Add plugins to 4.0 branch

.JuliaFormatter.toml

@@ -1,6 +1,6 @@
 style = "blue"
 indent = 4
-margin = 180
+margin = 140
 always_for_in = true
 whitespace_typedefs = true
 whitespace_ops_in_indices = true

.github/workflows/ci.yml

@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.9'
+          - '1.10'
           - 'nightly'
         os:
           - ubuntu-latest
@@ -33,18 +33,9 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-runtest@latest
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v3
         env:
@@ -56,8 +47,8 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
-        with:
-          version: '1.9'
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

.gitignore

@@ -48,3 +48,4 @@ Coverage.ipynb
 
 examples/*Compiled
 statprof
+profile.pb.gz

Project.toml

@@ -6,6 +6,7 @@ version = "3.1.0"
 [deps]
 BitSetTuples = "0f2f92aa-23a3-4d05-b791-88071d064721"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+Dictionaries = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73"
 MetaGraphsNext = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
@@ -30,6 +31,7 @@ BitSetTuples = "1"
 Cairo = "1.0"
 Compose = "0.9"
 DataStructures = "0.18"
+Dictionaries = "0.4"
 Distributions = "0.25"
 Documenter = "1.0"
 GraphPlot = "0.5"

benchmark/benchmarks.jl

@@ -3,7 +3,7 @@ using BenchmarkTools
 const SUITE = BenchmarkGroup()
 include("graph_engine.jl")
 include("model_creation.jl")
-include("constraints_engine.jl")
-SUITE["constraints_engine"] = benchmark_constraints_engine()
+# include("constraints_engine.jl")
+# SUITE["constraints_engine"] = benchmark_constraints_engine()
 SUITE["graph_engine"] = benchmark_graph_engine()
 SUITE["model_creation"] = benchmark_model_creation()

benchmark/graph_engine.jl

@@ -20,14 +20,14 @@ function factor_node_creation()
             x = GraphPPL.getorcreate!(model, ctx, :x, j)
         end
         y = GraphPPL.getorcreate!(model, ctx, :y, nothing)
-        SUITE["Create factor node with $i edges"] = @benchmarkable GraphPPL.make_node!(m, c, sum, $y, [$x]) setup=(m=deepcopy($model);c=deepcopy($ctx)) evals=1
+        SUITE["Create factor node with $i edges"] = @benchmarkable GraphPPL.make_node!(m, c, sum, $y, (in = $x,)) setup=(m=deepcopy($model);c=deepcopy($ctx)) evals=1
     end
     return SUITE
 end
 
 function add_n_nodes(n::Int, model, ctx)
     for i in 1:n
-        GraphPPL.add_variable_node!(model, ctx, :x; index=i)
+        GraphPPL.add_variable_node!(model, ctx, :x, i)
     end
 end
 
@@ -43,14 +43,13 @@ function variable_node_creation()
     SUITE = BenchmarkGroup(["node_creation"])
     model = GraphPPL.create_model()
     ctx = GraphPPL.getcontext(model)
-    SUITE["add_variable_node"] = @benchmarkable GraphPPL.add_variable_node!(m, c, :x) setup=(m=deepcopy($model);c=deepcopy($ctx)) evals=1
+    SUITE["add_variable_node"] = @benchmarkable GraphPPL.add_variable_node!(m, c, :x, nothing) setup=(m=deepcopy($model);c=deepcopy($ctx)) evals=1
 
     for j in 10 .^ range(1, stop=3)
         j = convert(Int, j)
         model = GraphPPL.create_model()
         ctx = GraphPPL.getcontext(model)
-        x = GraphPPL.ResizableArray(GraphPPL.NodeLabel, Val(1))
-        ctx.vector_variables[:x] = x
+        x = GraphPPL.getorcreate!(model, ctx, :x, 1)
         SUITE["add $j variable nodes"] = @benchmarkable add_n_nodes($j, m, c) setup=(m=deepcopy($model);c=deepcopy($ctx)) evals=1
         SUITE["getorcreate $j variable nodes ascending"] = @benchmarkable getorcreate_n_nodes($j, m, c) setup=(m=deepcopy($model);c=deepcopy($ctx)) evals=1
         SUITE["getorcreate $j variable nodes descending"] = @benchmarkable getorcreate_n_nodes($j, m, c; asc=false) setup=(m=deepcopy($model);c=deepcopy($ctx)) evals=1

benchmark/model_zoo.jl

@@ -22,12 +22,11 @@ function create_hgf(n::Int)
     ω = GraphPPL.getorcreate!(model, ctx, :ω, nothing)
     θ = GraphPPL.getorcreate!(model, ctx, :θ, nothing)
     x_begin = GraphPPL.getorcreate!(model, ctx, :x_begin, nothing)
-    GraphPPL.add_terminated_submodel!(
+    GraphPPL.add_toplevel_model!(
         model,
         ctx,
         hgf,
-        (κ = κ, ω = ω, θ = θ, x_begin = x_begin, depth = n);
-        __debug__ = false,
+        (κ = κ, ω = ω, θ = θ, x_begin = x_begin, depth = n)
     )
     return model
 end
@@ -58,7 +57,6 @@ function create_longarray(n::Int)
         ctx,
         long_array,
         (μ = μ, σ = σ, depth=n);
-        __debug__ = false,
     )
     return model
 end

docs/src/developers_guide.md

@@ -57,12 +57,11 @@ x = GraphPPL.getorcreate!(model, context, :x, nothing; options = GraphPPL.Variab
 y = GraphPPL.getorcreate!(model, context, :y, nothing; options = GraphPPL.VariableNodeOptions(datavar=true))
 
 # Add the gcv model
-GraphPPL.add_terminated_submodel!(
+GraphPPL.add_toplevel_model!(
         model,
         context,
         gcv,
         (κ = κ, ω = ω, z = z, x = x, y = y);
-        __debug__ = false,
     )
 
 # Apply the constraints

ext/GraphPPLDistributionsExt.jl

@@ -4,7 +4,7 @@ using GraphPPL, Distributions, Static
 
 GraphPPL.NodeBehaviour(::Type{<:Distributions.Distribution}) = GraphPPL.Stochastic()
 
-function GraphPPL.default_parametrization(::GraphPPL.Atomic, t::Type{<:Distributions.Distribution}, interface_values) 
+function GraphPPL.default_parametrization(::GraphPPL.Atomic, t::Type{<:Distributions.Distribution}, interface_values::Tuple) 
     return distributions_ext_default_parametrization(t, distributions_ext_input_interfaces(t), interface_values)
 end
 

src/GraphPPL.jl

@@ -3,13 +3,14 @@ module GraphPPL
 using MacroTools
 
 include("resizable_array.jl")
-include("indexedvariable.jl")
+include("plugins_collection.jl")
+
 include("graph_engine.jl")
 include("model_macro.jl")
-include("constraints_engine.jl")
-include("constraints_macro.jl")
-include("meta_engine.jl")
-include("meta_macro.jl")
+
+include("plugins/node_created_by.jl")
+include("plugins/variational_constraints/variational_constraints.jl")
+include("plugins/meta/meta.jl")
 
 include("old/old.jl")