rename a few folders for clarity (#2073)

* rename a few folders for clarity * move abstractmcmc into mcmc * rename AdvancedSMC to particle_mcmc * more moves. * Reorganised some files. (#2055) * Moved some files. * Merge branch 'hg/reorg-algorithms' into hg/reorg * Merge branch 'hg/reorg-algorithms' into hg/reorg * remove empty test file * Update Optimisation.jl
TuringLang · Sep 4, 2023 · c0c8130 · c0c8130 · yebai · Sep 4, 2023
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diff --git a/src/Turing.jl b/src/Turing.jl
@@ -46,13 +46,13 @@ include("stdlib/RandomMeasures.jl")
 include("essential/Essential.jl")
 Base.@deprecate_binding Core Essential false
 using .Essential
-include("inference/Inference.jl")  # inference algorithms
+include("mcmc/Inference.jl")  # inference algorithms
 using .Inference
 include("variational/VariationalInference.jl")
 using .Variational
 
-include("modes/ModeEstimation.jl")
-using .ModeEstimation
+include("optimisation/Optimisation.jl")
+using .Optimisation
 
 ###########
 # Exports #

diff --git a/src/inference/Inference.jl → src/mcmc/Inference.jl b/src/inference/Inference.jl → src/mcmc/Inference.jl
@@ -507,12 +507,12 @@ include("ess.jl")
 include("hmc.jl")
 include("mh.jl")
 include("is.jl")
-include("AdvancedSMC.jl")
+include("particle_mcmc.jl")
 include("gibbs_conditional.jl")
 include("gibbs.jl")
-include("../contrib/inference/sghmc.jl")
+include("sghmc.jl")
 include("emcee.jl")
-include("../contrib/inference/abstractmcmc.jl")
+include("abstractmcmc.jl")
 
 ################
 # Typing tools #

diff --git a/src/contrib/inference/abstractmcmc.jl → src/mcmc/abstractmcmc.jl b/src/contrib/inference/abstractmcmc.jl → src/mcmc/abstractmcmc.jl
diff --git a/src/inference/emcee.jl → src/mcmc/emcee.jl b/src/inference/emcee.jl → src/mcmc/emcee.jl
diff --git a/src/inference/ess.jl → src/mcmc/ess.jl b/src/inference/ess.jl → src/mcmc/ess.jl
diff --git a/src/inference/gibbs.jl → src/mcmc/gibbs.jl b/src/inference/gibbs.jl → src/mcmc/gibbs.jl
diff --git a/src/inference/gibbs_conditional.jl → src/mcmc/gibbs_conditional.jl b/src/inference/gibbs_conditional.jl → src/mcmc/gibbs_conditional.jl
diff --git a/src/inference/hmc.jl → src/mcmc/hmc.jl b/src/inference/hmc.jl → src/mcmc/hmc.jl
diff --git a/src/inference/is.jl → src/mcmc/is.jl b/src/inference/is.jl → src/mcmc/is.jl
diff --git a/src/inference/mh.jl → src/mcmc/mh.jl b/src/inference/mh.jl → src/mcmc/mh.jl
diff --git a/src/inference/AdvancedSMC.jl → src/mcmc/particle_mcmc.jl b/src/inference/AdvancedSMC.jl → src/mcmc/particle_mcmc.jl
diff --git a/src/contrib/inference/sghmc.jl → src/mcmc/sghmc.jl b/src/contrib/inference/sghmc.jl → src/mcmc/sghmc.jl
diff --git a/src/modes/ModeEstimation.jl → src/optimisation/Optimisation.jl b/src/modes/ModeEstimation.jl → src/optimisation/Optimisation.jl
@@ -1,4 +1,4 @@
-module ModeEstimation
+module Optimisation
 
 using ..Turing
 using Bijectors

diff --git a/test/contrib/inference/AdvancedSMCExtenstions.jl b/test/contrib/inference/AdvancedSMCExtenstions.jl
diff --git a/test/modes/ModeEstimation.jl → test/ext/Optimisation.jl b/test/modes/ModeEstimation.jl → test/ext/Optimisation.jl
@@ -1,4 +1,4 @@
-@testset "ModeEstimation.jl" begin
+@testset "ext/Optimisation.jl" begin
     @testset "gdemo" begin
         @testset "MLE" begin
             Random.seed!(222)

diff --git a/test/contrib/inference/dynamichmc.jl → test/ext/dynamichmc.jl b/test/contrib/inference/dynamichmc.jl → test/ext/dynamichmc.jl
diff --git a/test/inference/Inference.jl → test/mcmc/Inference.jl b/test/inference/Inference.jl → test/mcmc/Inference.jl
diff --git a/test/contrib/inference/abstractmcmc.jl → test/mcmc/abstractmcmc.jl b/test/contrib/inference/abstractmcmc.jl → test/mcmc/abstractmcmc.jl
diff --git a/test/inference/emcee.jl → test/mcmc/emcee.jl b/test/inference/emcee.jl → test/mcmc/emcee.jl
diff --git a/test/inference/ess.jl → test/mcmc/ess.jl b/test/inference/ess.jl → test/mcmc/ess.jl
diff --git a/test/inference/gibbs.jl → test/mcmc/gibbs.jl b/test/inference/gibbs.jl → test/mcmc/gibbs.jl
diff --git a/test/inference/gibbs_conditional.jl → test/mcmc/gibbs_conditional.jl b/test/inference/gibbs_conditional.jl → test/mcmc/gibbs_conditional.jl
diff --git a/test/inference/hmc.jl → test/mcmc/hmc.jl b/test/inference/hmc.jl → test/mcmc/hmc.jl
diff --git a/test/inference/is.jl → test/mcmc/is.jl b/test/inference/is.jl → test/mcmc/is.jl
diff --git a/test/inference/mh.jl → test/mcmc/mh.jl b/test/inference/mh.jl → test/mcmc/mh.jl
diff --git a/test/inference/AdvancedSMC.jl → test/mcmc/particle_mcmc.jl b/test/inference/AdvancedSMC.jl → test/mcmc/particle_mcmc.jl
diff --git a/test/contrib/inference/sghmc.jl → test/mcmc/sghmc.jl b/test/contrib/inference/sghmc.jl → test/mcmc/sghmc.jl
diff --git a/test/inference/utilities.jl → test/mcmc/utilities.jl b/test/inference/utilities.jl → test/mcmc/utilities.jl
diff --git a/test/modes/OptimInterface.jl → test/optimisation/OptimInterface.jl b/test/modes/OptimInterface.jl → test/optimisation/OptimInterface.jl
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -58,10 +58,10 @@ macro timeit_include(path::AbstractString) :(@timeit TIMEROUTPUT $path include($
     end
 
     @testset "samplers (without AD)" begin
-        @timeit_include("inference/AdvancedSMC.jl")
-        @timeit_include("inference/emcee.jl")
-        @timeit_include("inference/ess.jl")
-        @timeit_include("inference/is.jl")
+        @timeit_include("mcmc/particle_mcmc.jl")
+        @timeit_include("mcmc/emcee.jl")
+        @timeit_include("mcmc/ess.jl")
+        @timeit_include("mcmc/is.jl")
     end
 
     Turing.setrdcache(false)
@@ -71,24 +71,24 @@ macro timeit_include(path::AbstractString) :(@timeit TIMEROUTPUT $path include($
             @info "Testing $(adbackend)"
             @testset "inference: $adbackend" begin
                 @testset "samplers" begin
-                    @timeit_include("inference/gibbs.jl")
-                    @timeit_include("inference/gibbs_conditional.jl")
-                    @timeit_include("inference/hmc.jl")
-                    @timeit_include("inference/Inference.jl")
-                    @timeit_include("contrib/inference/dynamichmc.jl")
-                    @timeit_include("contrib/inference/sghmc.jl")
-                    @timeit_include("contrib/inference/abstractmcmc.jl")
-                    @timeit_include("inference/mh.jl")
+                    @timeit_include("mcmc/gibbs.jl")
+                    @timeit_include("mcmc/gibbs_conditional.jl")
+                    @timeit_include("mcmc/hmc.jl")
+                    @timeit_include("mcmc/Inference.jl")
+                    @timeit_include("mcmc/sghmc.jl")
+                    @timeit_include("mcmc/abstractmcmc.jl")
+                    @timeit_include("mcmc/mh.jl")
+                    @timeit_include("ext/dynamichmc.jl")
                 end
             end
 
             @testset "variational algorithms : $adbackend" begin
                 @timeit_include("variational/advi.jl")
             end
 
-            @testset "modes : $adbackend" begin
-                @timeit_include("modes/ModeEstimation.jl")
-                @timeit_include("modes/OptimInterface.jl")
+            @testset "mode estimation : $adbackend" begin
+                @timeit_include("optimisation/OptimInterface.jl")
+                @timeit_include("ext/Optimisation.jl")
             end
 
         end
@@ -105,7 +105,7 @@ macro timeit_include(path::AbstractString) :(@timeit TIMEROUTPUT $path include($
     end
 
     @testset "utilities" begin
-        @timeit_include("inference/utilities.jl")
+        @timeit_include("mcmc/utilities.jl")
     end
 end