Merge pull request ReactiveBayes#20 from biaslab/dev_addons

Add addons

Project.toml

@@ -19,16 +19,15 @@ Rocket = "df971d30-c9d6-4b37-b8ff-e965b2cb3a40"
 TupleTools = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6"
 
 [compat]
-Distributions = "0.25"
 DataStructures = "0.18"
+Distributions = "0.25"
 DomainSets = "0.5.2, 0.6"
 GraphPPL = "3.1.0"
 MacroTools = "0.5.6"
 Optim = "1.0.0"
 ProgressMeter = "1.0.0"
-ReactiveMP = "~3.2.0"
+ReactiveMP = "~3.3.0"
 Reexport = "1.2.0"
-Rocket = "1.6.0"
 TupleTools = "1.2.0"
 julia = "1.6"
 
@@ -37,10 +36,10 @@ Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 BenchmarkCI = "20533458-34a3-403d-a444-e18f38190b5b"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"
-Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"

docs/make.jl

@@ -55,6 +55,7 @@ makedocs(;
                 "Overview" => "manuals/inference/overview.md",
                 "Static dataset" => "manuals/inference/inference.md",
                 "Real-time dataset / reactive inference" => "manuals/inference/rxinference.md",
+                "Inference results postprocessing"  => "manuals/inference/postprocess.md",
                 "Manual inference specification" => "manuals/inference/manual.md"
             ]
         ],

docs/src/manuals/inference/inference.md

@@ -8,4 +8,4 @@ For manual inference specification see the [Manual Inference](@ref user-guide-ma
 ```@docs
 inference
 InferenceResult
-```
+```

docs/src/manuals/inference/postprocess.md

@@ -0,0 +1,14 @@
+# [Inference results postprocessing](@id user-guide-inference-postprocess)
+
+Both [`inference`](@ref) and [`rxinference`](@ref) allow users to postprocess 
+the inference result with the `postprocess = ...` keyword argument. The inference engine 
+operates on __wrapper__ types to distinguish between marginals and messages. By default 
+these wrapper types are removed from the inference results if no addons option is present.
+Together with the enabled addons, however, the wrapper types are preserved in the 
+inference result output value. Use the options below to change this behaviour:
+
+```@docs
+DefaultPostprocess
+UnpackMarginalPostprocess
+NoopPostprocess
+```

examples/.meta.jl

@@ -103,6 +103,12 @@ return [
         description = "This example implements one of the Gamma mixture experiments outlined in https://biaslab.github.io/publication/mp-based-inference-in-gmm/ .",
         hidden = false
     ),
+    (
+        path  = "Universal Mixtures.ipynb", 
+        title = "Universal Mixtures", 
+        description = "Universal mixture modeling.",
+        hidden = false
+    ),
     (
         path = "Global Parameter Optimisation.ipynb",
         title = "Global Parameter Optimisation",
@@ -192,5 +198,5 @@ return [
         title = "Tiny Benchmark", 
         description = "Tiny Benchmark for Internal testing.",
         hidden = true
-    )
+    ),
 ]

examples/Project.toml

@@ -11,9 +11,7 @@ Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
-ReactiveMP = "a194aa59-28ba-4574-a09c-4a745416d6e3"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
-Rocket = "df971d30-c9d6-4b37-b8ff-e965b2cb3a40"
 RxInfer = "86711068-29c9-4ff7-b620-ae75d7495b3d"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"

scripts/examples.jl

@@ -188,8 +188,15 @@ function Base.run(examplesrunner::ExamplesRunner)
             # Check if example failed with an error
             # TODO: we might have better heurstic here? But I couldn't find a way to tell `Weave.jl` if an error has occured
             # TODO: try to improve this later
-            if !isnothing(findnext("```\nError:", mdtext, 1))
+            erroridx = findnext("```\nError:", mdtext, 1)
+            if !isnothing(erroridx)
                 @error "`Error` block found in the `$(mdpath)` example. Check the logs for more details."
+                # We print a part of the file, which (hopefully) should be enough to identify the issue
+                # For more logs check the actual output
+                errwindow = 500 # We need to iterate over the text with `prevind` and `nextind`, because strings are UTF8
+                errstart = reduce((idx, _) -> max(firstindex(mdtext), prevind(mdtext, idx)), 1:errwindow; init = first(erroridx))
+                errend = reduce((idx, _) -> min(lastindex(mdtext), nextind(mdtext, idx)), 1:errwindow; init = last(erroridx))
+                @error "Part of the error message:\n\n$(mdtext[errstart:errend])\n"
                 error(-1)
             end
 

src/constraints/form/form_point_mass.jl

@@ -102,6 +102,18 @@ function default_point_mass_form_constraint_optimizer(::Type{Univariate}, ::Type
     end
 end
 
+function default_point_mass_form_constraint_optimizer(::Type{Univariate}, ::Type{Discrete}, constraint::PointMassFormConstraint, distribution)
+
+    # fetch probvec
+    p = probvec(distribution)
+
+    # create new probvec
+    p_new = zeros(length(p))
+    p_new[argmax(p)] = 1
+
+    return PointMass(p_new)
+end
+
 function default_point_mass_form_constraint_boundaries(::Type{Univariate}, ::Type{Continuous}, constraint::PointMassFormConstraint, distribution)
     support = Distributions.support(distribution)
     lower   = Distributions.minimum(support)