Fix duplicate of include and some bugs in tests (#343)

* Fix duplicate include of common.jl

* Bugfix.

* bump version

* Bugfix

Author: yebai

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"

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)

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

test/contrib.jl

@@ -1,7 +1,5 @@
 using ReTest, AdvancedHMC, ForwardDiff, Zygote
 
-include("common.jl")
-
 @testset "contrib" begin
     @testset "ad" begin
         metric = UnitEuclideanMetric(D)

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

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

test/integrator.jl

@@ -1,5 +1,4 @@
 using ReTest, Random, AdvancedHMC, ForwardDiff
-include("common.jl")
 
 using OrdinaryDiffEq
 using LinearAlgebra: dot

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)

test/models.jl

@@ -1,7 +1,5 @@
 using ReTest, Random, AdvancedHMC, ForwardDiff
 using Statistics: mean
-include("common.jl")
-
 
 @testset "Models" begin
     @testset "gdemo" begin

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
 

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

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},

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)