From 2015afa8db991c11b0d05ca756e8636c9dfb0d6f Mon Sep 17 00:00:00 2001
From: Joseph Campolongo <joseph.campolongo@gmail.com>
Date: Tue, 15 Nov 2022 14:15:19 -0500
Subject: [PATCH 01/13] Avi's code adding default implementations Adding unit
 tests

---
 src/operators/op_defs.jl          |   4 +-
 src/sfuncs/conddist/invertible.jl |   2 +-
 src/sfuncs/op_impls/basic_ops.jl  |  23 +++++-
 test/runtests.jl                  |   1 +
 test/test_core.jl                 |   2 +-
 test/test_ops.jl                  | 122 ++++++++++++++++++++++++++++++
 6 files changed, 147 insertions(+), 7 deletions(-)
 create mode 100644 test/test_ops.jl

diff --git a/src/operators/op_defs.jl b/src/operators/op_defs.jl
index 858c6e16..e2e95f1e 100644
--- a/src/operators/op_defs.jl
+++ b/src/operators/op_defs.jl
@@ -18,10 +18,12 @@ __Opt{T} = Union{Nothing, T}
 # to support 
 MultiInterface.get_imp(::Nothing, args...) = nothing
 
+@interface forward(sf::SFunc{I,O}, i::I)::Dist{O} where {I,O}
+@interface inverse(sf::SFunc{I,O}, o::O)::Score{I} where {I,O}
 @interface is_deterministic(sf::SFunc)::Bool
 @interface sample(sf::SFunc{I,O}, i::I)::O where {I,O}
 @interface sample_logcpdf(sf::SFunc{I,O}, i::I)::Tuple{O, AbstractFloat} where {I,O}
-@interface invert(sf::SFunc{I,O}, o::O)::I where {I,O}
+# @interface invert(sf::SFunc{I,O}, o::O)::I where {I,O}
 @interface lambda_msg(sf::SFunc{I,O}, i::SFunc{<:__Opt{Tuple{}}, O})::SFunc{<:__Opt{Tuple{}}, I} where {I,O}
 @interface marginalize(sf::SFunc{I,O}, i::SFunc{<:__Opt{Tuple{}}, I})::SFunc{<:__Opt{Tuple{}}, O} where {I,O}
 @interface logcpdf(sf::SFunc{I,O}, i::I, o::O)::AbstractFloat where {I,O}
diff --git a/src/sfuncs/conddist/invertible.jl b/src/sfuncs/conddist/invertible.jl
index fddb8139..f10b17ef 100644
--- a/src/sfuncs/conddist/invertible.jl
+++ b/src/sfuncs/conddist/invertible.jl
@@ -2,7 +2,7 @@ export
     Invertible
 
 """
-    struct Invertible{I,O} <: SFunc{Tuple{I},O,Nothing}
+    struct Invertible{I,O} <: SFunc{Tuple{I},O}
 
 An invertible sfunc, with both a `forward` and a `inverse` function provided.
 
diff --git a/src/sfuncs/op_impls/basic_ops.jl b/src/sfuncs/op_impls/basic_ops.jl
index 3a3ac64d..ada1c2fa 100644
--- a/src/sfuncs/op_impls/basic_ops.jl
+++ b/src/sfuncs/op_impls/basic_ops.jl
@@ -1,17 +1,32 @@
-# Default implementations of basic operators
+#= 
+# Default implementations of operators. These are defined using other operators.
+# They will always be called if a more specific implementation is not provided.
+# If the operators they rely on are not implemented, they will produce a runtime error.
+# Writers of default implementations should avoid infinite loops.
+=#
 
-# cpdf and logcpdf have default operators in terms of the other. Sfuncs should implement one or the other.
+# if forward is defined, we get a default implementation of sample
+@impl begin
+    struct DefaultSample end
+    # This should not produce an infinite loop, because a dist should not implement forward,
+    # since forwards maps a parent to a dist, but here the parent is empty.
+    function sample(sf::SFunc{I,O}, i::I)::O where {I,O}
+        d = forward(sf, i)
+        return sample(d, tuple())
+    end
+end
 
 @impl begin
-    struct SFuncCpdf end
     function cpdf(sf::SFunc{I,O}, i::I, o::O)::AbstractFloat where {I,O}
         exp(logcpdf(sf, i, o))
     end
 end
 
 @impl begin
-    struct SFuncLogcpdf end
     function logcpdf(sf::SFunc{I,O}, i::I, o::O)::AbstractFloat where {I,O}
         log(cpdf(sf, i, o))
     end
 end
+
+# TODO: Create default implementations of compute_pi and send_lambda
+# TODO: Create weighted_sample operator with default implementation using inverse
diff --git a/test/runtests.jl b/test/runtests.jl
index 44895a4d..7b2865ed 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -8,6 +8,7 @@ using Test
     include("test_sfuncs.jl")
     include("test_score.jl")
     include("test_utils.jl")
+    include("test_ops.jl")
     include("test_ve.jl")
     include("test_lsfi.jl")
     include("test_bp.jl")
diff --git a/test/test_core.jl b/test/test_core.jl
index 23505052..1c2d05cc 100644
--- a/test/test_core.jl
+++ b/test/test_core.jl
@@ -11,7 +11,7 @@ using Scruff.SFuncs
 
 import Scruff: make_initial, make_transition
 import Scruff.Models: get_dt
-import Scruff.Operators: Sample, sample, Logcpdf, logcpdf, Marginalize, marginalize
+import Scruff.Operators: Sample, sample, Logcpdf, logcpdf, Marginalize, marginalize, expectation
 
 struct MyModel <: Model{Tuple{}, Tuple{Int}, Tuple{Int, Int}} end
 
diff --git a/test/test_ops.jl b/test/test_ops.jl
new file mode 100644
index 00000000..381a567c
--- /dev/null
+++ b/test/test_ops.jl
@@ -0,0 +1,122 @@
+using Test
+
+import Logging
+
+using Scruff
+using Scruff.Operators
+using Scruff.MultiInterface: @impl
+
+import Scruff.Operators: sample, forward, cpdf, logcpdf
+import Scruff.SFuncs: Constant
+
+# Test default implementation of operators
+
+logger = Logging.SimpleLogger(stderr, Logging.Error+1)
+
+struct SF1 <: SFunc{Tuple{Int},Int} end
+
+@impl begin
+    struct SF1Forward end
+    function forward(sf::SF1, i::Tuple{Int})::Dist{Int}
+        Constant(1)
+    end
+end
+
+@impl begin
+    struct SF1Sample end
+    function sample(sf::SF1, i::Tuple{Int})::Int
+        0
+    end
+end
+
+struct SF2 <: SFunc{Tuple{Int},Int} end
+
+@impl begin
+    struct SF2Forward end
+    function forward(sf::SF2, i::Tuple{Int})::Dist{Int}
+        Constant(1)
+    end
+end
+
+struct SF3 <: SFunc{Tuple{Int}, Int} end
+
+struct SF4 <: SFunc{Tuple{Int}, Int} end
+
+@impl begin
+    struct SF4Cpdf end
+    function cpdf(sf::SF4, i::Tuple{Int}, o::Int)
+        0.0
+    end
+end
+
+@impl begin
+    struct SF4Logcpdf end
+    function logcpdf(sf::SF4, i::Tuple{Int}, o::Int)
+        0.0 # so cpdf is 1.0
+    end
+end
+
+struct SF5 <: SFunc{Tuple{Int}, Int} end
+
+@impl begin
+    struct SF5Cpdf end
+    function cpdf(sf::SF5, i::Tuple{Int}, o::Int)
+        0.0
+    end
+end
+
+struct SF6 <: SFunc{Tuple{Int}, Int} end
+
+@impl begin
+    struct SF6Logcpdf end
+    function logcpdf(sf::SF6, i::Tuple{Int}, o::Int)
+        0.0
+    end
+end
+
+struct SF7 <: SFunc{Tuple{Int}, Int} end
+
+Logging.with_logger(logger) do
+
+@testset "Implementation of sample using forward" begin
+    @testset "When explicit sample defined that is different" begin
+        # To test the calls, we implement forward and sample in contradictory ways
+        # The explicit sample should be used
+        @test sample(SF1(), (2,)) == 0
+    end
+
+    @testset "When forward is implemented explicitly but not sample" begin
+        # sample should use forward
+        @test sample(SF2(), (2,)) == 1
+    end
+
+    @testset "When neither sample nor forward are implemented explicitly" begin
+        # Should throw a MethodError because forward is not found when using the default implemenation of sample``
+        @test_throws MethodError sample(SF3(), (2,))
+    end
+end
+
+@testset "Default implementations of cpdf and logcpdf in terms of each other" begin
+    @testset "When both cpdf and logcpdf are implemented explicitly" begin
+        # To test the calls, we implement cpdf and logcpdf in contradictory ways
+        @test cpdf(SF4(), (2,), 1) == 0.0
+        @test logcpdf(SF4(), (2,), 1) == 0.0
+    end
+
+    @testset "When only cpdf is implemented explicitly" begin
+        @test cpdf(SF5(), (2,), 1) == 0.0
+        @test logcpdf(SF5(), (2,), 1) == -Inf64
+    end
+    
+    @testset "When only cpdf is implemented explicitly" begin
+        @test cpdf(SF6(), (2,), 1) == 1.0
+        @test logcpdf(SF6(), (2,), 1) == 0.0
+    end
+
+    # @testset "When neither cpdf nor logcpdf are implemented explicitly" begin
+    #     # should detect infinite loop and throw error
+    #     @test_throws ErrorException cpdf(SF7(), (2,), 1)
+    #     @test_throws ErrorException logcpdf(SF7(), (2,), 1)
+    # end
+end
+end
\ No newline at end of file

From 3f43ce039d23f2130142e4c659a502075814ab4b Mon Sep 17 00:00:00 2001
From: Joseph Campolongo <jcampolongo@cra.com>
Date: Fri, 10 Feb 2023 11:26:58 -0500
Subject: [PATCH 02/13] Increment version to 0.8.2

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index d5ed0c7f..22caa470 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,6 +1,6 @@
 name = "Scruff"
 uuid = "6c98c146-7a27-4df0-99b1-e6e7c9a81876"
-version = "0.8.1"
+version = "0.8.2"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"

From 738f5cb4bfa8c9509f243a190fc172072313459d Mon Sep 17 00:00:00 2001
From: Joseph Campolongo <joseph.campolongo@gmail.com>
Date: Fri, 10 Feb 2023 12:47:18 -0500
Subject: [PATCH 03/13] Updating compats to have upper bounds

---
 Project.toml | 33 ++++++++++++++++-----------------
 1 file changed, 16 insertions(+), 17 deletions(-)

diff --git a/Project.toml b/Project.toml
index 22caa470..fdeac771 100644
--- a/Project.toml
+++ b/Project.toml
@@ -28,23 +28,22 @@ TensorOperations = "6aa20fa7-93e2-5fca-9bc0-fbd0db3c71a2"
 UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [compat]
-AbstractTrees = ">= 0.3.4"
-Cassette = ">= 0.3.10"
-Clustering = ">= 0.14.2"
-DataStructures = ">= 0.18.11"
-Distributions = ">= 0.25.52"
-Folds = ">= 0.2.7"
-MLDatasets = ">= 0.5.15"
-MacroTools = ">= 0.5.9"
-MetaGraphs = ">= 0.7.1"
-Parameters = ">= 0.12.3"
-Plots = ">= 1.27.2"
-PrettyPrint = ">= 0.2"
-PyPlot = ">= 2.10"
-SimpleTraits = ">= 0.9.4"
-StatsBase = ">= 0.33.16"
-StatsFuns = ">= 0.9.16"
-TensorOperations = ">= 3.2.3"
+AbstractTrees = "0.3.4 - 0.4"
+Cassette = "0.3.10"
+Clustering = "0.14.2"
+DataStructures = "0.18.11"
+Distributions = "0.25.52"
+Folds = "0.2.7"
+MacroTools = "0.5.9"
+Parameters = "0.12.3"
+Plots = "1.27.2"
+PrettyPrint = "0.2"
+PyCall = "1.95.1"
+PyPlot = "2.10"
+SimpleTraits = "0.9.4"
+StatsBase = "0.33.16"
+StatsFuns = "1"
+TensorOperations = "3.2.3"
 julia = "^1.6"
 
 [extras]

From f5dff8a6351e01dea9107d7edbc93393fd5af008 Mon Sep 17 00:00:00 2001
From: Joseph Campolongo <jcampolongo@cra.com>
Date: Fri, 10 Feb 2023 13:11:54 -0500
Subject: [PATCH 04/13] Update Project.toml

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index fdeac771..d49ea7e8 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,6 +1,6 @@
 name = "Scruff"
 uuid = "6c98c146-7a27-4df0-99b1-e6e7c9a81876"
-version = "0.8.2"
+version = "0.8.3"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"

From 457add0d5c040b48a60d62c1241ccd0c54e23a78 Mon Sep 17 00:00:00 2001
From: Joseph Campolongo <jcampolongo@cra.com>
Date: Fri, 10 Feb 2023 13:32:19 -0500
Subject: [PATCH 05/13] Change for auto-registry

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index d49ea7e8..fdeac771 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,6 +1,6 @@
 name = "Scruff"
 uuid = "6c98c146-7a27-4df0-99b1-e6e7c9a81876"
-version = "0.8.3"
+version = "0.8.2"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"

From 5d562092f9a079bae3be913d07fa8df673f20a71 Mon Sep 17 00:00:00 2001
From: apfeffer <apfeffer@cra.com>
Date: Wed, 29 Mar 2023 15:52:31 -0400
Subject: [PATCH 06/13] Uniform

---
 src/sfuncs.jl              |   1 +
 src/sfuncs/dist/uniform.jl | 123 +++++++++++++++++++++++++++++++++++++
 test/test_bp.jl            |  14 ++---
 test/test_bp_logger.jl     |  12 ++--
 test/test_core.jl          |  10 +--
 test/test_filter.jl        |  14 ++---
 test/test_importance.jl    |  12 ++--
 test/test_logger.jl        |  12 ++--
 test/test_lsfi.jl          |  14 ++---
 test/test_net.jl           |   6 +-
 test/test_score.jl         |   8 +--
 test/test_sfuncs.jl        |  38 ++++++++++--
 test/test_utils.jl         |   6 +-
 test/test_ve.jl            |  14 ++---
 14 files changed, 218 insertions(+), 66 deletions(-)
 create mode 100644 src/sfuncs/dist/uniform.jl
 mode change 100644 => 100755 test/test_sfuncs.jl

diff --git a/src/sfuncs.jl b/src/sfuncs.jl
index ea46d34b..72bdfc7c 100644
--- a/src/sfuncs.jl
+++ b/src/sfuncs.jl
@@ -14,6 +14,7 @@ include("sfuncs/dist/cat.jl")
 include("sfuncs/dist/constant.jl")
 include("sfuncs/dist/flip.jl")
 include("sfuncs/dist/normal.jl")
+include("sfuncs/dist/uniform.jl")
 
 include("sfuncs/score/score.jl")
 include("sfuncs/score/hardscore.jl")
diff --git a/src/sfuncs/dist/uniform.jl b/src/sfuncs/dist/uniform.jl
new file mode 100644
index 00000000..a3cc3f73
--- /dev/null
+++ b/src/sfuncs/dist/uniform.jl
@@ -0,0 +1,123 @@
+# Continuous uniform sfunc
+
+export Uniform
+
+import Distributions
+
+mutable struct Uniform <: Dist{Float64}
+    params :: Tuple{Float64, Float64}
+    Uniform(l, u) = new((l,u))
+end
+
+lb(u::Uniform) = u.params[1]
+ub(u::Uniform) = u.params[2]
+
+mean(u::Uniform) = (lb(u) + ub(u)) / 2.0
+
+sd(u::Uniform) = (ub(u) - lb(u)) / sqrt(12.0)
+
+dist(u::Uniform) = Distributions.Uniform(lb(u), ub(u))
+
+@impl begin
+    struct UniformSupport end
+    function support(
+        sf::Uniform,
+        ::NTuple,
+        size::Integer,
+        curr::Vector{Float64}
+    )
+        newsize = size - length(curr)
+        result = curr
+        if newsize > 0
+            x = lb(sf)
+            push!(result, x)
+            numsteps = newsize - 1
+            step = (ub(sf) - lb(sf)) / numsteps
+            for i in 1:numsteps
+                x += step
+                push!(result, x)
+            end
+        end
+        unique(result)
+    end
+end
+
+
+@impl begin
+    struct UniformSupportQuality end
+    function support_quality(::Uniform, parranges)
+        :IncrementalSupport
+    end
+end
+
+
+@impl begin
+    struct UniformSample end
+    function sample(sf::Uniform, x::Tuple{})::Float64
+        rand(dist(sf))
+    end
+end
+
+@impl begin
+    struct UniformLogcpdf end
+    function logcpdf(sf::Uniform, i::Tuple{}, o::Float64)::AbstractFloat
+        Distributions.logpdf(dist(sf), o)
+    end
+end
+
+@impl begin
+    struct UniformBoundedProbs end
+
+    # assumes range is sorted
+    function bounded_probs(
+        sf::Uniform,
+        range::Vector{Float64},
+        ::NTuple
+    )
+        l = lb(sf)
+        u = ub(sf)
+        d = u - l
+        n = length(range)
+
+        # Each element in the range is associated with the interval between the midpoint
+        # of it and the point below and the midpoint between it and the point above,
+        # except for the end intervals which go to negative or positive infinity.
+        points = [-Inf64]
+        for i in 2:n
+            push!(points, (range[i-1] + range[i]) / 2)
+        end
+        push!(points, Inf64)
+
+        # Each interval might be completely, partially, or not contained in the bounds
+        # of the uniform distribution. The following code determines the length of each
+        # interval that is in the bounds.
+        lengthsinbound = Float64[]
+        for i in 1:n
+            a = max(points[i], l)
+            b = min(points[i+1], u)
+            push!(lengthsinbound, max(b-a, 0.0))
+        end
+
+        ps = [lengthsinbound[i] / d for i in 1:n]
+        return (ps, ps)
+    end
+
+end
+
+@impl begin
+    struct UniformComputePi end
+
+    function compute_pi(sf::Uniform,
+                    range::Vector{Float64}, 
+                    ::NTuple, 
+                    ::Tuple)::Cat{Float64}
+
+        ps = bounded_probs(sf, range, ())[1]
+        Cat(range, ps)
+    end
+end
+
+
+
+
+
diff --git a/test/test_bp.jl b/test/test_bp.jl
index b0e8fc35..cebbfd31 100644
--- a/test/test_bp.jl
+++ b/test/test_bp.jl
@@ -5,13 +5,13 @@ import Scruff.Operators.bounded_probs
 import Scruff.Operators.range
 
 using Test
-using Scruff
-using Scruff.Utils
-using Scruff.RTUtils
-using Scruff.SFuncs
-using Scruff.Models
-using Scruff.Operators
-import Scruff.Algorithms: three_pass_BP, loopy_BP, ThreePassBP, LoopyBP, infer, probability
+using ..Scruff
+using ..Scruff.Utils
+using ..Scruff.RTUtils
+using ..Scruff.SFuncs
+using ..Scruff.Models
+using ..Scruff.Operators
+import ..Scruff.Algorithms: three_pass_BP, loopy_BP, ThreePassBP, LoopyBP, infer, probability
 
 @testset "BP" begin
 
diff --git a/test/test_bp_logger.jl b/test/test_bp_logger.jl
index d7988d79..5d8db55f 100644
--- a/test/test_bp_logger.jl
+++ b/test/test_bp_logger.jl
@@ -1,11 +1,11 @@
 include("..//src//utils//logplots.jl")
 
-using Scruff
-using Scruff.SFuncs
-using Scruff.Utils
-using Scruff.RTUtils
-using Scruff.Models
-import Scruff.Algorithms
+using ..Scruff
+using ..Scruff.SFuncs
+using ..Scruff.Utils
+using ..Scruff.RTUtils
+using ..Scruff.Models
+import ..Scruff.Algorithms
 
 pyplot()
 
diff --git a/test/test_core.jl b/test/test_core.jl
index 9ad7d0c0..4c0a3f51 100644
--- a/test/test_core.jl
+++ b/test/test_core.jl
@@ -5,11 +5,11 @@ using Plots
 
 import Distributions
 
-using Scruff
-using Scruff.Operators
-using Scruff.MultiInterface
-using Scruff.Models
-using Scruff.SFuncs
+using ..Scruff
+using ..Scruff.Operators
+using ..Scruff.MultiInterface
+using ..Scruff.Models
+using ..Scruff.SFuncs
 
 import Scruff: make_initial, make_transition
 import Scruff.Models: get_dt
diff --git a/test/test_filter.jl b/test/test_filter.jl
index 9a4fb7ce..c3986c60 100644
--- a/test/test_filter.jl
+++ b/test/test_filter.jl
@@ -1,12 +1,12 @@
 using Test
 
-using Scruff
-using Scruff.Utils
-using Scruff.RTUtils
-using Scruff.Models
-using Scruff.SFuncs
-using Scruff.Algorithms
-import Scruff: make_initial, make_transition
+using ..Scruff
+using ..Scruff.Utils
+using ..Scruff.RTUtils
+using ..Scruff.Models
+using ..Scruff.SFuncs
+using ..Scruff.Algorithms
+import ..Scruff: make_initial, make_transition
 
 @testset "Filtering" begin
     
diff --git a/test/test_importance.jl b/test/test_importance.jl
index c6333fde..fbdefb0c 100644
--- a/test/test_importance.jl
+++ b/test/test_importance.jl
@@ -3,12 +3,12 @@ import Base.isapprox
 import PrettyPrint
 
 using Test
-using Scruff
-using Scruff.Utils
-using Scruff.RTUtils
-using Scruff.SFuncs
-using Scruff.Algorithms
-import Scruff.Operators: cpdf
+using ..Scruff
+using ..Scruff.Utils
+using ..Scruff.RTUtils
+using ..Scruff.SFuncs
+using ..Scruff.Algorithms
+import ..Scruff.Operators: cpdf
 
 @testset "Importance" begin
     
diff --git a/test/test_logger.jl b/test/test_logger.jl
index 781d1c80..c1c12bf5 100644
--- a/test/test_logger.jl
+++ b/test/test_logger.jl
@@ -1,12 +1,12 @@
 using Test
 
 using Logging
-using Scruff
-using Scruff.Models
-using Scruff.Utils
-using Scruff.RTUtils
-using Scruff.SFuncs
-using Scruff.Operators
+using ..Scruff
+using ..Scruff.Models
+using ..Scruff.Utils
+using ..Scruff.RTUtils
+using ..Scruff.SFuncs
+using ..Scruff.Operators
 
 @testset "test loggers" begin
     x1 = Cat([1,2], [0.1, 0.9])()(:x1)
diff --git a/test/test_lsfi.jl b/test/test_lsfi.jl
index 1476aa70..e69d26bc 100644
--- a/test/test_lsfi.jl
+++ b/test/test_lsfi.jl
@@ -3,13 +3,13 @@ import Base.isapprox
 import PrettyPrint
 
 using Test
-using Scruff
-using Scruff.Utils
-using Scruff.RTUtils
-using Scruff.Models
-using Scruff.SFuncs
-using Scruff.Operators
-import Scruff.Algorithms: LSFI, probability_bounds, prepare, refine, ve
+using ..Scruff
+using ..Scruff.Utils
+using ..Scruff.RTUtils
+using ..Scruff.Models
+using ..Scruff.SFuncs
+using ..Scruff.Operators
+import ..Scruff.Algorithms: LSFI, probability_bounds, prepare, refine, ve
 
 using Scruff.MultiInterface
 
diff --git a/test/test_net.jl b/test/test_net.jl
index 4e96ff7c..1711c610 100644
--- a/test/test_net.jl
+++ b/test/test_net.jl
@@ -1,7 +1,7 @@
 using Test
-using Scruff
-using Scruff.SFuncs
-using Scruff.Operators
+using ..Scruff
+using ..Scruff.SFuncs
+using ..Scruff.Operators
 
 @testset "net" begin
     @testset "Build NetworkSFunc" begin
diff --git a/test/test_score.jl b/test/test_score.jl
index b1c1c059..c7201516 100644
--- a/test/test_score.jl
+++ b/test/test_score.jl
@@ -1,8 +1,8 @@
 using Test
-using Scruff
-using Scruff.Operators
-using Scruff.SFuncs
-using Scruff.Utils
+using ..Scruff
+using ..Scruff.Operators
+using ..Scruff.SFuncs
+using ..Scruff.Utils
 
 @testset "Score" begin
 
diff --git a/test/test_sfuncs.jl b/test/test_sfuncs.jl
old mode 100644
new mode 100755
index 5ce563c4..4256c578
--- a/test/test_sfuncs.jl
+++ b/test/test_sfuncs.jl
@@ -1,9 +1,9 @@
 using Test
-using Scruff
-using Scruff.Operators
-using Scruff.MultiInterface
-using Scruff.SFuncs
-using Scruff.Utils
+using ..Scruff
+using ..Scruff.Operators
+using ..Scruff.MultiInterface
+using ..Scruff.SFuncs
+using ..Scruff.Utils
 import Distributions
 
 function test_support(sf::SFunc{I,O}, parranges, target, quality; 
@@ -145,6 +145,34 @@ end
         @test isapprox(compute_pi(f, [false, true], (), ()).params, [0.3, 0.7])
     end
 
+    @testset "Uniform" begin
+        u = SFuncs.Uniform(-1.0, 3.0)
+        
+        test_support(u, (), [-1.0, 0.0, 1.0, 2.0, 3.0], :IncrementalSupport; size = 5)
+        test_support(u, (), [-1.0, -0.5, 0.0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0], :IncrementalSupport; 
+            size = 9, curr = [-0.5, 0.5, 1.5, 2.5])
+        test_support(u, (), [-1.0, -0.5, 0.0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0], :IncrementalSupport; 
+            size = 10, curr = [-0.5, 0.5, 1.0, 1.5, 2.5])
+        
+        cs = [0.0, 0.0, 0.0, 0.0]
+        tot = 1000
+        for i in 1:tot
+            x = sample(u, ())
+            cs[Int(floor(x)) + 2] += 1
+        end
+        for j in 1:4
+            @test isapprox(cs[j] / tot, 0.25; atol = 0.05)
+        end
+        @test isapprox(logcpdf(u, (), 0.0), log(0.25))
+        @test isapprox(logcpdf(u, (), 5.0), -Inf64)
+
+        @test isapprox(bounded_probs(u, [-1.0, 0.0, 1.0, 2.0, 3.0], ())[1],
+                        [0.125, 0.25, 0.25, 0.25, 0.125])
+        @test isapprox(bounded_probs(u, [-1.0, 0.0, 1.0, 2.0, 3.0], ())[2],
+                        [0.125, 0.25, 0.25, 0.25, 0.125])
+        @test isapprox(bounded_probs(u, [-1.0, -9.0, -8.0], ())[1], [0.0, 0.0, 1.0])
+    end
+    
     @testset "Normal" begin
         n = SFuncs.Normal(-1.0,1.0)
         dist = Distributions.Normal(-1.0, 1.0)
diff --git a/test/test_utils.jl b/test/test_utils.jl
index 0ed1533f..d8996a88 100644
--- a/test/test_utils.jl
+++ b/test/test_utils.jl
@@ -1,7 +1,7 @@
 using Test
-using Scruff
-using Scruff.Utils
-using Scruff.RTUtils
+using ..Scruff
+using ..Scruff.Utils
+using ..Scruff.RTUtils
 using AbstractTrees
 using DataStructures
 
diff --git a/test/test_ve.jl b/test/test_ve.jl
index 27bf7241..9f2fec19 100644
--- a/test/test_ve.jl
+++ b/test/test_ve.jl
@@ -1,11 +1,11 @@
 using Test
-using Scruff
-using Scruff.Utils
-using Scruff.RTUtils
-using Scruff.Models
-using Scruff.SFuncs
-using Scruff.Operators
-import Scruff.Algorithms: VE, ve, infer, probability, greedy_order, unconnected_neighbors, cost, copy_graph, eliminate
+using ..Scruff
+using ..Scruff.Utils
+using ..Scruff.RTUtils
+using ..Scruff.Models
+using ..Scruff.SFuncs
+using ..Scruff.Operators
+import ..Scruff.Algorithms: VE, ve, infer, probability, greedy_order, unconnected_neighbors, cost, copy_graph, eliminate
 
 @testset "VE" begin
 

From b99c0fc8f61658dc04f751be297cd537d1a7244d Mon Sep 17 00:00:00 2001
From: apfeffer <apfeffer@cra.com>
Date: Fri, 31 Mar 2023 14:12:37 -0400
Subject: [PATCH 07/13] MultipleScore

---
 src/sfuncs.jl                     |  1 +
 src/sfuncs/score/multiplescore.jl | 15 +++++++++++++++
 test/test_score.jl                |  9 +++++++++
 3 files changed, 25 insertions(+)
 create mode 100644 src/sfuncs/score/multiplescore.jl

diff --git a/src/sfuncs.jl b/src/sfuncs.jl
index 72bdfc7c..ab47241e 100644
--- a/src/sfuncs.jl
+++ b/src/sfuncs.jl
@@ -19,6 +19,7 @@ include("sfuncs/dist/uniform.jl")
 include("sfuncs/score/score.jl")
 include("sfuncs/score/hardscore.jl")
 include("sfuncs/score/softscore.jl")
+include("sfuncs/score/multiplescore.jl")
 include("sfuncs/score/logscore.jl")
 include("sfuncs/score/functionalscore.jl")
 include("sfuncs/score/normalscore.jl")
diff --git a/src/sfuncs/score/multiplescore.jl b/src/sfuncs/score/multiplescore.jl
new file mode 100644
index 00000000..06c3a6ef
--- /dev/null
+++ b/src/sfuncs/score/multiplescore.jl
@@ -0,0 +1,15 @@
+# MultipleScore lets you assert multiple evidence on the same variable
+export MultipleScore
+
+struct MultipleScore{I} <: Score{I}
+    components :: Vector{<:Score{I}}
+end
+
+function get_log_score(ms::MultipleScore{I}, i::I) where I
+    tot = 0.0
+    for m in ms.components
+        tot += get_log_score(m, i)
+    end
+    tot
+end
+
diff --git a/test/test_score.jl b/test/test_score.jl
index c7201516..10c47dda 100644
--- a/test/test_score.jl
+++ b/test/test_score.jl
@@ -34,6 +34,15 @@ using ..Scruff.Utils
             @test get_log_score(s, :b) == -2.0
         end
 
+        @testset "Multiple score" begin
+            s1 = SoftScore([:a, :b], [0.1, 0.2])
+            s2 = LogScore([:b, :c], [-1.0, -2.0])
+            s = MultipleScore([s1, s2])
+            @test isapprox(get_log_score(s, :a), -Inf64)
+            @test isapprox(get_log_score(s, :b), log(0.2) - 1.0)
+            @test isapprox(get_log_score(s, :c), -Inf64)
+        end
+
         @testset "Functional score" begin
             f(x) = 1.0 / x
             s = FunctionalScore{Float64}(f)

From 728bc6fff5389833c5b6368c0158dcf15e799275 Mon Sep 17 00:00:00 2001
From: Michael Harradon <mharradon@cra.com>
Date: Fri, 22 Mar 2024 13:41:58 -0400
Subject: [PATCH 08/13] Add soccer example to docs

---
 docs/src/tutorial/examples.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/src/tutorial/examples.md b/docs/src/tutorial/examples.md
index 8b43393e..48b6b216 100644
--- a/docs/src/tutorial/examples.md
+++ b/docs/src/tutorial/examples.md
@@ -4,3 +4,4 @@
 * [novelty_example.jl](https://github.com/p2t2/Scruff.jl/tree/main/docs/examples/novelty_example.jl)
 * [novelty_lazy.jl](https://github.com/p2t2/Scruff.jl/tree/main/docs/examples/novelty_lazy.jl)
 * [novelty_filtering.jl](https://github.com/p2t2/Scruff.jl/tree/main/docs/examples/novelty_filtering.jl)
+* [soccer_example.jl](https://github.com/charles-river-analytics/Scruff.jl/tree/main/docs/examples/soccer_example.jl)

From 6d10977e8b339e05141b88a29e596d1ade0c2f3f Mon Sep 17 00:00:00 2001
From: Michael Harradon <mharradon@cra.com>
Date: Fri, 22 Mar 2024 13:53:21 -0400
Subject: [PATCH 09/13] Update

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2cbdb956..184384bd 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,9 +19,9 @@ jobs:
     strategy:
       matrix:
         version:
-          - '1.6'
-          - '1.7'
           - '1.8'
+          - '1.9'
+          - '1.10'
           - 'nightly'
         os:
           - ubuntu-latest

From d0ac4747500c350d7ad0dcecada2100e2fd5b501 Mon Sep 17 00:00:00 2001
From: Michael Harradon <mharradon@cra.com>
Date: Fri, 22 Mar 2024 13:58:38 -0400
Subject: [PATCH 10/13] Get rid of relative paths in tests

---
 test/test_bp.jl         | 14 +++++++-------
 test/test_bp_logger.jl  | 12 ++++++------
 test/test_core.jl       | 10 +++++-----
 test/test_filter.jl     | 14 +++++++-------
 test/test_importance.jl | 12 ++++++------
 test/test_logger.jl     | 12 ++++++------
 test/test_lsfi.jl       | 14 +++++++-------
 test/test_net.jl        |  6 +++---
 test/test_score.jl      |  8 ++++----
 test/test_sfuncs.jl     | 10 +++++-----
 test/test_utils.jl      |  6 +++---
 test/test_ve.jl         | 14 +++++++-------
 12 files changed, 66 insertions(+), 66 deletions(-)

diff --git a/test/test_bp.jl b/test/test_bp.jl
index cebbfd31..b0e8fc35 100644
--- a/test/test_bp.jl
+++ b/test/test_bp.jl
@@ -5,13 +5,13 @@ import Scruff.Operators.bounded_probs
 import Scruff.Operators.range
 
 using Test
-using ..Scruff
-using ..Scruff.Utils
-using ..Scruff.RTUtils
-using ..Scruff.SFuncs
-using ..Scruff.Models
-using ..Scruff.Operators
-import ..Scruff.Algorithms: three_pass_BP, loopy_BP, ThreePassBP, LoopyBP, infer, probability
+using Scruff
+using Scruff.Utils
+using Scruff.RTUtils
+using Scruff.SFuncs
+using Scruff.Models
+using Scruff.Operators
+import Scruff.Algorithms: three_pass_BP, loopy_BP, ThreePassBP, LoopyBP, infer, probability
 
 @testset "BP" begin
 
diff --git a/test/test_bp_logger.jl b/test/test_bp_logger.jl
index 5d8db55f..d7988d79 100644
--- a/test/test_bp_logger.jl
+++ b/test/test_bp_logger.jl
@@ -1,11 +1,11 @@
 include("..//src//utils//logplots.jl")
 
-using ..Scruff
-using ..Scruff.SFuncs
-using ..Scruff.Utils
-using ..Scruff.RTUtils
-using ..Scruff.Models
-import ..Scruff.Algorithms
+using Scruff
+using Scruff.SFuncs
+using Scruff.Utils
+using Scruff.RTUtils
+using Scruff.Models
+import Scruff.Algorithms
 
 pyplot()
 
diff --git a/test/test_core.jl b/test/test_core.jl
index a0243fdf..b1819d7d 100644
--- a/test/test_core.jl
+++ b/test/test_core.jl
@@ -5,11 +5,11 @@ using Plots
 
 import Distributions
 
-using ..Scruff
-using ..Scruff.Operators
-using ..Scruff.MultiInterface
-using ..Scruff.Models
-using ..Scruff.SFuncs
+using Scruff
+using Scruff.Operators
+using Scruff.MultiInterface
+using Scruff.Models
+using Scruff.SFuncs
 
 import Scruff: make_initial, make_transition
 import Scruff.Models: get_dt
diff --git a/test/test_filter.jl b/test/test_filter.jl
index c3986c60..9a4fb7ce 100644
--- a/test/test_filter.jl
+++ b/test/test_filter.jl
@@ -1,12 +1,12 @@
 using Test
 
-using ..Scruff
-using ..Scruff.Utils
-using ..Scruff.RTUtils
-using ..Scruff.Models
-using ..Scruff.SFuncs
-using ..Scruff.Algorithms
-import ..Scruff: make_initial, make_transition
+using Scruff
+using Scruff.Utils
+using Scruff.RTUtils
+using Scruff.Models
+using Scruff.SFuncs
+using Scruff.Algorithms
+import Scruff: make_initial, make_transition
 
 @testset "Filtering" begin
     
diff --git a/test/test_importance.jl b/test/test_importance.jl
index fbdefb0c..c6333fde 100644
--- a/test/test_importance.jl
+++ b/test/test_importance.jl
@@ -3,12 +3,12 @@ import Base.isapprox
 import PrettyPrint
 
 using Test
-using ..Scruff
-using ..Scruff.Utils
-using ..Scruff.RTUtils
-using ..Scruff.SFuncs
-using ..Scruff.Algorithms
-import ..Scruff.Operators: cpdf
+using Scruff
+using Scruff.Utils
+using Scruff.RTUtils
+using Scruff.SFuncs
+using Scruff.Algorithms
+import Scruff.Operators: cpdf
 
 @testset "Importance" begin
     
diff --git a/test/test_logger.jl b/test/test_logger.jl
index c1c12bf5..781d1c80 100644
--- a/test/test_logger.jl
+++ b/test/test_logger.jl
@@ -1,12 +1,12 @@
 using Test
 
 using Logging
-using ..Scruff
-using ..Scruff.Models
-using ..Scruff.Utils
-using ..Scruff.RTUtils
-using ..Scruff.SFuncs
-using ..Scruff.Operators
+using Scruff
+using Scruff.Models
+using Scruff.Utils
+using Scruff.RTUtils
+using Scruff.SFuncs
+using Scruff.Operators
 
 @testset "test loggers" begin
     x1 = Cat([1,2], [0.1, 0.9])()(:x1)
diff --git a/test/test_lsfi.jl b/test/test_lsfi.jl
index e69d26bc..1476aa70 100644
--- a/test/test_lsfi.jl
+++ b/test/test_lsfi.jl
@@ -3,13 +3,13 @@ import Base.isapprox
 import PrettyPrint
 
 using Test
-using ..Scruff
-using ..Scruff.Utils
-using ..Scruff.RTUtils
-using ..Scruff.Models
-using ..Scruff.SFuncs
-using ..Scruff.Operators
-import ..Scruff.Algorithms: LSFI, probability_bounds, prepare, refine, ve
+using Scruff
+using Scruff.Utils
+using Scruff.RTUtils
+using Scruff.Models
+using Scruff.SFuncs
+using Scruff.Operators
+import Scruff.Algorithms: LSFI, probability_bounds, prepare, refine, ve
 
 using Scruff.MultiInterface
 
diff --git a/test/test_net.jl b/test/test_net.jl
index 1711c610..4e96ff7c 100644
--- a/test/test_net.jl
+++ b/test/test_net.jl
@@ -1,7 +1,7 @@
 using Test
-using ..Scruff
-using ..Scruff.SFuncs
-using ..Scruff.Operators
+using Scruff
+using Scruff.SFuncs
+using Scruff.Operators
 
 @testset "net" begin
     @testset "Build NetworkSFunc" begin
diff --git a/test/test_score.jl b/test/test_score.jl
index 10c47dda..53a91a54 100644
--- a/test/test_score.jl
+++ b/test/test_score.jl
@@ -1,8 +1,8 @@
 using Test
-using ..Scruff
-using ..Scruff.Operators
-using ..Scruff.SFuncs
-using ..Scruff.Utils
+using Scruff
+using Scruff.Operators
+using Scruff.SFuncs
+using Scruff.Utils
 
 @testset "Score" begin
 
diff --git a/test/test_sfuncs.jl b/test/test_sfuncs.jl
index 4256c578..18be3e82 100755
--- a/test/test_sfuncs.jl
+++ b/test/test_sfuncs.jl
@@ -1,9 +1,9 @@
 using Test
-using ..Scruff
-using ..Scruff.Operators
-using ..Scruff.MultiInterface
-using ..Scruff.SFuncs
-using ..Scruff.Utils
+using Scruff
+using Scruff.Operators
+using Scruff.MultiInterface
+using Scruff.SFuncs
+using Scruff.Utils
 import Distributions
 
 function test_support(sf::SFunc{I,O}, parranges, target, quality; 
diff --git a/test/test_utils.jl b/test/test_utils.jl
index d8996a88..0ed1533f 100644
--- a/test/test_utils.jl
+++ b/test/test_utils.jl
@@ -1,7 +1,7 @@
 using Test
-using ..Scruff
-using ..Scruff.Utils
-using ..Scruff.RTUtils
+using Scruff
+using Scruff.Utils
+using Scruff.RTUtils
 using AbstractTrees
 using DataStructures
 
diff --git a/test/test_ve.jl b/test/test_ve.jl
index 9f2fec19..27bf7241 100644
--- a/test/test_ve.jl
+++ b/test/test_ve.jl
@@ -1,11 +1,11 @@
 using Test
-using ..Scruff
-using ..Scruff.Utils
-using ..Scruff.RTUtils
-using ..Scruff.Models
-using ..Scruff.SFuncs
-using ..Scruff.Operators
-import ..Scruff.Algorithms: VE, ve, infer, probability, greedy_order, unconnected_neighbors, cost, copy_graph, eliminate
+using Scruff
+using Scruff.Utils
+using Scruff.RTUtils
+using Scruff.Models
+using Scruff.SFuncs
+using Scruff.Operators
+import Scruff.Algorithms: VE, ve, infer, probability, greedy_order, unconnected_neighbors, cost, copy_graph, eliminate
 
 @testset "VE" begin
 

From dc6fc7c4183dbea28a6f26a9cb6bfd37f851864a Mon Sep 17 00:00:00 2001
From: Michael Harradon <mharradon@cra.com>
Date: Fri, 22 Mar 2024 14:02:16 -0400
Subject: [PATCH 11/13] Remove some unused deps

---
 Project.toml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/Project.toml b/Project.toml
index fdeac771..a660bf0a 100644
--- a/Project.toml
+++ b/Project.toml
@@ -17,8 +17,6 @@ Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PrettyPrint = "8162dcfd-2161-5ef2-ae6c-7681170c5f98"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
-PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 SimpleTraits = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
@@ -38,8 +36,6 @@ MacroTools = "0.5.9"
 Parameters = "0.12.3"
 Plots = "1.27.2"
 PrettyPrint = "0.2"
-PyCall = "1.95.1"
-PyPlot = "2.10"
 SimpleTraits = "0.9.4"
 StatsBase = "0.33.16"
 StatsFuns = "1"

From 2a35f43b0cc299b32a4ad0a239d92b6d9dc28213 Mon Sep 17 00:00:00 2001
From: Michael Harradon <mharradon@cra.com>
Date: Fri, 22 Mar 2024 14:21:38 -0400
Subject: [PATCH 12/13] Bump version number

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index a660bf0a..12d66c59 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,6 +1,6 @@
 name = "Scruff"
 uuid = "6c98c146-7a27-4df0-99b1-e6e7c9a81876"
-version = "0.8.2"
+version = "0.8.3"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"

From 2901596f667afe764618d12aeae1491ca3aa6f89 Mon Sep 17 00:00:00 2001
From: Michael Harradon <mharradon@cra.com>
Date: Fri, 22 Mar 2024 15:32:12 -0400
Subject: [PATCH 13/13] Update README

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 7253fc65..a771c48d 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 
 Scruff is an AI framework to build agents that sense, reason, and learn in the world using a variety of models.  It aims to integrate many different kinds of models in a coherent framework, provide flexibility in spatiotemporal modeling, and provide tools to compose, share, and reuse models and model components.
 
-Scruff is provided as a [Julia](https://julialang.org/) package and is licensed under the BSD-3-Clause License.  It should be run using Julia v1.6 or v1.7.
+Scruff is provided as a [Julia](https://julialang.org/) package and is licensed under the BSD-3-Clause License.
 
 > *Warning*: Scruff is rapidly evolving beta research software. Although the software already has a lot of functionality, we intend to expand on this in the future and cannot promise stability of the code or the APIs at the moment.