropout ratio of 0.6 inside and outside each GATConv call, and uses a hidden_channels dimensions of 8 per head.

``` ## Conclusion ```@raw html
-

In this tutorial, we have seen how to apply GNNs to real-world problems, and, in particular, how they can effectively be used for boosting a model's performance. In the next section, we will look into how GNNs can be used for the task of graph classification.

Next tutorial: Graph Classification with Graph Neural Networks

+

In this tutorial, we have seen how to apply GNNs to real-world problems, and, in particular, how they can effectively be used for boosting a model's performance. In the next tutorial, we will look into how GNNs can be used for the task of graph classification.

``` diff --git a/docs/src/dev.md b/docs/src/dev.md index 5c617fa28..23f7e38e8 100644 --- a/docs/src/dev.md +++ b/docs/src/dev.md @@ -39,7 +39,7 @@ julia> compare(dfpr, dfmaster) Tutorials in GraphNeuralNetworks.jl are written in Pluto and rendered using [DemoCards.jl](https://github.com/JuliaDocs/DemoCards.jl) and [PlutoStaticHTML.jl](https://github.com/rikhuijzer/PlutoStaticHTML.jl). Rendering a Pluto notebook is time and resource-consuming, especially in a CI environment. So we use the [caching functionality](https://huijzer.xyz/PlutoStaticHTML.jl/dev/#Caching) provided by PlutoStaticHTML.jl to reduce CI time. -If you are contributing a new tutorial or making changes to the existing notebook, generate the docs locally before committing/pushing. For caching to work, the cache environment(your local) and the documenter CI should have the same Julia version. So use the [documenter CI Julia version](https://github.com/CarloLucibello/GraphNeuralNetworks.jl/blob/master/.github/workflows/docs.yml#L17) for generating docs locally. +If you are contributing a new tutorial or making changes to the existing notebook, generate the docs locally before committing/pushing. For caching to work, the cache environment(your local) and the documenter CI should have the same Julia version (e.g. "v1.9.1", also the patch number must match). So use the [documenter CI Julia version](https://github.com/CarloLucibello/GraphNeuralNetworks.jl/blob/master/.github/workflows/docs.yml#L17) for generating docs locally. ```console julia --version # check julia version before generating docs diff --git a/docs/tutorials/introductory_tutorials/gnn_intro_pluto.jl b/docs/tutorials/introductory_tutorials/gnn_intro_pluto.jl index df1ea058c..87cce8e4f 100644 --- a/docs/tutorials/introductory_tutorials/gnn_intro_pluto.jl +++ b/docs/tutorials/introductory_tutorials/gnn_intro_pluto.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.19 +# v0.19.26 #> [frontmatter] #> author = "[Carlo Lucibello](https://github.com/CarloLucibello)" @@ -26,7 +26,7 @@ end # ╔═╡ 03a9e023-e682-4ea3-a10b-14c4d101b291 md""" -*This Pluto notebook is a julia adaptation of the Pytorch Geometric tutorials that can be found [here](https://pytorch-geometric.readthedocs.io/en/latest/notes/colabs.html).* +*This Pluto notebook is a Julia adaptation of the Pytorch Geometric tutorials that can be found [here](https://pytorch-geometric.readthedocs.io/en/latest/notes/colabs.html).* Recently, deep learning on graphs has emerged to one of the hottest research fields in the deep learning community. Here, **Graph Neural Networks (GNNs)** aim to generalize classical deep learning concepts to irregular structured data (in contrast to images or texts) and to enable neural networks to reason about objects and their relations. @@ -120,9 +120,9 @@ Each graph in GraphNeuralNetworks.jl is represented by a `GNNGraph` object, whi We can print the data object anytime via `print(g)` to receive a short summary about its attributes and their shapes. The `g` object holds 3 attributes: -- `g.ndata` contains node related information; -- `g.edata` holds edge-related information; -- `g.gdata`: this stores the global data, therefore neither node nor edge specific features. +- `g.ndata`: contains node-related information. +- `g.edata`: holds edge-related information. +- `g.gdata`: this stores the global data, therefore neither node nor edge-specific features. These attributes are `NamedTuples` that can store multiple feature arrays: we can access a specific set of features e.g. `x`, with `g.ndata.x`. @@ -130,7 +130,7 @@ These attributes are `NamedTuples` that can store multiple feature arrays: we ca In our task, `g.ndata.train_mask` describes for which nodes we already know their community assignments. In total, we are only aware of the ground-truth labels of 4 nodes (one for each community), and the task is to infer the community assignment for the remaining nodes. The `g` object also provides some **utility functions** to infer some basic properties of the underlying graph. -For example, we can easily infer whether there exists isolated nodes in the graph (*i.e.* there exists no edge to any node), whether the graph contains self-loops (*i.e.*, ``(v, v) \in \mathcal{E}``), or whether the graph is bidirected (*i.e.*, for each edge ``(v, w) \in \mathcal{E}`` there also exists the edge ``(w, v) \in \mathcal{E}``). +For example, we can easily infer whether there exist isolated nodes in the graph (*i.e.* there exists no edge to any node), whether the graph contains self-loops (*i.e.*, ``(v, v) \in \mathcal{E}``), or whether the graph is bidirected (*i.e.*, for each edge ``(v, w) \in \mathcal{E}`` there also exists the edge ``(w, v) \in \mathcal{E}``). Let us now inspect the `edge_index` method: @@ -337,8 +337,8 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" CairoMakie = "~0.10.0" Flux = "~0.13.10" GraphMakie = "~0.5.0" -GraphNeuralNetworks = "~0.5.2" -Graphs = "~1.7.4" +GraphNeuralNetworks = "~0.6.6" +Graphs = "~1.8.0" MLDatasets = "~0.7.8" PlutoUI = "~0.7.49" """ @@ -347,15 +347,19 @@ PlutoUI = "~0.7.49" PLUTO_MANIFEST_TOML_CONTENTS = """ # This file is machine-generated - editing it directly is not advised -julia_version = "1.8.3" +julia_version = "1.9.1" manifest_format = "2.0" -project_hash = "565ce867f785b122494abba41dfa93706b554a45" +project_hash = "720d4fac59d155679da4880798ab24be8b9165d7" [[deps.AbstractFFTs]] -deps = ["ChainRulesCore", "LinearAlgebra"] -git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" +deps = ["LinearAlgebra"] +git-tree-sha1 = "16b6dbc4cf7caee4e1e75c49485ec67b667098a0" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.2.1" +version = "1.3.1" +weakdeps = ["ChainRulesCore"] + + [deps.AbstractFFTs.extensions] + AbstractFFTsChainRulesCoreExt = "ChainRulesCore" [[deps.AbstractPlutoDingetjes]] deps = ["Pkg"] @@ -364,21 +368,37 @@ uuid = "6e696c72-6542-2067-7265-42206c756150" version = "1.1.4" [[deps.AbstractTrees]] -git-tree-sha1 = "52b3b436f8f73133d7bc3a6c71ee7ed6ab2ab754" +git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.4.3" +version = "0.4.4" [[deps.Accessors]] -deps = ["Compat", "CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Requires", "Test"] -git-tree-sha1 = "3fa8cc751763c91a5ea33331e523221009cb1e6f" +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Requires", "Test"] +git-tree-sha1 = "954634616d5846d8e216df1298be2298d55280b2" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.23" +version = "0.1.32" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" [[deps.Adapt]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.4.0" +version = "3.6.2" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" [[deps.Animations]] deps = ["Colors"] @@ -404,6 +424,12 @@ version = "0.2.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +[[deps.Atomix]] +deps = ["UnsafeAtomics"] +git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" +uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" +version = "0.1.0" + [[deps.Automa]] deps = ["Printf", "ScanByte", "TranscodingStreams"] git-tree-sha1 = "d50976f217489ce799e366d9561d56a98a30d7fe" @@ -424,15 +450,29 @@ version = "0.4.6" [[deps.BFloat16s]] deps = ["LinearAlgebra", "Printf", "Random", "Test"] -git-tree-sha1 = "a598ecb0d717092b5539dbbe890c98bac842b072" +git-tree-sha1 = "dbf84058d0a8cbbadee18d25cf606934b22d7c66" uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" -version = "0.2.0" +version = "0.4.2" [[deps.BangBang]] -deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] -git-tree-sha1 = "7fe6d92c4f281cf4ca6f2fba0ce7b299742da7ca" +deps = ["Compat", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables"] +git-tree-sha1 = "e28912ce94077686443433c2800104b061a827ed" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.3.37" +version = "0.3.39" + + [deps.BangBang.extensions] + BangBangChainRulesCoreExt = "ChainRulesCore" + BangBangDataFramesExt = "DataFrames" + BangBangStaticArraysExt = "StaticArrays" + BangBangStructArraysExt = "StructArrays" + BangBangTypedTablesExt = "TypedTables" + + [deps.BangBang.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -442,21 +482,15 @@ git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" -[[deps.BinaryProvider]] -deps = ["Libdl", "Logging", "SHA"] -git-tree-sha1 = "ecdec412a9abc8db54c0efc5548c64dfce072058" -uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232" -version = "0.5.10" - [[deps.BitFlags]] git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" version = "0.1.7" [[deps.BufferedStreams]] -git-tree-sha1 = "bb065b14d7f941b8617bc323063dbe79f55d16ea" +git-tree-sha1 = "5bcb75a2979e40b29eb250cb26daab67aa8f97f5" uuid = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d" -version = "1.1.0" +version = "1.2.0" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -469,17 +503,44 @@ git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.4.2" +[[deps.CRC32c]] +uuid = "8bf52ea8-c179-5cab-976a-9e18b702a9bc" + [[deps.CSV]] -deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "SnoopPrecompile", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] -git-tree-sha1 = "8c73e96bd6817c2597cfd5615b91fca5deccf1af" +deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] +git-tree-sha1 = "44dbf560808d49041989b8a96cae4cffbeb7966a" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.8" +version = "0.10.11" [[deps.CUDA]] -deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CompilerSupportLibraries_jll", "ExprTools", "GPUArrays", "GPUCompiler", "LLVM", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "SpecialFunctions", "TimerOutputs"] -git-tree-sha1 = "49549e2c28ffb9cc77b3689dc10e46e6271e9452" +deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CUDA_Driver_jll", "CUDA_Runtime_Discovery", "CUDA_Runtime_jll", "CompilerSupportLibraries_jll", "ExprTools", "GPUArrays", "GPUCompiler", "KernelAbstractions", "LLVM", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "Preferences", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "SpecialFunctions", "UnsafeAtomicsLLVM"] +git-tree-sha1 = "442d989978ed3ff4e174c928ee879dc09d1ef693" uuid = "052768ef-5323-5732-b1bb-66c8b64840ba" -version = "3.12.0" +version = "4.3.2" + +[[deps.CUDA_Driver_jll]] +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] +git-tree-sha1 = "498f45593f6ddc0adff64a9310bb6710e851781b" +uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc" +version = "0.5.0+1" + +[[deps.CUDA_Runtime_Discovery]] +deps = ["Libdl"] +git-tree-sha1 = "bcc4a23cbbd99c8535a5318455dcf0f2546ec536" +uuid = "1af6417a-86b4-443c-805f-a4643ffb695f" +version = "0.2.2" + +[[deps.CUDA_Runtime_jll]] +deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "5248d9c45712e51e27ba9b30eebec65658c6ce29" +uuid = "76a88914-d11a-5bdc-97e0-2f5a05c973a2" +version = "0.6.0+0" + +[[deps.CUDNN_jll]] +deps = ["Artifacts", "CUDA_Runtime_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "2918fbffb50e3b7a0b9127617587afa76d4276e8" +uuid = "62b44479-cb7b-5706-934f-f13b2eb2e645" +version = "8.8.1+0" [[deps.Cairo]] deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] @@ -488,13 +549,13 @@ uuid = "159f3aea-2a34-519c-b102-8c37f9878175" version = "1.0.5" [[deps.CairoMakie]] -deps = ["Base64", "Cairo", "Colors", "FFTW", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "SHA", "SnoopPrecompile"] -git-tree-sha1 = "a1889ac0cfd046d62404ac3e0a1cb718575ee017" +deps = ["Base64", "Cairo", "Colors", "FFTW", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools", "SHA"] +git-tree-sha1 = "bfc7d54b3c514f8015055e6ad0d5997da64d99fc" uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" -version = "0.10.0" +version = "0.10.6" [[deps.Cairo_jll]] -deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] +deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.16.1+1" @@ -507,39 +568,33 @@ version = "0.5.1" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "99a39b0f807499510e2ea14b0eef8422082aa372" +git-tree-sha1 = "61549d9b52c88df34d21bd306dba1d43bb039c87" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.46.0" +version = "1.51.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" +git-tree-sha1 = "e30f2f4e20f7f186dc36529910beaedc60cfa644" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.6" - -[[deps.ChangesOfVariables]] -deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" -uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.4" +version = "1.16.0" [[deps.Chemfiles]] -deps = ["BinaryProvider", "Chemfiles_jll", "DocStringExtensions", "Libdl"] -git-tree-sha1 = "3b4a49a0a4c9b2ff8c0c6ec035c16f32955531a8" +deps = ["Chemfiles_jll", "DocStringExtensions"] +git-tree-sha1 = "6951fe6a535a07041122a3a6860a63a7a83e081e" uuid = "46823bd8-5fb3-5f92-9aa0-96921f3dd015" -version = "0.10.3" +version = "0.10.40" [[deps.Chemfiles_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d4e54b053fc584e7a0f37e9d3a5c4500927b343a" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f3743181e30d87c23d9c8ebd493b77f43d8f1890" uuid = "78a364fa-1a3c-552a-b4bb-8fa0f9c1fcca" -version = "0.10.3+0" +version = "0.10.4+0" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" +git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.0" +version = "0.7.1" [[deps.ColorBrewer]] deps = ["Colors", "JSON", "Test"] @@ -548,10 +603,10 @@ uuid = "a2cac450-b92f-5266-8821-25eda20663c8" version = "0.4.0" [[deps.ColorSchemes]] -deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] -git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] +git-tree-sha1 = "be6ab11021cd29f0344d5c4357b163af05a48cba" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.20.0" +version = "3.21.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -561,9 +616,9 @@ version = "0.11.4" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] -git-tree-sha1 = "d08c20eef1f2cbc6e60fd3612ac4340b89fea322" +git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.9.9" +version = "0.9.10" [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] @@ -578,26 +633,45 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[deps.Compat]] -deps = ["Dates", "LinearAlgebra", "UUIDs"] -git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" +deps = ["UUIDs"] +git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.5.0" +version = "4.6.1" +weakdeps = ["Dates", "LinearAlgebra"] + + [deps.Compat.extensions] + CompatLinearAlgebraExt = "LinearAlgebra" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "0.5.2+0" +version = "1.0.2+0" [[deps.CompositionsBase]] -git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" -version = "0.1.1" +version = "0.1.2" +weakdeps = ["InverseFunctions"] + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" + +[[deps.ConcurrentUtilities]] +deps = ["Serialization", "Sockets"] +git-tree-sha1 = "96d823b94ba8d187a6d8f0826e731195a74b90e9" +uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" +version = "2.2.0" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fb21ddd70a051d882a1686a5a550990bbe371a95" +git-tree-sha1 = "738fec4d684a9a6ee9598a8bfee305b26831f28c" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.4.1" +version = "1.5.2" +weakdeps = ["IntervalSets", "StaticArrays"] + + [deps.ConstructionBase.extensions] + ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.ContextVariablesX]] deps = ["Compat", "Logging", "UUIDs"] @@ -616,9 +690,9 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.DataAPI]] -git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" +git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.14.0" +version = "1.15.0" [[deps.DataDeps]] deps = ["HTTP", "Libdl", "Reexport", "SHA", "p7zip_jll"] @@ -627,10 +701,10 @@ uuid = "124859b0-ceae-595e-8997-d05f6a7a8dfe" version = "0.7.10" [[deps.DataFrames]] -deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "d4f69885afa5e6149d0cab3818491565cf41446d" +deps = ["Compat", "DataAPI", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "aa51303df86f8626a962fccb878430cdb0a97eee" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.4.4" +version = "1.5.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -654,13 +728,9 @@ version = "0.1.2" [[deps.DelimitedFiles]] deps = ["Mmap"] +git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" - -[[deps.DensityInterface]] -deps = ["InverseFunctions", "Test"] -git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" -uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" -version = "0.4.0" +version = "1.9.1" [[deps.DiffResults]] deps = ["StaticArraysCore"] @@ -670,25 +740,33 @@ version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "c5b6685d53f933c11404a3ae9822afe30d522494" +git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.12.2" +version = "1.15.1" [[deps.Distances]] deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" +git-tree-sha1 = "49eba9ad9f7ead780bfb7ee319f962c811c6d3b2" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.7" +version = "0.10.8" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "a7756d098cbabec6b3ac44f369f74915e8cfd70a" +deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Test"] +git-tree-sha1 = "c72970914c8a21b36bbc244e9df0ed1834a0360b" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.79" +version = "0.25.95" + + [deps.Distributions.extensions] + DistributionsChainRulesCoreExt = "ChainRulesCore" + DistributionsDensityInterfaceExt = "DensityInterface" + + [deps.Distributions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -720,9 +798,9 @@ uuid = "2e619515-83b5-522b-bb60-26c02a35a201" version = "2.4.8+0" [[deps.ExprTools]] -git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d" +git-tree-sha1 = "c1d06d129da9f55715c6c212866f5b1bddc5fa00" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" -version = "0.1.8" +version = "0.1.9" [[deps.Extents]] git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" @@ -743,9 +821,9 @@ version = "4.4.2+2" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "90630efff0894f8142308e334473eba54c433549" +git-tree-sha1 = "06bf20fcecd258eccf9a6ef7b99856a4dfe7b64c" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.5.0" +version = "1.7.0" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -767,9 +845,9 @@ version = "0.1.1" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "7be5f99f7d15578798f338f5433b6c432ea8037b" +git-tree-sha1 = "299dc33549f68299137e51e6d49a13b5b1da9673" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.0" +version = "1.16.1" [[deps.FilePathsBase]] deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] @@ -782,9 +860,9 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "9a0472ec2f5409db243160a8b030f94c380167a3" +git-tree-sha1 = "589d3d3bff204bdd80ecc53293896b4f39175723" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.6" +version = "1.1.1" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -793,10 +871,16 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.4" [[deps.Flux]] -deps = ["Adapt", "CUDA", "ChainRulesCore", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "OneHotArrays", "Optimisers", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Zygote"] -git-tree-sha1 = "96e29bb33cc05cc053751b1299f84e6b34cb7afd" +deps = ["Adapt", "CUDA", "ChainRulesCore", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote", "cuDNN"] +git-tree-sha1 = "64005071944bae14fc145661f617eb68b339189c" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.13.10" +version = "0.13.16" + + [deps.Flux.extensions] + AMDGPUExt = "AMDGPU" + + [deps.Flux.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" [[deps.FoldsThreads]] deps = ["Accessors", "FunctionWrappers", "InitialValues", "SplittablesBase", "Transducers"] @@ -817,10 +901,14 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[deps.ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "a69dd6db8a809f78846ff259298678f0d6212180" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] +git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.34" +version = "0.10.35" +weakdeps = ["StaticArrays"] + + [deps.ForwardDiff.extensions] + ForwardDiffStaticArraysExt = "StaticArrays" [[deps.FreeType]] deps = ["CEnum", "FreeType2_jll"] @@ -853,9 +941,9 @@ version = "1.1.3" [[deps.Functors]] deps = ["LinearAlgebra"] -git-tree-sha1 = "a2657dd0f3e8a61dbe70fc7c122038bd33790af5" +git-tree-sha1 = "478f8c3145bb91d82c2cf20433e8c1b30df454cc" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.3.0" +version = "0.4.4" [[deps.Future]] deps = ["Random"] @@ -863,21 +951,21 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "45d7deaf05cbb44116ba785d147c518ab46352d7" +git-tree-sha1 = "a3351bc577a6b49297248aadc23a4add1097c2ac" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.5.0" +version = "8.7.1" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "6872f5ec8fd1a38880f027a26739d42dcda6691f" +git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.2" +version = "0.1.5" [[deps.GPUCompiler]] -deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "30488903139ebf4c88f965e7e396f2d652f988ac" +deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"] +git-tree-sha1 = "cb090aea21c6ca78d59672a7e7d13bd56d09de64" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.16.7" +version = "0.20.3" [[deps.GZip]] deps = ["Libdl"] @@ -887,15 +975,15 @@ version = "0.5.1" [[deps.GeoInterface]] deps = ["Extents"] -git-tree-sha1 = "fb28b5dc239d0174d7297310ef7b84a11804dfab" +git-tree-sha1 = "bb198ff907228523f3dee1070ceee63b9359b6ab" uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" -version = "1.0.1" +version = "1.3.1" [[deps.GeometryBasics]] deps = ["EarCut_jll", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "fe9aea4ed3ec6afdfbeb5a4f39a2208909b162a6" +git-tree-sha1 = "659140c9375afa2f685e37c1a0b9c9a60ef56b40" uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.4.5" +version = "0.4.7" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -910,21 +998,21 @@ uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" version = "2.74.0+2" [[deps.Glob]] -git-tree-sha1 = "4df9f7e06108728ebf00a0a11edee4b29a482bb2" +git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" uuid = "c27321d9-0574-5035-807b-f59d2c89b15c" -version = "1.3.0" +version = "1.3.1" [[deps.GraphMakie]] -deps = ["GeometryBasics", "Graphs", "LinearAlgebra", "Makie", "NetworkLayout", "StaticArrays"] -git-tree-sha1 = "da596204780670d848c5bf35aff1f8580b885e09" +deps = ["GeometryBasics", "Graphs", "LinearAlgebra", "Makie", "NetworkLayout", "PolynomialRoots", "StaticArrays"] +git-tree-sha1 = "f07cb696d6f9caf070ebfede9f8a7b4c9e1451fc" uuid = "1ecd5474-83a3-4783-bb4f-06765db800d2" -version = "0.5.0" +version = "0.5.4" [[deps.GraphNeuralNetworks]] deps = ["Adapt", "CUDA", "ChainRulesCore", "DataStructures", "Flux", "Functors", "Graphs", "KrylovKit", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "NearestNeighbors", "Random", "Reexport", "SparseArrays", "Statistics", "StatsBase"] -git-tree-sha1 = "8005f6c7b6d395a07eb92454e646beaee44b8019" +git-tree-sha1 = "9f6e956209a673862fccc1f467a91a8b8cbc4e88" uuid = "cffab07f-9bc2-4db1-8861-388f63bf7694" -version = "0.5.2" +version = "0.6.6" [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] @@ -940,9 +1028,9 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "ba2d094a88b6b287bd25cfa86f301e7693ffae2f" +git-tree-sha1 = "1cf1d7dcb4bc32d7b4a5add4232db3750c27ecb4" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.7.4" +version = "1.8.0" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] @@ -957,9 +1045,9 @@ version = "1.0.2" [[deps.HDF5]] deps = ["Compat", "HDF5_jll", "Libdl", "Mmap", "Random", "Requires", "UUIDs"] -git-tree-sha1 = "b5df7c3cab3a00c33c2e09c6bd23982a75e2fbb2" +git-tree-sha1 = "c73fdc3d9da7700691848b78c61841274076932a" uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" -version = "0.16.13" +version = "0.16.15" [[deps.HDF5_jll]] deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"] @@ -968,10 +1056,10 @@ uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" version = "1.12.2+2" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "2e13c9956c82f5ae8cbdb8335327e63badb8c4ff" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "5e77dbf117412d4f164a464d610ee6050cc75272" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.6.2" +version = "1.9.6" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -980,10 +1068,10 @@ uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" version = "2.8.1+1" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] -git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" +deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "0ec02c648befc2f94156eaef13b0f38106212f3f" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.11" +version = "0.3.17" [[deps.Hyperscript]] deps = ["Test"] @@ -999,15 +1087,15 @@ version = "0.9.4" [[deps.IOCapture]] deps = ["Logging", "Random"] -git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +git-tree-sha1 = "d75853a0bdbfb1ac815478bacd89cd27b550ace6" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.2" +version = "0.2.3" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "2e99184fca5eb6f075944b04c22edec29beb4778" +git-tree-sha1 = "eac00994ce3229a464c2847e956d77a2c64ad3a5" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.7" +version = "0.4.10" [[deps.ImageAxes]] deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"] @@ -1040,16 +1128,16 @@ uuid = "bc367c6b-8a6b-528e-b4bd-a4b897500b49" version = "0.9.8" [[deps.ImageShow]] -deps = ["Base64", "FileIO", "ImageBase", "ImageCore", "OffsetArrays", "StackViews"] -git-tree-sha1 = "b563cf9ae75a635592fc73d3eb78b86220e55bd8" +deps = ["Base64", "ColorSchemes", "FileIO", "ImageBase", "ImageCore", "OffsetArrays", "StackViews"] +git-tree-sha1 = "ce28c68c900eed3cdbfa418be66ed053e54d4f56" uuid = "4e3cecfd-b093-5904-9786-8bbb286a6a31" -version = "0.3.6" +version = "0.3.7" [[deps.Imath_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "87f7662e03a649cffa2e05bf19c303e168732d3e" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "3d09a9f60edf77f8a4d99f9e015e8fbf9989605d" uuid = "905a6f67-0a94-5f89-b386-d35d92009cd1" -version = "3.1.2+0" +version = "3.1.7+0" [[deps.IndirectArrays]] git-tree-sha1 = "012e604e1c7458645cb8b436f8fba789a51b257f" @@ -1061,11 +1149,6 @@ git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" version = "0.1.3" -[[deps.IniFile]] -git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" -uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" -version = "0.5.1" - [[deps.InitialValues]] git-tree-sha1 = "4da0f88e9a39111c2fa3add390ab15f3a44f3ca3" uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" @@ -1073,15 +1156,15 @@ version = "0.3.1" [[deps.InlineStrings]] deps = ["Parsers"] -git-tree-sha1 = "0cf92ec945125946352f3d46c96976ab972bde6f" +git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461" uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.3.2" +version = "1.4.0" [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d979e54b71da82f3a65b62553da4fc3d18c9004c" +git-tree-sha1 = "0cb9352ef2e01574eeebdb102948a58740dcaf83" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2018.0.3+2" +version = "2023.1.0+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -1107,19 +1190,19 @@ version = "0.7.4" [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" +git-tree-sha1 = "6667aadd1cdee2c6cd068128b3d226ebc4fb0c67" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.8" +version = "0.1.9" [[deps.InvertedIndices]] -git-tree-sha1 = "82aec7a3dd64f4d9584659dc0b62ef7db2ef3e19" +git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.2.0" +version = "1.3.0" [[deps.IrrationalConstants]] -git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.1" +version = "0.2.2" [[deps.Isoband]] deps = ["isoband_jll"] @@ -1128,9 +1211,9 @@ uuid = "f1662d9f-8043-43de-a69a-05efc1cc6ff4" version = "0.1.1" [[deps.IterTools]] -git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" +git-tree-sha1 = "4ced6667f9974fc5c5943fa5e2ef1ca43ea9e450" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.4.0" +version = "1.8.0" [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -1138,10 +1221,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLD2]] -deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "ec8a9c9f0ecb1c687e34c1fda2699de4d054672a" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "42c17b18ced77ff0be65957a591d34f4ed57c631" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.29" +version = "0.4.31" [[deps.JLLWrappers]] deps = ["Preferences"] @@ -1151,27 +1234,27 @@ version = "1.4.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" +git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.3" +version = "0.21.4" [[deps.JSON3]] -deps = ["Dates", "Mmap", "Parsers", "SnoopPrecompile", "StructTypes", "UUIDs"] -git-tree-sha1 = "84b10656a41ef564c39d2d477d7236966d2b5683" +deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] +git-tree-sha1 = "5b62d93f2582b09e469b3099d839c2d2ebf5066d" uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -version = "1.12.0" +version = "1.13.1" [[deps.JpegTurbo]] deps = ["CEnum", "FileIO", "ImageCore", "JpegTurbo_jll", "TOML"] -git-tree-sha1 = "a77b273f1ddec645d1b7c4fd5fb98c8f90ad10a5" +git-tree-sha1 = "106b6aa272f294ba47e96bd3acbabdc0407b5c60" uuid = "b835a17e-a41a-41e7-81f0-2f016b05efe0" -version = "0.1.1" +version = "0.1.2" [[deps.JpegTurbo_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6f2675ef130a300a112286de91973805fcc5ffbc" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.2+0" +version = "2.1.91+0" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -1179,11 +1262,17 @@ git-tree-sha1 = "49fb3cb53362ddadb4415e9b73926d6b40709e70" uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" version = "0.2.4" +[[deps.KernelAbstractions]] +deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] +git-tree-sha1 = "47be64f040a7ece575c2b5f53ca6da7b548d69f4" +uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" +version = "0.9.4" + [[deps.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] -git-tree-sha1 = "9816b296736292a80b9a3200eb7fbb57aaa3917a" +git-tree-sha1 = "90442c50e202a5cdf21a7899c66b240fdef14035" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" -version = "0.6.5" +version = "0.6.7" [[deps.KrylovKit]] deps = ["ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Printf"] @@ -1199,15 +1288,21 @@ version = "3.100.1+0" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "088dd02b2797f0233d92583562ab669de8517fd1" +git-tree-sha1 = "5007c1421563108110bbd57f63d8ad4565808818" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "4.14.1" +version = "5.2.0" [[deps.LLVMExtra_jll]] -deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg", "TOML"] -git-tree-sha1 = "771bfe376249626d3ca12bcd58ba243d3f961576" +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "1222116d7313cdefecf3d45a2bc1a89c4e7c9217" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.16+0" +version = "0.0.22+0" + +[[deps.LLVMOpenMP_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "f689897ccbe049adb19a065c495e75f372ecd42b" +uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" +version = "15.0.4+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1288,14 +1383,24 @@ uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" version = "2.36.0+0" [[deps.LinearAlgebra]] -deps = ["Libdl", "libblastrampoline_jll"] +deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LogExpFunctions]] -deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239" +deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.19" +version = "0.3.24" + + [deps.LogExpFunctions.extensions] + LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" + LogExpFunctionsChangesOfVariablesExt = "ChangesOfVariables" + LogExpFunctionsInverseFunctionsExt = "InverseFunctions" + + [deps.LogExpFunctions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -1308,9 +1413,9 @@ version = "1.0.0" [[deps.MAT]] deps = ["BufferedStreams", "CodecZlib", "HDF5", "SparseArrays"] -git-tree-sha1 = "971be550166fe3f604d28715302b58a3f7293160" +git-tree-sha1 = "79fd0b5ee384caf8ebba6c8fb3f365ca3e2c5493" uuid = "23992714-dd62-5051-b70f-ba57cb901cac" -version = "0.10.3" +version = "0.10.5" [[deps.MIMEs]] git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" @@ -1325,20 +1430,20 @@ version = "2022.2.0+0" [[deps.MLDatasets]] deps = ["CSV", "Chemfiles", "DataDeps", "DataFrames", "DelimitedFiles", "FileIO", "FixedPointNumbers", "GZip", "Glob", "HDF5", "ImageShow", "JLD2", "JSON3", "LazyModules", "MAT", "MLUtils", "NPZ", "Pickle", "Printf", "Requires", "SparseArrays", "Tables"] -git-tree-sha1 = "d995d90956fd27e83b8e15eca67276848a0876d2" +git-tree-sha1 = "498b37aa3ebb4407adea36df1b244fa4e397de5e" uuid = "eb30cadb-4394-5ae3-aed4-317e484a6458" -version = "0.7.8" +version = "0.7.9" [[deps.MLStyle]] -git-tree-sha1 = "060ef7956fef2dc06b0e63b294f7dbfbcbdc7ea2" +git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" uuid = "d8e11817-5142-5d16-987a-aa16d5891078" -version = "0.4.16" +version = "0.4.17" [[deps.MLUtils]] -deps = ["ChainRulesCore", "DataAPI", "DelimitedFiles", "FLoops", "FoldsThreads", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] -git-tree-sha1 = "82c1104919d664ab1024663ad851701415300c5f" +deps = ["ChainRulesCore", "Compat", "DataAPI", "DelimitedFiles", "FLoops", "FoldsThreads", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] +git-tree-sha1 = "ca31739905ddb08c59758726e22b9e25d0d1521b" uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" -version = "0.3.1" +version = "0.4.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1347,21 +1452,21 @@ uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" version = "0.5.10" [[deps.Makie]] -deps = ["Animations", "Base64", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Distributions", "DocStringExtensions", "FFMPEG", "FileIO", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MakieCore", "Markdown", "Match", "MathTeXEngine", "MiniQhull", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "Printf", "Random", "RelocatableFolders", "Serialization", "Setfield", "Showoff", "SignedDistanceFields", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun"] -git-tree-sha1 = "7154536d78dcde1c4321b50e0e8dda90995f1f6f" +deps = ["Animations", "Base64", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG", "FileIO", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "Match", "MathTeXEngine", "MiniQhull", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Setfield", "Showoff", "SignedDistanceFields", "SparseArrays", "StableHashTraits", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun"] +git-tree-sha1 = "a6695a632992a2e19ae1a1d0c9bee0e137e2f3cb" uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" -version = "0.19.0" +version = "0.19.6" [[deps.MakieCore]] deps = ["Observables"] -git-tree-sha1 = "5357b0696f7c245941389995e193c127190d45f8" +git-tree-sha1 = "9926529455a331ed73c19ff06d16906737a876ed" uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b" -version = "0.6.0" +version = "0.6.3" [[deps.MappedArrays]] -git-tree-sha1 = "e8b359ef06ec72e8c030463fe02efe5527ee5142" +git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" -version = "0.4.1" +version = "0.4.2" [[deps.Markdown]] deps = ["Base64"] @@ -1374,9 +1479,9 @@ version = "1.2.0" [[deps.MathTeXEngine]] deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "Test", "UnicodeFun"] -git-tree-sha1 = "f04120d9adf4f49be242db0b905bea0be32198d1" +git-tree-sha1 = "8f52dbaa1351ce4cb847d95568cb29e62a307d93" uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53" -version = "0.5.4" +version = "0.5.6" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] @@ -1387,13 +1492,13 @@ version = "1.1.7" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.0+0" +version = "2.28.2+0" [[deps.MicroCollections]] deps = ["BangBang", "InitialValues", "Setfield"] -git-tree-sha1 = "4d5917a26ca33c66c8e5ca3247bd163624d35493" +git-tree-sha1 = "629afd7d10dbc6935ec59b32daeb33bc4460a42e" uuid = "128add7d-3638-4c79-886c-908ea0c25c34" -version = "0.1.3" +version = "0.1.4" [[deps.MiniQhull]] deps = ["QhullMiniWrapper_jll"] @@ -1403,9 +1508,9 @@ version = "0.4.0" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" +git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.0.2" +version = "1.1.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -1418,19 +1523,25 @@ version = "0.3.4" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.2.1" +version = "2022.10.11" [[deps.NNlib]] -deps = ["Adapt", "ChainRulesCore", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "37596c26f107f2fd93818166ed3dab1a2e6b2f05" +deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] +git-tree-sha1 = "99e6dbb50d8a96702dc60954569e9fe7291cc55d" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.8.11" +version = "0.8.20" + + [deps.NNlib.extensions] + NNlibAMDGPUExt = "AMDGPU" + + [deps.NNlib.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" [[deps.NNlibCUDA]] -deps = ["Adapt", "CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics"] -git-tree-sha1 = "4429261364c5ea5b7308aecaa10e803ace101631" +deps = ["Adapt", "CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics", "cuDNN"] +git-tree-sha1 = "f94a9684394ff0d325cc12b06da7032d8be01aaf" uuid = "a00861dc-f156-4864-bf3c-e6376f28a68d" -version = "0.2.4" +version = "0.2.7" [[deps.NPZ]] deps = ["FileIO", "ZipFile"] @@ -1440,9 +1551,9 @@ version = "0.4.3" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" +git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.1" +version = "1.0.2" [[deps.NameResolution]] deps = ["PrettyPrint"] @@ -1463,10 +1574,10 @@ uuid = "f09324ee-3d7c-5217-9330-fc30815ba969" version = "1.1.0" [[deps.NetworkLayout]] -deps = ["GeometryBasics", "LinearAlgebra", "Random", "Requires", "SparseArrays"] -git-tree-sha1 = "cac8fc7ba64b699c678094fa630f49b80618f625" +deps = ["GeometryBasics", "LinearAlgebra", "Random", "Requires", "SparseArrays", "StaticArrays"] +git-tree-sha1 = "2bfd8cd7fba3e46ce48139ae93904ee848153660" uuid = "46757867-2c16-5918-afeb-47bfcb05e46a" -version = "0.4.4" +version = "0.4.5" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" @@ -1479,9 +1590,9 @@ version = "0.5.4" [[deps.OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "f71d8950b724e9ff6110fc948dff5a329f901d64" +git-tree-sha1 = "82d7c9e310fe55aa54996e6f7f94674e2a38fcb4" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.8" +version = "1.12.9" [[deps.Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1491,14 +1602,14 @@ version = "1.3.5+1" [[deps.OneHotArrays]] deps = ["Adapt", "ChainRulesCore", "Compat", "GPUArraysCore", "LinearAlgebra", "NNlib"] -git-tree-sha1 = "97af68a840d83df94053f45e68b944e645a2262c" +git-tree-sha1 = "f511fca956ed9e70b80cd3417bb8c2dde4b68644" uuid = "0b1bfda6-eb8a-41d2-88d8-f5af5cad476f" -version = "0.2.1" +version = "0.2.3" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.20+0" +version = "0.3.21+4" [[deps.OpenEXR]] deps = ["Colors", "FileIO", "OpenEXR_jll"] @@ -1507,10 +1618,10 @@ uuid = "52e1d378-f018-4a11-a4be-720524705ac7" version = "0.3.2" [[deps.OpenEXR_jll]] -deps = ["Artifacts", "Imath_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "923319661e9a22712f24596ce81c54fc0366f304" +deps = ["Artifacts", "Imath_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "a4ca623df1ae99d09bc9868b008262d0c0ac1e4f" uuid = "18a262bb-aa17-5467-a713-aee519bc75cb" -version = "3.1.1+0" +version = "3.1.4+0" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -1519,15 +1630,15 @@ version = "0.8.1+0" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "df6830e37943c7aaa10023471ca47fb3065cc3c4" +git-tree-sha1 = "51901a49222b09e3743c65b8847687ae5fc78eb2" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.3.2" +version = "1.4.1" [[deps.OpenSSL_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1aa4b74f80b01c6bc2b89992b861b5f210e665b5" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.19+0" +version = "1.1.21+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1537,9 +1648,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "e657acef119cc0de2a8c0762666d3b64727b053b" +git-tree-sha1 = "6a01f65dd8583dee82eecc2a19b0ff21521aa749" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.14" +version = "0.2.18" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1548,20 +1659,20 @@ uuid = "91d4177d-7536-5919-b921-800302f37372" version = "1.3.2+0" [[deps.OrderedCollections]] -git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" +git-tree-sha1 = "d321bf2de576bf25ec4d3e4360faca399afca282" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.4.1" +version = "1.6.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" -version = "10.40.0+0" +version = "10.42.0+0" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" +git-tree-sha1 = "67eae2738d63117a196f497d7db789821bce61d1" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.16" +version = "0.11.17" [[deps.PNGFiles]] deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] @@ -1571,15 +1682,15 @@ version = "0.3.17" [[deps.Packing]] deps = ["GeometryBasics"] -git-tree-sha1 = "1155f6f937fa2b94104162f01fa400e192e4272f" +git-tree-sha1 = "ec3edfe723df33528e085e632414499f26650501" uuid = "19eb6ba3-879d-56ad-ad62-d5c202156566" -version = "0.4.2" +version = "0.5.0" [[deps.PaddedViews]] deps = ["OffsetArrays"] -git-tree-sha1 = "03a7a85b76381a3d04c7a1656039197e70eda03d" +git-tree-sha1 = "0fac6313486baae819364c52b4f483450a9d793f" uuid = "5432bcbf-9aad-5242-b902-cca2824c8663" -version = "0.5.11" +version = "0.5.12" [[deps.Pango_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1588,10 +1699,10 @@ uuid = "36c8627f-9965-5494-a995-c6b170f724f3" version = "1.50.9+0" [[deps.Parsers]] -deps = ["Dates", "SnoopPrecompile"] -git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559" +deps = ["Dates", "PrecompileTools", "UUIDs"] +git-tree-sha1 = "5a6ab2f64388fd1175effdf73fe5933ef1e0bac0" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.5.2" +version = "2.7.0" [[deps.Pickle]] deps = ["DataStructures", "InternedStrings", "Serialization", "SparseArrays", "Strided", "StringEncodings", "ZipFile"] @@ -1600,15 +1711,15 @@ uuid = "fbb45041-c46e-462f-888f-7c521cafbc2c" version = "0.3.2" [[deps.Pixman_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] +git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.40.1+0" +version = "0.42.2+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.8.0" +version = "1.9.0" [[deps.PkgVersion]] deps = ["Pkg"] @@ -1617,33 +1728,44 @@ uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688" version = "0.3.2" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] -git-tree-sha1 = "5b7690dd212e026bbab1860016a6601cb077ab66" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] +git-tree-sha1 = "f92e1315dadf8c46561fb9396e525f7200cdc227" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.2" +version = "1.3.5" [[deps.PlutoUI]] deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] -git-tree-sha1 = "eadad7b14cf046de6eb41f13c9275e5aa2711ab6" +git-tree-sha1 = "b478a748be27bd2f2c73a7690da219d0844db305" uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" -version = "0.7.49" +version = "0.7.51" [[deps.PolygonOps]] git-tree-sha1 = "77b3d3605fc1cd0b42d95eba87dfcd2bf67d5ff6" uuid = "647866c9-e3ac-4575-94e7-e3d426903924" version = "0.1.2" +[[deps.PolynomialRoots]] +git-tree-sha1 = "5f807b5345093487f733e520a1b7395ee9324825" +uuid = "3a141323-8675-5d76-9d11-e1df1406c778" +version = "1.0.0" + [[deps.PooledArrays]] deps = ["DataAPI", "Future"] git-tree-sha1 = "a6062fe4063cdafe78f4a0a81cfffb89721b30e7" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" version = "1.4.2" +[[deps.PrecompileTools]] +deps = ["Preferences"] +git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" +version = "1.1.2" + [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" +git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.3.0" +version = "1.4.0" [[deps.PrettyPrint]] git-tree-sha1 = "632eb4abab3449ab30c5e1afaa874f0b98b586e4" @@ -1652,9 +1774,9 @@ version = "0.2.0" [[deps.PrettyTables]] deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "96f6db03ab535bdb901300f88335257b0018689d" +git-tree-sha1 = "213579618ec1f42dea7dd637a42785a608b1ea9c" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.2.2" +version = "2.2.4" [[deps.Printf]] deps = ["Unicode"] @@ -1685,16 +1807,16 @@ uuid = "460c41e3-6112-5d7f-b78c-b6823adb3f2d" version = "1.0.0+1" [[deps.Qhull_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "238dd7e2cc577281976b9681702174850f8d4cbc" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "be2449911f4d6cfddacdf7efc895eceda3eee5c1" uuid = "784f63db-0788-585a-bace-daefebcd302b" -version = "8.0.1001+0" +version = "8.0.1003+0" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "97aa253e65b784fd13e83774cadc95b38011d734" +git-tree-sha1 = "6ec7ac8412e83d57e313393220879ede1740f9ee" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.6.0" +version = "2.8.2" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -1706,9 +1828,9 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.Random123]] deps = ["Random", "RandomNumbers"] -git-tree-sha1 = "7a1a306b72cfa60634f03a911405f4e64d1b718b" +git-tree-sha1 = "552f30e847641591ba3f39fd1bed559b9deb0ef3" uuid = "74087812-796a-5b5d-8853-05524746bad3" -version = "1.6.0" +version = "1.6.1" [[deps.RandomNumbers]] deps = ["Random", "Requires"] @@ -1723,9 +1845,13 @@ version = "0.3.2" [[deps.Ratios]] deps = ["Requires"] -git-tree-sha1 = "dc84268fe0e3335a62e315a3a7cf2afa7178a734" +git-tree-sha1 = "1342a47bf3260ee108163042310d26f2be5ec90b" uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" -version = "0.4.3" +version = "0.4.5" +weakdeps = ["FixedPointNumbers"] + + [deps.Ratios.extensions] + RatiosFixedPointNumbersExt = "FixedPointNumbers" [[deps.RealDot]] deps = ["LinearAlgebra"] @@ -1752,24 +1878,25 @@ version = "1.3.0" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" +git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.0" +version = "0.7.1" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" +git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.3.0+0" +version = "0.4.0+0" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SIMD]] -git-tree-sha1 = "bc12e315740f3a36a6db85fa2c0212a848bd239e" +deps = ["PrecompileTools"] +git-tree-sha1 = "0e270732477b9e551d884e6b07e23bb2ec947790" uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.4.2" +version = "3.4.5" [[deps.ScanByte]] deps = ["Libdl", "SIMD"] @@ -1779,15 +1906,15 @@ version = "0.3.3" [[deps.Scratch]] deps = ["Dates"] -git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" +git-tree-sha1 = "30449ee12237627992a99d5e30ae63e4d78cd24a" uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.1.1" +version = "1.2.0" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "efd23b378ea5f2db53a55ae53d3133de4e080aa9" +git-tree-sha1 = "04bdff0b09c65ff3e06a05e3eb7b120223da3d39" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.3.16" +version = "1.4.0" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1837,9 +1964,10 @@ uuid = "45858cf5-a6b0-47a3-bbea-62219f50df47" version = "0.1.2" [[deps.SnoopPrecompile]] -git-tree-sha1 = "f604441450a3c0569830946e5b33b78c928e1a85" +deps = ["Preferences"] +git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" -version = "1.0.1" +version = "1.0.3" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -1851,14 +1979,18 @@ uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" version = "1.1.0" [[deps.SparseArrays]] -deps = ["LinearAlgebra", "Random"] +deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" +deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.1.7" +version = "2.2.0" +weakdeps = ["ChainRulesCore"] + + [deps.SpecialFunctions.extensions] + SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] @@ -1866,6 +1998,12 @@ git-tree-sha1 = "e08a62abc517eb79667d0a29dc08a3b589516bb5" uuid = "171d559e-b47b-412a-8079-5efa626c420e" version = "0.1.15" +[[deps.StableHashTraits]] +deps = ["CRC32c", "Compat", "Dates", "SHA", "Tables", "TupleTools", "UUIDs"] +git-tree-sha1 = "0b8b801b8f03a329a4e86b44c5e8a7d7f4fe10a3" +uuid = "c5dd0088-6c3f-4803-b00e-f31a60c170fa" +version = "0.3.1" + [[deps.StackViews]] deps = ["OffsetArrays"] git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c" @@ -1874,9 +2012,9 @@ version = "0.1.1" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "ffc098086f35909741f71ce21d03dadf0d2bfa76" +git-tree-sha1 = "832afbae2a45b4ae7e831f86965469a24d1d8a83" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.11" +version = "1.5.26" [[deps.StaticArraysCore]] git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" @@ -1886,24 +2024,30 @@ version = "1.4.0" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" +git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.5.0" +version = "1.6.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" +git-tree-sha1 = "75ebe04c5bed70b91614d684259b661c9e6274a4" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.21" +version = "0.34.0" [[deps.StatsFuns]] -deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "ab6083f09b3e617e34a956b43e9d51b824206932" +deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.1.1" +version = "1.3.0" +weakdeps = ["ChainRulesCore", "InverseFunctions"] + + [deps.StatsFuns.extensions] + StatsFunsChainRulesCoreExt = "ChainRulesCore" + StatsFunsInverseFunctionsExt = "InverseFunctions" [[deps.Strided]] deps = ["LinearAlgebra", "TupleTools"] @@ -1913,9 +2057,9 @@ version = "1.2.3" [[deps.StringEncodings]] deps = ["Libiconv_jll"] -git-tree-sha1 = "50ccd5ddb00d19392577902f0079267a72c5ab04" +git-tree-sha1 = "33c0da881af3248dafefb939a21694b97cfece76" uuid = "69024149-9ee7-55f6-a4c4-859efe599b68" -version = "0.3.5" +version = "0.3.6" [[deps.StringManipulation]] git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" @@ -1924,9 +2068,9 @@ version = "0.3.0" [[deps.StructArrays]] deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "b03a3b745aa49b566f128977a7dd1be8711c5e71" +git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.14" +version = "0.6.15" [[deps.StructTypes]] deps = ["Dates", "UUIDs"] @@ -1938,10 +2082,15 @@ version = "1.10.0" deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" +[[deps.SuiteSparse_jll]] +deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] +uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" +version = "5.10.1+6" + [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" -version = "1.0.0" +version = "1.0.3" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -1951,14 +2100,14 @@ version = "1.0.1" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" +git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.10.0" +version = "1.10.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" -version = "1.10.1" +version = "1.10.0" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -1972,32 +2121,32 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TiffImages]] deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "UUIDs"] -git-tree-sha1 = "7e6b0e3e571be0b4dd4d2a9a3a83b65c04351ccc" +git-tree-sha1 = "8621f5c499a8aa4aa970b1ae381aae0ef1576966" uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" -version = "0.6.3" +version = "0.6.4" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "f2fd3f288dfc6f507b0c3a2eb3bac009251e548b" +git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.22" +version = "0.5.23" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "e4bdc63f5c6d62e80eb1c0043fcc0360d5950ff7" +git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.10" +version = "0.9.13" [[deps.Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] -git-tree-sha1 = "c42fa452a60f022e9e087823b47e5a5f8adc53d5" +git-tree-sha1 = "25358a5f2384c490e98abd565ed321ffae2cbb37" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.75" +version = "0.4.76" [[deps.Tricks]] -git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" +git-tree-sha1 = "aadb748be58b492045b4f56166b5188aa63ce549" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.6" +version = "0.1.7" [[deps.TriplotBase]] git-tree-sha1 = "4d4ed7f294cda19382ff7de4c137d24d16adc89b" @@ -2010,9 +2159,9 @@ uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6" version = "1.3.0" [[deps.URIs]] -git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348" +git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.4.1" +version = "1.4.2" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -2027,6 +2176,17 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" +[[deps.UnsafeAtomics]] +git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" +uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" +version = "0.2.1" + +[[deps.UnsafeAtomicsLLVM]] +deps = ["LLVM", "UnsafeAtomics"] +git-tree-sha1 = "ea37e6066bf194ab78f4e747f5245261f17a7175" +uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" +version = "0.1.2" + [[deps.WeakRefStrings]] deps = ["DataAPI", "InlineStrings", "Parsers"] git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" @@ -2113,19 +2273,35 @@ version = "0.10.1" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.12+3" +version = "1.2.13+0" [[deps.Zygote]] -deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "a6f1287943ac05fae56fa06049d1a7846dfbc65f" +deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] +git-tree-sha1 = "5be3ddb88fc992a7d8ea96c3f10a49a7e98ebc7b" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.51" +version = "0.6.62" + + [deps.Zygote.extensions] + ZygoteColorsExt = "Colors" + ZygoteDistancesExt = "Distances" + ZygoteTrackerExt = "Tracker" + + [deps.Zygote.weakdeps] + Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" + Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ZygoteRules]] -deps = ["MacroTools"] -git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" +deps = ["ChainRulesCore", "MacroTools"] +git-tree-sha1 = "977aed5d006b840e2e40c0b48984f7463109046d" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.2" +version = "0.2.3" + +[[deps.cuDNN]] +deps = ["CEnum", "CUDA", "CUDNN_jll"] +git-tree-sha1 = "f65490d187861d6222cb38bcbbff3fd949a7ec3e" +uuid = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" +version = "1.0.4" [[deps.isoband_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2146,9 +2322,9 @@ uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" [[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.1.1+0" +version = "5.8.0+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] diff --git a/docs/tutorials/introductory_tutorials/graph_classification_pluto.jl b/docs/tutorials/introductory_tutorials/graph_classification_pluto.jl index f8241044a..76d6c59ef 100644 --- a/docs/tutorials/introductory_tutorials/graph_classification_pluto.jl +++ b/docs/tutorials/introductory_tutorials/graph_classification_pluto.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.19 +# v0.19.26 #> [frontmatter] #> author = "[Carlo Lucibello](https://github.com/CarloLucibello)" @@ -89,13 +89,13 @@ train_data, test_data = splitobs((graphs, y), at = 150, shuffle = true) |> getob # ╔═╡ 3c3d5038-0ef6-47d7-a1b7-50880c5f3a0b begin - train_loader = DataLoader(train_data, batchsize = 64, shuffle = true) - test_loader = DataLoader(test_data, batchsize = 64, shuffle = false) + train_loader = DataLoader(train_data, batchsize = 32, shuffle = true) + test_loader = DataLoader(test_data, batchsize = 32, shuffle = false) end # ╔═╡ f7778e2d-2e2a-4fc8-83b0-5242e4ec5eb4 md""" -Here, we opt for a `batch_size` of 64, leading to 3 (randomly shuffled) mini-batches, containing all ``2 \cdot 64+22 = 150`` graphs. +Here, we opt for a `batch_size` of 32, leading to 5 (randomly shuffled) mini-batches, containing all ``4 \cdot 32+22 = 150`` graphs. """ # ╔═╡ 2a1c501e-811b-4ddd-887b-91e8c929c8b7 @@ -266,36 +266,56 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [compat] Flux = "~0.13.10" -GraphNeuralNetworks = "~0.5.2" +GraphNeuralNetworks = "~0.6.6" MLDatasets = "~0.7.8" -MLUtils = "~0.3.1" +MLUtils = "~0.4.2" """ # ╔═╡ 00000000-0000-0000-0000-000000000002 PLUTO_MANIFEST_TOML_CONTENTS = """ # This file is machine-generated - editing it directly is not advised -julia_version = "1.8.3" +julia_version = "1.9.1" manifest_format = "2.0" -project_hash = "2086ed67641fd3a73826d065ab6b1f8a5f7341ce" +project_hash = "f04cc096e9556fbdca6d876a64aac2129abb528a" [[deps.AbstractFFTs]] -deps = ["ChainRulesCore", "LinearAlgebra"] -git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" +deps = ["LinearAlgebra"] +git-tree-sha1 = "16b6dbc4cf7caee4e1e75c49485ec67b667098a0" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.2.1" +version = "1.3.1" +weakdeps = ["ChainRulesCore"] + + [deps.AbstractFFTs.extensions] + AbstractFFTsChainRulesCoreExt = "ChainRulesCore" [[deps.Accessors]] -deps = ["Compat", "CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Requires", "Test"] -git-tree-sha1 = "3fa8cc751763c91a5ea33331e523221009cb1e6f" +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Requires", "Test"] +git-tree-sha1 = "954634616d5846d8e216df1298be2298d55280b2" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.23" +version = "0.1.32" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" [[deps.Adapt]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.4.0" +version = "3.6.2" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -315,17 +335,37 @@ version = "0.2.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +[[deps.Atomix]] +deps = ["UnsafeAtomics"] +git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" +uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" +version = "0.1.0" + [[deps.BFloat16s]] deps = ["LinearAlgebra", "Printf", "Random", "Test"] -git-tree-sha1 = "a598ecb0d717092b5539dbbe890c98bac842b072" +git-tree-sha1 = "dbf84058d0a8cbbadee18d25cf606934b22d7c66" uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" -version = "0.2.0" +version = "0.4.2" [[deps.BangBang]] -deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] -git-tree-sha1 = "7fe6d92c4f281cf4ca6f2fba0ce7b299742da7ca" +deps = ["Compat", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables"] +git-tree-sha1 = "e28912ce94077686443433c2800104b061a827ed" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.3.37" +version = "0.3.39" + + [deps.BangBang.extensions] + BangBangChainRulesCoreExt = "ChainRulesCore" + BangBangDataFramesExt = "DataFrames" + BangBangStaticArraysExt = "StaticArrays" + BangBangStructArraysExt = "StructArrays" + BangBangTypedTablesExt = "TypedTables" + + [deps.BangBang.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -335,21 +375,15 @@ git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" -[[deps.BinaryProvider]] -deps = ["Libdl", "Logging", "SHA"] -git-tree-sha1 = "ecdec412a9abc8db54c0efc5548c64dfce072058" -uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232" -version = "0.5.10" - [[deps.BitFlags]] git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" version = "0.1.7" [[deps.BufferedStreams]] -git-tree-sha1 = "bb065b14d7f941b8617bc323063dbe79f55d16ea" +git-tree-sha1 = "5bcb75a2979e40b29eb250cb26daab67aa8f97f5" uuid = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d" -version = "1.1.0" +version = "1.2.0" [[deps.CEnum]] git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" @@ -357,52 +391,76 @@ uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.4.2" [[deps.CSV]] -deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "SnoopPrecompile", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] -git-tree-sha1 = "8c73e96bd6817c2597cfd5615b91fca5deccf1af" +deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] +git-tree-sha1 = "44dbf560808d49041989b8a96cae4cffbeb7966a" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.8" +version = "0.10.11" [[deps.CUDA]] -deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CompilerSupportLibraries_jll", "ExprTools", "GPUArrays", "GPUCompiler", "LLVM", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "SpecialFunctions", "TimerOutputs"] -git-tree-sha1 = "49549e2c28ffb9cc77b3689dc10e46e6271e9452" +deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CUDA_Driver_jll", "CUDA_Runtime_Discovery", "CUDA_Runtime_jll", "CompilerSupportLibraries_jll", "ExprTools", "GPUArrays", "GPUCompiler", "KernelAbstractions", "LLVM", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "Preferences", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "SpecialFunctions", "UnsafeAtomicsLLVM"] +git-tree-sha1 = "442d989978ed3ff4e174c928ee879dc09d1ef693" uuid = "052768ef-5323-5732-b1bb-66c8b64840ba" -version = "3.12.0" +version = "4.3.2" + +[[deps.CUDA_Driver_jll]] +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] +git-tree-sha1 = "498f45593f6ddc0adff64a9310bb6710e851781b" +uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc" +version = "0.5.0+1" + +[[deps.CUDA_Runtime_Discovery]] +deps = ["Libdl"] +git-tree-sha1 = "bcc4a23cbbd99c8535a5318455dcf0f2546ec536" +uuid = "1af6417a-86b4-443c-805f-a4643ffb695f" +version = "0.2.2" + +[[deps.CUDA_Runtime_jll]] +deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "5248d9c45712e51e27ba9b30eebec65658c6ce29" +uuid = "76a88914-d11a-5bdc-97e0-2f5a05c973a2" +version = "0.6.0+0" + +[[deps.CUDNN_jll]] +deps = ["Artifacts", "CUDA_Runtime_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "2918fbffb50e3b7a0b9127617587afa76d4276e8" +uuid = "62b44479-cb7b-5706-934f-f13b2eb2e645" +version = "8.8.1+0" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "99a39b0f807499510e2ea14b0eef8422082aa372" +git-tree-sha1 = "61549d9b52c88df34d21bd306dba1d43bb039c87" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.46.0" +version = "1.51.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" +git-tree-sha1 = "e30f2f4e20f7f186dc36529910beaedc60cfa644" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.6" - -[[deps.ChangesOfVariables]] -deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" -uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.4" +version = "1.16.0" [[deps.Chemfiles]] -deps = ["BinaryProvider", "Chemfiles_jll", "DocStringExtensions", "Libdl"] -git-tree-sha1 = "3b4a49a0a4c9b2ff8c0c6ec035c16f32955531a8" +deps = ["Chemfiles_jll", "DocStringExtensions"] +git-tree-sha1 = "6951fe6a535a07041122a3a6860a63a7a83e081e" uuid = "46823bd8-5fb3-5f92-9aa0-96921f3dd015" -version = "0.10.3" +version = "0.10.40" [[deps.Chemfiles_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d4e54b053fc584e7a0f37e9d3a5c4500927b343a" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f3743181e30d87c23d9c8ebd493b77f43d8f1890" uuid = "78a364fa-1a3c-552a-b4bb-8fa0f9c1fcca" -version = "0.10.3+0" +version = "0.10.4+0" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" +git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.0" +version = "0.7.1" + +[[deps.ColorSchemes]] +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] +git-tree-sha1 = "be6ab11021cd29f0344d5c4357b163af05a48cba" +uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" +version = "3.21.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -412,9 +470,9 @@ version = "0.11.4" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] -git-tree-sha1 = "d08c20eef1f2cbc6e60fd3612ac4340b89fea322" +git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.9.9" +version = "0.9.10" [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] @@ -429,26 +487,48 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[deps.Compat]] -deps = ["Dates", "LinearAlgebra", "UUIDs"] -git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" +deps = ["UUIDs"] +git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.5.0" +version = "4.6.1" +weakdeps = ["Dates", "LinearAlgebra"] + + [deps.Compat.extensions] + CompatLinearAlgebraExt = "LinearAlgebra" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "0.5.2+0" +version = "1.0.2+0" [[deps.CompositionsBase]] -git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" -version = "0.1.1" +version = "0.1.2" +weakdeps = ["InverseFunctions"] + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" + +[[deps.ConcurrentUtilities]] +deps = ["Serialization", "Sockets"] +git-tree-sha1 = "96d823b94ba8d187a6d8f0826e731195a74b90e9" +uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" +version = "2.2.0" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fb21ddd70a051d882a1686a5a550990bbe371a95" +git-tree-sha1 = "738fec4d684a9a6ee9598a8bfee305b26831f28c" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.4.1" +version = "1.5.2" + + [deps.ConstructionBase.extensions] + ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseStaticArraysExt = "StaticArrays" + + [deps.ConstructionBase.weakdeps] + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.ContextVariablesX]] deps = ["Compat", "Logging", "UUIDs"] @@ -462,9 +542,9 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.DataAPI]] -git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" +git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.14.0" +version = "1.15.0" [[deps.DataDeps]] deps = ["HTTP", "Libdl", "Reexport", "SHA", "p7zip_jll"] @@ -473,10 +553,10 @@ uuid = "124859b0-ceae-595e-8997-d05f6a7a8dfe" version = "0.7.10" [[deps.DataFrames]] -deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "d4f69885afa5e6149d0cab3818491565cf41446d" +deps = ["Compat", "DataAPI", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "aa51303df86f8626a962fccb878430cdb0a97eee" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.4.4" +version = "1.5.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -500,7 +580,9 @@ version = "0.1.2" [[deps.DelimitedFiles]] deps = ["Mmap"] +git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" +version = "1.9.1" [[deps.DiffResults]] deps = ["StaticArraysCore"] @@ -510,15 +592,15 @@ version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "c5b6685d53f933c11404a3ae9822afe30d522494" +git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.12.2" +version = "1.15.1" [[deps.Distances]] deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" +git-tree-sha1 = "49eba9ad9f7ead780bfb7ee319f962c811c6d3b2" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.7" +version = "0.10.8" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -536,9 +618,9 @@ uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" [[deps.ExprTools]] -git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d" +git-tree-sha1 = "c1d06d129da9f55715c6c212866f5b1bddc5fa00" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" -version = "0.1.8" +version = "0.1.9" [[deps.FLoops]] deps = ["BangBang", "Compat", "FLoopsBase", "InitialValues", "JuliaVariables", "MLStyle", "Serialization", "Setfield", "Transducers"] @@ -554,9 +636,9 @@ version = "0.1.1" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "7be5f99f7d15578798f338f5433b6c432ea8037b" +git-tree-sha1 = "299dc33549f68299137e51e6d49a13b5b1da9673" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.0" +version = "1.16.1" [[deps.FilePathsBase]] deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] @@ -569,9 +651,9 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "9a0472ec2f5409db243160a8b030f94c380167a3" +git-tree-sha1 = "589d3d3bff204bdd80ecc53293896b4f39175723" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.6" +version = "1.1.1" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -580,10 +662,16 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.4" [[deps.Flux]] -deps = ["Adapt", "CUDA", "ChainRulesCore", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "OneHotArrays", "Optimisers", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Zygote"] -git-tree-sha1 = "96e29bb33cc05cc053751b1299f84e6b34cb7afd" +deps = ["Adapt", "CUDA", "ChainRulesCore", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote", "cuDNN"] +git-tree-sha1 = "64005071944bae14fc145661f617eb68b339189c" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.13.10" +version = "0.13.16" + + [deps.Flux.extensions] + AMDGPUExt = "AMDGPU" + + [deps.Flux.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" [[deps.FoldsThreads]] deps = ["Accessors", "FunctionWrappers", "InitialValues", "SplittablesBase", "Transducers"] @@ -598,10 +686,14 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[deps.ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "a69dd6db8a809f78846ff259298678f0d6212180" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] +git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.34" +version = "0.10.35" +weakdeps = ["StaticArrays"] + + [deps.ForwardDiff.extensions] + ForwardDiffStaticArraysExt = "StaticArrays" [[deps.FunctionWrappers]] git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" @@ -610,9 +702,9 @@ version = "1.1.3" [[deps.Functors]] deps = ["LinearAlgebra"] -git-tree-sha1 = "a2657dd0f3e8a61dbe70fc7c122038bd33790af5" +git-tree-sha1 = "478f8c3145bb91d82c2cf20433e8c1b30df454cc" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.3.0" +version = "0.4.4" [[deps.Future]] deps = ["Random"] @@ -620,21 +712,21 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "45d7deaf05cbb44116ba785d147c518ab46352d7" +git-tree-sha1 = "a3351bc577a6b49297248aadc23a4add1097c2ac" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.5.0" +version = "8.7.1" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "6872f5ec8fd1a38880f027a26739d42dcda6691f" +git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.2" +version = "0.1.5" [[deps.GPUCompiler]] -deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "30488903139ebf4c88f965e7e396f2d652f988ac" +deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"] +git-tree-sha1 = "cb090aea21c6ca78d59672a7e7d13bd56d09de64" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.16.7" +version = "0.20.3" [[deps.GZip]] deps = ["Libdl"] @@ -643,15 +735,15 @@ uuid = "92fee26a-97fe-5a0c-ad85-20a5f3185b63" version = "0.5.1" [[deps.Glob]] -git-tree-sha1 = "4df9f7e06108728ebf00a0a11edee4b29a482bb2" +git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" uuid = "c27321d9-0574-5035-807b-f59d2c89b15c" -version = "1.3.0" +version = "1.3.1" [[deps.GraphNeuralNetworks]] deps = ["Adapt", "CUDA", "ChainRulesCore", "DataStructures", "Flux", "Functors", "Graphs", "KrylovKit", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "NearestNeighbors", "Random", "Reexport", "SparseArrays", "Statistics", "StatsBase"] -git-tree-sha1 = "8005f6c7b6d395a07eb92454e646beaee44b8019" +git-tree-sha1 = "9f6e956209a673862fccc1f467a91a8b8cbc4e88" uuid = "cffab07f-9bc2-4db1-8861-388f63bf7694" -version = "0.5.2" +version = "0.6.6" [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] @@ -661,33 +753,33 @@ version = "1.1.2" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "ba2d094a88b6b287bd25cfa86f301e7693ffae2f" +git-tree-sha1 = "1cf1d7dcb4bc32d7b4a5add4232db3750c27ecb4" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.7.4" +version = "1.8.0" [[deps.HDF5]] deps = ["Compat", "HDF5_jll", "Libdl", "Mmap", "Random", "Requires", "UUIDs"] -git-tree-sha1 = "b5df7c3cab3a00c33c2e09c6bd23982a75e2fbb2" +git-tree-sha1 = "c73fdc3d9da7700691848b78c61841274076932a" uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" -version = "0.16.13" +version = "0.16.15" [[deps.HDF5_jll]] -deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "4cc2bb72df6ff40b055295fdef6d92955f9dede8" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"] +git-tree-sha1 = "3b20c3ce9c14aedd0adca2bc8c882927844bd53d" uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" -version = "1.12.2+2" +version = "1.14.0+0" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "2e13c9956c82f5ae8cbdb8335327e63badb8c4ff" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "5e77dbf117412d4f164a464d610ee6050cc75272" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.6.2" +version = "1.9.6" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "2e99184fca5eb6f075944b04c22edec29beb4778" +git-tree-sha1 = "eac00994ce3229a464c2847e956d77a2c64ad3a5" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.7" +version = "0.4.10" [[deps.ImageBase]] deps = ["ImageCore", "Reexport"] @@ -702,21 +794,16 @@ uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534" version = "0.9.4" [[deps.ImageShow]] -deps = ["Base64", "FileIO", "ImageBase", "ImageCore", "OffsetArrays", "StackViews"] -git-tree-sha1 = "b563cf9ae75a635592fc73d3eb78b86220e55bd8" +deps = ["Base64", "ColorSchemes", "FileIO", "ImageBase", "ImageCore", "OffsetArrays", "StackViews"] +git-tree-sha1 = "ce28c68c900eed3cdbfa418be66ed053e54d4f56" uuid = "4e3cecfd-b093-5904-9786-8bbb286a6a31" -version = "0.3.6" +version = "0.3.7" [[deps.Inflate]] git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" version = "0.1.3" -[[deps.IniFile]] -git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" -uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" -version = "0.5.1" - [[deps.InitialValues]] git-tree-sha1 = "4da0f88e9a39111c2fa3add390ab15f3a44f3ca3" uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" @@ -724,9 +811,9 @@ version = "0.3.1" [[deps.InlineStrings]] deps = ["Parsers"] -git-tree-sha1 = "0cf92ec945125946352f3d46c96976ab972bde6f" +git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461" uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.3.2" +version = "1.4.0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -740,19 +827,19 @@ version = "0.7.0" [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" +git-tree-sha1 = "6667aadd1cdee2c6cd068128b3d226ebc4fb0c67" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.8" +version = "0.1.9" [[deps.InvertedIndices]] -git-tree-sha1 = "82aec7a3dd64f4d9584659dc0b62ef7db2ef3e19" +git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.2.0" +version = "1.3.0" [[deps.IrrationalConstants]] -git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.1" +version = "0.2.2" [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -760,10 +847,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLD2]] -deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "ec8a9c9f0ecb1c687e34c1fda2699de4d054672a" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "42c17b18ced77ff0be65957a591d34f4ed57c631" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.29" +version = "0.4.31" [[deps.JLLWrappers]] deps = ["Preferences"] @@ -772,10 +859,10 @@ uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" version = "1.4.1" [[deps.JSON3]] -deps = ["Dates", "Mmap", "Parsers", "SnoopPrecompile", "StructTypes", "UUIDs"] -git-tree-sha1 = "84b10656a41ef564c39d2d477d7236966d2b5683" +deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] +git-tree-sha1 = "5b62d93f2582b09e469b3099d839c2d2ebf5066d" uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -version = "1.12.0" +version = "1.13.1" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -783,6 +870,12 @@ git-tree-sha1 = "49fb3cb53362ddadb4415e9b73926d6b40709e70" uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" version = "0.2.4" +[[deps.KernelAbstractions]] +deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] +git-tree-sha1 = "47be64f040a7ece575c2b5f53ca6da7b548d69f4" +uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" +version = "0.9.4" + [[deps.KrylovKit]] deps = ["ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Printf"] git-tree-sha1 = "1a5e1d9941c783b0119897d29f2eb665d876ecf3" @@ -791,15 +884,21 @@ version = "0.6.0" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "088dd02b2797f0233d92583562ab669de8517fd1" +git-tree-sha1 = "5007c1421563108110bbd57f63d8ad4565808818" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "4.14.1" +version = "5.2.0" [[deps.LLVMExtra_jll]] -deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg", "TOML"] -git-tree-sha1 = "771bfe376249626d3ca12bcd58ba243d3f961576" +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "1222116d7313cdefecf3d45a2bc1a89c4e7c9217" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.16+0" +version = "0.0.22+0" + +[[deps.LLVMOpenMP_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "f689897ccbe049adb19a065c495e75f372ecd42b" +uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" +version = "15.0.4+0" [[deps.LaTeXStrings]] git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" @@ -844,14 +943,24 @@ uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" version = "1.16.1+2" [[deps.LinearAlgebra]] -deps = ["Libdl", "libblastrampoline_jll"] +deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LogExpFunctions]] -deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239" +deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.19" +version = "0.3.24" + + [deps.LogExpFunctions.extensions] + LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" + LogExpFunctionsChangesOfVariablesExt = "ChangesOfVariables" + LogExpFunctionsInverseFunctionsExt = "InverseFunctions" + + [deps.LogExpFunctions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -864,26 +973,44 @@ version = "1.0.0" [[deps.MAT]] deps = ["BufferedStreams", "CodecZlib", "HDF5", "SparseArrays"] -git-tree-sha1 = "971be550166fe3f604d28715302b58a3f7293160" +git-tree-sha1 = "79fd0b5ee384caf8ebba6c8fb3f365ca3e2c5493" uuid = "23992714-dd62-5051-b70f-ba57cb901cac" -version = "0.10.3" +version = "0.10.5" [[deps.MLDatasets]] deps = ["CSV", "Chemfiles", "DataDeps", "DataFrames", "DelimitedFiles", "FileIO", "FixedPointNumbers", "GZip", "Glob", "HDF5", "ImageShow", "JLD2", "JSON3", "LazyModules", "MAT", "MLUtils", "NPZ", "Pickle", "Printf", "Requires", "SparseArrays", "Tables"] -git-tree-sha1 = "d995d90956fd27e83b8e15eca67276848a0876d2" +git-tree-sha1 = "498b37aa3ebb4407adea36df1b244fa4e397de5e" uuid = "eb30cadb-4394-5ae3-aed4-317e484a6458" -version = "0.7.8" +version = "0.7.9" [[deps.MLStyle]] -git-tree-sha1 = "060ef7956fef2dc06b0e63b294f7dbfbcbdc7ea2" +git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" uuid = "d8e11817-5142-5d16-987a-aa16d5891078" -version = "0.4.16" +version = "0.4.17" [[deps.MLUtils]] -deps = ["ChainRulesCore", "DataAPI", "DelimitedFiles", "FLoops", "FoldsThreads", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] -git-tree-sha1 = "82c1104919d664ab1024663ad851701415300c5f" +deps = ["ChainRulesCore", "Compat", "DataAPI", "DelimitedFiles", "FLoops", "FoldsThreads", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] +git-tree-sha1 = "ca31739905ddb08c59758726e22b9e25d0d1521b" uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" -version = "0.3.1" +version = "0.4.2" + +[[deps.MPICH_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "d790fbd913f85e8865c55bf4725aff197c5155c8" +uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" +version = "4.1.1+1" + +[[deps.MPIPreferences]] +deps = ["Libdl", "Preferences"] +git-tree-sha1 = "d86a788b336e8ae96429c0c42740ccd60ac0dfcc" +uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267" +version = "0.1.8" + +[[deps.MPItrampoline_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "b3dcf8e1c610a10458df3c62038c8cc3a4d6291d" +uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" +version = "5.3.0+0" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -892,9 +1019,9 @@ uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" version = "0.5.10" [[deps.MappedArrays]] -git-tree-sha1 = "e8b359ef06ec72e8c030463fe02efe5527ee5142" +git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" -version = "0.4.1" +version = "0.4.2" [[deps.Markdown]] deps = ["Base64"] @@ -909,19 +1036,25 @@ version = "1.1.7" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.0+0" +version = "2.28.2+0" [[deps.MicroCollections]] deps = ["BangBang", "InitialValues", "Setfield"] -git-tree-sha1 = "4d5917a26ca33c66c8e5ca3247bd163624d35493" +git-tree-sha1 = "629afd7d10dbc6935ec59b32daeb33bc4460a42e" uuid = "128add7d-3638-4c79-886c-908ea0c25c34" -version = "0.1.3" +version = "0.1.4" + +[[deps.MicrosoftMPI_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "a8027af3d1743b3bfae34e54872359fdebb31422" +uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf" +version = "10.1.3+4" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" +git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.0.2" +version = "1.1.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -934,19 +1067,25 @@ version = "0.3.4" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.2.1" +version = "2022.10.11" [[deps.NNlib]] -deps = ["Adapt", "ChainRulesCore", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "37596c26f107f2fd93818166ed3dab1a2e6b2f05" +deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] +git-tree-sha1 = "99e6dbb50d8a96702dc60954569e9fe7291cc55d" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.8.11" +version = "0.8.20" + + [deps.NNlib.extensions] + NNlibAMDGPUExt = "AMDGPU" + + [deps.NNlib.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" [[deps.NNlibCUDA]] -deps = ["Adapt", "CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics"] -git-tree-sha1 = "4429261364c5ea5b7308aecaa10e803ace101631" +deps = ["Adapt", "CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics", "cuDNN"] +git-tree-sha1 = "f94a9684394ff0d325cc12b06da7032d8be01aaf" uuid = "a00861dc-f156-4864-bf3c-e6376f28a68d" -version = "0.2.4" +version = "0.2.7" [[deps.NPZ]] deps = ["FileIO", "ZipFile"] @@ -956,9 +1095,9 @@ version = "0.4.3" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" +git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.1" +version = "1.0.2" [[deps.NameResolution]] deps = ["PrettyPrint"] @@ -978,37 +1117,43 @@ version = "1.2.0" [[deps.OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "f71d8950b724e9ff6110fc948dff5a329f901d64" +git-tree-sha1 = "82d7c9e310fe55aa54996e6f7f94674e2a38fcb4" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.8" +version = "1.12.9" [[deps.OneHotArrays]] deps = ["Adapt", "ChainRulesCore", "Compat", "GPUArraysCore", "LinearAlgebra", "NNlib"] -git-tree-sha1 = "97af68a840d83df94053f45e68b944e645a2262c" +git-tree-sha1 = "f511fca956ed9e70b80cd3417bb8c2dde4b68644" uuid = "0b1bfda6-eb8a-41d2-88d8-f5af5cad476f" -version = "0.2.1" +version = "0.2.3" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.20+0" +version = "0.3.21+4" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" version = "0.8.1+0" +[[deps.OpenMPI_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "f3080f4212a8ba2ceb10a34b938601b862094314" +uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" +version = "4.1.5+0" + [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "df6830e37943c7aaa10023471ca47fb3065cc3c4" +git-tree-sha1 = "51901a49222b09e3743c65b8847687ae5fc78eb2" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.3.2" +version = "1.4.1" [[deps.OpenSSL_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "cae3153c7f6cf3f069a853883fd1919a6e5bab5b" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.19+0" +version = "3.0.9+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1018,26 +1163,26 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "e657acef119cc0de2a8c0762666d3b64727b053b" +git-tree-sha1 = "6a01f65dd8583dee82eecc2a19b0ff21521aa749" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.14" +version = "0.2.18" [[deps.OrderedCollections]] -git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" +git-tree-sha1 = "d321bf2de576bf25ec4d3e4360faca399afca282" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.4.1" +version = "1.6.0" [[deps.PaddedViews]] deps = ["OffsetArrays"] -git-tree-sha1 = "03a7a85b76381a3d04c7a1656039197e70eda03d" +git-tree-sha1 = "0fac6313486baae819364c52b4f483450a9d793f" uuid = "5432bcbf-9aad-5242-b902-cca2824c8663" -version = "0.5.11" +version = "0.5.12" [[deps.Parsers]] -deps = ["Dates", "SnoopPrecompile"] -git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559" +deps = ["Dates", "PrecompileTools", "UUIDs"] +git-tree-sha1 = "5a6ab2f64388fd1175effdf73fe5933ef1e0bac0" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.5.2" +version = "2.7.0" [[deps.Pickle]] deps = ["DataStructures", "InternedStrings", "Serialization", "SparseArrays", "Strided", "StringEncodings", "ZipFile"] @@ -1046,9 +1191,9 @@ uuid = "fbb45041-c46e-462f-888f-7c521cafbc2c" version = "0.3.2" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.8.0" +version = "1.9.0" [[deps.PooledArrays]] deps = ["DataAPI", "Future"] @@ -1056,11 +1201,17 @@ git-tree-sha1 = "a6062fe4063cdafe78f4a0a81cfffb89721b30e7" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" version = "1.4.2" +[[deps.PrecompileTools]] +deps = ["Preferences"] +git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" +version = "1.1.2" + [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" +git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.3.0" +version = "1.4.0" [[deps.PrettyPrint]] git-tree-sha1 = "632eb4abab3449ab30c5e1afaa874f0b98b586e4" @@ -1069,9 +1220,9 @@ version = "0.2.0" [[deps.PrettyTables]] deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "96f6db03ab535bdb901300f88335257b0018689d" +git-tree-sha1 = "213579618ec1f42dea7dd637a42785a608b1ea9c" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.2.2" +version = "2.2.4" [[deps.Printf]] deps = ["Unicode"] @@ -1093,9 +1244,9 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.Random123]] deps = ["Random", "RandomNumbers"] -git-tree-sha1 = "7a1a306b72cfa60634f03a911405f4e64d1b718b" +git-tree-sha1 = "552f30e847641591ba3f39fd1bed559b9deb0ef3" uuid = "74087812-796a-5b5d-8853-05524746bad3" -version = "1.6.0" +version = "1.6.1" [[deps.RandomNumbers]] deps = ["Random", "Requires"] @@ -1124,11 +1275,17 @@ version = "1.3.0" uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" +[[deps.Scratch]] +deps = ["Dates"] +git-tree-sha1 = "30449ee12237627992a99d5e30ae63e4d78cd24a" +uuid = "6c6a2e73-6563-6170-7368-637461726353" +version = "1.2.0" + [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "efd23b378ea5f2db53a55ae53d3133de4e080aa9" +git-tree-sha1 = "04bdff0b09c65ff3e06a05e3eb7b120223da3d39" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.3.16" +version = "1.4.0" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1160,9 +1317,10 @@ uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" version = "0.9.4" [[deps.SnoopPrecompile]] -git-tree-sha1 = "f604441450a3c0569830946e5b33b78c928e1a85" +deps = ["Preferences"] +git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" -version = "1.0.1" +version = "1.0.3" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -1174,14 +1332,18 @@ uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" version = "1.1.0" [[deps.SparseArrays]] -deps = ["LinearAlgebra", "Random"] +deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" +deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.1.7" +version = "2.2.0" +weakdeps = ["ChainRulesCore"] + + [deps.SpecialFunctions.extensions] + SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] @@ -1197,9 +1359,9 @@ version = "0.1.1" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "ffc098086f35909741f71ce21d03dadf0d2bfa76" +git-tree-sha1 = "832afbae2a45b4ae7e831f86965469a24d1d8a83" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.11" +version = "1.5.26" [[deps.StaticArraysCore]] git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" @@ -1209,18 +1371,19 @@ version = "1.4.0" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" +git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.5.0" +version = "1.6.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" +git-tree-sha1 = "75ebe04c5bed70b91614d684259b661c9e6274a4" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.21" +version = "0.34.0" [[deps.Strided]] deps = ["LinearAlgebra", "TupleTools"] @@ -1230,9 +1393,9 @@ version = "1.2.3" [[deps.StringEncodings]] deps = ["Libiconv_jll"] -git-tree-sha1 = "50ccd5ddb00d19392577902f0079267a72c5ab04" +git-tree-sha1 = "33c0da881af3248dafefb939a21694b97cfece76" uuid = "69024149-9ee7-55f6-a4c4-859efe599b68" -version = "0.3.5" +version = "0.3.6" [[deps.StringManipulation]] git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" @@ -1241,9 +1404,9 @@ version = "0.3.0" [[deps.StructArrays]] deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "b03a3b745aa49b566f128977a7dd1be8711c5e71" +git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.14" +version = "0.6.15" [[deps.StructTypes]] deps = ["Dates", "UUIDs"] @@ -1251,10 +1414,15 @@ git-tree-sha1 = "ca4bccb03acf9faaf4137a9abc1881ed1841aa70" uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" version = "1.10.0" +[[deps.SuiteSparse_jll]] +deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] +uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" +version = "5.10.1+6" + [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" -version = "1.0.0" +version = "1.0.3" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -1264,14 +1432,14 @@ version = "1.0.1" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" +git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.10.0" +version = "1.10.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" -version = "1.10.1" +version = "1.10.0" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -1285,21 +1453,21 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "f2fd3f288dfc6f507b0c3a2eb3bac009251e548b" +git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.22" +version = "0.5.23" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "e4bdc63f5c6d62e80eb1c0043fcc0360d5950ff7" +git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.10" +version = "0.9.13" [[deps.Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] -git-tree-sha1 = "c42fa452a60f022e9e087823b47e5a5f8adc53d5" +git-tree-sha1 = "25358a5f2384c490e98abd565ed321ffae2cbb37" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.75" +version = "0.4.76" [[deps.TupleTools]] git-tree-sha1 = "3c712976c47707ff893cf6ba4354aa14db1d8938" @@ -1307,9 +1475,9 @@ uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6" version = "1.3.0" [[deps.URIs]] -git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348" +git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.4.1" +version = "1.4.2" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -1318,6 +1486,17 @@ uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" +[[deps.UnsafeAtomics]] +git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" +uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" +version = "0.2.1" + +[[deps.UnsafeAtomicsLLVM]] +deps = ["LLVM", "UnsafeAtomics"] +git-tree-sha1 = "ea37e6066bf194ab78f4e747f5245261f17a7175" +uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" +version = "0.1.2" + [[deps.WeakRefStrings]] deps = ["DataAPI", "InlineStrings", "Parsers"] git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" @@ -1338,24 +1517,46 @@ version = "0.10.1" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.12+3" +version = "1.2.13+0" [[deps.Zygote]] -deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "a6f1287943ac05fae56fa06049d1a7846dfbc65f" +deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] +git-tree-sha1 = "5be3ddb88fc992a7d8ea96c3f10a49a7e98ebc7b" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.51" +version = "0.6.62" + + [deps.Zygote.extensions] + ZygoteColorsExt = "Colors" + ZygoteDistancesExt = "Distances" + ZygoteTrackerExt = "Tracker" + + [deps.Zygote.weakdeps] + Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" + Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ZygoteRules]] -deps = ["MacroTools"] -git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" +deps = ["ChainRulesCore", "MacroTools"] +git-tree-sha1 = "977aed5d006b840e2e40c0b48984f7463109046d" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.2" +version = "0.2.3" + +[[deps.cuDNN]] +deps = ["CEnum", "CUDA", "CUDNN_jll"] +git-tree-sha1 = "f65490d187861d6222cb38bcbbff3fd949a7ec3e" +uuid = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" +version = "1.0.4" + +[[deps.libaec_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "eddd19a8dea6b139ea97bdc8a0e2667d4b661720" +uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0" +version = "1.0.6+1" [[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.1.1+0" +version = "5.8.0+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] diff --git a/docs/tutorials/introductory_tutorials/node_classification_pluto.jl b/docs/tutorials/introductory_tutorials/node_classification_pluto.jl index 2e88ba08f..e1cf01f96 100644 --- a/docs/tutorials/introductory_tutorials/node_classification_pluto.jl +++ b/docs/tutorials/introductory_tutorials/node_classification_pluto.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.19 +# v0.19.26 #> [frontmatter] #> author = "[Deeptendu Santra](https://github.com/Dsantra92)" @@ -26,12 +26,10 @@ begin ENV["DATADEPS_ALWAYS_ACCEPT"] = "true" Random.seed!(17) # for reproducibility -end +end; # ╔═╡ ca2f0293-7eac-4d9a-9a2f-fda47fd95a99 md""" -Following our previous tutorial in GNNs, we covered how to create graph neural networks. - In this tutorial, we will be learning how to use Graph Neural Networks (GNNs) for node classification. Given the ground-truth labels of only a small subset of nodes, and want to infer the labels for all the remaining nodes (transductive learning). """ @@ -123,7 +121,7 @@ begin num_features = size(x)[1] hidden_channels = 16 num_classes = dataset.metadata["num_classes"] -end +end; # ╔═╡ fa743000-604f-4d28-99f1-46ab2f884b8e md""" @@ -280,12 +278,12 @@ function train(model::GCN, g::GNNGraph, x::AbstractMatrix, epochs::Int, opt) Flux.trainmode!(model) for epoch in 1:epochs - loss, grad[1] = Flux.withgradient(model) do model + loss, grad = Flux.withgradient(model) do model ŷ = model(g, x) logitcrossentropy(ŷ[:, train_mask], y[:, train_mask]) end - Flux.update!(opt, model, grad) + Flux.update!(opt, model, grad[1]) if epoch % 200 == 0 @show epoch, loss end @@ -354,13 +352,9 @@ end md""" ## (Optional) Exercises -1. To achieve better model performance and to avoid overfitting, it is usually a good idea to select the best model based on an additional validation set. -The `Cora` dataset provides a validation node set as `g.ndata.val_mask`, but we haven't used it yet. -Can you modify the code to select and test the model with the highest validation performance? -This should bring test performance to **82% accuracy**. +1. To achieve better model performance and to avoid overfitting, it is usually a good idea to select the best model based on an additional validation set. The `Cora` dataset provides a validation node set as `g.ndata.val_mask`, but we haven't used it yet. Can you modify the code to select and test the model with the highest validation performance? This should bring test performance to **82% accuracy**. -2. How does `GCN` behave when increasing the hidden feature dimensionality or the number of layers? -Does increasing the number of layers help at all? +2. How does `GCN` behave when increasing the hidden feature dimensionality or the number of layers? Does increasing the number of layers help at all? 3. You can try to use different GNN layers to see how model performance changes. What happens if you swap out all `GCNConv` instances with [`GATConv`](https://carlolucibello.github.io/GraphNeuralNetworks.jl/dev/api/conv/#GraphNeuralNetworks.GATConv) layers that make use of attention? Try to write a 2-layer `GAT` model that makes use of 8 attention heads in the first layer and 1 attention head in the second layer, uses a `dropout` ratio of `0.6` inside and outside each `GATConv` call, and uses a `hidden_channels` dimensions of `8` per head. """ @@ -368,9 +362,7 @@ Does increasing the number of layers help at all? # ╔═╡ c343419f-a1d7-45a0-b600-2c868588b33a md""" ## Conclusion -In this tutorial, we have seen how to apply GNNs to real-world problems, and, in particular, how they can effectively be used for boosting a model's performance. In the next section, we will look into how GNNs can be used for the task of graph classification. - -[Next tutorial: Graph Classification with Graph Neural Networks]() +In this tutorial, we have seen how to apply GNNs to real-world problems, and, in particular, how they can effectively be used for boosting a model's performance. In the next tutorial, we will look into how GNNs can be used for the task of graph classification. """ # ╔═╡ 00000000-0000-0000-0000-000000000001 @@ -386,11 +378,11 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" TSne = "24678dba-d5e9-5843-a4c6-250288b04835" [compat] -Flux = "~0.13.10" -GraphNeuralNetworks = "~0.5.2" -MLDatasets = "~0.7.8" -Plots = "~1.38.0" -PlutoUI = "~0.7.49" +Flux = "~0.13.16" +GraphNeuralNetworks = "~0.6.6" +MLDatasets = "~0.7.9" +Plots = "~1.38.16" +PlutoUI = "~0.7.51" TSne = "~1.3.0" """ @@ -398,15 +390,19 @@ TSne = "~1.3.0" PLUTO_MANIFEST_TOML_CONTENTS = """ # This file is machine-generated - editing it directly is not advised -julia_version = "1.8.3" +julia_version = "1.9.1" manifest_format = "2.0" -project_hash = "f443ac87d03cacaf5b7c5411eb7e2fc3efd634e7" +project_hash = "e6a3d73a547b07b276f328b7d279f88621b88446" [[deps.AbstractFFTs]] -deps = ["ChainRulesCore", "LinearAlgebra"] -git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" +deps = ["LinearAlgebra"] +git-tree-sha1 = "16b6dbc4cf7caee4e1e75c49485ec67b667098a0" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.2.1" +version = "1.3.1" +weakdeps = ["ChainRulesCore"] + + [deps.AbstractFFTs.extensions] + AbstractFFTsChainRulesCoreExt = "ChainRulesCore" [[deps.AbstractPlutoDingetjes]] deps = ["Pkg"] @@ -415,16 +411,32 @@ uuid = "6e696c72-6542-2067-7265-42206c756150" version = "1.1.4" [[deps.Accessors]] -deps = ["Compat", "CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Requires", "Test"] -git-tree-sha1 = "3fa8cc751763c91a5ea33331e523221009cb1e6f" +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Requires", "Test"] +git-tree-sha1 = "954634616d5846d8e216df1298be2298d55280b2" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.23" +version = "0.1.32" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" [[deps.Adapt]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.4.0" +version = "3.6.2" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -444,17 +456,37 @@ version = "0.2.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +[[deps.Atomix]] +deps = ["UnsafeAtomics"] +git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" +uuid = 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"StructArrays" + BangBangTypedTablesExt = "TypedTables" + + [deps.BangBang.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -464,21 +496,15 @@ git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" -[[deps.BinaryProvider]] -deps = ["Libdl", "Logging", "SHA"] -git-tree-sha1 = "ecdec412a9abc8db54c0efc5548c64dfce072058" -uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232" -version = "0.5.10" - [[deps.BitFlags]] git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" version = "0.1.7" [[deps.BufferedStreams]] -git-tree-sha1 = "bb065b14d7f941b8617bc323063dbe79f55d16ea" +git-tree-sha1 = "5bcb75a2979e40b29eb250cb26daab67aa8f97f5" uuid = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d" -version = "1.1.0" +version = "1.2.0" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -492,64 +518,82 @@ uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.4.2" [[deps.CSV]] -deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "SnoopPrecompile", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] -git-tree-sha1 = "8c73e96bd6817c2597cfd5615b91fca5deccf1af" +deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] +git-tree-sha1 = "44dbf560808d49041989b8a96cae4cffbeb7966a" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.8" +version = "0.10.11" [[deps.CUDA]] -deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", 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= "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.6" - -[[deps.ChangesOfVariables]] -deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" -uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.4" +version = "1.16.0" [[deps.Chemfiles]] -deps = ["BinaryProvider", "Chemfiles_jll", "DocStringExtensions", "Libdl"] -git-tree-sha1 = "3b4a49a0a4c9b2ff8c0c6ec035c16f32955531a8" +deps = ["Chemfiles_jll", "DocStringExtensions"] +git-tree-sha1 = "6951fe6a535a07041122a3a6860a63a7a83e081e" uuid = "46823bd8-5fb3-5f92-9aa0-96921f3dd015" -version = "0.10.3" +version = "0.10.40" [[deps.Chemfiles_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d4e54b053fc584e7a0f37e9d3a5c4500927b343a" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f3743181e30d87c23d9c8ebd493b77f43d8f1890" uuid = "78a364fa-1a3c-552a-b4bb-8fa0f9c1fcca" -version = "0.10.3+0" +version = "0.10.4+0" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" +git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.0" +version = "0.7.1" [[deps.ColorSchemes]] -deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] -git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] +git-tree-sha1 = "be6ab11021cd29f0344d5c4357b163af05a48cba" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.20.0" +version = "3.21.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -559,9 +603,9 @@ version = "0.11.4" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] -git-tree-sha1 = "d08c20eef1f2cbc6e60fd3612ac4340b89fea322" +git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.9.9" +version = "0.9.10" [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] @@ -576,26 +620,48 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[deps.Compat]] -deps = ["Dates", "LinearAlgebra", "UUIDs"] -git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" +deps = ["UUIDs"] +git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.5.0" +version = "4.6.1" +weakdeps = ["Dates", "LinearAlgebra"] + + [deps.Compat.extensions] + CompatLinearAlgebraExt = "LinearAlgebra" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "0.5.2+0" +version = "1.0.2+0" [[deps.CompositionsBase]] -git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" -version = "0.1.1" +version = "0.1.2" +weakdeps = ["InverseFunctions"] + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" + +[[deps.ConcurrentUtilities]] +deps = ["Serialization", "Sockets"] +git-tree-sha1 = "96d823b94ba8d187a6d8f0826e731195a74b90e9" +uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" +version = "2.2.0" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fb21ddd70a051d882a1686a5a550990bbe371a95" +git-tree-sha1 = "738fec4d684a9a6ee9598a8bfee305b26831f28c" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.4.1" +version = "1.5.2" + + [deps.ConstructionBase.extensions] + ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseStaticArraysExt = "StaticArrays" + + [deps.ConstructionBase.weakdeps] + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.ContextVariablesX]] deps = ["Compat", "Logging", "UUIDs"] @@ -614,9 +680,9 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.DataAPI]] -git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" +git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.14.0" +version = "1.15.0" [[deps.DataDeps]] deps = ["HTTP", "Libdl", "Reexport", "SHA", "p7zip_jll"] @@ -625,10 +691,10 @@ uuid = "124859b0-ceae-595e-8997-d05f6a7a8dfe" version = "0.7.10" [[deps.DataFrames]] -deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "d4f69885afa5e6149d0cab3818491565cf41446d" +deps = ["Compat", "DataAPI", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "aa51303df86f8626a962fccb878430cdb0a97eee" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.4.4" +version = "1.5.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -652,7 +718,9 @@ version = "0.1.2" [[deps.DelimitedFiles]] deps = ["Mmap"] +git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" +version = "1.9.1" [[deps.DiffResults]] deps = ["StaticArraysCore"] @@ -662,15 +730,15 @@ version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "c5b6685d53f933c11404a3ae9822afe30d522494" +git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.12.2" +version = "1.15.1" [[deps.Distances]] deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" +git-tree-sha1 = "49eba9ad9f7ead780bfb7ee319f962c811c6d3b2" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.7" +version = "0.10.8" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -694,9 +762,9 @@ uuid = "2e619515-83b5-522b-bb60-26c02a35a201" version = "2.4.8+0" [[deps.ExprTools]] -git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d" +git-tree-sha1 = "c1d06d129da9f55715c6c212866f5b1bddc5fa00" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" -version = "0.1.8" +version = "0.1.9" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] @@ -724,9 +792,9 @@ version = "0.1.1" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "7be5f99f7d15578798f338f5433b6c432ea8037b" +git-tree-sha1 = "299dc33549f68299137e51e6d49a13b5b1da9673" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.0" +version = "1.16.1" [[deps.FilePathsBase]] deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] @@ -739,9 +807,9 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "9a0472ec2f5409db243160a8b030f94c380167a3" +git-tree-sha1 = "589d3d3bff204bdd80ecc53293896b4f39175723" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.6" +version = "1.1.1" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -750,10 +818,16 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.4" [[deps.Flux]] -deps = ["Adapt", "CUDA", "ChainRulesCore", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "OneHotArrays", "Optimisers", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Zygote"] -git-tree-sha1 = "96e29bb33cc05cc053751b1299f84e6b34cb7afd" +deps = ["Adapt", "CUDA", "ChainRulesCore", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote", "cuDNN"] +git-tree-sha1 = "64005071944bae14fc145661f617eb68b339189c" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.13.10" +version = "0.13.16" + + [deps.Flux.extensions] + AMDGPUExt = "AMDGPU" + + [deps.Flux.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" [[deps.FoldsThreads]] deps = ["Accessors", "FunctionWrappers", "InitialValues", "SplittablesBase", "Transducers"] @@ -774,10 +848,14 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[deps.ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "a69dd6db8a809f78846ff259298678f0d6212180" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] +git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.34" +version = "0.10.35" +weakdeps = ["StaticArrays"] + + [deps.ForwardDiff.extensions] + ForwardDiffStaticArraysExt = "StaticArrays" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -798,9 +876,9 @@ version = "1.1.3" [[deps.Functors]] deps = ["LinearAlgebra"] -git-tree-sha1 = "a2657dd0f3e8a61dbe70fc7c122038bd33790af5" +git-tree-sha1 = "478f8c3145bb91d82c2cf20433e8c1b30df454cc" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.3.0" +version = "0.4.4" [[deps.Future]] deps = ["Random"] @@ -814,33 +892,33 @@ version = "3.3.8+0" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "45d7deaf05cbb44116ba785d147c518ab46352d7" +git-tree-sha1 = "a3351bc577a6b49297248aadc23a4add1097c2ac" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.5.0" +version = "8.7.1" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "6872f5ec8fd1a38880f027a26739d42dcda6691f" +git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.2" +version = "0.1.5" [[deps.GPUCompiler]] -deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "30488903139ebf4c88f965e7e396f2d652f988ac" +deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"] +git-tree-sha1 = "cb090aea21c6ca78d59672a7e7d13bd56d09de64" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.16.7" +version = "0.20.3" [[deps.GR]] deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "bcc737c4c3afc86f3bbc55eb1b9fabcee4ff2d81" +git-tree-sha1 = "8b8a2fd4536ece6e554168c21860b6820a8a83db" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.71.2" +version = "0.72.7" [[deps.GR_jll]] -deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "64ef06fa8f814ff0d09ac31454f784c488e22b29" +deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "19fad9cd9ae44847fe842558a744748084a722d1" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.71.2+0" +version = "0.72.7+0" [[deps.GZip]] deps = ["Libdl"] @@ -861,15 +939,15 @@ uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" version = "2.74.0+2" [[deps.Glob]] -git-tree-sha1 = "4df9f7e06108728ebf00a0a11edee4b29a482bb2" +git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" uuid = "c27321d9-0574-5035-807b-f59d2c89b15c" -version = "1.3.0" +version = "1.3.1" [[deps.GraphNeuralNetworks]] deps = ["Adapt", "CUDA", "ChainRulesCore", "DataStructures", "Flux", "Functors", "Graphs", "KrylovKit", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "NearestNeighbors", "Random", "Reexport", "SparseArrays", "Statistics", "StatsBase"] -git-tree-sha1 = "8005f6c7b6d395a07eb92454e646beaee44b8019" +git-tree-sha1 = "9f6e956209a673862fccc1f467a91a8b8cbc4e88" uuid = "cffab07f-9bc2-4db1-8861-388f63bf7694" -version = "0.5.2" +version = "0.6.6" [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] @@ -885,9 +963,9 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "ba2d094a88b6b287bd25cfa86f301e7693ffae2f" +git-tree-sha1 = "1cf1d7dcb4bc32d7b4a5add4232db3750c27ecb4" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.7.4" +version = "1.8.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -896,9 +974,9 @@ version = "1.0.2" [[deps.HDF5]] deps = ["Compat", "HDF5_jll", "Libdl", "Mmap", "Random", "Requires", "UUIDs"] -git-tree-sha1 = "b5df7c3cab3a00c33c2e09c6bd23982a75e2fbb2" +git-tree-sha1 = "c73fdc3d9da7700691848b78c61841274076932a" uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" -version = "0.16.13" +version = "0.16.15" [[deps.HDF5_jll]] deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"] @@ -907,10 +985,10 @@ uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" version = "1.12.2+2" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "2e13c9956c82f5ae8cbdb8335327e63badb8c4ff" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "5e77dbf117412d4f164a464d610ee6050cc75272" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.6.2" +version = "1.9.6" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -932,15 +1010,15 @@ version = "0.9.4" [[deps.IOCapture]] deps = ["Logging", "Random"] -git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +git-tree-sha1 = "d75853a0bdbfb1ac815478bacd89cd27b550ace6" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.2" +version = "0.2.3" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "2e99184fca5eb6f075944b04c22edec29beb4778" +git-tree-sha1 = "eac00994ce3229a464c2847e956d77a2c64ad3a5" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.7" +version = "0.4.10" [[deps.ImageBase]] deps = ["ImageCore", "Reexport"] @@ -955,21 +1033,16 @@ uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534" version = "0.9.4" [[deps.ImageShow]] -deps = ["Base64", "FileIO", "ImageBase", "ImageCore", "OffsetArrays", "StackViews"] -git-tree-sha1 = "b563cf9ae75a635592fc73d3eb78b86220e55bd8" +deps = ["Base64", "ColorSchemes", "FileIO", "ImageBase", "ImageCore", "OffsetArrays", "StackViews"] +git-tree-sha1 = "ce28c68c900eed3cdbfa418be66ed053e54d4f56" uuid = "4e3cecfd-b093-5904-9786-8bbb286a6a31" -version = "0.3.6" +version = "0.3.7" [[deps.Inflate]] git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" version = "0.1.3" -[[deps.IniFile]] -git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" -uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" -version = "0.5.1" - [[deps.InitialValues]] git-tree-sha1 = "4da0f88e9a39111c2fa3add390ab15f3a44f3ca3" uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" @@ -977,9 +1050,9 @@ version = "0.3.1" [[deps.InlineStrings]] deps = ["Parsers"] -git-tree-sha1 = "0cf92ec945125946352f3d46c96976ab972bde6f" +git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461" uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.3.2" +version = "1.4.0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -993,19 +1066,19 @@ version = "0.7.0" [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" +git-tree-sha1 = "6667aadd1cdee2c6cd068128b3d226ebc4fb0c67" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.8" +version = "0.1.9" [[deps.InvertedIndices]] -git-tree-sha1 = "82aec7a3dd64f4d9584659dc0b62ef7db2ef3e19" +git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.2.0" +version = "1.3.0" [[deps.IrrationalConstants]] -git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.1" +version = "0.2.2" [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -1013,10 +1086,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLD2]] -deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "ec8a9c9f0ecb1c687e34c1fda2699de4d054672a" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "42c17b18ced77ff0be65957a591d34f4ed57c631" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.29" +version = "0.4.31" [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] @@ -1032,21 +1105,21 @@ version = "1.4.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" +git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.3" +version = "0.21.4" [[deps.JSON3]] -deps = ["Dates", "Mmap", "Parsers", "SnoopPrecompile", "StructTypes", "UUIDs"] -git-tree-sha1 = "84b10656a41ef564c39d2d477d7236966d2b5683" +deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] +git-tree-sha1 = "5b62d93f2582b09e469b3099d839c2d2ebf5066d" uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -version = "1.12.0" +version = "1.13.1" [[deps.JpegTurbo_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6f2675ef130a300a112286de91973805fcc5ffbc" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.2+0" +version = "2.1.91+0" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -1054,6 +1127,12 @@ git-tree-sha1 = "49fb3cb53362ddadb4415e9b73926d6b40709e70" uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" version = "0.2.4" +[[deps.KernelAbstractions]] +deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] +git-tree-sha1 = "47be64f040a7ece575c2b5f53ca6da7b548d69f4" +uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" +version = "0.9.4" + [[deps.KrylovKit]] deps = ["ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Printf"] git-tree-sha1 = "1a5e1d9941c783b0119897d29f2eb665d876ecf3" @@ -1074,15 +1153,21 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "088dd02b2797f0233d92583562ab669de8517fd1" +git-tree-sha1 = "5007c1421563108110bbd57f63d8ad4565808818" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "4.14.1" +version = "5.2.0" [[deps.LLVMExtra_jll]] -deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg", "TOML"] -git-tree-sha1 = "771bfe376249626d3ca12bcd58ba243d3f961576" +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "1222116d7313cdefecf3d45a2bc1a89c4e7c9217" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.16+0" +version = "0.0.22+0" + +[[deps.LLVMOpenMP_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "f689897ccbe049adb19a065c495e75f372ecd42b" +uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" +version = "15.0.4+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1097,9 +1182,17 @@ version = "1.3.0" [[deps.Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] -git-tree-sha1 = "ab9aa169d2160129beb241cb2750ca499b4e90e9" +git-tree-sha1 = "f428ae552340899a935973270b8d98e5a31c49fe" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.17" +version = "0.16.1" + + [deps.Latexify.extensions] + DataFramesExt = "DataFrames" + SymEngineExt = "SymEngine" + + [deps.Latexify.weakdeps] + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -1181,14 +1274,24 @@ uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" version = "2.36.0+0" [[deps.LinearAlgebra]] -deps = ["Libdl", "libblastrampoline_jll"] +deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LogExpFunctions]] -deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239" +deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.19" +version = "0.3.24" + + [deps.LogExpFunctions.extensions] + LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" + LogExpFunctionsChangesOfVariablesExt = "ChangesOfVariables" + LogExpFunctionsInverseFunctionsExt = "InverseFunctions" + + [deps.LogExpFunctions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -1201,9 +1304,9 @@ version = "1.0.0" [[deps.MAT]] deps = ["BufferedStreams", "CodecZlib", "HDF5", "SparseArrays"] -git-tree-sha1 = "971be550166fe3f604d28715302b58a3f7293160" +git-tree-sha1 = "79fd0b5ee384caf8ebba6c8fb3f365ca3e2c5493" uuid = "23992714-dd62-5051-b70f-ba57cb901cac" -version = "0.10.3" +version = "0.10.5" [[deps.MIMEs]] git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" @@ -1212,20 +1315,20 @@ version = "0.1.4" [[deps.MLDatasets]] deps = ["CSV", "Chemfiles", "DataDeps", "DataFrames", "DelimitedFiles", "FileIO", "FixedPointNumbers", "GZip", "Glob", "HDF5", "ImageShow", "JLD2", "JSON3", "LazyModules", "MAT", "MLUtils", "NPZ", "Pickle", "Printf", "Requires", "SparseArrays", "Tables"] -git-tree-sha1 = "d995d90956fd27e83b8e15eca67276848a0876d2" +git-tree-sha1 = "498b37aa3ebb4407adea36df1b244fa4e397de5e" uuid = "eb30cadb-4394-5ae3-aed4-317e484a6458" -version = "0.7.8" +version = "0.7.9" [[deps.MLStyle]] -git-tree-sha1 = "060ef7956fef2dc06b0e63b294f7dbfbcbdc7ea2" +git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" uuid = "d8e11817-5142-5d16-987a-aa16d5891078" -version = "0.4.16" +version = "0.4.17" [[deps.MLUtils]] -deps = ["ChainRulesCore", "DataAPI", "DelimitedFiles", "FLoops", "FoldsThreads", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] -git-tree-sha1 = "82c1104919d664ab1024663ad851701415300c5f" +deps = ["ChainRulesCore", "Compat", "DataAPI", "DelimitedFiles", "FLoops", "FoldsThreads", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] +git-tree-sha1 = "ca31739905ddb08c59758726e22b9e25d0d1521b" uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" -version = "0.3.1" +version = "0.4.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1234,9 +1337,9 @@ uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" version = "0.5.10" [[deps.MappedArrays]] -git-tree-sha1 = "e8b359ef06ec72e8c030463fe02efe5527ee5142" +git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" -version = "0.4.1" +version = "0.4.2" [[deps.Markdown]] deps = ["Base64"] @@ -1251,7 +1354,7 @@ version = "1.1.7" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.0+0" +version = "2.28.2+0" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -1260,15 +1363,15 @@ version = "0.3.2" [[deps.MicroCollections]] deps = ["BangBang", "InitialValues", "Setfield"] -git-tree-sha1 = "4d5917a26ca33c66c8e5ca3247bd163624d35493" +git-tree-sha1 = "629afd7d10dbc6935ec59b32daeb33bc4460a42e" uuid = "128add7d-3638-4c79-886c-908ea0c25c34" -version = "0.1.3" +version = "0.1.4" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" +git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.0.2" +version = "1.1.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -1281,19 +1384,25 @@ version = "0.3.4" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.2.1" +version = "2022.10.11" [[deps.NNlib]] -deps = ["Adapt", "ChainRulesCore", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "37596c26f107f2fd93818166ed3dab1a2e6b2f05" +deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] +git-tree-sha1 = "99e6dbb50d8a96702dc60954569e9fe7291cc55d" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.8.11" +version = "0.8.20" + + [deps.NNlib.extensions] + NNlibAMDGPUExt = "AMDGPU" + + [deps.NNlib.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" [[deps.NNlibCUDA]] -deps = ["Adapt", "CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics"] -git-tree-sha1 = "4429261364c5ea5b7308aecaa10e803ace101631" +deps = ["Adapt", "CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics", "cuDNN"] +git-tree-sha1 = "f94a9684394ff0d325cc12b06da7032d8be01aaf" uuid = "a00861dc-f156-4864-bf3c-e6376f28a68d" -version = "0.2.4" +version = "0.2.7" [[deps.NPZ]] deps = ["FileIO", "ZipFile"] @@ -1303,9 +1412,9 @@ version = "0.4.3" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" +git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.1" +version = "1.0.2" [[deps.NameResolution]] deps = ["PrettyPrint"] @@ -1325,9 +1434,9 @@ version = "1.2.0" [[deps.OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "f71d8950b724e9ff6110fc948dff5a329f901d64" +git-tree-sha1 = "82d7c9e310fe55aa54996e6f7f94674e2a38fcb4" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.8" +version = "1.12.9" [[deps.Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1337,14 +1446,14 @@ version = "1.3.5+1" [[deps.OneHotArrays]] deps = ["Adapt", "ChainRulesCore", "Compat", "GPUArraysCore", "LinearAlgebra", "NNlib"] -git-tree-sha1 = "97af68a840d83df94053f45e68b944e645a2262c" +git-tree-sha1 = "f511fca956ed9e70b80cd3417bb8c2dde4b68644" uuid = "0b1bfda6-eb8a-41d2-88d8-f5af5cad476f" -version = "0.2.1" +version = "0.2.3" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.20+0" +version = "0.3.21+4" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -1353,15 +1462,15 @@ version = "0.8.1+0" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "df6830e37943c7aaa10023471ca47fb3065cc3c4" +git-tree-sha1 = "51901a49222b09e3743c65b8847687ae5fc78eb2" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.3.2" +version = "1.4.1" [[deps.OpenSSL_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1aa4b74f80b01c6bc2b89992b861b5f210e665b5" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.19+0" +version = "1.1.21+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1371,9 +1480,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "e657acef119cc0de2a8c0762666d3b64727b053b" +git-tree-sha1 = "6a01f65dd8583dee82eecc2a19b0ff21521aa749" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.14" +version = "0.2.18" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1382,26 +1491,26 @@ uuid = "91d4177d-7536-5919-b921-800302f37372" version = "1.3.2+0" [[deps.OrderedCollections]] -git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" +git-tree-sha1 = "d321bf2de576bf25ec4d3e4360faca399afca282" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.4.1" +version = "1.6.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" -version = "10.40.0+0" +version = "10.42.0+0" [[deps.PaddedViews]] deps = ["OffsetArrays"] -git-tree-sha1 = "03a7a85b76381a3d04c7a1656039197e70eda03d" +git-tree-sha1 = "0fac6313486baae819364c52b4f483450a9d793f" uuid = "5432bcbf-9aad-5242-b902-cca2824c8663" -version = "0.5.11" +version = "0.5.12" [[deps.Parsers]] -deps = ["Dates", "SnoopPrecompile"] -git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559" +deps = ["Dates", "PrecompileTools", "UUIDs"] +git-tree-sha1 = "5a6ab2f64388fd1175effdf73fe5933ef1e0bac0" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.5.2" +version = "2.7.0" [[deps.Pickle]] deps = ["DataStructures", "InternedStrings", "Serialization", "SparseArrays", "Strided", "StringEncodings", "ZipFile"] @@ -1415,15 +1524,15 @@ uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" version = "1.3.0" [[deps.Pixman_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] +git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.40.1+0" +version = "0.42.2+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.8.0" +version = "1.9.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] @@ -1432,22 +1541,36 @@ uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" version = "3.1.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] -git-tree-sha1 = "5b7690dd212e026bbab1860016a6601cb077ab66" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] +git-tree-sha1 = "f92e1315dadf8c46561fb9396e525f7200cdc227" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.2" +version = "1.3.5" [[deps.Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "513084afca53c9af3491c94224997768b9af37e8" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] +git-tree-sha1 = "75ca67b2c6512ad2d0c767a7cfc55e75075f8bbc" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.0" +version = "1.38.16" + + [deps.Plots.extensions] + FileIOExt = "FileIO" + GeometryBasicsExt = "GeometryBasics" + IJuliaExt = "IJulia" + ImageInTerminalExt = "ImageInTerminal" + UnitfulExt = "Unitful" + + [deps.Plots.weakdeps] + FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" + GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326" + IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a" + ImageInTerminal = "d8c32880-2388-543b-8c61-d9f865259254" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.PlutoUI]] deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] -git-tree-sha1 = "eadad7b14cf046de6eb41f13c9275e5aa2711ab6" +git-tree-sha1 = "b478a748be27bd2f2c73a7690da219d0844db305" uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" -version = "0.7.49" +version = "0.7.51" [[deps.PooledArrays]] deps = ["DataAPI", "Future"] @@ -1455,11 +1578,17 @@ git-tree-sha1 = "a6062fe4063cdafe78f4a0a81cfffb89721b30e7" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" version = "1.4.2" +[[deps.PrecompileTools]] +deps = ["Preferences"] +git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" +version = "1.1.2" + [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" +git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.3.0" +version = "1.4.0" [[deps.PrettyPrint]] git-tree-sha1 = "632eb4abab3449ab30c5e1afaa874f0b98b586e4" @@ -1468,9 +1597,9 @@ version = "0.2.0" [[deps.PrettyTables]] deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "96f6db03ab535bdb901300f88335257b0018689d" +git-tree-sha1 = "213579618ec1f42dea7dd637a42785a608b1ea9c" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.2.2" +version = "2.2.4" [[deps.Printf]] deps = ["Unicode"] @@ -1504,9 +1633,9 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.Random123]] deps = ["Random", "RandomNumbers"] -git-tree-sha1 = "7a1a306b72cfa60634f03a911405f4e64d1b718b" +git-tree-sha1 = "552f30e847641591ba3f39fd1bed559b9deb0ef3" uuid = "74087812-796a-5b5d-8853-05524746bad3" -version = "1.6.0" +version = "1.6.1" [[deps.RandomNumbers]] deps = ["Random", "Requires"] @@ -1521,16 +1650,16 @@ uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" version = "0.1.0" [[deps.RecipesBase]] -deps = ["SnoopPrecompile"] -git-tree-sha1 = "18c35ed630d7229c5584b945641a73ca83fb5213" +deps = ["PrecompileTools"] +git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.3.2" +version = "1.3.4" [[deps.RecipesPipeline]] -deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"] -git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f" +deps = ["Dates", "NaNMath", "PlotUtils", "PrecompileTools", "RecipesBase"] +git-tree-sha1 = "45cf9fd0ca5839d06ef333c8201714e888486342" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.6.11" +version = "0.6.12" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1555,15 +1684,15 @@ version = "0.7.0" [[deps.Scratch]] deps = ["Dates"] -git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" +git-tree-sha1 = "30449ee12237627992a99d5e30ae63e4d78cd24a" uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.1.1" +version = "1.2.0" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "efd23b378ea5f2db53a55ae53d3133de4e080aa9" +git-tree-sha1 = "04bdff0b09c65ff3e06a05e3eb7b120223da3d39" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.3.16" +version = "1.4.0" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1601,9 +1730,10 @@ uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" version = "0.9.4" [[deps.SnoopPrecompile]] -git-tree-sha1 = "f604441450a3c0569830946e5b33b78c928e1a85" +deps = ["Preferences"] +git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" -version = "1.0.1" +version = "1.0.3" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -1615,14 +1745,18 @@ uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" version = "1.1.0" [[deps.SparseArrays]] -deps = ["LinearAlgebra", "Random"] +deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" +deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.1.7" +version = "2.2.0" +weakdeps = ["ChainRulesCore"] + + [deps.SpecialFunctions.extensions] + SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] @@ -1638,9 +1772,9 @@ version = "0.1.1" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "ffc098086f35909741f71ce21d03dadf0d2bfa76" +git-tree-sha1 = "832afbae2a45b4ae7e831f86965469a24d1d8a83" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.11" +version = "1.5.26" [[deps.StaticArraysCore]] git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" @@ -1650,18 +1784,19 @@ version = "1.4.0" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" +git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.5.0" +version = "1.6.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" +git-tree-sha1 = "75ebe04c5bed70b91614d684259b661c9e6274a4" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.21" +version = "0.34.0" [[deps.Strided]] deps = ["LinearAlgebra", "TupleTools"] @@ -1671,9 +1806,9 @@ version = "1.2.3" [[deps.StringEncodings]] deps = ["Libiconv_jll"] -git-tree-sha1 = "50ccd5ddb00d19392577902f0079267a72c5ab04" +git-tree-sha1 = "33c0da881af3248dafefb939a21694b97cfece76" uuid = "69024149-9ee7-55f6-a4c4-859efe599b68" -version = "0.3.5" +version = "0.3.6" [[deps.StringManipulation]] git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" @@ -1682,9 +1817,9 @@ version = "0.3.0" [[deps.StructArrays]] deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "b03a3b745aa49b566f128977a7dd1be8711c5e71" +git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.14" +version = "0.6.15" [[deps.StructTypes]] deps = ["Dates", "UUIDs"] @@ -1692,10 +1827,15 @@ git-tree-sha1 = "ca4bccb03acf9faaf4137a9abc1881ed1841aa70" uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" version = "1.10.0" +[[deps.SuiteSparse_jll]] +deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] +uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" +version = "5.10.1+6" + [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" -version = "1.0.0" +version = "1.0.3" [[deps.TSne]] deps = ["Distances", "LinearAlgebra", "Printf", "ProgressMeter", "Statistics"] @@ -1711,14 +1851,14 @@ version = "1.0.1" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" +git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.10.0" +version = "1.10.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" -version = "1.10.1" +version = "1.10.0" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -1732,26 +1872,26 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "f2fd3f288dfc6f507b0c3a2eb3bac009251e548b" +git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.22" +version = "0.5.23" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "e4bdc63f5c6d62e80eb1c0043fcc0360d5950ff7" +git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.10" +version = "0.9.13" [[deps.Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] -git-tree-sha1 = "c42fa452a60f022e9e087823b47e5a5f8adc53d5" +git-tree-sha1 = "25358a5f2384c490e98abd565ed321ffae2cbb37" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.75" +version = "0.4.76" [[deps.Tricks]] -git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" +git-tree-sha1 = "aadb748be58b492045b4f56166b5188aa63ce549" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.6" +version = "0.1.7" [[deps.TupleTools]] git-tree-sha1 = "3c712976c47707ff893cf6ba4354aa14db1d8938" @@ -1759,9 +1899,9 @@ uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6" version = "1.3.0" [[deps.URIs]] -git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348" +git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.4.1" +version = "1.4.2" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -1776,6 +1916,33 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" +[[deps.Unitful]] +deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"] +git-tree-sha1 = "ba4aa36b2d5c98d6ed1f149da916b3ba46527b2b" +uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" +version = "1.14.0" +weakdeps = ["InverseFunctions"] + + [deps.Unitful.extensions] + InverseFunctionsUnitfulExt = "InverseFunctions" + +[[deps.UnitfulLatexify]] +deps = ["LaTeXStrings", "Latexify", "Unitful"] +git-tree-sha1 = "e2d817cc500e960fdbafcf988ac8436ba3208bfd" +uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" +version = "1.6.3" + +[[deps.UnsafeAtomics]] +git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" +uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" +version = "0.2.1" + +[[deps.UnsafeAtomicsLLVM]] +deps = ["LLVM", "UnsafeAtomics"] +git-tree-sha1 = "ea37e6066bf194ab78f4e747f5245261f17a7175" +uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" +version = "0.1.2" + [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" @@ -1783,9 +1950,9 @@ version = "0.2.0" [[deps.Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" +git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" -version = "1.19.0+0" +version = "1.21.0+0" [[deps.Wayland_protocols_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1951,25 +2118,41 @@ version = "0.10.1" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.12+3" +version = "1.2.13+0" [[deps.Zstd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.2+0" +version = "1.5.5+0" [[deps.Zygote]] -deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "a6f1287943ac05fae56fa06049d1a7846dfbc65f" +deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] +git-tree-sha1 = "5be3ddb88fc992a7d8ea96c3f10a49a7e98ebc7b" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.51" +version = "0.6.62" + + [deps.Zygote.extensions] + ZygoteColorsExt = "Colors" + ZygoteDistancesExt = "Distances" + ZygoteTrackerExt = "Tracker" + + [deps.Zygote.weakdeps] + Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" + Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ZygoteRules]] -deps = ["MacroTools"] -git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" +deps = ["ChainRulesCore", "MacroTools"] +git-tree-sha1 = "977aed5d006b840e2e40c0b48984f7463109046d" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.2" +version = "0.2.3" + +[[deps.cuDNN]] +deps = ["CEnum", "CUDA", "CUDNN_jll"] +git-tree-sha1 = "f65490d187861d6222cb38bcbbff3fd949a7ec3e" +uuid = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" +version = "1.0.4" [[deps.fzf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1990,9 +2173,9 @@ uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" [[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.1.1+0" +version = "5.8.0+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] From 973181724534c9097e0cceea1cfa4d0a6b807d0b Mon Sep 17 00:00:00 2001 From: Carlo Lucibello Date: Wed, 14 Jun 2023 12:32:22 +0200 Subject: [PATCH 4/4] change test --- .github/workflows/docs.yml | 2 +- test/layers/basic.jl | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 5b6ea9893..9990411ed 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -14,7 +14,7 @@ jobs: - uses: actions/checkout@v3 - uses: julia-actions/setup-julia@latest with: - version: '1.8.2' + version: '1.9.1' - name: Install dependencies run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()' - name: Build and deploy diff --git a/test/layers/basic.jl b/test/layers/basic.jl index 94567d699..9a3b6ee9f 100644 --- a/test/layers/basic.jl +++ b/test/layers/basic.jl @@ -43,15 +43,15 @@ @testset "Parallel" begin AddResidual(l) = Parallel(+, identity, l) - gnn = GNNChain(ResGatedGraphConv(din => d, tanh), + gnn = GNNChain(GraphConv(din => d, tanh), LayerNorm(d), - AddResidual(ResGatedGraphConv(d => d, tanh)), + AddResidual(GraphConv(d => d, tanh)), BatchNorm(d), Dense(d, dout)) trainmode!(gnn) - test_layer(gnn, g, rtol = 1e-5, atol=1e-5, exclude_grad_fields = [:μ, :σ²]) + test_layer(gnn, g, rtol = 1e-4, atol=1e-4, exclude_grad_fields = [:μ, :σ²]) end @testset "Only graph input" begin