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Inferencedata dimarray tests #71

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Inferencedata dimarray tests #71

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b7f7e38
Rel 7.3.0
goedman Feb 18, 2023
ae8a2f7
Rel 7.3.0 - Test branch for both using :dimarray(s) and inferencedata()
goedman Feb 18, 2023
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37 changes: 20 additions & 17 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
CompatHelperLocal = "5224ae11-6099-4aaa-941d-3aab004bd678"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
InferenceObjects = "b5cf5a8d-e756-4ee3-b014-01d49d192c00"
Expand All @@ -29,13 +30,30 @@ TableOperations = "ab02a1b2-a7df-11e8-156e-fb1833f50b87"
Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
Unicode = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

[weakdeps]
AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5"
BridgeStan = "c88b6f0a-829e-4b0b-94b7-f06ab5908f5a"
DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
InferenceObjects = "b5cf5a8d-e756-4ee3-b014-01d49d192c00"
MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca"

[extensions]
AxisKeysExt = "AxisKeys"
BridgeStanExt = "BridgeStan"
DimensionalDataExt = "DimensionalData"
InferenceObjectsExt = "InferenceObjects"
MCMCChainsExt = "MCMCChains"
MonteCarloMeasurementsExt = "MonteCarloMeasurements"

[compat]
AxisKeys = "0.2"
BridgeStan = "1.0.1"
CSV = "0.10"
CompatHelperLocal = "0.1"
DataFrames = "1.3"
DelimitedFiles = "1.8, 1.9"
DimensionalData = "0.24.2"
DocStringExtensions = "0.8, 0.9"
InferenceObjects = "0.3.2"
JSON = "0.21"
Expand All @@ -52,17 +70,11 @@ TableOperations = "1.0"
Tables = "1.5"
julia = "1.8"

[extensions]
AxisKeysExt = "AxisKeys"
BridgeStanExt = "BridgeStan"
InferenceObjectsExt = "InferenceObjects"
MCMCChainsExt = "MCMCChains"
MonteCarloMeasurementsExt = "MonteCarloMeasurements"

[extras]
AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5"
BridgeStan = "c88b6f0a-829e-4b0b-94b7-f06ab5908f5a"
CPUSummary = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"
DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
InferenceObjects = "b5cf5a8d-e756-4ee3-b014-01d49d192c00"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Expand All @@ -74,13 +86,4 @@ StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[targets]
test = ["AxisKeys", "BridgeStan", "Distributions", "Statistics", "LinearAlgebra", "MCMCChains",
"MonteCarloMeasurements", "InferenceObjects", "StatsBase", "StatsFuns", "Test"]

[weakdeps]
AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5"
BridgeStan = "c88b6f0a-829e-4b0b-94b7-f06ab5908f5a"
InferenceObjects = "b5cf5a8d-e756-4ee3-b014-01d49d192c00"
MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca"

test = ["AxisKeys", "BridgeStan", "DimensionalData", "Distributions", "Statistics", "LinearAlgebra", "MCMCChains", "MonteCarloMeasurements", "InferenceObjects", "StatsBase", "StatsFuns", "Test"]
49 changes: 49 additions & 0 deletions ext/DimensionalDataExt.jl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,49 @@
module DimensionalDataExt

using StanSample, DocStringExtensions

StanSample.EXTENSIONS_SUPPORTED ? (using DimensionalData) : (using ..DimensionalData)

import StanSample: convert_a3d, matrix
import DimensionalData: @dim, XDim, YDim, ZDim, DimArray, Dimensions, dims, At

@dim iteration XDim "iterations"
@dim chain YDim "chains"
@dim param ZDim "parameters"

function convert_a3d(a3d_array, cnames, ::Val{:dimarrays})
psymbols= Symbol.(cnames)
pa = permutedims(a3d_array, [1, 3, 2])

DimArray(pa, (iteration, chain, param(psymbols)); name=:draws)
end

function convert_a3d(a3d_array, cnames, ::Val{:dimarray})
psymbols= Symbol.(cnames)

# Permute [draws, params, chains] to [draws, chains, params]
a3dp = permutedims(a3d_array, [1, 3, 2])

# Append all chains
iters, chains, pars = size(a3dp)
a3dpa = reshape(a3dp, iters*chains, pars)

# Create the DimArray
DimArray(a3dpa, (iteration, param(psymbols)); name=:draws)
end

function matrix(da::DimArray, sym::Union{Symbol, String})
n = string.(dims(da, :param).val)
syms = string(sym)
sel = String[]
for (i, s) in enumerate(n)
if length(s) > length(syms) && syms == n[i][1:length(syms)] &&
n[i][length(syms)+1] in ['[', '.', '_']
append!(sel, [n[i]])
end
end
length(sel) == 0 && error("$syms not in $n")
da[param=At(Symbol.(sel))]
end

end
1 change: 1 addition & 0 deletions src/StanSample.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@ function __init__()
@require MCMCChains="c7f686f2-ff18-58e9-bc7b-31028e88f75d" include("../ext/MCMCChainsExt.jl")
@require AxisKeys="94b1ba4f-4ee9-5380-92f1-94cde586c3c5" include("../ext/AxisKeysExt.jl")
@require InferenceObjects="b5cf5a8d-e756-4ee3-b014-01d49d192c00" include("../ext/InferenceObjectsExt.jl")
@require DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0" include("../ext/DimensionalDataExt.jl")
end
end

Expand Down
30 changes: 12 additions & 18 deletions test/runtests.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -56,8 +56,6 @@ if haskey(ENV, "CMDSTAN") || haskey(ENV, "JULIA_CMDSTAN_HOME")

end

#if Int(VERSION.minor) > 8

test_bridgestan = [
"test_bridgestan/test_bridgestan.jl",
]
Expand All @@ -70,9 +68,19 @@ if haskey(ENV, "CMDSTAN") || haskey(ENV, "JULIA_CMDSTAN_HOME")
end
println()
end

#end

test_dimensionaldata = [
"test_dimensionaldata/test_dimensionaldata.jl",
]

@testset "DimensionalData interface" begin
for test in test_dimensionaldata
println("\nTesting: $test.")
include(joinpath(TestDir, test))
end
println()
end

println()
test_inferencedata = [
"test_inferencedata/test_inferencedata.jl",
Expand Down Expand Up @@ -175,20 +183,6 @@ if haskey(ENV, "CMDSTAN") || haskey(ENV, "JULIA_CMDSTAN_HOME")
println()
end

test_dimensionaldata = [
"test_dimensionaldata/test_dimensionaldata.jl",
]

#=
@testset "DimensionalData interface" begin
for test in test_dimensionaldata
println("\nTesting: $test.")
include(joinpath(TestDir, test))
end
println()
end
=#

test_keywords = [
"test_keywords/test_bernoulli_keyedarray_01.jl",
"test_keywords/test_bernoulli_keyedarray_02.jl",
Expand Down