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Merged
merged 4 commits into from
Jun 7, 2024
Merged

Add Aqua to tests #2257

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46e66c0
Add running Aqua to test suite
mhauru Jun 6, 2024
374413f
Remove undefined imports
mhauru Jun 6, 2024
ea18b6e
Add compat entries for stdlib dependencies
mhauru Jun 6, 2024
16e5ab7
Disable Aqua checking method ambiguities
mhauru Jun 6, 2024
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3 changes: 3 additions & 0 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -68,13 +68,16 @@ Compat = "4.15.0"
EllipticalSliceSampling = "0.5, 1, 2"
ForwardDiff = "0.10.3"
Libtask = "0.7, 0.8"
LinearAlgebra = "1"
LogDensityProblems = "2"
LogDensityProblemsAD = "1.7.0"
MCMCChains = "5, 6"
NamedArrays = "0.9, 0.10"
Optimization = "3"
OptimizationOptimJL = "0.1, 0.2, 0.3"
OrderedCollections = "1"
Printf = "1"
Random = "1"
Optim = "1"
Reexport = "0.2, 1"
Requires = "0.5, 1.0"
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3 changes: 0 additions & 3 deletions src/Turing.jl
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Expand Up @@ -92,8 +92,6 @@ export @model, # modelling
SGHMC,
HMCDA,
NUTS,
DynamicNUTS,
ANUTS,
PolynomialStepsize,
IS, # particle-based sampling
SMC,
Expand Down Expand Up @@ -121,7 +119,6 @@ export @model, # modelling
NamedDist, # Exports from DynamicPPL
predict,
pointwise_loglikelihoods,
elementwise_loglikelihoods,
generated_quantities,
logprior,
logjoint,
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17 changes: 0 additions & 17 deletions src/essential/Essential.jl
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Expand Up @@ -19,27 +19,10 @@ include("container.jl")

export @model,
@varname,
generate_observe,
translate_tilde!,
get_vars,
get_data,
get_default_values,
ParticleContainer,
Particle,
Trace,
fork,
forkr,
current_trace,
getweights,
getweight,
effectiveSampleSize,
sweep!,
ResampleWithESSThreshold,
AutoForwardDiff,
AutoTracker,
AutoZygote,
AutoReverseDiff,
value,
@logprob_str,
@prob_str

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2 changes: 0 additions & 2 deletions src/mcmc/Inference.jl
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Expand Up @@ -38,7 +38,6 @@ import StatsBase: predict

export InferenceAlgorithm,
Hamiltonian,
GibbsComponent,
StaticHamiltonian,
AdaptiveHamiltonian,
SampleFromUniform,
Expand All @@ -54,7 +53,6 @@ export InferenceAlgorithm,
SGHMC,
HMCDA,
NUTS, # Hamiltonian-like sampling
DynamicNUTS,
IS,
SMC,
CSMC,
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10 changes: 10 additions & 0 deletions test/Aqua.jl
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@@ -0,0 +1,10 @@
module AquaTests

using Aqua: Aqua
using Turing

# TODO(mhauru) We skip testing for method ambiguities because it catches a lot of problems
# in dependencies. Would like to check it for just Turing.jl itself though.
Aqua.test_all(Turing; ambiguities=false)
Comment on lines +6 to +8
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@devmotion devmotion Jun 6, 2024 •
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If you want to test ambiguities, I suggest

Suggested change
# TODO(mhauru) We skip testing for method ambiguities because it catches a lot of problems
# in dependencies. Would like to check it for just Turing.jl itself though.
Aqua.test_all(Turing; ambiguities=false)
@testset "Aqua" begin
# Test ambiguities separately without Base and Core
# Ref: https://github.com/JuliaTesting/Aqua.jl/issues/77
Aqua.test_all(Turing; ambiguities = false)
Aqua.test_ambiguities(Turing)
end

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@mhauru mhauru Jun 7, 2024

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Nice, thanks. I'll see if I can fix all the ambiguities, and if yes then commit this.

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@mhauru mhauru Jun 7, 2024

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I won't get to this today, and next week I'm off this project, so I'll merge what's here now and open an issue to come back to method ambiguities.


end
5 changes: 5 additions & 0 deletions test/Project.toml
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Expand Up @@ -3,6 +3,7 @@ AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
AdvancedMH = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170"
AdvancedPS = "576499cb-2369-40b2-a588-c64705576edc"
AdvancedVI = "b5ca4192-6429-45e5-a2d9-87aec30a685c"
Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
DistributionsAD = "ced4e74d-a319-5a8a-b0ac-84af2272839c"
Expand Down Expand Up @@ -39,6 +40,7 @@ AbstractMCMC = "5"
AdvancedMH = "0.6, 0.7, 0.8"
AdvancedPS = "0.6.0"
AdvancedVI = "0.2"
Aqua = "0.8"
Clustering = "0.14, 0.15"
Distributions = "0.25"
DistributionsAD = "0.6.3"
Expand All @@ -47,6 +49,7 @@ DynamicPPL = "0.27"
FiniteDifferences = "0.10.8, 0.11, 0.12"
ForwardDiff = "0.10.12 - 0.10.32, 0.10"
HypothesisTests = "0.11"
LinearAlgebra = "1"
LogDensityProblems = "2"
LogDensityProblemsAD = "1.4"
MCMCChains = "5, 6"
Expand All @@ -57,6 +60,8 @@ OptimizationBBO = "0.1, 0.2"
OptimizationNLopt = "0.1, 0.2"
OptimizationOptimJL = "0.1, 0.2, 0.3"
PDMats = "0.10, 0.11"
Pkg = "1"
Random = "1"
ReverseDiff = "1.4.2"
SpecialFunctions = "0.10.3, 1, 2"
StableRNGs = "1"
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4 changes: 4 additions & 0 deletions test/runtests.jl
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Expand Up @@ -26,6 +26,10 @@ macro timeit_include(path::AbstractString)
end

@testset "Turing" begin
@testset "Aqua" begin
@timeit_include("Aqua.jl")
end

@testset "essential" begin
@timeit_include("essential/ad.jl")
@timeit_include("essential/container.jl")
Expand Down