From af812b88c87b144ae6e31447679cb4ac7367898c Mon Sep 17 00:00:00 2001
From: Markus Hauru <markus@mhauru.org>
Date: Fri, 7 Jun 2024 18:21:43 +0200
Subject: [PATCH] Add Aqua to tests (#2257)

* Add running Aqua to test suite

* Remove undefined imports

* Add compat entries for stdlib dependencies

See
https://discourse.julialang.org/t/psa-compat-requirements-in-the-general-registry-are-changing/104958
for why this is necessary

* Disable Aqua checking method ambiguities
---
 Project.toml               |  3 +++
 src/Turing.jl              |  3 ---
 src/essential/Essential.jl | 17 -----------------
 src/mcmc/Inference.jl      |  2 --
 test/Aqua.jl               | 10 ++++++++++
 test/Project.toml          |  5 +++++
 test/runtests.jl           |  4 ++++
 7 files changed, 22 insertions(+), 22 deletions(-)
 create mode 100644 test/Aqua.jl

diff --git a/Project.toml b/Project.toml
index 99e7b316b..a870ae9ff 100644
--- a/Project.toml
+++ b/Project.toml
@@ -68,6 +68,7 @@ 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"
@@ -75,6 +76,8 @@ 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"
diff --git a/src/Turing.jl b/src/Turing.jl
index e3ba2f81d..8dfb8df28 100644
--- a/src/Turing.jl
+++ b/src/Turing.jl
@@ -92,8 +92,6 @@ export @model,                 # modelling
     SGHMC,
     HMCDA,
     NUTS,
-    DynamicNUTS,
-    ANUTS,
     PolynomialStepsize,
     IS,                     # particle-based sampling
     SMC,
@@ -121,7 +119,6 @@ export @model,                 # modelling
     NamedDist,              # Exports from DynamicPPL
     predict,
     pointwise_loglikelihoods,
-    elementwise_loglikelihoods,
     generated_quantities,
     logprior,
     logjoint,
diff --git a/src/essential/Essential.jl b/src/essential/Essential.jl
index 12413bef2..778e2a62f 100644
--- a/src/essential/Essential.jl
+++ b/src/essential/Essential.jl
@@ -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
 
diff --git a/src/mcmc/Inference.jl b/src/mcmc/Inference.jl
index 311632a3b..b70426992 100644
--- a/src/mcmc/Inference.jl
+++ b/src/mcmc/Inference.jl
@@ -38,7 +38,6 @@ import StatsBase: predict
 
 export  InferenceAlgorithm,
         Hamiltonian,
-        GibbsComponent,
         StaticHamiltonian,
         AdaptiveHamiltonian,
         SampleFromUniform,
@@ -54,7 +53,6 @@ export  InferenceAlgorithm,
         SGHMC,
         HMCDA,
         NUTS,       # Hamiltonian-like sampling
-        DynamicNUTS,
         IS,
         SMC,
         CSMC,
diff --git a/test/Aqua.jl b/test/Aqua.jl
new file mode 100644
index 000000000..0b536770b
--- /dev/null
+++ b/test/Aqua.jl
@@ -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)
+
+end
diff --git a/test/Project.toml b/test/Project.toml
index 77df264f5..6515b17b3 100644
--- a/test/Project.toml
+++ b/test/Project.toml
@@ -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"
@@ -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"
@@ -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"
@@ -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"
diff --git a/test/runtests.jl b/test/runtests.jl
index f4f0ca9b3..52205d86e 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -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")