JuliaGraphs · CarloLucibello · Sep 26, 2024 · Sep 26, 2024 · Sep 26, 2024 · Sep 26, 2024
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -16,14 +16,14 @@ 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();'
       - name: Build and deploy
         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
diff --git 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
diff --git a/GNNLux/LICENSE b/GNNLux/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2024 Carlo Lucibello <[email protected]> and contributors
+Copyright (c) 2021 Carlo Lucibello <[email protected]> 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
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Carlo Lucibello <[email protected]> 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 → GraphNeuralNetworks/Project.toml b/Project.toml → GraphNeuralNetworks/Project.toml
diff --git a/GraphNeuralNetworks/README.md b/GraphNeuralNetworks/README.md
@@ -0,0 +1,55 @@
+<img align="right" width="300px" src="https://raw.githubusercontent.com/CarloLucibello/GraphNeuralNetworks.jl/master/docs/src/assets/logo.svg">
+
+
+# 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 → GraphNeuralNetworks/docs/Project.toml b/docs/Project.toml → GraphNeuralNetworks/docs/Project.toml
diff --git a/docs/make.jl → GraphNeuralNetworks/docs/make.jl b/docs/make.jl → GraphNeuralNetworks/docs/make.jl
diff --git a/docs/pluto_output/gnn_intro_pluto.md → ...orks/docs/pluto_output/gnn_intro_pluto.md b/docs/pluto_output/gnn_intro_pluto.md → ...orks/docs/pluto_output/gnn_intro_pluto.md
diff --git a/...luto_output/graph_classification_pluto.md → ...luto_output/graph_classification_pluto.md b/...luto_output/graph_classification_pluto.md → ...luto_output/graph_classification_pluto.md
diff --git a/...pluto_output/node_classification_pluto.md → ...pluto_output/node_classification_pluto.md b/...pluto_output/node_classification_pluto.md → ...pluto_output/node_classification_pluto.md
diff --git a/docs/src/api/basic.md → GraphNeuralNetworks/docs/src/api/basic.md b/docs/src/api/basic.md → GraphNeuralNetworks/docs/src/api/basic.md
diff --git a/docs/src/api/conv.md → GraphNeuralNetworks/docs/src/api/conv.md b/docs/src/api/conv.md → GraphNeuralNetworks/docs/src/api/conv.md
diff --git a/docs/src/api/gnngraph.md → GraphNeuralNetworks/docs/src/api/gnngraph.md b/docs/src/api/gnngraph.md → GraphNeuralNetworks/docs/src/api/gnngraph.md
diff --git a/docs/src/api/heterograph.md → ...euralNetworks/docs/src/api/heterograph.md b/docs/src/api/heterograph.md → ...euralNetworks/docs/src/api/heterograph.md
diff --git a/docs/src/api/messagepassing.md → ...alNetworks/docs/src/api/messagepassing.md b/docs/src/api/messagepassing.md → ...alNetworks/docs/src/api/messagepassing.md
diff --git a/docs/src/api/pool.md → GraphNeuralNetworks/docs/src/api/pool.md b/docs/src/api/pool.md → GraphNeuralNetworks/docs/src/api/pool.md
diff --git a/docs/src/api/temporalconv.md → ...uralNetworks/docs/src/api/temporalconv.md b/docs/src/api/temporalconv.md → ...uralNetworks/docs/src/api/temporalconv.md
diff --git a/docs/src/api/temporalgraph.md → ...ralNetworks/docs/src/api/temporalgraph.md b/docs/src/api/temporalgraph.md → ...ralNetworks/docs/src/api/temporalgraph.md
diff --git a/docs/src/api/utils.md → GraphNeuralNetworks/docs/src/api/utils.md b/docs/src/api/utils.md → GraphNeuralNetworks/docs/src/api/utils.md
diff --git a/docs/src/assets/logo.png → GraphNeuralNetworks/docs/src/assets/logo.png b/docs/src/assets/logo.png → GraphNeuralNetworks/docs/src/assets/logo.png
diff --git a/docs/src/assets/logo.svg → GraphNeuralNetworks/docs/src/assets/logo.svg b/docs/src/assets/logo.svg → GraphNeuralNetworks/docs/src/assets/logo.svg
diff --git a/docs/src/assets/logo_alternatives/V1.svg → .../docs/src/assets/logo_alternatives/V1.svg b/docs/src/assets/logo_alternatives/V1.svg → .../docs/src/assets/logo_alternatives/V1.svg
diff --git a/docs/src/assets/logo_alternatives/V10.svg → ...docs/src/assets/logo_alternatives/V10.svg b/docs/src/assets/logo_alternatives/V10.svg → ...docs/src/assets/logo_alternatives/V10.svg
diff --git a/docs/src/assets/logo_alternatives/V2.svg → .../docs/src/assets/logo_alternatives/V2.svg b/docs/src/assets/logo_alternatives/V2.svg → .../docs/src/assets/logo_alternatives/V2.svg
diff --git a/docs/src/assets/logo_alternatives/V3.svg → .../docs/src/assets/logo_alternatives/V3.svg b/docs/src/assets/logo_alternatives/V3.svg → .../docs/src/assets/logo_alternatives/V3.svg
diff --git a/docs/src/assets/logo_alternatives/V4.svg → .../docs/src/assets/logo_alternatives/V4.svg b/docs/src/assets/logo_alternatives/V4.svg → .../docs/src/assets/logo_alternatives/V4.svg
diff --git a/docs/src/assets/logo_alternatives/V5.svg → .../docs/src/assets/logo_alternatives/V5.svg b/docs/src/assets/logo_alternatives/V5.svg → .../docs/src/assets/logo_alternatives/V5.svg
diff --git a/docs/src/assets/logo_alternatives/V6.svg → .../docs/src/assets/logo_alternatives/V6.svg b/docs/src/assets/logo_alternatives/V6.svg → .../docs/src/assets/logo_alternatives/V6.svg
diff --git a/docs/src/assets/logo_alternatives/V7.svg → .../docs/src/assets/logo_alternatives/V7.svg b/docs/src/assets/logo_alternatives/V7.svg → .../docs/src/assets/logo_alternatives/V7.svg
diff --git a/docs/src/assets/logo_alternatives/V8.svg → .../docs/src/assets/logo_alternatives/V8.svg b/docs/src/assets/logo_alternatives/V8.svg → .../docs/src/assets/logo_alternatives/V8.svg
diff --git a/docs/src/assets/logo_alternatives/V9.svg → .../docs/src/assets/logo_alternatives/V9.svg b/docs/src/assets/logo_alternatives/V9.svg → .../docs/src/assets/logo_alternatives/V9.svg
diff --git a/docs/src/datasets.md → GraphNeuralNetworks/docs/src/datasets.md b/docs/src/datasets.md → GraphNeuralNetworks/docs/src/datasets.md
diff --git a/docs/src/dev.md → GraphNeuralNetworks/docs/src/dev.md b/docs/src/dev.md → GraphNeuralNetworks/docs/src/dev.md
diff --git a/docs/src/gnngraph.md → GraphNeuralNetworks/docs/src/gnngraph.md b/docs/src/gnngraph.md → GraphNeuralNetworks/docs/src/gnngraph.md
diff --git a/docs/src/gsoc.md → GraphNeuralNetworks/docs/src/gsoc.md b/docs/src/gsoc.md → GraphNeuralNetworks/docs/src/gsoc.md
diff --git a/docs/src/heterograph.md → GraphNeuralNetworks/docs/src/heterograph.md b/docs/src/heterograph.md → GraphNeuralNetworks/docs/src/heterograph.md
diff --git a/docs/src/index.md → GraphNeuralNetworks/docs/src/index.md b/docs/src/index.md → GraphNeuralNetworks/docs/src/index.md
diff --git a/docs/src/messagepassing.md → ...NeuralNetworks/docs/src/messagepassing.md b/docs/src/messagepassing.md → ...NeuralNetworks/docs/src/messagepassing.md
diff --git a/docs/src/models.md → GraphNeuralNetworks/docs/src/models.md b/docs/src/models.md → GraphNeuralNetworks/docs/src/models.md
diff --git a/docs/src/temporalgraph.md → ...hNeuralNetworks/docs/src/temporalgraph.md b/docs/src/temporalgraph.md → ...hNeuralNetworks/docs/src/temporalgraph.md
diff --git a/docs/tutorials/config.json → ...NeuralNetworks/docs/tutorials/config.json b/docs/tutorials/config.json → ...NeuralNetworks/docs/tutorials/config.json
diff --git a/docs/tutorials/index.md → GraphNeuralNetworks/docs/tutorials/index.md b/docs/tutorials/index.md → GraphNeuralNetworks/docs/tutorials/index.md
diff --git a/...troductory_tutorials/assets/brain_gnn.gif → ...troductory_tutorials/assets/brain_gnn.gif b/...troductory_tutorials/assets/brain_gnn.gif → ...troductory_tutorials/assets/brain_gnn.gif
diff --git a/...tutorials/assets/graph_classification.gif → ...tutorials/assets/graph_classification.gif b/...tutorials/assets/graph_classification.gif → ...tutorials/assets/graph_classification.gif
diff --git a/...introductory_tutorials/assets/intro_1.png → ...introductory_tutorials/assets/intro_1.png b/...introductory_tutorials/assets/intro_1.png → ...introductory_tutorials/assets/intro_1.png
diff --git a/...tutorials/assets/node_classsification.gif → ...tutorials/assets/node_classsification.gif b/...tutorials/assets/node_classsification.gif → ...tutorials/assets/node_classsification.gif
diff --git a/...introductory_tutorials/assets/traffic.gif → ...introductory_tutorials/assets/traffic.gif b/...introductory_tutorials/assets/traffic.gif → ...introductory_tutorials/assets/traffic.gif
diff --git a/...introductory_tutorials/gnn_intro_pluto.jl → ...introductory_tutorials/gnn_intro_pluto.jl b/...introductory_tutorials/gnn_intro_pluto.jl → ...introductory_tutorials/gnn_intro_pluto.jl
diff --git a/...y_tutorials/graph_classification_pluto.jl → ...y_tutorials/graph_classification_pluto.jl b/...y_tutorials/graph_classification_pluto.jl → ...y_tutorials/graph_classification_pluto.jl
diff --git a/...ry_tutorials/node_classification_pluto.jl → ...ry_tutorials/node_classification_pluto.jl b/...ry_tutorials/node_classification_pluto.jl → ...ry_tutorials/node_classification_pluto.jl
diff --git a/...en/temporal_graph_classification_pluto.jl → ...en/temporal_graph_classification_pluto.jl b/...en/temporal_graph_classification_pluto.jl → ...en/temporal_graph_classification_pluto.jl
diff --git a/docs/tutorials_broken/traffic_prediction.jl → ...cs/tutorials_broken/traffic_prediction.jl b/docs/tutorials_broken/traffic_prediction.jl → ...cs/tutorials_broken/traffic_prediction.jl
diff --git a/examples/Project.toml → GraphNeuralNetworks/examples/Project.toml b/examples/Project.toml → GraphNeuralNetworks/examples/Project.toml
diff --git a/...es/graph_classification_temporalbrains.jl → ...es/graph_classification_temporalbrains.jl b/...es/graph_classification_temporalbrains.jl → ...es/graph_classification_temporalbrains.jl
diff --git a/examples/graph_classification_tudataset.jl → ...xamples/graph_classification_tudataset.jl b/examples/graph_classification_tudataset.jl → ...xamples/graph_classification_tudataset.jl
diff --git a/examples/link_prediction_pubmed.jl → ...tworks/examples/link_prediction_pubmed.jl b/examples/link_prediction_pubmed.jl → ...tworks/examples/link_prediction_pubmed.jl
diff --git a/examples/neural_ode_cora.jl → ...euralNetworks/examples/neural_ode_cora.jl b/examples/neural_ode_cora.jl → ...euralNetworks/examples/neural_ode_cora.jl
diff --git a/examples/node_classification_cora.jl → ...orks/examples/node_classification_cora.jl b/examples/node_classification_cora.jl → ...orks/examples/node_classification_cora.jl
diff --git a/examples/traffic_prediction.jl → ...alNetworks/examples/traffic_prediction.jl b/examples/traffic_prediction.jl → ...alNetworks/examples/traffic_prediction.jl
diff --git a/notebooks/gnn_intro.ipynb → ...hNeuralNetworks/notebooks/gnn_intro.ipynb b/notebooks/gnn_intro.ipynb → ...hNeuralNetworks/notebooks/gnn_intro.ipynb
diff --git a/notebooks/graph_classification.ipynb → ...orks/notebooks/graph_classification.ipynb b/notebooks/graph_classification.ipynb → ...orks/notebooks/graph_classification.ipynb
diff --git a/notebooks/graph_classification_solved.ipynb → ...tebooks/graph_classification_solved.ipynb b/notebooks/graph_classification_solved.ipynb → ...tebooks/graph_classification_solved.ipynb
diff --git a/perf/Project.toml → GraphNeuralNetworks/perf/Project.toml b/perf/Project.toml → GraphNeuralNetworks/perf/Project.toml
diff --git a/perf/bench_gnn.jl → GraphNeuralNetworks/perf/bench_gnn.jl b/perf/bench_gnn.jl → GraphNeuralNetworks/perf/bench_gnn.jl
diff --git a/perf/neural_ode_mnist.jl → GraphNeuralNetworks/perf/neural_ode_mnist.jl b/perf/neural_ode_mnist.jl → GraphNeuralNetworks/perf/neural_ode_mnist.jl
diff --git a/...node_classification_cora_geometricflux.jl → ...node_classification_cora_geometricflux.jl b/...node_classification_cora_geometricflux.jl → ...node_classification_cora_geometricflux.jl
diff --git a/perf/perf.jl → GraphNeuralNetworks/perf/perf.jl b/perf/perf.jl → GraphNeuralNetworks/perf/perf.jl
diff --git a/perf/perf_master_20210830_carlodsba.jld2 → .../perf/perf_master_20210830_carlodsba.jld2 b/perf/perf_master_20210830_carlodsba.jld2 → .../perf/perf_master_20210830_carlodsba.jld2
diff --git a/src/GraphNeuralNetworks.jl → ...NeuralNetworks/src/GraphNeuralNetworks.jl b/src/GraphNeuralNetworks.jl → ...NeuralNetworks/src/GraphNeuralNetworks.jl
diff --git a/src/deprecations.jl → GraphNeuralNetworks/src/deprecations.jl b/src/deprecations.jl → GraphNeuralNetworks/src/deprecations.jl
diff --git a/src/layers/basic.jl → GraphNeuralNetworks/src/layers/basic.jl b/src/layers/basic.jl → GraphNeuralNetworks/src/layers/basic.jl
diff --git a/src/layers/conv.jl → GraphNeuralNetworks/src/layers/conv.jl b/src/layers/conv.jl → GraphNeuralNetworks/src/layers/conv.jl
diff --git a/src/layers/heteroconv.jl → GraphNeuralNetworks/src/layers/heteroconv.jl b/src/layers/heteroconv.jl → GraphNeuralNetworks/src/layers/heteroconv.jl
diff --git a/src/layers/pool.jl → GraphNeuralNetworks/src/layers/pool.jl b/src/layers/pool.jl → GraphNeuralNetworks/src/layers/pool.jl
diff --git a/src/layers/temporalconv.jl → ...NeuralNetworks/src/layers/temporalconv.jl b/src/layers/temporalconv.jl → ...NeuralNetworks/src/layers/temporalconv.jl
diff --git a/test/examples/node_classification_cora.jl → ...test/examples/node_classification_cora.jl b/test/examples/node_classification_cora.jl → ...test/examples/node_classification_cora.jl
diff --git a/test/layers/basic.jl → GraphNeuralNetworks/test/layers/basic.jl b/test/layers/basic.jl → GraphNeuralNetworks/test/layers/basic.jl
diff --git a/test/layers/conv.jl → GraphNeuralNetworks/test/layers/conv.jl b/test/layers/conv.jl → GraphNeuralNetworks/test/layers/conv.jl
diff --git a/test/layers/heteroconv.jl → ...hNeuralNetworks/test/layers/heteroconv.jl b/test/layers/heteroconv.jl → ...hNeuralNetworks/test/layers/heteroconv.jl
diff --git a/test/layers/pool.jl → GraphNeuralNetworks/test/layers/pool.jl b/test/layers/pool.jl → GraphNeuralNetworks/test/layers/pool.jl
diff --git a/test/layers/temporalconv.jl → ...euralNetworks/test/layers/temporalconv.jl b/test/layers/temporalconv.jl → ...euralNetworks/test/layers/temporalconv.jl
diff --git a/test/runtests.jl → GraphNeuralNetworks/test/runtests.jl b/test/runtests.jl → GraphNeuralNetworks/test/runtests.jl
diff --git a/test/test_utils.jl → GraphNeuralNetworks/test/test_utils.jl b/test/test_utils.jl → GraphNeuralNetworks/test/test_utils.jl
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-<img align="right" width="300px" src="https://raw.githubusercontent.com/CarloLucibello/GraphNeuralNetworks.jl/master/docs/src/assets/logo.svg">
+<img align="right" width="300px" src="https://raw.githubusercontent.com/CarloLucibello/GraphNeuralNetworks.jl/master/GraphNeuralNetworks/docs/src/assets/logo.svg">
 
 
 # GraphNeuralNetworks.jl