[WIP] Add docs and tests

.github/workflows/CI.yml

@@ -29,6 +29,9 @@ jobs:
           - ubuntu-latest
         arch:
           - x64
+    env:
+      DATADEPS_ALWAYS_ACCEPT: true
+      LD_LIBRARY_PATH: ""
     steps:
       - name: Install matplotlib
         run: if [ "$RUNNER_OS" = "Linux" ]; then sudo apt-get install -y python3-matplotlib; fi
@@ -40,6 +43,13 @@ jobs:
           arch: ${{ matrix.arch }}
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
+      - name: Configure test environment
+        shell: julia --color=yes {0}
+        run: |
+          using Pkg
+          Pkg.develop(PackageSpec(path=pwd()))
+          Pkg.instantiate()
+          Pkg.add(name="OpenSSL_jll", version="3")
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v5
@@ -54,6 +64,8 @@ jobs:
       actions: write # needed to allow julia-actions/cache to proactively delete old caches that it has created
       contents: write
       statuses: write
+    env:
+      LD_LIBRARY_PATH: ""
     steps:
       - name: Install matplotlib
         run: if [ "$RUNNER_OS" = "Linux" ]; then sudo apt-get install -y python3-matplotlib; fi
@@ -65,14 +77,14 @@ jobs:
           arch: x64
           os: ubuntu-latest
       - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
       - name: Configure doc environment
         shell: julia --project=docs --color=yes {0}
         run: |
           using Pkg
           Pkg.develop(PackageSpec(path=pwd()))
           Pkg.instantiate()
           Pkg.add(name="OpenSSL_jll", version="3.0")
-      - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-docdeploy@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/CompatHelper.yml

@@ -3,14 +3,42 @@ on:
   schedule:
     - cron: 0 0 * * *
   workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
       - name: CompatHelper.main()
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}

Project.toml

@@ -11,6 +11,7 @@ Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
 GNNGraphs = "aed8fd31-079b-4b5a-b342-a13352159b8c"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 InvertedIndices = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Lux = "b2108857-7c20-44ae-9111-449ecde12c47"
 MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54"
 NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
@@ -22,7 +23,8 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
-julia = ">= 1.10.0"
+LinearAlgebra = ">= 1.10.0"
 Reactant = ">= 0.2.0"
+SimpleDirectedHypergraphs = "0.1.0"
 SimpleHypergraphs = "0.3.0"
-SimpleDirectedHypergraphs = "0.1.0" 
+julia = ">= 1.10.0"

src/HyperGraphNeuralNetworks.jl

@@ -3,11 +3,12 @@ module HyperGraphNeuralNetworks
 using Random
 using DataStructures: counter
 using StatsBase: FrequencyWeights, sample
+using LinearAlgebra
+using InvertedIndices
 using Graphs
 using GNNGraphs
 import GNNGraphs: getn, getdata, normalize_graphdata, cat_features, shortsummary
 using MLUtils
-using InvertedIndices
 using SimpleHypergraphs
 using SimpleDirectedHypergraphs
 
@@ -27,22 +28,26 @@ include("core/query.jl")
 
 export hyperedge_index, get_hyperedge_weight, get_hyperedge_weights
 export has_vertex, vertices, isolated_vertices
-export degree, indegree, outdegree
-export all_neighbors, in_neighbors, out_neighbors, hyperedge_neighbors
-export incidence_matrix, complex_incidence_matrix, hyperedge_weight_matrix, vertex_weight_matrix
-export normalized_laplacian
-export hypergraph_ids, has_self_loops, has_multi_hyperedges
+export hyperedge_neighbors
+export hyperedge_weight_matrix, hyperedge_degree_matrix, vertex_weight_matrix, vertex_degree_matrix
+export complex_incidence_matrix, normalized_laplacian_matrix
+export hypergraph_ids, has_multi_hyperedges
 
 include("core/transform.jl")
 
 export add_self_loops, remove_self_loops, remove_multi_hyperedges
 export rewire_hyperedges, to_undirected
-export combine_hypergraphs, get_hypergraph, negative_sample
-export random_split_vertices, random_split_hyperedges
+export combine_hypergraphs, get_hypergraph
+export AbstractNegativeSamplingStrategy, UniformSample, SizedSample, MotifSample, CliqueSample, negative_sample_hyperedge
+
+include("core/split.jl")
+
+export split_vertices, split_hyperedges, split_hypergraphs
+export random_split_vertices, random_split_hyperedges, random_split_hypergraphs
 
 include("core/utils.jl")
 
 export check_num_vertices, check_num_hyperedges
 export normalize_graphdata
 
-end
+end

src/core/generate.jl

@@ -17,7 +17,7 @@
         kws...
     ) where {H <: AbstractHGNNDiHypergraph}
 
-    Generate a *random* undirected hypergraph (in the style of Erdős–Rényi random graphs) without any structural
+    Generate a *random* hypergraph (in the style of Erdős–Rényi random graphs) without any structural
     constraints. See `SimpleHypergraphs.random_model`. The user can optionally seed the random number
     generator with kwarg `seed`. The default value is -1; if the value is greater than or equal to 0, then `seed` will
     be used.
@@ -30,7 +30,7 @@ function erdos_renyi_hypergraph(
     kws...
 ) where {H <: AbstractHGNNHypergraph}
     if seed >= 0
-        seed!(seed)
+        Random.seed!(seed)
     end
 
     basic = random_model(nVertices, nEdges, Hypergraph)
@@ -47,7 +47,7 @@ function erdos_renyi_hypergraph(
     kws...
 ) where {H <: AbstractHGNNDiHypergraph}
     if seed >= 0
-        seed!(seed)
+        Random.seed!(seed)
     end
 
     basic = random_model(
@@ -94,7 +94,7 @@ function random_kuniform_hypergraph(
     kws...
 ) where {H <: AbstractHGNNHypergraph}
     if seed >= 0
-        seed!(seed)
+        Random.seed!(seed)
     end
 
     kuniform = random_kuniform_model(nVertices, nEdges, k, Hypergraph)
@@ -112,7 +112,7 @@ function random_kuniform_hypergraph(
     kws...
 ) where {H <: AbstractHGNNDiHypergraph}
     if seed >= 0
-        seed!(seed)
+        Random.seed!(seed)
     end
 
     kuniform = random_kuniform_model(
@@ -159,7 +159,7 @@ function random_dregular_hypergraph(
     kws...
 ) where {H <: AbstractHGNNHypergraph}
     if seed >= 0
-        seed!(seed)
+        Random.seed!(seed)
     end
 
     dregular = random_dregular_model(nVertices, nEdges, d, Hypergraph)
@@ -177,7 +177,7 @@ function random_dregular_hypergraph(
     kws...
 ) where {H <: AbstractHGNNDiHypergraph}
     if seed >= 0
-        seed!(seed)
+        Random.seed!(seed)
     end
 
     dregular = random_dregular_model(
@@ -214,11 +214,11 @@ function random_preferential_hypergraph(
     HType::Type{HO};
     seed::Int = -1,
     HTypeStart::Type{HI} = Hypergraph,
-    hg::HI = random_model(5,5, HI),
+    hg::HI = random_model(5,5, HTypeStart),
     kws...
 ) where {HI<:AbstractSimpleHypergraph, HO<:AbstractHGNNHypergraph}
     if seed >= 0
-        seed!(seed)
+        Random.seed!(seed)
     end
 
     pref_hg = random_preferential_model(