Merge branch 'main' into make-formatting-a-separate-action

ReactiveBayes · Jan 6, 2025 · 1f55b93 · 1f55b93
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -95,6 +95,8 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1.10' # 1.11 is not supported by Cairo/GraphViz
       - uses: actions/cache@v3
         id: examples
         with:

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "RxInfer"
 uuid = "86711068-29c9-4ff7-b620-ae75d7495b3d"
 authors = ["Bagaev Dmitry <[email protected]> and contributors"]
-version = "3.7.1"
+version = "3.8.3"
 
 [deps]
 BayesBase = "b4ee3484-f114-42fe-b91c-797d54a0c67e"
@@ -36,13 +36,13 @@ DomainSets = "0.5.2, 0.6, 0.7"
 ExponentialFamily = "1.5"
 ExponentialFamilyProjection = "1.1"
 FastCholesky = "1.3.0"
-GraphPPL = "~4.3.0"
+GraphPPL = "~4.5.0"
 LinearAlgebra = "1.9"
 MacroTools = "0.5.6"
 Optim = "1.0.0"
 ProgressMeter = "1.0.0"
 Random = "1.9"
-ReactiveMP = "~4.4.1"
+ReactiveMP = "~4.4.4"
 Reexport = "1.2.0"
 Rocket = "1.8.0"
 Static = "0.8.10, 1"

diff --git a/README.md b/README.md
@@ -166,40 +166,49 @@ Our high-level project roadmap outlines the key milestones and focus areas for t
 
 | Q1/Q2 2024          | Q3/Q4 2024                | 2025                | 
 |---------------------|---------------------------|--------------------|
-| 🧩 **Nested models with [GraphPPL.jl](https://github.com/reactivebayes/GraphPPL.jl)** ✅    | 🌐 **Graph structure visualization** | 🔀 **Stochastic Processes** |
-| 🔄 **Development of [ExponentialFamilyProjection.jl]()** ✅                | 🧠 **Automated inference with [ExponentialFamilyProjection.jl](https://github.com/reactivebayes/ExponentialFamilyProjection.jl)** | 🚀 **Robustness & Memory-efficiency** |
+| 🧩 **Nested models with [GraphPPL.jl](https://github.com/reactivebayes/GraphPPL.jl)** ✅    | 🌐 **Graph structure visualization** ✅ | 🧠🧠 **Automated Inference** |
+| 🔄 **Development of [ExponentialFamilyProjection.jl]()** ✅                | 🧠 **Semi-automated inference with [ExponentialFamilyProjection.jl](https://github.com/reactivebayes/ExponentialFamilyProjection.jl)** ✅| 🚀 **Stochastic Processes** |
 
 For a more granular view of our progress and ongoing tasks, check out our [project board](https://github.com/orgs/reactivebayes/projects/2/views/4) or join our 4-weekly [public meetings](https://dynalist.io/d/F4aA-Z2c8X-M1iWTn9hY_ndN).
 
-# External Contributors
 
-RxInfer has benefited from the contributions and development efforts of external collaborators and organizations. We're grateful for their involvement in advancing the project.
+## Ecosystem
 
-## Active Inference Institute
+The `RxInfer` framework consists of three *core* packages developed by [ReactiveBayes](https://github.com/reactivebayes/):
 
-Members of the [Active Inference Institute](https://www.activeinference.org/) have been working on improving the visualization capabilities of RxInfer/GraphPPL. Their efforts focus on developing better model visualization capabilities, creating various summary/subgraph visualization modalities, implementing different graph layout algorithms, and improving the ability to inspect and understand models.
+- [`ReactiveMP.jl`](https://github.com/reactivebayes/ReactiveMP.jl) - the underlying message passing-based inference engine
+- [`GraphPPL.jl`](https://github.com/reactivebayes/GraphPPL.jl) - model and constraints specification package
+- [`Rocket.jl`](https://github.com/reactivebayes/Rocket.jl) - reactive extensions package for Julia 
 
-For more details on their ongoing work, see the [RxInfer development project board](https://coda.io/d/RxInfer-2024-Active-Inference-Institute_ddtS-XZ4BJb/Developing-RxInfer-jl_sufeCeIa#_lutfq_7F).
+# Where to go next?
 
-## Educational Content
+There are a set of [examples](https://reactivebayes.github.io/RxInfer.jl/stable/examples/overview/) available in `RxInfer` repository that demonstrate the more advanced features of the package. Alternatively, you can head to the [documentation](https://reactivebayes.github.io/RxInfer.jl/stable/) that provides more detailed information of how to use `RxInfer` to specify more complex probabilistic models.
 
-Educational content and tutorials related to RxInfer are being developed and can be found on [Learnable Loop](https://learnableloop.com/#category=RxInfer). These resources cover a range of topics including visualizing Forney Factor Graphs, sales forecasting with time-varying autoregressive models, hidden Markov models with control, and various applications of Active Inference across different domains.
 
-# Contributing
+# Join Our Community and Contribute to RxInfer
 
-We welcome contributions from the community. If you are interested in contributing to the development of `RxInfer.jl`, please check out our [contributing guide](https://reactivebayes.github.io/RxInfer.jl/stable/contributing/guide), the [contributing guidelines](https://reactivebayes.github.io/RxInfer.jl/stable/contributing/guidelines), or look at the [issues linked with the `good first issue` label](https://github.com/ReactiveBayes/RxInfer.jl/issues?q=is%3Aopen+is%3Aissue+label%3A%22good+first+issue%22) to get started.
+RxInfer is a community-driven project and we welcome all contributions! To get started:
+- Check out our [contributing guide](https://reactivebayes.github.io/RxInfer.jl/stable/contributing/guide)
+- Review the [contributing guidelines](https://reactivebayes.github.io/RxInfer.jl/stable/contributing/guidelines)
+- Browse [beginner-friendly issues](https://github.com/ReactiveBayes/RxInfer.jl/issues?q=is%3Aopen+is%3Aissue+label%3A%22good+first+issue%22) to find something that interests you
 
-# Where to go next?
+## Active Inference Institute Collaboration
 
-There are a set of [examples](https://reactivebayes.github.io/RxInfer.jl/stable/examples/overview/) available in `RxInfer` repository that demonstrate the more advanced features of the package. Alternatively, you can head to the [documentation](https://reactivebayes.github.io/RxInfer.jl/stable/) that provides more detailed information of how to use `RxInfer` to specify more complex probabilistic models.
+The [Active Inference Institute](https://www.activeinference.org/) community members are enhancing RxInfer/GraphPPL's visualization capabilities. Their work includes:
+- Developing advanced model visualization features ✅ ([PR](https://github.com/ReactiveBayes/GraphPPL.jl/pull/251))
+- Creating summary and subgraph visualization modalities
+- Implementing various graph layout algorithms
+- Improving model inspection and understanding tools
 
-## Ecosystem
+For more details on ongoing work, see the [RxInfer development project board](https://coda.io/d/RxInfer-2024-Active-Inference-Institute_ddtS-XZ4BJb/Developing-RxInfer-jl_sufeCeIa#_lutfq_7F).
 
-The `RxInfer` framework consists of three *core* packages developed by [ReactiveBayes](https://github.com/reactivebayes/):
+## Learning Resources
 
-- [`ReactiveMP.jl`](https://github.com/reactivebayes/ReactiveMP.jl) - the underlying message passing-based inference engine
-- [`GraphPPL.jl`](https://github.com/reactivebayes/GraphPPL.jl) - model and constraints specification package
-- [`Rocket.jl`](https://github.com/reactivebayes/Rocket.jl) - reactive extensions package for Julia 
+The community maintains educational content and tutorials on [Learnable Loop](https://learnableloop.com/#category=RxInfer), covering topics such as:
+- Visualizing Forney Factor Graphs
+- Sales forecasting with time-varying autoregressive models
+- Hidden Markov models with control
+- Applications of Active Inference across different domains
 
 ## JuliaCon 2023 presentation
 
@@ -217,6 +226,7 @@ Also check out the recorded presentation at the Julia User Group Munich meetup f
     <a href="https://www.youtube.com/watch?v=KuluqEzFtm8"><img style="width: 100%" src="https://img.youtube.com/vi/KuluqEzFtm8/0.jpg"></a>
 </p>
 
+
 # License
 
 [MIT License](LICENSE) Copyright (c) 2021-2024 BIASlab, 2024-present ReactiveBayes
diff --git a/codemeta.json b/codemeta.json
@@ -9,12 +9,12 @@
     "downloadUrl": "https://github.com/reactivebayes/RxInfer.jl/releases",
     "issueTracker": "https://github.com/reactivebayes/RxInfer.jl/issues",
     "name": "RxInfer.jl",
-    "version": "3.7.1",
+    "version": "3.8.3",
     "description": "Julia package for automated, scalable and efficient Bayesian inference on factor graphs with reactive message passing. ",
     "applicationCategory": "Statistics",
     "developmentStatus": "active",
     "readme": "https://reactivebayes.github.io/RxInfer.jl/stable/",
-    "softwareVersion": "3.7.1",
+    "softwareVersion": "3.8.3",
     "keywords": [
         "Bayesian inference",
         "message passing",

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -4,10 +4,12 @@ BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 Cairo = "159f3aea-2a34-519c-b102-8c37f9878175"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterMermaid = "a078cd44-4d9c-4618-b545-3ab9d77f9177"
 ExponentialFamily = "62312e5e-252a-4322-ace9-a5f4bf9b357b"
 ExponentialFamilyProjection = "17f509fa-9a96-44ba-99b2-1c5f01f0931b"
 GraphPPL = "b3f8163a-e979-4e85-b43e-1f63d8c8b42c"
 GraphPlot = "a2cc645c-3eea-5389-862e-a155d0052231"
+GraphViz = "f526b714-d49f-11e8-06ff-31ed36ee7ee0"
 Optimisers = "3bd65402-5787-11e9-1adc-39752487f4e2"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 ReactiveMP = "a194aa59-28ba-4574-a09c-4a745416d6e3"

diff --git a/docs/make.jl b/docs/make.jl
@@ -1,5 +1,6 @@
 using RxInfer
 using Documenter
+using DocumenterMermaid
 
 ## https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988
 ## https://gr-framework.org/workstations.html#no-output
@@ -69,10 +70,13 @@ foreach(vcat(ExamplesOverviewPath, ExamplesCategoriesOverviewPaths)) do path
         @warn "`$(path)` does not exist. Generating an empty overview. Use the `make examples` command to generate the overview and all examples."
         mkpath(dirname(path))
         open(path, "w") do f
-            write(f, """
-            $(isequal(path, ExamplesOverviewPath) ? "# [Examples overview](@id examples-overview)" : "")
-            The overview is missing. Use the `make examples` command to generate the overview and all examples.
-            """)
+            write(
+                f,
+                """
+       $(isequal(path, ExamplesOverviewPath) ? "# [Examples overview](@id examples-overview)" : "")
+       The overview is missing. Use the `make examples` command to generate the overview and all examples.
+       """
+            )
         end
     end
 end
@@ -82,8 +86,10 @@ ExamplesPages = map(collect(pairs(ExamplesCategoriesPages))) do (label, info)
     return info.title => info.pages
 end
 
+draft = get(ENV, "DOCS_DRAFT", "false") == "true"
+
 makedocs(;
-    draft = false,
+    draft = draft,
     warnonly = false,
     modules = [RxInfer],
     authors = "Bagaev Dmitry <[email protected]> and contributors",
@@ -105,22 +111,16 @@ makedocs(;
             "Model specification"       => "manuals/model-specification.md",
             "Constraints specification" => "manuals/constraints-specification.md",
             "Meta specification"        => "manuals/meta-specification.md",
-            "Inference specification"   => [
-                "Overview" => "manuals/inference/overview.md", 
-                "Static inference" => "manuals/inference/static.md", 
-                "Streamline inference" => "manuals/inference/streamlined.md",
-                "Initialization"   => "manuals/inference/initialization.md",
-                "Auto-updates"   => "manuals/inference/autoupdates.md",
-                "Deterministic nodes" => "manuals/inference/delta-node.md",
-                "Non-conjugate inference" => "manuals/inference/nonconjugate.md",
-                "Undefined message update rules" => "manuals/inference/undefinedrules.md"
-            ],
-            "Inference customization"   => [
-                "Defining a custom node and rules" => "manuals/customization/custom-node.md",
-                "Inference results postprocessing" => "manuals/customization/postprocess.md", 
-            ],
-            "Debugging" => "manuals/debugging.md",
-            "Migration from v2 to v3" => "manuals/migration-guide-v2-v3.md"
+            "Inference specification"   => ["Overview" => "manuals/inference/overview.md", "Static inference" => "manuals/inference/static.md", "Streamline inference" => "manuals/inference/streamlined.md", "Initialization" => "manuals/inference/initialization.md", "Auto-updates" => "manuals/inference/autoupdates.md", "Deterministic nodes" => "manuals/inference/delta-node.md", "Non-conjugate inference" => "manuals/inference/nonconjugate.md", "Undefined message update rules" => "manuals/inference/undefinedrules.md"],
+            "Inference customization"   => ["Defining a custom node and rules" => "manuals/customization/custom-node.md", "Inference results postprocessing" => "manuals/customization/postprocess.md"],
+            "Debugging"                 => "manuals/debugging.md",
+            "Migration from v2 to v3"   => "manuals/migration-guide-v2-v3.md",
+            "Sharp bits of RxInfer"     => [
+                "Overview" => "manuals/sharpbits/overview.md",
+                "Rule Not Found Error" => "manuals/sharpbits/rule-not-found.md",
+                "Stack Overflow in Message Computations" => "manuals/sharpbits/stack-overflow-inference.md",
+                "Using `=` instead of `:=` for deterministic nodes" => "manuals/sharpbits/usage-colon-equality.md"
+            ]
         ],
         "Library" => [
             "Model construction" => "library/model-construction.md",
@@ -131,11 +131,11 @@ makedocs(;
         "Examples" => [
             "Overview" => "examples/overview.md", # This must be auto-generated with `make examples`
             ExamplesPages...,
-            "External examples" => "contributing/external-examples.md"
+            "Contribute with examples" => "contributing/examples.md"
         ],
         "Contributing" => [
             "Contribution guide" => "contributing/guide.md",
-            "Contribution guidelines"=> "contributing/guidelines.md",
+            "Contribution guidelines" => "contributing/guidelines.md",
             "Contributing to the documentation" => "contributing/new-documentation.md",
             "Contributing to the examples" => "contributing/new-example.md",
             "Publishing a new release" => "contributing/new-release.md"

diff --git a/docs/src/contributing/examples.md b/docs/src/contributing/examples.md
@@ -0,0 +1,11 @@
+# [Contribute with examples](@id examples)
+
+We welcome examples from the community that showcase RxInfer.jl in action! Whether you're working in machine learning, signal processing, robotics, computational biology, or any other domain - your contributions help others learn and explore probabilistic modeling with RxInfer.jl.
+
+## Featured Examples
+
+- **Active Inference with RxInfer.jl** - Dive into the realm of Active Inference guided by [Kobus Esterhuysen](https://www.linkedin.com/in/kobusesterhuysen/) at [Learnable Loop](https://learnableloop.com/#category=RxInfer).
+- **Tutorial Series on RxInfer.jl** - Explore a series of engaging tutorial videos on RxInfer.jl's functionalities, presented by [@doggotodjl](https://www.youtube.com/@doggodotjl/search?query=RxInfer).
+
+!!! note 
+    If you're interested in contributing an example, we'd love to hear from you! Please initiate an issue or start a new discussion on our [GitHub repository](https://github.com/reactivebayes/RxInfer.jl) to get involved.
diff --git a/docs/src/contributing/external-examples.md b/docs/src/contributing/external-examples.md
diff --git a/docs/src/manuals/comparison.md b/docs/src/manuals/comparison.md
@@ -67,7 +67,12 @@ end
 end
 ```
 
-- **Expressiveness**: `RxInfer.jl` empowers users to elegantly and concisely craft models, closely mirroring probabilistic notation, thanks to Julia's macro capabilities. To illustrate this, let's consider the following model:
+- **Expressiveness**: `RxInfer.jl` empowers users to elegantly and concisely craft models, closely mirroring probabilistic notation, thanks to Julia's macro capabilities.
+
+!!! note
+    RxInfer uses `:=` for deterministic relationships (see [Using `=` instead of `:=` for deterministic nodes](@ref usage-colon-equality)) which might differ from other frameworks but enables powerful message-passing capabilities.
+
+To illustrate the expressiveness, let's consider the following model:
 
 $$\begin{aligned}
  x & \sim \mathrm{Normal}(0.0, 1.0)\\