add dummy julia code block to enable jmd building

tutorials/using-turing-sampler-viz/Manifest.toml

@@ -124,11 +124,6 @@ git-tree-sha1 = "a3704b8e5170f9339dff4e6cb286ad49464d3646"
 uuid = "76274a88-744f-5084-9051-94815aaf08c4"
 version = "0.10.6"
 
-[[deps.BitFlags]]
-git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d"
-uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
-version = "0.1.7"
-
 [[deps.Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2"
@@ -171,12 +166,6 @@ git-tree-sha1 = "64df3da1d2a26f4de23871cd1b6482bb68092bd5"
 uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
 version = "0.14.3"
 
-[[deps.CodecZlib]]
-deps = ["TranscodingStreams", "Zlib_jll"]
-git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83"
-uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
-version = "0.7.1"
-
 [[deps.ColorSchemes]]
 deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"]
 git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3"
@@ -331,9 +320,9 @@ version = "0.6.43"
 
 [[deps.DocStringExtensions]]
 deps = ["LibGit2"]
-git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d"
+git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b"
 uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-version = "0.9.3"
+version = "0.8.6"
 
 [[deps.Downloads]]
 deps = ["ArgTools", "LibCURL", "NetworkOptions"]
@@ -508,10 +497,10 @@ uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe"
 version = "1.0.2"
 
 [[deps.HTTP]]
-deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
-git-tree-sha1 = "37e4657cd56b11abe3d10cd4a1ec5fbdb4180263"
+deps = ["Base64", "Dates", "IniFile", "MbedTLS", "Sockets"]
+git-tree-sha1 = "c7ec02c4c6a039a98a15f955462cd7aea5df4508"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "1.7.4"
+version = "0.8.19"
 
 [[deps.HarfBuzz_jll]]
 deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"]
@@ -902,12 +891,6 @@ uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
 deps = ["Artifacts", "Libdl"]
 uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
 
-[[deps.OpenSSL]]
-deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"]
-git-tree-sha1 = "6503b77492fd7fcb9379bf73cd31035670e3c509"
-uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c"
-version = "1.3.3"
-
 [[deps.OpenSSL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004"
@@ -1064,10 +1047,10 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c"
 version = "0.6.11"
 
 [[deps.RecursiveArrayTools]]
-deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "ZygoteRules"]
-git-tree-sha1 = "fcf0962b399f3bc0fa13ae7274db7879c3ef9f1e"
+deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "Tables", "ZygoteRules"]
+git-tree-sha1 = "a5ce741acddc02f0d4fc6505463ca89697d7fb23"
 uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
-version = "2.35.0"
+version = "2.32.3"
 
 [[deps.Reexport]]
 git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
@@ -1155,11 +1138,6 @@ git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de"
 uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f"
 version = "1.0.3"
 
-[[deps.SimpleBufferStream]]
-git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1"
-uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7"
-version = "1.1.0"
-
 [[deps.SnoopPrecompile]]
 deps = ["Preferences"]
 git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c"
@@ -1251,12 +1229,6 @@ version = "0.6.14"
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
 uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
 
-[[deps.SymbolicIndexingInterface]]
-deps = ["DocStringExtensions"]
-git-tree-sha1 = "6b764c160547240d868be4e961a5037f47ad7379"
-uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
-version = "0.2.1"
-
 [[deps.TOML]]
 deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
@@ -1305,12 +1277,6 @@ git-tree-sha1 = "77817887c4b414b9c6914c61273910e3234eb21c"
 uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
 version = "0.2.23"
 
-[[deps.TranscodingStreams]]
-deps = ["Random", "Test"]
-git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f"
-uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
-version = "0.9.11"
-
 [[deps.Transducers]]
 deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"]
 git-tree-sha1 = "c42fa452a60f022e9e087823b47e5a5f8adc53d5"
@@ -1323,11 +1289,6 @@ git-tree-sha1 = "8a40377bcc4b054ebdc8f680e96cd73a4a6fe2e6"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
 version = "0.22.0"
 
-[[deps.URIs]]
-git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348"
-uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
-version = "1.4.1"
-
 [[deps.UUIDs]]
 deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"

tutorials/using-turing-sampler-viz/Project.toml

@@ -1,6 +1,4 @@
 [deps]
-Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"
-DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"

tutorials/using-turing-sampler-viz/sampler-viz.jmd

@@ -21,9 +21,7 @@ ENV["GKS_ENCODING"] = "utf-8" # Allows the use of unicode characters in Plots.jl
 using Plots
 using StatsPlots
 using Turing
-using Bijectors
 using Random
-using DynamicPPL: getlogp, settrans!, getval, reconstruct, vectorize, setval!
 
 # Set a seed.
 Random.seed!(0)
@@ -45,25 +43,9 @@ x = [1.5, 2.0, 13.0, 2.1, 0.0]
 
 # Set up the model call, sample from the prior.
 model = gdemo(x)
-vi = Turing.VarInfo(model)
-
-# Convert the variance parameter to the real line before sampling.
-# Note: We only have to do this here because we are being very hands-on.
-# Turing will handle all of this for you during normal sampling.
-dist = InverseGamma(2, 3)
-svn = vi.metadata.s².vns[1]
-mvn = vi.metadata.m.vns[1]
-setval!(vi, vectorize(dist, Bijectors.link(dist, reconstruct(dist, getval(vi, svn)))), svn)
-settrans!(vi, true, svn)
 
 # Evaluate surface at coordinates.
-function evaluate(m1, m2)
-    spl = Turing.SampleFromPrior()
-    vi[svn] = [m1]
-    vi[mvn] = [m2]
-    model(vi, spl)
-    return getlogp(vi)
-end
+evaluate(m1, m2) = logjoint(model, (m=m2, s²=m1))
 
 function plot_sampler(chain; label="")
     # Extract values from chain.
@@ -125,7 +107,7 @@ end;
 Gibbs sampling tends to exhibit a "jittery" trajectory. The example below combines `HMC` and `PG` sampling to traverse the posterior.
 
 ```julia
-c = sample(model, Gibbs(HMC(0.01, 5, :s), PG(20, :m)), 1000)
+c = sample(model, Gibbs(HMC(0.01, 5, :s²), PG(20, :m)), 1000)
 plot_sampler(c)
 ```
 
@@ -203,4 +185,4 @@ Next, we plot using 50 particles.
 ```julia
 c = sample(model, PG(50), 1000)
 plot_sampler(c)
-```
+```

tutorials/using-turing/using-turing.jmd → tutorials/using-turing/index.jmd

@@ -7,11 +7,14 @@ weave_options:
 
 # Turing Documentation
 
-Welcome to the documentation for Turing.
-
-Turing is a general-purpose probabilistic programming language for robust, efficient Bayesian inference and decision making. Current features include:
+Welcome to the documentation for Turing. Turing is a general-purpose probabilistic programming language for robust,
+efficient Bayesian inference and decision making. Current features include:
 
   - General-purpose probabilistic programming with an intuitive modelling interface;
   - Robust, efficient [Hamiltonian Monte Carlo (HMC)](https://github.com/TuringLang/AdvancedHMC.jl) sampling for differentiable posterior distributions;
   - Particle MCMC sampling for complex posterior distributions involving discrete variables and stochastic control flow; and
-  - Gibbs sampling combines particle MCMC, HMC and random-walk MH (RWMH) etc.
+  - Gibbs sampling that combines particle MCMC, HMC and random-walk MH (RWMH) etc.
+
+```julia
+
+```