From eb9b2e0d60ef3dd85768d6e6a9f19de15b8f7130 Mon Sep 17 00:00:00 2001
From: Hong Ge <3279477+yebai@users.noreply.github.com>
Date: Sat, 29 Jul 2023 00:54:06 +0100
Subject: [PATCH] Fix duplicate of include and some bugs in tests  (#343)

* Fix duplicate include of common.jl

* Bugfix.

* bump version

* Bugfix
---
 Project.toml         | 2 +-
 test/abstractmcmc.jl | 1 -
 test/constructors.jl | 9 ++++-----
 test/contrib.jl      | 2 --
 test/cuda.jl         | 2 --
 test/hamiltonian.jl  | 3 ---
 test/integrator.jl   | 1 -
 test/mcmcchains.jl   | 1 -
 test/models.jl       | 2 --
 test/runtests.jl     | 3 +++
 test/sampler-vec.jl  | 1 -
 test/sampler.jl      | 1 -
 test/trajectory.jl   | 1 -
 13 files changed, 8 insertions(+), 21 deletions(-)

diff --git a/Project.toml b/Project.toml
index 7e006f1b..f98be0f0 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,6 +1,6 @@
 name = "AdvancedHMC"
 uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.5.2"
+version = "0.5.3"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
diff --git a/test/abstractmcmc.jl b/test/abstractmcmc.jl
index 52d6c35c..4d895c72 100644
--- a/test/abstractmcmc.jl
+++ b/test/abstractmcmc.jl
@@ -1,6 +1,5 @@
 using ReTest, Random, AdvancedHMC, ForwardDiff, AbstractMCMC
 using Statistics: mean
-include("common.jl")
 
 @testset "AbstractMCMC w/ gdemo" begin
     rng = MersenneTwister(0)
diff --git a/test/constructors.jl b/test/constructors.jl
index 8d66a79e..49b0cf89 100644
--- a/test/constructors.jl
+++ b/test/constructors.jl
@@ -1,5 +1,4 @@
 using AdvancedHMC, AbstractMCMC, Random
-include("common.jl")
 
 get_kernel_hyperparams(spl::HMC, state) = state.κ.τ.termination_criterion.L
 get_kernel_hyperparams(spl::HMCDA, state) = state.κ.τ.termination_criterion.λ
@@ -169,13 +168,13 @@ end
         spl = NUTS(0.8)
         T = AdvancedHMC.sampler_eltype(spl)
 
-        metric = make_metric(spl, logdensity)
+        metric = AdvancedHMC.make_metric(spl, logdensity)
         hamiltonian = Hamiltonian(metric, model)
 
-        init_params1 = make_init_params(rng, spl, logdensity, nothing)
+        init_params1 = AdvancedHMC.make_init_params(rng, spl, logdensity, nothing)
         @test typeof(init_params1) == Vector{T}
         @test length(init_params1) == d
-        init_params2 = make_init_params(rng, spl, logdensity, θ_init)
-        @test init_params2 === θ_init
+        init_params2 = AdvancedHMC.make_init_params(rng, spl, logdensity, θ_init)
+        @test init_params2 == θ_init
     end
 end
diff --git a/test/contrib.jl b/test/contrib.jl
index 1bba01fb..38a5023a 100644
--- a/test/contrib.jl
+++ b/test/contrib.jl
@@ -1,7 +1,5 @@
 using ReTest, AdvancedHMC, ForwardDiff, Zygote
 
-include("common.jl")
-
 @testset "contrib" begin
     @testset "ad" begin
         metric = UnitEuclideanMetric(D)
diff --git a/test/cuda.jl b/test/cuda.jl
index fb9655a9..39c02f92 100644
--- a/test/cuda.jl
+++ b/test/cuda.jl
@@ -4,8 +4,6 @@ using AdvancedHMC: DualValue, PhasePoint
 using CUDA
 
 @testset "AdvancedHMC GPU" begin
-    include("common.jl")
-
     n_chains = 1000
     n_samples = 1000
     dim = 5
diff --git a/test/hamiltonian.jl b/test/hamiltonian.jl
index 91607280..47948325 100644
--- a/test/hamiltonian.jl
+++ b/test/hamiltonian.jl
@@ -2,9 +2,6 @@ using ReTest, AdvancedHMC
 using AdvancedHMC: GaussianKinetic, DualValue, PhasePoint
 using LinearAlgebra: dot, diagm
 
-
-include("common.jl")
-
 @testset "Hamiltonian" begin
     f = x -> dot(x, x)
     g = x -> 2x
diff --git a/test/integrator.jl b/test/integrator.jl
index 00582034..672b480e 100644
--- a/test/integrator.jl
+++ b/test/integrator.jl
@@ -1,5 +1,4 @@
 using ReTest, Random, AdvancedHMC, ForwardDiff
-include("common.jl")
 
 using OrdinaryDiffEq
 using LinearAlgebra: dot
diff --git a/test/mcmcchains.jl b/test/mcmcchains.jl
index 1c896884..a555a90a 100644
--- a/test/mcmcchains.jl
+++ b/test/mcmcchains.jl
@@ -1,6 +1,5 @@
 using ReTest, Random, AdvancedHMC, ForwardDiff, AbstractMCMC, MCMCChains
 using Statistics: mean
-include("common.jl")
 
 @testset "MCMCChains w/ gdemo" begin
     rng = MersenneTwister(0)
diff --git a/test/models.jl b/test/models.jl
index 08be9197..cdff6ef3 100644
--- a/test/models.jl
+++ b/test/models.jl
@@ -1,7 +1,5 @@
 using ReTest, Random, AdvancedHMC, ForwardDiff
 using Statistics: mean
-include("common.jl")
-
 
 @testset "Models" begin
     @testset "gdemo" begin
diff --git a/test/runtests.jl b/test/runtests.jl
index 0a58c56a..382bb871 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -3,6 +3,7 @@ using FillArrays
 using AdvancedHMC: AdvancedHMC
 using LogDensityProblems: LogDensityProblems
 using LogDensityProblemsAD: LogDensityProblemsAD
+using ReTest
 
 println("Environment variables for testing")
 println(ENV)
@@ -11,6 +12,8 @@ const DIRECTORY_AdvancedHMC = dirname(dirname(pathof(AdvancedHMC)))
 const DIRECTORY_Turing_tests = joinpath(DIRECTORY_AdvancedHMC, "test", "turing")
 const GROUP = get(ENV, "AHMC_TEST_GROUP", "AdvancedHMC")
 
+include("common.jl")
+
 if GROUP == "All" || GROUP == "AdvancedHMC"
     using ReTest, CUDA
 
diff --git a/test/sampler-vec.jl b/test/sampler-vec.jl
index 2b85614a..b629c538 100644
--- a/test/sampler-vec.jl
+++ b/test/sampler-vec.jl
@@ -1,6 +1,5 @@
 using ReTest, AdvancedHMC, LinearAlgebra, UnicodePlots, Random
 using Statistics: mean, var, cov
-include("common.jl")
 
 @testset "sample (vectorized)" begin
     n_chains_max = 20
diff --git a/test/sampler.jl b/test/sampler.jl
index 94b32122..109f01a4 100644
--- a/test/sampler.jl
+++ b/test/sampler.jl
@@ -6,7 +6,6 @@ using AdvancedHMC: StaticTerminationCriterion, DynamicTerminationCriterion
 using Setfield
 using Statistics: mean, var, cov
 unicodeplots()
-include("common.jl")
 
 function test_stats(
     ::Trajectory{TS,I,TC},
diff --git a/test/trajectory.jl b/test/trajectory.jl
index 06da7399..2ff8acbe 100644
--- a/test/trajectory.jl
+++ b/test/trajectory.jl
@@ -1,7 +1,6 @@
 using ReTest, AdvancedHMC, Random
 using Statistics: mean
 using LinearAlgebra: dot
-include("common.jl")
 
 function makeplot(plt, traj_θ, ts_list...)
     function plotturn!(traj_θ, ts)