Bump-deps

.gitignore

@@ -15,3 +15,7 @@
 
 .ipynb_checkpoints
 .ipynb_checkpoints/*
+
+.CondaPkg
+
+.DS_Store

CondaPkg.toml

@@ -0,0 +1,8 @@
+[deps]
+networkx = ""
+matplotlib = ""
+pandas = "<2.3"
+
+[pip.deps]
+hypernetx = ">=2.4.0,<3"
+fastjsonschema = ""

Project.toml

@@ -1,31 +1,31 @@
 name = "SimpleHypergraphs"
 uuid = "aa4a32ff-dd5d-5357-90e3-e7a9512f0501"
-version = "0.3.4"
-authors = ["Przemysław Szufel <pszufe@sgh.waw.pl>", "Bogumił Kamiński <bkamins@sgh.waw.pl>", "Carmine Spagnuolo <spagnuolocarmine@gmail.com>", "Alessia Antelmi <aless.antelmi@gmail.com>", "Evan Walter Clark Spotte-Smith <espottesmith@gmail.com>"]
+authors = ["Przemysław Szufel <pszufe@sgh.waw.pl>", "Bogumił Kamiński <bkamins@sgh.waw.pl>", "Carmine Spagnuolo <spagnuolocarmine@gmail.com>", "Alessia Antelmi <aless.antelmi@gmail.com>", "Evan Walter Clark Spotte-Smith <espottesmith@gmail.com>", "Daniele De Vinco <ddevinco@unisa.it>"]
+version = "0.4.0"
 
 [deps]
-Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
+CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
-PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
+PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
+PythonPlot = "274fc56d-3b97-40fa-a1cd-1b4a50311bf9"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SimpleTraits = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
 
 [compat]
-Conda = "^1.5.0"
+CondaPkg = "^0.2"
 DataFrames = "^1.7.0"
 DataStructures = "^0.18.11, ^0.19.1"
 Graphs = "^1.4.1"
-JSON = "^1.0.0"
-PyCall = "^1.91.2"
-PyPlot = "^2.8.2"
+JSON = "^1.3.0"
+PythonCall = "^0.9"
+PythonPlot = "^1.0"
 SimpleTraits = "^0.9.4"
 SparseArrays = "^1.0.0"
 StatsBase = "^0.34.0"

src/SimpleHypergraphs.jl

@@ -4,9 +4,9 @@ using Graphs
 using StatsBase
 using DataStructures
 using DataFrames
-using PyCall
-using Conda
-using PyPlot
+using PythonCall
+using CondaPkg
+using PythonPlot
 using JSON
 using Random
 using LinearAlgebra
@@ -48,28 +48,37 @@ export distance
 export HyperNetX, GraphBased
 export draw
 
-const hnx  = PyNULL()
-const nx = PyNULL()
+const hnx = Ref{Py}()
+const nx = Ref{Py}()
+const pyplot = Ref{Py}()
 const has_plotting = Ref(false)
 
 
 function __init__()
     has_networkx = false
     has_hypernetx = false
+    has_pyplot = false
     try
-        copy!(nx, pyimport("networkx"))
+        nx[] = pyimport("networkx")
         has_networkx = true
     catch e; end
     try
-        copy!(hnx, pyimport("hypernetx"))
+        hnx[] = pyimport("hypernetx")
         has_hypernetx = true
     catch e; end
-    has_plotting[] = has_networkx && has_hypernetx
+    try
+        pyplot[] = pyimport("matplotlib.pyplot")
+        has_pyplot = true
+    catch e; end
+    has_plotting[] = has_networkx && has_hypernetx && has_pyplot
     if !has_plotting[]
         @warn "The plotting functionality of HyperNetX will not work!\n"* 
-		(has_networkx ? "" : "Conda Python networkx not found.\n")*
-        (has_hypernetx ? "" : "Conda Python HyperNetX not found.\n")*        
-        "To test your installation try running `using PyCall;pyimport(\"networkx\");pyimport(\"hypernetx\")`"
+		(has_networkx ? "" : "CondaPkg Python networkx not found.\n")*
+        (has_hypernetx ? "" : "CondaPkg Python HyperNetX not found.\n")*
+        (has_pyplot ? "" : "CondaPkg Python matplotlib.pyplot not found.\n")*        
+        "To test your installation try running `using PythonCall;pyimport(\"networkx\");pyimport(\"hypernetx\");pyimport(\"matplotlib.pyplot\")`"
+    else
+        @info "HyperNetX plotting support loaded successfully"
     end
 end
 

src/io.jl

@@ -226,7 +226,7 @@ function hg_load(
         json_hg.he_meta = JSON.parse(json_hg.he_meta)
     end
     m = reshape(Vector{Union{T, Nothing}}(json_hg.m), json_hg.n, json_hg.k)
-    
+
     V2 = (V == :auto) ? ("v_meta" ∈ keys(json_hg) && length(json_hg.v_meta) > 0 ? elemtypes(json_hg.v_meta) : Nothing) : V
     E2 = (E == :auto) ? ("he_meta" ∈ keys(json_hg) && length(json_hg.he_meta) > 0 ? elemtypes(json_hg.he_meta) : Nothing) : E
 
@@ -253,9 +253,12 @@ end
         format::Abstract_HG_format = HGF_Format(),
         HType::Type{H} = Hypergraph,
         T::Type{U} = Bool,
-        D::Type{<:AbstractDict{Int, U}} = Dict{Int, T},
         V = Nothing,
-        E = Nothing
+        E = Nothing,
+        D::Type{<:AbstractDict{Int, U}} = Dict{Int, T}, 
+        show_warning::Bool=true,
+        sort_by_id::Bool=false,
+        add_original_id_to_meta::Union{Symbol, Nothing}=nothing
     ) where {U <: Real, H <: AbstractSimpleHypergraph}
 
 Loads a hypergraph from a file `fname`.

src/viz/drawing.jl

@@ -156,9 +156,9 @@ end
         with_color::Bool=true,
         with_node_counts::Bool=false,
         with_edge_counts::Bool=false,
-        layout::PyObject=nx.spring_layout,
+        layout::Py=nx[],
         layout_kwargs::Dict=Dict{String, Any}(),
-        ax::Union{PyObject, Nothing}=nothing,
+        ax::Union{Py, Nothing}=nothing,
         no_border::Bool=false,
         edges_kwargs::Dict=Dict{String, Any}(),
         nodes_kwargs::Dict=Dict{String, Any}(),
@@ -194,21 +194,20 @@ function draw(
         edge_labels::Union{Dict{Int, String}, Nothing}=nothing,
         collapse_nodes::Bool=false,
         collapse_edges::Bool=false,
+        node_radius::Union{Int, Nothing}=nothing,
         pos::Union{Dict{Int,Pair{Int,Int}}, Nothing}=nothing,
-        with_color::Bool=true,
-        with_node_counts::Bool=false,
-        with_edge_counts::Bool=false,
-        layout::PyObject=nx.spring_layout,
+        layout::Py=nx[].spring_layout,
         layout_kwargs::Dict=Dict{String, Any}(),
-        ax::Union{PyObject, Nothing}=nothing,
+        ax::Union{Py, Nothing}=nothing,
         no_border::Bool=false,
         edges_kwargs::Dict=Dict{String, Any}(),
         nodes_kwargs::Dict=Dict{String, Any}(),
         edge_labels_kwargs::Dict=Dict{String, Any}(),
         node_labels_kwargs::Dict=Dict{String, Any}(),
         with_edge_labels::Bool=true,
         with_node_labels::Bool=true,
-        label_alpha::Float64=.35
+        node_label_alpha::Float64=.35,
+        edge_label_alpha::Float64=.35
         ) where {H<:AbstractSimpleHypergraph}
     if (!SimpleHypergraphs.support_hypernetx())
         throw("HyperNetX is not installed in Python used by this Julia. Install HyperNetX and reload SimpleHypergraphs.jl")
@@ -227,30 +226,31 @@ function draw(
     end
 
     if ax === nothing #isnothing(ax)
-        fig = plt.figure(figsize=[width,height])
-        ax = plt.gca()
+        fig = pyplot[].figure(figsize=[width,height])
+        ax = pyplot[].gca()
 
         if no_border
             ax.axis("off")
         end
     end
 
-    hnx.draw(h_hnx,
+    hnx[].draw(h_hnx,
         pos=pos,
-        with_color=with_color,
-        with_node_counts=with_node_counts,
-        with_edge_counts=with_edge_counts,
         layout=layout,
         layout_kwargs=layout_kwargs,
         ax=ax,
+        node_radius=node_radius,
         edges_kwargs=edges_kwargs,
         nodes_kwargs=nodes_kwargs,
         edge_labels_kwargs=edge_labels_kwargs,
         node_labels_kwargs=node_labels_kwargs,
         with_edge_labels=with_edge_labels,
         with_node_labels=with_node_labels,
-        label_alpha=label_alpha
+        node_label_alpha=node_label_alpha,
+        edge_label_alpha=edge_label_alpha
     )
+
+    return pyplot[].gcf()
 end
 
 
@@ -271,23 +271,28 @@ function _convert_to_hnx(h::Hypergraph;
         node_labels::Union{Dict{Int, String}, Nothing}=nothing,
         edge_labels::Union{Dict{Int, String}, Nothing}=nothing,
         )
-    h_hnx = hnx.Hypergraph()
+    pybuiltins = pyimport("builtins")
+    edges_dict = pybuiltins.dict()
 
     for he=1:nhe(h)
-        if node_labels === nothing #isnothing(node_labels)
-            vertices = collect(keys(getvertices(h, he)))
+        vertices = collect(keys(getvertices(h, he)))
+
+        if node_labels === nothing
+            vertices = [string(v) for v in vertices]
         else
-            vertices = [get(node_labels, v, v) for v in collect(keys(getvertices(h, he)))]
+            vertices = [get(node_labels, v, string(v)) for v in vertices]
         end
-
-        if edge_labels === nothing #isnothing(edge_labels)
-            he_hnx = hnx.Entity(string(he), elements=vertices)
+        
+        edge_label = if edge_labels === nothing
+            string(he)
         else
-            he_hnx = hnx.Entity(get(edge_labels, he, string(he)), elements=vertices)
+            get(edge_labels, he, string(he))
         end
-
-        h_hnx.add_edge(he_hnx)
+        
+        edges_dict[edge_label] = pybuiltins.list(vertices)
     end
-
+
+    h_hnx = hnx[].Hypergraph(edges_dict)
+
     h_hnx
 end

test/hif-standard-tests.jl

@@ -69,6 +69,121 @@ end
     end
 end
 
+
+@testset "Tutorials JSON Data          " begin
+    pth = joinpath(dirname(dirname(pathof(SimpleHypergraphs))), "tutorials", "basics", "data");
+    pth2 = joinpath(dirname(dirname(pathof(SimpleHypergraphs))), "tutorials", "hif-standard", "data");
+    files = String[]
+    for (root, dirs, filenames) in walkdir(pth)
+        for file in filenames
+            if endswith(file, ".json")
+                if contains(file, "hif.json")
+                    continue
+                end
+                push!(files, joinpath(root, file))
+            end
+        end
+    end
+    for (root, dirs, filenames) in walkdir(pth2)
+        for file in filenames
+            if endswith(file, ".json")
+                if contains(file, "hif.json")
+                    continue
+                end
+                push!(files, joinpath(root, file))
+            end
+        end
+    end
+    for file in files
+        println("Testing tutorials JSON file: $(basename(file))")
+
+        flush(stdout)
+        flush(stderr)
+        if !endswith(file, "hg_seasons_min.json")
+            loaded_hg = hg_load(file; format=JSON_Format(), HType=Hypergraph, T=Bool, V=Symbol, E=Symbol)
+        else 
+            loaded_hg = hg_load(file; format=JSON_Format(), HType=Hypergraph, T=Int, V=Symbol, E=Symbol)
+        end
+        io_h = IOBuffer()
+        hg_save(io_h, loaded_hg, JSON_Format(); pretty=true)
+        if !endswith(file, "hg_seasons_min.json")
+            h_loaded = hg_load(seekstart(io_h), JSON_Format(); HType=Hypergraph, T=Bool, V=Symbol, E=Symbol)
+        else 
+            h_loaded = hg_load(seekstart(io_h), JSON_Format(); HType=Hypergraph, T=Int, V=Symbol, E=Symbol)
+        end
+        @test loaded_hg == h_loaded
+    end
+
+end;
+
+@testset "Tutorials as HIF Data          " begin
+    pth = joinpath(dirname(dirname(pathof(SimpleHypergraphs))), "tutorials", "basics", "data");
+    pth2 = joinpath(dirname(dirname(pathof(SimpleHypergraphs))), "tutorials", "hif-standard", "data");
+    files = String[]
+    for (root, dirs, filenames) in walkdir(pth)
+        for file in filenames
+            if endswith(file, "hif.json")
+                push!(files, joinpath(root, file))
+            end
+        end
+    end
+    for (root, dirs, filenames) in walkdir(pth2)
+        for file in filenames
+            if endswith(file, "hif.json")
+                push!(files, joinpath(root, file))
+            end
+        end
+    end
+    for file in files
+        println("Testing tutorials as HIF file: $(basename(file))")
+        flush(stdout)
+        flush(stderr)
+        if !endswith(file, "hg_seasons_min.json")
+            loaded_hg = hg_load(
+                    file;
+                    format=HIF_Format(),
+                    HType=Hypergraph,
+                    T=Bool, V=:auto, E=:auto
+                )
+        else 
+            loaded_hg = hg_load(
+                    file;
+                    format=HIF_Format(),
+                    HType=Hypergraph,
+                    T=Int, V=:auto, E=:auto
+                )
+        end
+        io_h = IOBuffer()
+        hg_save(io_h, loaded_hg, HIF_Format(); pretty=true)
+
+        if !endswith(file, "hg_seasons_min.json")
+            h_loaded = hg_load(seekstart(io_h), HIF_Format(); HType=Hypergraph, T=Bool, V=:auto, E=:auto)
+        else 
+            h_loaded = hg_load(seekstart(io_h), HIF_Format(); HType=Hypergraph, T=Int, V=:auto, E=:auto)
+        end
+
+        @test loaded_hg == h_loaded
+    end
+
+end;
+
+@testset "JSON and HIF correct load test" begin
+    path = joinpath(dirname(dirname(pathof(SimpleHypergraphs))), "tutorials", "basics", "data", "hg_seasons_min.json");
+
+    h1 = SimpleHypergraphs.hg_load(
+        path; format=JSON_Format(), HType=Hypergraph, T=Int, V=:auto, E=:auto
+    )
+
+    @test nhv(h1) == 149
+    @test nhe(h1) == 8
+
+    pth_hif = joinpath(dirname(dirname(pathof(SimpleHypergraphs))), "tutorials", "basics", "data", "hg_seasons_min.hif.json")
+    h2 = SimpleHypergraphs.hg_load(pth_hif; format=HIF_Format(), T=Int, V=:auto, E=:auto)
+
+    @test nhv(h2) == 149
+    @test nhe(h2) == 8 
+end
+
 #==
 using Revise
 using SimpleHypergraphs