Solve compatibility with Julia 0.6 (#341, #330, #293)

* Initial support for infix ~ (#173).

* seperate model wrapper call in sample.jl test

* update ForwardDiff.Dual signature

* sample.jl test passed

* fix some tests for Julia 0.6

* remove typealias for 0.6

* make some functions 0.6-ish

* make abstract 0.6-ish

* change some decpreated functions

* Update .travis.yml

* Update appveyor.yml

* Update appveyor.yml

* fix test

* Deprecations on package loading fixed

* fix deprecations

* implement callbacks for inner function

* fix model type bug

* Fix type

* update Dual in benchmark

* update Dual constructor

* Bump up required Julia version to 0.6

* Disable depreciated warning messages for `consume/produce`.

* Remove duplicate definition of produce.

* fix floor, tanh, abs, log

* fix logpdf warning and bug

* fix vec assume init

* Travis: Allow `Benchmarking` test to fail.

Author: yebai

.travis.yml

@@ -8,7 +8,7 @@ addons:
            - g++-5
 language: julia
 julia:
-  - 0.5
+  - 0.6
 os:
   - linux
   - osx
@@ -36,6 +36,7 @@ matrix:
     allow_failures:
        - env: GROUP=Test
          os: osx
+       - env: GROUP=Bench
        - env: GROUP=LDA
        - env: GROUP=MOC
        - env: GROUP=SV

REQUIRE

@@ -1,4 +1,4 @@
-julia 0.5
+julia 0.6
 
 Stan
 Distributions 0.11.0

appveyor.yml

@@ -1,11 +1,11 @@
 environment:
   matrix:
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.5/julia-0.5.0-win64.exe"
+  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6.0-win64.exe"
     MINGW_DIR: mingw64
     # MINGW_URL: https://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win64/Personal%20Builds/mingw-builds/5.3.0/threads-win32/seh/x86_64-5.3.0-release-win32-seh-rt_v4-rev0.7z/download
     MINGW_URL: http://mlg.eng.cam.ac.uk/hong/x86_64-5.3.0-release-win32-seh-rt_v4-rev0.7z
     MINGW_ARCHIVE: x86_64-5.3.0-release-win32-seh-rt_v4-rev0.7z
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x86/0.5/julia-0.5.0-win32.exe"
+  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x86/0.6/julia-0.6.0-win32.exe"
     MINGW_DIR: mingw32
     # MINGW_URL: https://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win32/Personal%20Builds/mingw-builds/5.3.0/threads-win32/dwarf/i686-5.3.0-release-win32-dwarf-rt_v4-rev0.7z/download
     MINGW_URL: http://mlg.eng.cam.ac.uk/hong/i686-5.3.0-release-win32-dwarf-rt_v4-rev0.7z

benchmarks/optimization.jl

@@ -290,7 +290,7 @@ optRes *= "realpart(): \n"
 
 using ForwardDiff: Dual
 
-ds = [Dual{10,Float64}(rand()) for i = 1:1000]
+ds = [Dual{Void,Float64,10}(rand()) for i = 1:1000]
 
 t_map = @elapsed for i = 1:1000 map(d -> d.value, ds) end
 t_list = @elapsed for i = 1:1000 Float64[ds[i].value for i = 1:length(ds)] end
@@ -304,7 +304,7 @@ optRes *= "Constructing Dual numbers: \n"
 
 dps = zeros(44); dps[11] = 1;
 
-t_dualnumbers = @elapsed for _ = 1:(44*2000*5) ForwardDiff.Dual(1.1, dps...) end
+t_dualnumbers = @elapsed for _ = 1:(44*2000*5) ForwardDiff.Dual{Void, Float64, 44}(1.1, dps) end
 
 optRes *= "44*2000*5 times: $t_dualnumbers\n"
 

example-models/nips-2017/gmm.model.jl

@@ -28,4 +28,4 @@ p = [ 0.2,  0.2,   0.2, 0.2,  0.2]
 # μ = [   0,    1,     2, 3.5, 4.25] + 0.5 * collect(0:4)
 μ = [   0,    1,     2, 3.5, 4.25] + 2.5 * collect(0:4)
 s = [-0.5, -1.5, -0.75,  -2, -0.5]
-σ = exp(s)
+σ = exp.(s)

example-models/nips-2017/sv.model.jl

@@ -5,9 +5,9 @@
   μ ~ Cauchy(0, 10)
   h = tzeros(Real, T)
   h[1] ~ Normal(μ, σ / sqrt(1 - ϕ^2))
-  y[1] ~ Normal(0, exp(h[1] / 2))
+  y[1] ~ Normal(0, exp.(h[1] / 2))
   for t = 2:T
     h[t] ~ Normal(μ + ϕ * (h[t-1] - μ) , σ)
-    y[t] ~ Normal(0, exp(h[t] / 2))
+    y[t] ~ Normal(0, exp.(h[t] / 2))
   end
 end

example-models/nips-2017/sv.sim.jl

@@ -16,7 +16,7 @@ for t in 2:T
 end
 y = Vector{Float64}(T);
 for t in 1:T
-  y[t] = rand(Normal(0, exp(h[t] / 2)));
+  y[t] = rand(Normal(0, exp.(h[t] / 2)));
 end
 
 

example-models/nuts-paper/lr_helper.jl

@@ -7,7 +7,7 @@ readlrdata() = begin
   open("lr_nuts.data") do f
     while !eof(f)
       raw_line = readline(f)
-      data_str = filter(str -> length(str) > 0, split(raw_line, r"[ ]+")[1:end-1])
+      data_str = Iterators.filter(str -> length(str) > 0, split(raw_line, r"[ ]+")[1:end-1])
       data = map(str -> parse(str), data_str)
       x = cat(1, x, data[1:end-1]')
       y = cat(1, y, data[end] - 1)  # turn {1, 2} to {0, 1}

example-models/nuts-paper/sv_nuts.jl

@@ -14,7 +14,7 @@ y = readsvdata()
   s[1] ~ Exponential(1/100)
   for i = 2:N
     s[i] ~ Normal(log(s[i-1]), τ)
-    s[i] = exp(s[i])
+    s[i] = exp.(s[i])
     dy = log(y[i] / y[i-1]) / s[i]
     dy ~ TDist(ν)
   end

example-models/sgld-paper/lr_helper.jl

@@ -8,7 +8,7 @@ readlrdata() = begin
   open("a9a2000.data") do f
     while !eof(f)
       raw_line = readline(f)
-      data_str = filter(str -> length(str) > 0, split(raw_line, r"[ ]+")[1:end-1])
+      data_str = Iterators.filter(str -> length(str) > 0, split(raw_line, r"[ ]+")[1:end-1])
       data = map(str -> parse(str), data_str)
       x_tmp = zeros(Int32, d)
       x_tmp[data[2:end]] = 1

example-models/stan-models/normal-mixture.model.jl

@@ -8,7 +8,7 @@ using ForwardDiff: Dual
 
   theta ~ Uniform(0, 1)
 
-  mu = tzeros(Dual, 2)
+  mu = Vector{Real}(2) # mu is sampled by HMC
   for i = 1:2
     mu[i] ~ Normal(0, 10)
   end
@@ -25,6 +25,6 @@ using ForwardDiff: Dual
   # logtheta_p = map(yᵢ -> [log(theta) + logpdf(Normal(mu[1], 1.0), yᵢ), log(1 - theta) + logpdf(Normal(mu[2], 1.0), yᵢ)], y)
   # map!(logtheta_pᵢ -> logtheta_pᵢ - logsumexp(logtheta_pᵢ), logtheta_p)   # normalization
   # for i = 1:N
-  #   k[i] ~ Categorical(exp(logtheta_p[i]))
+  #   k[i] ~ Categorical(exp.(logtheta_p[i]))
   # end
 end

src/Turing.jl

@@ -55,8 +55,8 @@ global const CACHERANGES = 0b01
 # Sampler abstraction #
 #######################
 
-abstract InferenceAlgorithm
-abstract Hamiltonian <: InferenceAlgorithm
+abstract type InferenceAlgorithm end
+abstract type Hamiltonian <: InferenceAlgorithm end
 
 doc"""
     Sampler{T}

src/core/ad.jl

@@ -55,12 +55,12 @@ gradient(vi::VarInfo, model::Function, spl::Union{Void, Sampler}) = begin
       vals = getval(vi, vns[i])
       if vns[i] in vn_chunk        # for each variable to compute gradient in this round
         for i = 1:l
-          vi[range[i]] = ForwardDiff.Dual{CHUNKSIZE, Float64}(realpart(vals[i]), SEEDS[dim_count])
+          vi[range[i]] = ForwardDiff.Dual{Void, Float64, CHUNKSIZE}(realpart(vals[i]), SEEDS[dim_count])
           dim_count += 1      # count
         end
       else                    # for other varilables (no gradient in this round)
         for i = 1:l
-          vi[range[i]] = ForwardDiff.Dual{CHUNKSIZE, Float64}(realpart(vals[i]))
+          vi[range[i]] = ForwardDiff.Dual{Void, Float64, CHUNKSIZE}(realpart(vals[i]))
         end
       end
     end
@@ -83,7 +83,7 @@ gradient(vi::VarInfo, model::Function, spl::Union{Void, Sampler}) = begin
 end
 
 verifygrad(grad::Vector{Float64}) = begin
-  if any(isnan(grad)) || any(isinf(grad))
+  if any(isnan.(grad)) || any(isinf.(grad))
     dwarn(0, "Numerical error has been found in gradients.")
     dwarn(1, "grad = $(grad)")
     false

src/core/compiler.jl

@@ -7,8 +7,8 @@ macro VarName(ex::Union{Expr, Symbol})
   #    return: (:x,[1,2],6,45,3)
   s = string(gensym())
   if isa(ex, Symbol)
-    _ = string(ex)
-    return :(Symbol($_), Symbol($s))
+    ex_str = string(ex)
+    return :(Symbol($ex_str), Symbol($s))
   elseif ex.head == :ref
     _2 = ex
     _1 = ""
@@ -143,9 +143,9 @@ Example:
 ```julia
 @model gauss() = begin
   s ~ InverseGamma(2,3)
-  m ~ Normal(0,sqrt(s))
-  1.5 ~ Normal(m, sqrt(s))
-  2.0 ~ Normal(m, sqrt(s))
+  m ~ Normal(0,sqrt.(s))
+  1.5 ~ Normal(m, sqrt.(s))
+  2.0 ~ Normal(m, sqrt.(s))
   return(s, m)
 end
 ```
@@ -154,7 +154,7 @@ macro model(fexpr)
    # Compiler design: sample(fname_compiletime(x,y), sampler)
    #   fname_compiletime(x=nothing,y=nothing; data=data,compiler=compiler) = begin
    #      ex = quote
-   #          fname_runtime(;vi=VarInfo,sampler=nothing) = begin
+   #          fname_runtime(vi::VarInfo,sampler::Sampler) = begin
    #              x=x,y=y
    #              # pour all variables in data dictionary, e.g.
    #              k = data[:k]
@@ -168,6 +168,7 @@ macro model(fexpr)
 
 
   dprintln(1, fexpr)
+  fexpr = translate(fexpr)
 
   fname = fexpr.args[1].args[1]      # Get model name f
   fargs = fexpr.args[1].args[2:end]  # Get model parameters (x,y;z=..)
@@ -178,31 +179,32 @@ macro model(fexpr)
   #       ==> f(x,y;)
   #   f(x,y; c=1)
   #       ==> unchanged
+
   if (length(fargs) == 0 ||         # e.g. f()
           isa(fargs[1], Symbol) ||  # e.g. f(x,y)
           fargs[1].head == :kw)     # e.g. f(x,y=1)
     insert!(fargs, 1, Expr(:parameters))
   end
 
   dprintln(1, fname)
-  dprintln(1, fargs)
+  # dprintln(1, fargs)
   dprintln(1, fbody)
 
   # Remove positional arguments from inner function, e.g.
   #  f((x,y; c=1)
   #      ==> f(; c=1)
   #  f(x,y;)
   #      ==> f(;)
-  fargs_inner = deepcopy(fargs)[1:1]
+  # fargs_inner = deepcopy(fargs)[1:1]
 
   # Add keyword arguments, e.g.
   #  f(; c=1)
   #      ==> f(; c=1, :vi=VarInfo(), :sample=nothing)
   #  f(;)
   #      ==> f(; :vi=VarInfo(), :sample=nothing)
-  push!(fargs_inner[1].args, Expr(:kw, :vi, :(Turing.VarInfo())))
-  push!(fargs_inner[1].args, Expr(:kw, :sampler, :(nothing)))
-  dprintln(1, fargs_inner)
+  # push!(fargs_inner[1].args, Expr(:kw, :vi, :(Turing.VarInfo())))
+  # push!(fargs_inner[1].args, Expr(:kw, :sampler, :(nothing)))
+  # dprintln(1, fargs_inner)
 
   # Modify fbody, so that we always return VarInfo
   fbody_inner = deepcopy(fbody)
@@ -234,19 +236,31 @@ macro model(fexpr)
 
   dprintln(1, fbody_inner)
 
-  fname_inner = Symbol("$(fname)_model")
+  fname_inner_str = "$(fname)_model"
+  fname_inner = Symbol(fname_inner_str)
   fdefn_inner = Expr(:(=), fname_inner,
           Expr(:function, Expr(:call, fname_inner))) # fdefn = :( $fname() )
-  push!(fdefn_inner.args[2].args[1].args, fargs_inner...)   # set parameters (x,y;data..)
+  # push!(fdefn_inner.args[2].args[1].args, fargs_inner...)   # set parameters (x,y;data..)
+
+  push!(fdefn_inner.args[2].args[1].args, :(vi::Turing.VarInfo))
+  push!(fdefn_inner.args[2].args[1].args, :(sampler::Union{Void,Turing.Sampler}))
+
   push!(fdefn_inner.args[2].args, deepcopy(fbody_inner))    # set function definition
   dprintln(1, fdefn_inner)
+  
+  fdefn_inner_callback_1 = parse("$fname_inner_str(vi::Turing.VarInfo)=$fname_inner_str(vi,nothing)")
+  fdefn_inner_callback_2 = parse("$fname_inner_str(sampler::Turing.Sampler)=$fname_inner_str(Turing.VarInfo(),nothing)")
+  fdefn_inner_callback_3 = parse("$fname_inner_str()=$fname_inner_str(Turing.VarInfo(),nothing)")
 
   compiler = Dict(:fname => fname,
                   :fargs => fargs,
                   :fbody => fbody,
                   :dvars => Set{Symbol}(),  # data
                   :pvars => Set{Symbol}(),  # parameter
-                  :fdefn_inner => fdefn_inner)
+                  :fdefn_inner => fdefn_inner,
+                  :fdefn_inner_callback_1 => fdefn_inner_callback_1,
+                  :fdefn_inner_callback_2 => fdefn_inner_callback_2,
+                  :fdefn_inner_callback_3 => fdefn_inner_callback_3)
 
   # Outer function defintion 1: f(x,y) ==> f(x,y;data=Dict())
   fargs_outer = deepcopy(fargs)
@@ -263,14 +277,34 @@ macro model(fexpr)
 
   fdefn_outer = Expr(:function, Expr(:call, fname, fargs_outer...),
                         Expr(:block, Expr(:return, fname_inner)))
-
+  
+  unshift!(fdefn_outer.args[2].args, :(Main.eval(fdefn_inner_callback_3)))
+  unshift!(fdefn_outer.args[2].args, :(Main.eval(fdefn_inner_callback_2)))
+  unshift!(fdefn_outer.args[2].args, :(Main.eval(fdefn_inner_callback_1)))
   unshift!(fdefn_outer.args[2].args, :(Main.eval(fdefn_inner)))
   unshift!(fdefn_outer.args[2].args,  quote
       # Check fargs, data
       eval(Turing, :(_compiler_ = deepcopy($compiler)))
-      fargs    = Turing._compiler_[:fargs];
-      fdefn_inner   = Turing._compiler_[:fdefn_inner];
-      fdefn_inner.args[2].args[1].args[1] = gensym((fdefn_inner.args[2].args[1].args[1]))
+      fargs = Turing._compiler_[:fargs];
+
+      # Copy the expr of function definition and callbacks
+      fdefn_inner = Turing._compiler_[:fdefn_inner];
+      fdefn_inner_callback_1 = Turing._compiler_[:fdefn_inner_callback_1];
+      fdefn_inner_callback_2 = Turing._compiler_[:fdefn_inner_callback_2];
+      fdefn_inner_callback_3 = Turing._compiler_[:fdefn_inner_callback_3];
+
+      # Add gensym to function name
+      fname_inner_with_gensym = gensym((fdefn_inner.args[2].args[1].args[1]));
+      
+      # Change the name of inner function definition to the one with gensym()
+      fdefn_inner.args[2].args[1].args[1] = fname_inner_with_gensym
+      fdefn_inner_callback_1.args[1].args[1] = fname_inner_with_gensym
+      fdefn_inner_callback_1.args[2].args[2].args[1] = fname_inner_with_gensym
+      fdefn_inner_callback_2.args[1].args[1] = fname_inner_with_gensym
+      fdefn_inner_callback_2.args[2].args[2].args[1] = fname_inner_with_gensym
+      fdefn_inner_callback_3.args[1].args[1] = fname_inner_with_gensym
+      fdefn_inner_callback_3.args[2].args[2].args[1] = fname_inner_with_gensym
+
       # Copy data dictionary
       for k in keys(data)
         if fdefn_inner.args[2].args[2].args[1].head == :line
@@ -295,7 +329,7 @@ macro model(fexpr)
     if _k != nothing
       _k_str = string(_k)
       dprintln(1, _k_str, " = ", _k)
-      _ = quote
+      data_check_ex = quote
             if haskey(data, keytype(data)($_k_str))
               if nothing != $_k
                 Turing.dwarn(0, " parameter "*$_k_str*" found twice, value in data dictionary will be used.")
@@ -305,7 +339,7 @@ macro model(fexpr)
               data[keytype(data)($_k_str)] == nothing && Turing.derror(0, "Data `"*$_k_str*"` is not provided.")
             end
           end
-      unshift!(fdefn_outer.args[2].args, _)
+      unshift!(fdefn_outer.args[2].args, data_check_ex)
     end
   end
   unshift!(fdefn_outer.args[2].args, quote data = copy(data) end)
@@ -331,3 +365,15 @@ getvsym(expr::Expr) = begin
   end
   curr
 end
+
+
+translate!(ex::Any) = ex
+translate!(ex::Expr) = begin
+  if (ex.head === :call && ex.args[1] === :(~))
+    ex.head = :macrocall; ex.args[1] = Symbol("@~")
+  else
+    map(translate!, ex.args)
+  end
+  ex
+end
+translate(ex::Expr) = translate!(deepcopy(ex))

src/core/container.jl

@@ -5,7 +5,7 @@ Data structure for particle filters
 - consume(pc::ParticleContainer): return incremental likelihood
 """
 
-typealias Particle Trace
+const Particle = Trace
 
 type ParticleContainer{T<:Particle}
   model :: Function
@@ -16,7 +16,7 @@ type ParticleContainer{T<:Particle}
   # conditional :: Union{Void,Conditional} # storing parameters, helpful for implementing rejuvenation steps
   conditional :: Void # storing parameters, helpful for implementing rejuvenation steps
   n_consume :: Int # helpful for rejuvenation steps, e.g. in SMC2
-  ParticleContainer(m::Function,n::Int) = new(m,n,Array{Particle,1}(),Array{Float64,1}(),0.0,nothing,0)
+  ParticleContainer{T}(m::Function,n::Int) where {T} = new(m,n,Array{Particle,1}(),Array{Float64,1}(),0.0,nothing,0)
 end
 
 (::Type{ParticleContainer{T}}){T}(m) = ParticleContainer{T}(m, 0)
@@ -127,7 +127,7 @@ end
 function weights(pc :: ParticleContainer)
   @assert pc.num_particles == length(pc)
   logWs = pc.logWs
-  Ws = exp(logWs-maximum(logWs))
+  Ws = exp.(logWs-maximum(logWs))
   logZ = log(sum(Ws)) + maximum(logWs)
   Ws = Ws ./ sum(Ws)
   return Ws, logZ
@@ -196,5 +196,5 @@ getsample(pc :: ParticleContainer) = begin
   w = pc.logE
   Ws, z = weights(pc)
   s = map((i)->getsample(pc, i, Ws[i]), 1:length(pc))
-  return exp(w), s
+  return exp.(w), s
 end

src/core/io.jl

@@ -17,14 +17,14 @@ getjuliatype(s::Sample, v::Symbol, cached_syms=nothing) = begin
   # NOTE: cached_syms is used to cache the filter entiries in svalue. This is helpful when the dimension of model is huge.
   if cached_syms == nothing
     # Get all keys associated with the given symbol
-    syms = collect(filter(k -> search(string(k), string(v)*"[") != 0:-1, keys(s.value)))
+    syms = collect(Iterators.filter(k -> search(string(k), string(v)*"[") != 0:-1, keys(s.value)))
   else
-    syms = filter(k -> search(string(k), string(v)) != 0:-1, cached_syms)
+    syms = collect((Iterators.filter(k -> search(string(k), string(v)) != 0:-1, cached_syms)))
   end
   # Map to the corresponding indices part
   idx_str = map(sym -> replace(string(sym), string(v), ""), syms)
   # Get the indexing component
-  idx_comp = map(idx -> filter(str -> str != "", split(string(idx), [']','['])), idx_str)
+  idx_comp = map(idx -> collect(Iterators.filter(str -> str != "", split(string(idx), [']','[']))), idx_str)
 
   # Deal with v is really a symbol, e.g. :x
   if length(idx_comp) == 0