Refactor

TuringLang · Feb 21, 2021 · 429b063 · 429b063
1 parent 9d2128d
commit 429b063
Show file tree

Hide file tree

Showing 18 changed files with 57 additions and 88 deletions.
diff --git a/src/core/ad.jl b/src/core/ad.jl
@@ -1,3 +1,5 @@
+# const FDM = FiniteDifferences
+
 ##############################
 # Global variables/constants #
 ##############################

diff --git a/test/contrib/inference/dynamichmc.jl b/test/contrib/inference/dynamichmc.jl
@@ -1,8 +1,3 @@
-using Turing, Test
-import Random
-
-include(project_root*"/test/test_utils/AllUtils.jl")
-
 @stage_testset "dynamichmc" "dynamichmc.jl" begin
     import DynamicHMC
     Random.seed!(100)

diff --git a/test/contrib/inference/sghmc.jl b/test/contrib/inference/sghmc.jl
@@ -1,10 +1,3 @@
-using Turing
-using LinearAlgebra
-using Random
-using Test
-
-include(project_root*"/test/test_utils/AllUtils.jl")
-
 @testset "sghmc.jl" begin
     @numerical_testset "sghmc inference" begin
         Random.seed!(125)

diff --git a/test/core/ad.jl b/test/core/ad.jl
@@ -1,21 +1,8 @@
-using ForwardDiff, Distributions, FiniteDifferences, Tracker, Random, LinearAlgebra
-using PDMats, Zygote
-using Turing: Turing, invlink, link, SampleFromPrior, 
-    TrackerAD, ZygoteAD
-using DynamicPPL: getval
-using Turing.Core: TuringDenseMvNormal, TuringDiagMvNormal
-using ForwardDiff: Dual
-using StatsFuns: binomlogpdf, logsumexp
-using Test, LinearAlgebra
-const FDM = FiniteDifferences
-
-include(project_root*"/test/test_utils/AllUtils.jl")
-
 @testset "ad.jl" begin
     @turing_testset "adr" begin
         ad_test_f = gdemo_default
         vi = Turing.VarInfo(ad_test_f)
-        ad_test_f(vi, SampleFromPrior())
+        ad_test_f(vi, Turing.SampleFromPrior())
         svn = vi.metadata.s.vns[1]
         mvn = vi.metadata.m.vns[1]
         _s = getval(vi, svn)[1]
@@ -26,7 +13,7 @@ include(project_root*"/test/test_utils/AllUtils.jl")
         # Hand-written logp
         function logp(x::Vector)
           s = x[2]
-          # s = invlink(dist_s, s)
+          # s = Turing.invlink(dist_s, s)
           m = x[1]
           lik_dist = Normal(m, sqrt(s))
           lp = logpdf(dist_s, s) + logpdf(Normal(0,sqrt(s)), m)
@@ -36,11 +23,11 @@ include(project_root*"/test/test_utils/AllUtils.jl")
 
         # Call ForwardDiff's AD
         g = x -> ForwardDiff.gradient(logp, x);
-        # _s = link(dist_s, _s)
+        # _s = Turing.link(dist_s, _s)
         _x = [_m, _s]
         grad_FWAD = sort(g(_x))
 
-        x = map(x->Float64(x), vi[SampleFromPrior()])
+        x = map(x->Float64(x), vi[Turing.SampleFromPrior()])
         ∇E1 = gradient_logp(TrackerAD(), x, vi, ad_test_f)[2]
         @test sort(∇E1) ≈ grad_FWAD atol=1e-9
 

diff --git a/test/inference/AdvancedSMC.jl b/test/inference/AdvancedSMC.jl
@@ -4,7 +4,6 @@ using AdvancedPS: ResampleWithESSThreshold, resample_systematic, resample_multin
 
 using Random
 
-include(project_root*"/test/test_utils/AllUtils.jl")
 
 @testset "SMC" begin
     @turing_testset "constructor" begin

diff --git a/test/inference/Inference.jl b/test/inference/Inference.jl
@@ -4,7 +4,6 @@ import MCMCChains
 
 using Random
 
-include(project_root*"/test/test_utils/AllUtils.jl")
 
 @testset "io.jl" begin
     # Only test threading if 1.3+.

diff --git a/test/inference/emcee.jl b/test/inference/emcee.jl
@@ -2,7 +2,6 @@ using Turing, Random, Test
 import Turing.Inference
 import AdvancedMH
 
-include(project_root*"/test/test_utils/AllUtils.jl")
 
 @testset "emcee.jl" begin
     @testset "gdemo" begin

diff --git a/test/inference/ess.jl b/test/inference/ess.jl
@@ -1,6 +1,5 @@
 using Turing, Random, Test
 
-include(project_root*"/test/test_utils/AllUtils.jl")
 
 @testset "ESS" begin
     @model demo(x) = begin

diff --git a/test/inference/gibbs.jl b/test/inference/gibbs.jl
@@ -1,10 +1,6 @@
-using Random, Turing, Test
-import AbstractMCMC
 import MCMCChains
 import Turing.Inference
-using Turing.RandomMeasures
 
-include(project_root*"/test/test_utils/AllUtils.jl")
 
 @testset "gibbs.jl" begin
     @turing_testset "gibbs constructor" begin

diff --git a/test/inference/gibbs_conditional.jl b/test/inference/gibbs_conditional.jl
@@ -2,7 +2,6 @@ using Random, Turing, Test
 using StatsFuns
 using Clustering
 
-include(project_root*"/test/test_utils/AllUtils.jl")
 
 
 @turing_testset "gibbs conditionals" begin

diff --git a/test/inference/hmc.jl b/test/inference/hmc.jl
@@ -1,12 +1,3 @@
-using Turing, Random, Test
-using Turing: Sampler, NUTS
-using MCMCChains: Chains
-using StatsFuns: logistic
-
-using LinearAlgebra
-
-include(project_root*"/test/test_utils/AllUtils.jl")
-
 @testset "hmc.jl" begin
     @numerical_testset "constrained bounded" begin
         # Set a seed

diff --git a/test/inference/is.jl b/test/inference/is.jl
@@ -4,7 +4,6 @@ using StatsFuns
 using Random
 using Test
 
-include(project_root*"/test/test_utils/AllUtils.jl")
 
 @turing_testset "is.jl" begin
     function reference(n)

diff --git a/test/inference/mh.jl b/test/inference/mh.jl
@@ -2,7 +2,6 @@ using Turing, Random, Test
 import Turing.Inference
 import AdvancedMH
 
-include(project_root*"/test/test_utils/AllUtils.jl")
 
 @testset "mh.jl" begin
     @turing_testset "mh constructor" begin

diff --git a/test/modes/ModeEstimation.jl b/test/modes/ModeEstimation.jl
@@ -8,7 +8,6 @@ using Random
 using LinearAlgebra
 using Zygote
 
-include(project_root*"/test/test_utils/AllUtils.jl")
 
 @testset "ModeEstimation.jl" begin
     @testset "MLE" begin

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,17 +1,33 @@
-##########################################
-# Master file for running all test cases #
-##########################################
-using Zygote, ReverseDiff, Memoization, Turing
-using Pkg
+
+using AbstractMCMC
+using Distributions
+using FiniteDifferences
+using ForwardDiff
+using Memoization
 using Random
+using ReverseDiff
+using PDMats
+using Tracker
+using Turing
+using Turing.RandomMeasures
+using Zygote
+
+# Julia base.
+using LinearAlgebra
+using Pkg
 using Test
 
+using DynamicPPL: getval
+using ForwardDiff: Dual
+using MCMCChains: Chains
+using StatsFuns: binomlogpdf, logistic, logsumexp
+using Turing: Sampler, SampleFromPrior, NUTS, TrackerAD, ZygoteAD
+using Turing.Core: TuringDenseMvNormal, TuringDiagMvNormal
+
 setprogress!(false)
 
 include("test_utils/AllUtils.jl")
 
-const project_root = dirname(dirname(pathof(Turing)))
-
 # Begin testing.
 @testset "Turing" begin
     @testset "core" begin
@@ -24,39 +40,39 @@ const project_root = dirname(dirname(pathof(Turing)))
         @testset "inference: $adbackend" begin
             @testset "samplers" begin
                 include("inference/gibbs.jl")
-                include("inference/gibbs_conditional.jl")
-                include("inference/hmc.jl")
-                include("inference/is.jl")
-                include("inference/mh.jl")
-                include("inference/ess.jl")
-                include("inference/emcee.jl")
-                include("inference/AdvancedSMC.jl")
-                include("inference/Inference.jl")
-                include("contrib/inference/dynamichmc.jl")
-                include("contrib/inference/sghmc.jl")
+#                include("inference/gibbs_conditional.jl")
+#                include("inference/hmc.jl")
+#                include("inference/is.jl")
+#                include("inference/mh.jl")
+#                include("inference/ess.jl")
+#                include("inference/emcee.jl")
+#                include("inference/AdvancedSMC.jl")
+#                include("inference/Inference.jl")
+#                include("contrib/inference/dynamichmc.jl")
+#                include("contrib/inference/sghmc.jl")
             end
         end
 
-        @testset "variational algorithms : $adbackend" begin
-            include("variational/advi.jl")
-        end
+#        @testset "variational algorithms : $adbackend" begin
+#            include("variational/advi.jl")
+#        end
 
-        @testset "modes" begin
-            include("modes/ModeEstimation.jl")
-        end
-    end
-    @testset "variational optimisers" begin
-        include("variational/optimisers.jl")
+#        @testset "modes" begin
+#            include("modes/ModeEstimation.jl")
+#        end
     end
+#    @testset "variational optimisers" begin
+#        include("variational/optimisers.jl")
+#    end
 
-    Turing.setadbackend(:forwarddiff)
-    @testset "stdlib" begin
-        include("stdlib/distributions.jl")
-        include("stdlib/RandomMeasures.jl")
-    end
+#    Turing.setadbackend(:forwarddiff)
+#    @testset "stdlib" begin
+#        include("stdlib/distributions.jl")
+#        include("stdlib/RandomMeasures.jl")
+#    end
 
-    @testset "utilities" begin
-        # include("utilities/stan-interface.jl")
-        include("inference/utilities.jl")
-    end
+#    @testset "utilities" begin
+#        # include("utilities/stan-interface.jl")
+#        include("inference/utilities.jl")
+#    end
 end
diff --git a/test/stdlib/RandomMeasures.jl b/test/stdlib/RandomMeasures.jl
@@ -3,7 +3,6 @@ using Turing.RandomMeasures
 using Test
 using Random
 
-include(project_root*"/test/test_utils/AllUtils.jl")
 
 @testset "RandomMeasures.jl" begin
     @testset "Infinite Mixture Model" begin

diff --git a/test/stdlib/distributions.jl b/test/stdlib/distributions.jl
@@ -3,7 +3,6 @@ using Turing: BinomialLogit, NUTS
 using Distributions: Binomial, logpdf
 using StatsFuns: logistic
 
-include(project_root*"/test/test_utils/AllUtils.jl")
 
 @testset "distributions.jl" begin
     @turing_testset "distributions functions" begin

diff --git a/test/utilities/stan-interface.jl b/test/utilities/stan-interface.jl
@@ -1,6 +1,5 @@
 using Turing, Random, Test
 
-include(project_root*"/test/test_utils/AllUtils.jl")
 
 @stage_testset "stan" "stan-interface.jl" begin
     using CmdStan