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Merged
merged 4 commits into from
Mar 5, 2022
Merged

Show timing and allocations for tests #48

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a4e6e4e
Show timing and allocations for tests
rikhuijzer Mar 5, 2022
9c5fb49
Merge branch 'main' into rh/measure-tests
rikhuijzer Mar 5, 2022
7c6a8e7
Revert removal of newline
rikhuijzer Mar 5, 2022
187aa25
Apply suggestions from code review
rikhuijzer Mar 5, 2022
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2 changes: 2 additions & 0 deletions test/Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,10 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"

[compat]
CSV = "0.9, 1"
CategoricalArrays = "0.10"
DataFrames = "1"
TimerOutputs = "0.5"
2 changes: 1 addition & 1 deletion test/data_constructors.jl
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@@ -1,4 +1,4 @@
@testset "data_constructors.jl" begin
@timed_testset "data_constructors" begin
@testset "data_response" begin
@testset "NamedTuples" begin
expected = [2, 3, 4, 5]
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2 changes: 1 addition & 1 deletion test/priors.jl
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@@ -1,4 +1,4 @@
@testset "prior.jl" begin
@timed_testset "priors" begin
@testset "types" begin
@test DefaultPrior() isa T.Prior

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17 changes: 16 additions & 1 deletion test/runtests.jl
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Expand Up @@ -5,6 +5,7 @@ using DataFrames
using CategoricalArrays: CategoricalValue
using CategoricalArrays: categorical, levels
using Statistics: mean, std
using TimerOutputs: TimerOutputs, @timeit
using Random: seed!

const T = TuringGLM
Expand All @@ -29,9 +30,23 @@ df_str = DataFrame(nt_str)

df_cat = DataFrame(nt_cat)

@testset "TuringGLM.jl" begin
# To capture time and allocation information.
const TIMEROUTPUT = TimerOutputs.TimerOutput()
macro timed_testset(str, block)
return quote
@timeit TIMEROUTPUT "$($(esc(str)))" begin
@testset "$($(esc(str)))" begin
$(esc(block))
end
end
end
end

@testset "TuringGLM" begin
include("data_constructors.jl")
include("utils.jl")
include("priors.jl")
include("turing_model.jl")
end

show(TIMEROUTPUT; compact=true, sortby=:firstexec)
14 changes: 7 additions & 7 deletions test/turing_model.jl
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@@ -1,10 +1,10 @@
@testset "turing_model.jl" begin
@timed_testset "turing_model" begin
DATA_DIR = joinpath("..", "data")
kidiq = CSV.read(joinpath(DATA_DIR, "kidiq.csv"), DataFrame)
wells = CSV.read(joinpath(DATA_DIR, "wells.csv"), DataFrame)
roaches = CSV.read(joinpath(DATA_DIR, "roaches.csv"), DataFrame)
cheese = CSV.read(joinpath(DATA_DIR, "cheese.csv"), DataFrame)
@testset "Gaussian Model" begin
@timed_testset "Gaussian Model" begin
f = @formula(kid_score ~ mom_iq * mom_hs)
@testset "standardize=false" begin
m = turing_model(f, kidiq)
Expand Down Expand Up @@ -38,7 +38,7 @@
@test quantile(chn)[Symbol("β[2]"), Symbol("50.0%")] ≈ 0.593 atol = 0.2
end
end
@testset "Student Model" begin
@timed_testset "TDist Model" begin
f = @formula(kid_score ~ mom_iq * mom_hs)
@testset "standardize=false" begin
m = turing_model(f, kidiq; model=TDist)
Expand All @@ -59,7 +59,7 @@
@test quantile(chn)[:ν, Symbol("50.0%")] ≈ 1.178 atol = 0.5
end
end
@testset "Logistic Model" begin
@timed_testset "Bernoulli Model" begin
f = @formula(switch ~ arsenic + dist + assoc + educ)
@testset "standardize=false" begin
m = turing_model(f, wells; model=Bernoulli)
Expand All @@ -78,7 +78,7 @@
@test quantile(chn)[Symbol("β[2]"), Symbol("50.0%")] ≈ -0.009 atol = 0.2
end
end
@testset "Pois Model" begin
@timed_testset "Poisson Model" begin
f = @formula(y ~ roach1 + treatment + senior + exposure2)
@testset "standardize=false" begin
m = turing_model(f, roaches; model=Poisson)
Expand All @@ -97,7 +97,7 @@
@test quantile(chn)[Symbol("β[2]"), Symbol("50.0%")] ≈ -0.5145 atol = 0.2
end
end
@testset "NegBin Model" begin
@timed_testset "NegativeBinomial Model" begin
f = @formula(y ~ roach1 + treatment + senior + exposure2)
@testset "standardize=false" begin
m = turing_model(f, roaches; model=NegativeBinomial)
Expand All @@ -118,7 +118,7 @@
@test quantile(chn)[:ϕ⁻, Symbol("50.0%")] ≈ 3.56 atol = 0.2
end
end
@testset "Hierarchical Model" begin
@timed_testset "Hierarchical Model" begin
f = @formula(y ~ (1 | cheese) + background)
m = turing_model(f, cheese)
chn = sample(seed!(123), m, NUTS(), MCMCThreads(), 2_000, 2)
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6 changes: 3 additions & 3 deletions test/utils.jl
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@@ -1,5 +1,5 @@
@testset "utils" begin
@testset "center_predictors" begin
@timed_testset "utils" begin
@timed_testset "center_predictors" begin
@testset "NamedTuples" begin
f = @formula(y_int ~ x_float + x_cat)
X = T.data_fixed_effects(f, nt_str)
Expand Down Expand Up @@ -29,7 +29,7 @@
end
end

@testset "standardize_predictors" begin
@timed_testset "standardize_predictors" begin
@testset "NamedTuples" begin
f = @formula(y_int ~ x_float + x_cat)
y = T.data_response(f, nt_str)
Expand Down