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License -Copyright (c) 2024 Carlo Lucibello and contributors +Copyright (c) 2021 Carlo Lucibello and contributors Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/GraphNeuralNetworks/LICENSE b/GraphNeuralNetworks/LICENSE new file mode 100644 index 000000000..e7410390d --- /dev/null +++ b/GraphNeuralNetworks/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2021 Carlo Lucibello and contributors + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/Project.toml b/GraphNeuralNetworks/Project.toml similarity index 100% rename from Project.toml rename to GraphNeuralNetworks/Project.toml diff --git a/GraphNeuralNetworks/README.md b/GraphNeuralNetworks/README.md new file mode 100644 index 000000000..434e4cd46 --- /dev/null +++ b/GraphNeuralNetworks/README.md @@ -0,0 +1,55 @@ + + + +# GraphNeuralNetworks.jl + +[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://CarloLucibello.github.io/GraphNeuralNetworks.jl/stable) +[![](https://img.shields.io/badge/docs-dev-blue.svg)](https://CarloLucibello.github.io/GraphNeuralNetworks.jl/dev) +![](https://github.com/CarloLucibello/GraphNeuralNetworks.jl/actions/workflows/ci.yml/badge.svg) +[![codecov](https://codecov.io/gh/CarloLucibello/GraphNeuralNetworks.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/CarloLucibello/GraphNeuralNetworks.jl) + + +GraphNeuralNetworks.jl is a graph neural network library written in Julia and based on the deep learning framework [Flux.jl](https://github.com/FluxML/Flux.jl). + +Among its features: + +* Implements common graph convolutional layers. +* Supports computations on batched graphs. +* Easy to define custom layers. +* 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 + +GraphNeuralNetworks.jl is a registered Julia package. You can easily install it through the package manager: + +```julia +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. + + +## Citing + +If you use GraphNeuralNetworks.jl in a scientific publication, we would appreciate the following reference: + +``` +@misc{Lucibello2021GNN, + author = {Carlo Lucibello and other contributors}, + title = {GraphNeuralNetworks.jl: a geometric deep learning library for the Julia programming language}, + year = 2021, + url = {https://github.com/CarloLucibello/GraphNeuralNetworks.jl} +} +``` + +## Acknowledgments + +GraphNeuralNetworks.jl is largely inspired by [PyTorch Geometric](https://pytorch-geometric.readthedocs.io/en/latest/), [Deep Graph Library](https://docs.dgl.ai/), +and [GeometricFlux.jl](https://fluxml.ai/GeometricFlux.jl/stable/). + + diff --git a/docs/Project.toml b/GraphNeuralNetworks/docs/Project.toml similarity index 100% rename from docs/Project.toml rename to GraphNeuralNetworks/docs/Project.toml diff 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GraphNeuralNetworks/notebooks/graph_classification_solved.ipynb diff --git a/perf/Project.toml b/GraphNeuralNetworks/perf/Project.toml similarity index 100% rename from perf/Project.toml rename to GraphNeuralNetworks/perf/Project.toml diff --git a/perf/bench_gnn.jl b/GraphNeuralNetworks/perf/bench_gnn.jl similarity index 100% rename from perf/bench_gnn.jl rename to GraphNeuralNetworks/perf/bench_gnn.jl diff --git a/perf/neural_ode_mnist.jl b/GraphNeuralNetworks/perf/neural_ode_mnist.jl similarity index 100% rename from perf/neural_ode_mnist.jl rename to GraphNeuralNetworks/perf/neural_ode_mnist.jl diff --git a/perf/node_classification_cora_geometricflux.jl b/GraphNeuralNetworks/perf/node_classification_cora_geometricflux.jl similarity index 100% rename from perf/node_classification_cora_geometricflux.jl rename to GraphNeuralNetworks/perf/node_classification_cora_geometricflux.jl diff --git a/perf/perf.jl b/GraphNeuralNetworks/perf/perf.jl similarity index 100% rename from perf/perf.jl rename to GraphNeuralNetworks/perf/perf.jl diff --git a/perf/perf_master_20210830_carlodsba.jld2 b/GraphNeuralNetworks/perf/perf_master_20210830_carlodsba.jld2 similarity index 100% rename from perf/perf_master_20210830_carlodsba.jld2 rename to GraphNeuralNetworks/perf/perf_master_20210830_carlodsba.jld2 diff --git a/src/GraphNeuralNetworks.jl b/GraphNeuralNetworks/src/GraphNeuralNetworks.jl similarity index 100% rename from src/GraphNeuralNetworks.jl rename to GraphNeuralNetworks/src/GraphNeuralNetworks.jl diff --git a/src/deprecations.jl b/GraphNeuralNetworks/src/deprecations.jl similarity index 100% rename from src/deprecations.jl rename to GraphNeuralNetworks/src/deprecations.jl diff --git a/src/layers/basic.jl b/GraphNeuralNetworks/src/layers/basic.jl similarity index 100% rename from src/layers/basic.jl rename to GraphNeuralNetworks/src/layers/basic.jl diff --git a/src/layers/conv.jl b/GraphNeuralNetworks/src/layers/conv.jl similarity index 100% rename from src/layers/conv.jl rename to GraphNeuralNetworks/src/layers/conv.jl diff --git a/src/layers/heteroconv.jl b/GraphNeuralNetworks/src/layers/heteroconv.jl similarity index 100% rename from src/layers/heteroconv.jl rename to GraphNeuralNetworks/src/layers/heteroconv.jl diff --git a/src/layers/pool.jl b/GraphNeuralNetworks/src/layers/pool.jl similarity index 100% rename from src/layers/pool.jl rename to GraphNeuralNetworks/src/layers/pool.jl diff --git a/src/layers/temporalconv.jl b/GraphNeuralNetworks/src/layers/temporalconv.jl similarity index 100% rename from src/layers/temporalconv.jl rename to GraphNeuralNetworks/src/layers/temporalconv.jl diff --git a/test/examples/node_classification_cora.jl b/GraphNeuralNetworks/test/examples/node_classification_cora.jl similarity index 100% rename from test/examples/node_classification_cora.jl rename to GraphNeuralNetworks/test/examples/node_classification_cora.jl diff --git a/test/layers/basic.jl b/GraphNeuralNetworks/test/layers/basic.jl similarity index 100% rename from test/layers/basic.jl rename to GraphNeuralNetworks/test/layers/basic.jl diff --git a/test/layers/conv.jl b/GraphNeuralNetworks/test/layers/conv.jl similarity index 100% rename from test/layers/conv.jl rename to GraphNeuralNetworks/test/layers/conv.jl diff --git a/test/layers/heteroconv.jl b/GraphNeuralNetworks/test/layers/heteroconv.jl similarity index 100% rename from test/layers/heteroconv.jl rename to GraphNeuralNetworks/test/layers/heteroconv.jl diff --git a/test/layers/pool.jl b/GraphNeuralNetworks/test/layers/pool.jl similarity index 100% rename from test/layers/pool.jl rename to GraphNeuralNetworks/test/layers/pool.jl diff --git a/test/layers/temporalconv.jl b/GraphNeuralNetworks/test/layers/temporalconv.jl similarity index 100% rename from test/layers/temporalconv.jl rename to GraphNeuralNetworks/test/layers/temporalconv.jl diff --git a/test/runtests.jl b/GraphNeuralNetworks/test/runtests.jl similarity index 100% rename from test/runtests.jl rename to GraphNeuralNetworks/test/runtests.jl diff --git a/test/test_utils.jl b/GraphNeuralNetworks/test/test_utils.jl similarity index 100% rename from test/test_utils.jl rename to GraphNeuralNetworks/test/test_utils.jl diff --git a/README.md b/README.md index 434e4cd46..68c49926a 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ - + # GraphNeuralNetworks.jl From 3bb5e8f9c3af018f75e326941f5cddc42c699a69 Mon Sep 17 00:00:00 2001 From: Carlo Lucibello Date: Thu, 26 Sep 2024 07:04:57 +0200 Subject: [PATCH 2/3] update ci --- .github/workflows/test_GraphNeuralNetworks.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test_GraphNeuralNetworks.yml b/.github/workflows/test_GraphNeuralNetworks.yml index 49e5e6074..bdc452541 100644 --- a/.github/workflows/test_GraphNeuralNetworks.yml +++ b/.github/workflows/test_GraphNeuralNetworks.yml @@ -37,12 +37,12 @@ jobs: # dev mono repo versions pkg"registry up" Pkg.update() - pkg"dev ./GNNGraphs ./GNNlib ." + pkg"dev ./GNNGraphs ./GNNlib ./GraphNeuralNetworks" Pkg.test("GraphNeuralNetworks"; coverage=true) - uses: julia-actions/julia-processcoverage@v1 with: - # directories: ./src, ./ext - directories: ./src + # directories: ./GraphNeuralNetworks/src, ./GraphNeuralNetworks/ext + directories: ./GraphNeuralNetworks/src - uses: codecov/codecov-action@v4 with: files: lcov.info From 082f239155e04995ed81424246bfe46162d7b49b Mon Sep 17 00:00:00 2001 From: Carlo Lucibello Date: Thu, 26 Sep 2024 07:07:17 +0200 Subject: [PATCH 3/3] update docs action --- .github/workflows/docs.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index a9c53cb36..ec69b388d 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -16,9 +16,9 @@ jobs: with: version: '1.10.4' - name: Install dependencies - run: julia --project=docs/ -e ' + run: julia --project=GraphNeuralNetworks/docs/ -e ' using Pkg; - Pkg.develop([PackageSpec(path=pwd()), + Pkg.develop([PackageSpec(path=joinpath(pwd(), "GraphNeuralNetworks")), PackageSpec(path=joinpath(pwd(), "GNNGraphs")), PackageSpec(path=joinpath(pwd(), "GNNlib"))]); Pkg.instantiate();' @@ -26,4 +26,4 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} - run: julia --project=docs/ docs/make.jl + run: julia --project=GraphNeuralNetworks/docs/ GraphNeuralNetworks/docs/make.jl