Merge pull request #204 from ReactiveBayes/dev-4.0.0

GraphPPL version 4.0.0

Author: bvdmitri

.JuliaFormatter.toml

@@ -0,0 +1,26 @@
+style = "blue"
+indent = 4
+margin = 140
+always_for_in = true
+whitespace_typedefs = true
+whitespace_ops_in_indices = true
+remove_extra_newlines = true
+import_to_using = false
+pipe_to_function_call = false
+short_to_long_function_def = false 
+long_to_short_function_def = false
+always_use_return = false
+whitespace_in_kwargs = true
+annotate_untyped_fields_with_any = false 
+format_docstrings = false
+conditional_to_if = true
+trailing_comma = false
+indent_submodule = false
+align_assignment = true
+align_struct_field = true
+align_conditional = true
+align_pair_arrow = true
+align_matrix = false
+join_lines_based_on_source = false
+separate_kwargs_with_semicolon = false
+surround_whereop_typeparameters = true

.github/codecov.yml

@@ -0,0 +1,3 @@
+ignore:
+  - "src/old/"
+  - "ext/"

.github/workflows/CompatHelper.yml

@@ -1,16 +1,45 @@
 name: CompatHelper
 on:
   schedule:
-    - cron: '00 00 * * *'
+    - 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: CompatHelper.main()
+      - 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@v1
+        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: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}  # optional
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/ci.yml

@@ -19,11 +19,8 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
-          - '1.7'
-          - '1.8'
-          - '1.9'
           - '1.10'
+          - 'nightly'
         os:
           - ubuntu-latest
         arch:
@@ -36,27 +33,22 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+      - 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:
-          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
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     needs: test
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
-        with:
-          version: '1.10'
+      - 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

@@ -33,7 +33,8 @@ demo/*wip.ipynb
 demo/*.jl
 
 .idea
-.vscode
+.vscode/
+
 
 **/*.aux
 **/*.log
@@ -46,5 +47,10 @@ Coverage.ipynb
 
 **/.DS_Store
 
+benchmark/tune.json
+benchmark_*md
+
 examples/*Compiled
 statprof
+profile.pb.gz
+.swp

Makefile

@@ -0,0 +1,20 @@
+scripts_init:
+	julia --startup-file=no --project=scripts/ -e 'using Pkg; Pkg.instantiate(); Pkg.update(); Pkg.precompile();'
+
+project_init:
+	julia --startup-file=no --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.update(); Pkg.precompile();'
+
+lint: scripts_init ## Code formating check
+	julia --startup-file=no --project=scripts/ scripts/format.jl
+
+format: scripts_init ## Code formating run
+	julia --startup-file=no --project=scripts/ scripts/format.jl --overwrite
+
+bench: ## Run benchmark, use `make bench branch=...` to test against a specific branch
+	julia --startup-file=no --project=scripts/ scripts/bench.jl $(branch)
+
+doc_init:
+	julia --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate();'
+
+docs: doc_init ## Generate documentation
+	julia --project=docs/ docs/make.jl

Project.toml

@@ -1,20 +1,48 @@
 name = "GraphPPL"
 uuid = "b3f8163a-e979-4e85-b43e-1f63d8c8b42c"
-authors = ["Dmitry Bagaev <bvdmitri@gmail.com>"]
-version = "3.1.0"
+authors = ["Wouter Nuijten <wouternuijten@gmail.com>", "Dmitry Bagaev <bvdmitri@gmail.com>"]
+version = "4.0.0"
 
 [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"
+MetaGraphsNext = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
+NamedTupleTools = "d9ec5142-1e00-5aa0-9d6a-321866360f50"
+Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 TupleTools = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6"
+Unrolled = "9602ed7d-8fef-5bc8-8597-8f21381861e8"
+
+[weakdeps]
+Cairo = "159f3aea-2a34-519c-b102-8c37f9878175"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+GraphPlot = "a2cc645c-3eea-5389-862e-a155d0052231"
+
+[extensions]
+GraphPPLDistributionsExt = "Distributions"
+GraphPPLPlottingExt = ["Cairo", "GraphPlot"]
 
 [compat]
-MacroTools = "0.5.6"
-TupleTools = "1.2.0"
+BitSetTuples = "1.1"
+Cairo = "1.0"
+DataStructures = "0.18"
+Dictionaries = "0.4"
+Distributions = "0.25"
+Documenter = "1.0"
+GraphPlot = "0.5"
+MacroTools = "0.5"
+MetaGraphsNext = "0.6, 0.7"
+NamedTupleTools = "0.14"
+Static = "0.8"
+StaticArrays = "1.6"
+TupleTools = "1.4"
+Unrolled = "0.1"
 julia = "1.6"
 
 [extras]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "Documenter"]
+test = ["Documenter"]

README.md

@@ -13,12 +13,46 @@
 [ci-img]: https://github.com/reactivebayes/GraphPPL.jl/actions/workflows/ci.yml/badge.svg?branch=master
 [ci-url]: https://github.com/reactivebayes/GraphPPL.jl/actions
 
-GraphPPL.jl is a probabilistic programming language focused on probabilistic graphical models. This repository is aimed for advanced users, please refer to the [ReactiveMP.jl](https://github.com/reactivebayes/ReactiveMP.jl) repository for more comprehensive and self-contained documentation and usages examples.
+GraphPPL.jl is a probabilistic programming language focused on probabilistic graphical models. GraphPPL.jl materializes a probabilistic model as a factor graph and provides a set of tools for model specification. GraphPPL.jl is a part of the [RxInfer](https://rxinfer.ml) ecosystem, but it does not explicitly depend on any inference backend. GraphPPL exports a high-level DSL for model specification and allows users to append arbitrary information to nodes in the model. This information can be used by inference backends to perform inference on the model.
+
+## Installation
+
+To install GraphPPL.jl, you can use the Julia package manager. From the Julia REPL, type `]` to enter the Pkg REPL mode and run:
+
+```julia
+pkg> add GraphPPL
+```
+
+# Model Specification in GraphPPL
+
+GraphPPL.jl provides a high-level DSL for model specification. The DSL is based on the [Julia's](https://julialang.org) macro system and allows users to specify probabilistic models in a concise and intuitive way. The DSL is based on the following principles:
+
+- **Model specification should read as a Julia program**. GraphPPL.jl introduces the `~` syntax for model specification. 
+- **Any GraphPPL model is a valid submodel**. GraphPPL.jl allows users to specify models as a composition of submodels. This allows users to reuse models and specify complex models in a modular way.
+- **Model specification should be extensible**. GraphPPL.jl allows users to extend the DSL with custom model specification procedures. This allows developers of inference backend to inject desired behavior to the model specification process.
+
+To achieve tihs, GraphPPL.jl specifies a protocol for the `@model` macro:
+```julia
+@model function beta_bernoulli(x)
+    θ ~ Beta(1, 1)
+    for i in eachindex(x)
+        x[i] ~ Bernoulli(θ)
+    end
+end
+```
 
 # Inference Backend
 
-GraphPPL.jl does not export any Bayesian inference backend. It provides a simple DSL parser, model generation, constraints specification and meta specification helpers. To run inference on 
-generated models user needs to have a Bayesian inference backend with GraphPPL.jl support (e.g. [ReactiveMP.jl](https://github.com/reactivebayes/ReactiveMP.jl)). 
+GraphPPL.jl does not export any Bayesian inference backend. It provides a complex DSL parser, model generation, constraints specification and meta specification helpers. To run inference on 
+generated models a user needs to have a Bayesian inference backend with GraphPPL.jl support (e.g. [RxInfer.jl](https://rxinfer.ml)). 
+
+# Documentation
+
+For more information about GraphPPL.jl please refer to the [documentation](https://biaslab.github.io/GraphPPL.jl/stable).
+
+> [!NOTE]
+> `GraphPPL.jl` API has been changed in version `4.0.0`. See [Migration Guide](https://reactivebayes.github.io/GraphPPL.jl/stable/) for more details.
+
 
 # License
 

benchmark/benchmarks.jl

@@ -0,0 +1,9 @@
+using BenchmarkTools
+
+const SUITE = BenchmarkGroup()
+
+include("graph_engine.jl")
+include("model_creation.jl")
+
+SUITE["graph_engine"] = benchmark_graph_engine()
+SUITE["model_creation"] = benchmark_model_creation()

benchmark/graph_engine.jl

@@ -0,0 +1,88 @@
+using BenchmarkTools
+using GraphPPL
+
+function benchmark_graph_engine()
+    SUITE = BenchmarkGroup(["graph_creation"])
+
+    # Benchmark how long it takes to create a model structure
+    SUITE["create_model"] = @benchmarkable GraphPPL.Model(identity, GraphPPL.PluginsCollection(), GraphPPL.DefaultBackend()) evals = 1
+
+    # Benchmark how long it takes to get the context of a model
+    SUITE["getcontext"] = @benchmarkable GraphPPL.getcontext(model) evals = 1 setup = begin
+        model = GraphPPL.Model(identity, GraphPPL.PluginsCollection(), GraphPPL.DefaultBackend())
+    end
+
+    # Benchmark how long it takes to create a factor node
+    SUITE["factor_node_creation"] = benchmark_factor_node_creation()
+
+    # Benchmark how long it takes to get or create a variable node
+    SUITE["variable_node_creation"] = benchmark_variable_node_creation()
+
+    return SUITE
+end
+
+# Benchmark how long it takes to create a factor node
+function benchmark_factor_node_creation()
+    SUITE = BenchmarkGroup()
+
+    # This SUITE benchmarks how long it takes to create a factor node `$f` with `n` variables as input
+    for f in (sum,), n in Int.(exp10.(0:4))
+        SUITE["make_node! (n inputs)", f, n] = @benchmarkable GraphPPL.make_node!(model, ctx, $f, y, (in = x,)) evals =
+            1 setup = begin
+            model = GraphPPL.Model(identity, GraphPPL.PluginsCollection(), GraphPPL.DefaultBackend())
+            ctx = GraphPPL.getcontext(model)
+            y = GraphPPL.getorcreate!(model, ctx, :y, nothing)
+            foreach(1:($n)) do i
+                GraphPPL.getorcreate!(model, ctx, :x, i)
+            end
+            x = GraphPPL.getorcreate!(model, ctx, :x, 1)
+        end
+    end
+
+    # This SUITE benchmarks how long it takes to create `n` factor nodes with the same variable as input
+    for f in (sum,), n in Int.(exp10.(0:4))
+        SUITE["make_node! (n nodes)", f, n] = @benchmarkable foreach(
+            _ -> GraphPPL.make_node!(model, ctx, $f, y, (in = x,)), 1:($n)
+        ) evals = 1 setup = begin
+            model = GraphPPL.Model(identity, GraphPPL.PluginsCollection(), GraphPPL.DefaultBackend())
+            ctx = GraphPPL.getcontext(model)
+            y = GraphPPL.getorcreate!(model, ctx, :y, nothing)
+            x = GraphPPL.getorcreate!(model, ctx, :x, nothing)
+        end
+    end
+
+    return SUITE
+end
+
+function benchmark_variable_node_creation()
+    SUITE = BenchmarkGroup()
+
+    # This SUITE benchmarks how long it takes to create a single variable node
+    SUITE["getorcreate! (individual)"] = @benchmarkable GraphPPL.getorcreate!(model, ctx, :x, nothing) evals = 1 setup =
+        begin
+            model = GraphPPL.Model(identity, GraphPPL.PluginsCollection(), GraphPPL.DefaultBackend())
+            ctx = GraphPPL.getcontext(model)
+        end
+
+    # This SUITE benchmarks how long it takes to add `n` individual variable nodes
+    for n in Int.(exp10.(0:4))
+        SUITE["getorcreate! (n individual)", n] = @benchmarkable foreach(
+            _ -> GraphPPL.getorcreate!(model, ctx, :x, nothing), 1:($n)
+        ) evals = 1 setup = begin
+            model = GraphPPL.Model(identity, GraphPPL.PluginsCollection(), GraphPPL.DefaultBackend())
+            ctx = GraphPPL.getcontext(model)
+        end
+    end
+
+    # THIS SUITE benchmarks how long it takes to add vector based bariables of size `n`
+    for n in Int.(exp10.(0:4))
+        SUITE["getorcreate! (n vector)", n] = @benchmarkable foreach(
+            i -> GraphPPL.getorcreate!(model, ctx, :x, i), 1:($n)
+        ) evals = 1 setup = begin
+            model = GraphPPL.Model(identity, GraphPPL.PluginsCollection(), GraphPPL.DefaultBackend())
+            ctx = GraphPPL.getcontext(model)
+        end
+    end
+
+    return SUITE
+end