Merge branch 'master' into phg/densityinterface

.github/workflows/CI.yml

@@ -56,19 +56,14 @@ jobs:
             ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest
-        with:
-          coverage: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.num_threads == 1 }}
         env:
           GROUP: All
           JULIA_NUM_THREADS: ${{ matrix.num_threads }}
       - uses: julia-actions/julia-processcoverage@v1
-        if: matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.num_threads == 1
       - uses: codecov/codecov-action@v1
-        if: matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.num_threads == 1
         with:
           file: lcov.info
       - uses: coverallsapp/github-action@master
-        if: matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.num_threads == 1
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: lcov.info

.gitignore

@@ -3,3 +3,4 @@
 *.jl.mem
 .DS_Store
 Manifest.toml
+**.~undo-tree~

Project.toml

@@ -1,39 +1,75 @@
 name = "DynamicPPL"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-version = "0.23.1"
+version = "0.25.3"
+
 
 [deps]
+ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
 AbstractPPL = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf"
+Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
 BangBang = "198e06fe-97b7-11e9-32a5-e1d131e6ad66"
 Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
 DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d"
 ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
+LogDensityProblemsAD = "996a588d-648d-4e1f-a8f0-a84b347e47b1"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
+Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"
 
+[weakdeps]
+ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
+ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
+ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
+ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"
+
+[extensions]
+DynamicPPLChainRulesCoreExt = ["ChainRulesCore"]
+DynamicPPLEnzymeCoreExt = ["EnzymeCore"]
+DynamicPPLForwardDiffExt = ["ForwardDiff"]
+DynamicPPLMCMCChainsExt = ["MCMCChains"]
+DynamicPPLReverseDiffExt = ["ReverseDiff"]
+DynamicPPLZygoteRulesExt = ["ZygoteRules"]
+
 [compat]
-AbstractMCMC = "2, 3.0, 4"
-AbstractPPL = "0.5.3"
-BangBang = "0.3"
-Bijectors = "0.13"
-ChainRulesCore = "0.9.7, 0.10, 1"
+ADTypes = "0.2, 1"
+AbstractMCMC = "5"
+AbstractPPL = "0.8.4"
+Accessors = "0.1"
+BangBang = "0.4.1"
+Bijectors = "0.13.9"
+ChainRulesCore = "1"
+Compat = "4"
+ConstructionBase = "1.5.4"
 DensityInterface = "0.4"
-ConstructionBase = "1"
-Distributions = "0.23.8, 0.24, 0.25"
-DocStringExtensions = "0.8, 0.9"
+Distributions = "0.25"
+DocStringExtensions = "0.9"
+EnzymeCore = "0.6, 0.7"
+LinearAlgebra = "1.6"
 LogDensityProblems = "2"
+LogDensityProblemsAD = "1.7.0"
+MCMCChains = "6"
 MacroTools = "0.5.6"
 OrderedCollections = "1"
-Setfield = "0.7.1, 0.8, 1"
+Random = "1.6"
+Requires = "1"
+Test = "1.6"
 ZygoteRules = "0.2"
 julia = "1.6"
+
+[extras]
+ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
+MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
+ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"

benchmarks/README.md

@@ -1,4 +1,5 @@
 To run the benchmarks, simply do:
+
 ```sh
 julia --project -e 'using DynamicPPLBenchmarks; weave_benchmarks();'
 ```

benchmarks/benchmark_body.jmd

@@ -20,7 +20,9 @@ results["evaluation_typed"]
 ```
 
 ```julia; echo=false; results="hidden";
-BenchmarkTools.save(joinpath("results", WEAVE_ARGS[:name], "$(nameof(m))_benchmarks.json"), results)
+BenchmarkTools.save(
+    joinpath("results", WEAVE_ARGS[:name], "$(nameof(m))_benchmarks.json"), results
+)
 ```
 
 ```julia; wrap=false
@@ -32,15 +34,16 @@ end
 ```julia; echo=false; results="hidden"
 if WEAVE_ARGS[:include_typed_code]
     # Serialize the output of `typed_code` so we can compare later.
-    haskey(WEAVE_ARGS, :name) && serialize(joinpath("results", WEAVE_ARGS[:name],"$(nameof(m)).jls"), string(typed));
+    haskey(WEAVE_ARGS, :name) &&
+        serialize(joinpath("results", WEAVE_ARGS[:name], "$(nameof(m)).jls"), string(typed))
 end
 ```
 
 ```julia; wrap=false; echo=false;
 if haskey(WEAVE_ARGS, :name_old)
     # We want to compare the generated code to the previous version.
-    import DiffUtils
-    typed_old = deserialize(joinpath("results", WEAVE_ARGS[:name_old], "$(nameof(m)).jls"));
-    DiffUtils.diff(typed_old, string(typed), width=130)
+    using DiffUtils: DiffUtils
+    typed_old = deserialize(joinpath("results", WEAVE_ARGS[:name_old], "$(nameof(m)).jls"))
+    DiffUtils.diff(typed_old, string(typed); width=130)
 end
 ```

benchmarks/benchmarks.jmd

@@ -19,21 +19,21 @@ import DynamicPPLBenchmarks: time_model_def, make_suite, typed_code, weave_child
     m ~ Normal()
     x ~ Normal(m, 1)
 
-    return (m = m, x = x)
+    return (m=m, x=x)
 end
 
 model_def = demo1;
 data = 1.0;
 ```
 
 ```julia; results="markup"; echo=false
-weave_child(WEAVE_ARGS[:benchmarkbody], mod = @__MODULE__, args = WEAVE_ARGS)
+weave_child(WEAVE_ARGS[:benchmarkbody]; mod=@__MODULE__, args=WEAVE_ARGS)
 ```
 
 ### `demo2`
 
 ```julia
-@model function demo2(y) 
+@model function demo2(y)
     # Our prior belief about the probability of heads in a coin.
     p ~ Beta(1, 1)
 
@@ -50,7 +50,7 @@ data = rand(0:1, 10);
 ```
 
 ```julia; results="markup"; echo=false
-weave_child(WEAVE_ARGS[:benchmarkbody], mod = @__MODULE__, args = WEAVE_ARGS)
+weave_child(WEAVE_ARGS[:benchmarkbody]; mod=@__MODULE__, args=WEAVE_ARGS)
 ```
 
 ### `demo3`
@@ -74,7 +74,7 @@ weave_child(WEAVE_ARGS[:benchmarkbody], mod = @__MODULE__, args = WEAVE_ARGS)
     k = Vector{Int}(undef, N)
     for i in 1:N
         k[i] ~ Categorical(w)
-        x[:,i] ~ MvNormal([μ[k[i]], μ[k[i]]], 1.)
+        x[:, i] ~ MvNormal([μ[k[i]], μ[k[i]]], 1.0)
     end
     return k
 end
@@ -88,11 +88,11 @@ N = 30
 μs = [-3.5, 0.0]
 
 # Construct the data points.
-data = mapreduce(c -> rand(MvNormal([μs[c], μs[c]], 1.), N), hcat, 1:2);
+data = mapreduce(c -> rand(MvNormal([μs[c], μs[c]], 1.0), N), hcat, 1:2);
 ```
 
 ```julia; echo=false
-weave_child(WEAVE_ARGS[:benchmarkbody], mod = @__MODULE__, args = WEAVE_ARGS)
+weave_child(WEAVE_ARGS[:benchmarkbody]; mod=@__MODULE__, args=WEAVE_ARGS)
 ```
 
 ### `demo4`: loads of indexing
@@ -107,24 +107,24 @@ weave_child(WEAVE_ARGS[:benchmarkbody], mod = @__MODULE__, args = WEAVE_ARGS)
 end
 
 model_def = demo4
-data = (100_000, );
+data = (100_000,);
 ```
 
 ```julia; echo=false
-weave_child(WEAVE_ARGS[:benchmarkbody], mod = @__MODULE__, args = WEAVE_ARGS)
+weave_child(WEAVE_ARGS[:benchmarkbody]; mod=@__MODULE__, args=WEAVE_ARGS)
 ```
 
 ```julia
 @model function demo4_dotted(n, ::Type{TV}=Vector{Float64}) where {TV}
     m ~ Normal()
     x = TV(undef, n)
-    x .~ Normal(m, 1.0)
+    return x .~ Normal(m, 1.0)
 end
 
 model_def = demo4_dotted
-data = (100_000, );
+data = (100_000,);
 ```
 
 ```julia; echo=false
-weave_child(WEAVE_ARGS[:benchmarkbody], mod = @__MODULE__, args = WEAVE_ARGS)
+weave_child(WEAVE_ARGS[:benchmarkbody]; mod=@__MODULE__, args=WEAVE_ARGS)
 ```

benchmarks/src/DynamicPPLBenchmarks.jl

@@ -8,6 +8,7 @@ using Markdown: Markdown
 
 using LibGit2: LibGit2
 using Pkg: Pkg
+using Random: Random
 
 export weave_benchmarks
 
@@ -33,9 +34,9 @@ function benchmark_typed_varinfo!(suite, m)
 end
 
 function typed_code(m, vi=VarInfo(m))
-    rng = DynamicPPL.Random.MersenneTwister(42)
-    spl = DynamicPPL.SampleFromPrior()
-    ctx = DynamicPPL.SamplingContext(rng, spl, DynamicPPL.DefaultContext())
+    rng = Random.MersenneTwister(42)
+    spl = SampleFromPrior()
+    ctx = SamplingContext(rng, spl, DefaultContext())
 
     results = code_typed(m.f, Base.typesof(m, vi, ctx, m.args...))
     return first(results)

docs/Project.toml

@@ -1,19 +1,19 @@
 [deps]
+Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
-MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54"
-Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
+MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 
 [compat]
+Accessors = "0.1"
 DataStructures = "0.18"
 Distributions = "0.25"
-Documenter = "0.27"
+Documenter = "1"
 FillArrays = "0.13, 1"
 LogDensityProblems = "2"
-MLUtils = "0.3, 0.4"
-Setfield = "0.7.1, 0.8, 1"
+MCMCChains = "5, 6"
 StableRNGs = "1"

docs/make.jl

@@ -1,11 +1,16 @@
 using Documenter
 using DynamicPPL
 using DynamicPPL: AbstractPPL
+# NOTE: This is necessary to ensure that if we print something from
+# Distributions.jl in a doctest, then the shown value will not include
+# a qualifier; that is, we don't want `Distributions.Normal{Float64}`
+# but rather `Normal{Float64}`. The latter is what will then be printed
+# in the doctest as run in `test/runtests.jl`, and so we need to stay
+# consistent with that.
+using Distributions
 
 # Doctest setup
-DocMeta.setdocmeta!(
-    DynamicPPL, :DocTestSetup, :(using DynamicPPL, Distributions); recursive=true
-)
+DocMeta.setdocmeta!(DynamicPPL, :DocTestSetup, :(using DynamicPPL); recursive=true)
 
 makedocs(;
     sitename="DynamicPPL",
@@ -16,7 +21,6 @@ makedocs(;
         "API" => "api.md",
         "Tutorials" => ["tutorials/prob-interface.md"],
     ],
-    strict=true,
     checkdocs=:exports,
 )