Merge pull request #144 from TuringLang/dev

Update master

Author: yebai

.github/workflows/CompatHelper.yml

@@ -8,12 +8,10 @@ jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: 1.3
       - name: Pkg.add("CompatHelper")
         run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
       - name: CompatHelper.main()
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
+        run: julia -e 'using CompatHelper; CompatHelper.main(; master_branch = "dev")'

.github/workflows/TagBot.yml

@@ -1,7 +1,7 @@
 name: TagBot
 on:
   schedule:
-    - cron: 0 * * * *
+    - cron: 0 0 * * *
 jobs:
   TagBot:
     runs-on: ubuntu-latest

Project.toml

@@ -12,8 +12,8 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"
 
 [compat]
-AbstractMCMC = "1.0"
-Bijectors = "0.5.2, 0.6, 0.7"
+AbstractMCMC = "1"
+Bijectors = "0.5.2, 0.6, 0.7, 0.8"
 Distributions = "0.22, 0.23"
 MacroTools = "0.5.1"
 ZygoteRules = "0.2"

src/context_implementations.jl

@@ -177,7 +177,7 @@ function dot_tilde(
     else
         vns, dist = get_vns_and_dist(right, left, vn)
     end
-    return _dot_tilde(rng, sampler, NoDist(dist), left, vns, vi)
+    return _dot_tilde(rng, sampler, NoDist.(dist), left, vns, vi)
 end
 function dot_tilde(rng, ctx::MiniBatchContext, sampler, right, left, vn::VarName, inds, vi)
     return dot_tilde(rng, ctx.ctx, sampler, right, left, vn, inds, vi)

src/prob_macro.jl

@@ -233,7 +233,7 @@ _setval!(vi::TypedVarInfo, c::AbstractChains) = _setval!(vi.metadata, vi, c)
     return Expr(:block, map(names) do n
         quote
             for vn in md.$n.vns
-                val = copy.(vec(c[Symbol(string(vn))].value))
+                val = vec(c[Symbol(vn)])
                 setval!(vi, val, vn)
                 settrans!(vi, false, vn)
             end

test/Turing/Turing.jl

@@ -12,7 +12,7 @@ using Requires, Reexport, ForwardDiff
 using DistributionsAD, Bijectors, StatsFuns, SpecialFunctions
 using Statistics, LinearAlgebra
 using Libtask
-@reexport using Distributions, MCMCChains, Libtask, AbstractMCMC
+@reexport using Distributions, MCMCChains, Libtask, AbstractMCMC, Bijectors
 using Tracker: Tracker
 
 import DynamicPPL: getspace, NoDist, NamedDist
@@ -58,6 +58,11 @@ using .Variational
     end
 end
 
+@init @require Optim="429524aa-4258-5aef-a3af-852621145aeb" @eval begin
+    include("modes/ModeEstimation.jl")
+    export MAP, MLE, optimize
+end
+
 ###########
 # Exports #
 ###########
@@ -71,6 +76,7 @@ export  @model,                 # modelling
 
         MH,                     # classic sampling
         RWMH,
+        Emcee,
         ESS,
         Gibbs,
 
@@ -87,7 +93,7 @@ export  @model,                 # modelling
         CSMC,
         PG,
 
-        vi,                    # variational inference
+        vi,                     # variational inference
         ADVI,
 
         sample,                 # inference

test/Turing/inference/AdvancedSMC.jl

@@ -170,6 +170,8 @@ struct PG{space,R} <: ParticleInference
     resampler::R
 end
 
+isgibbscomponent(::PG) = true
+
 """
     PG(n, space...)
     PG(n, [resampler = ResampleWithESSThreshold(), space = ()])