Merge branch 'master' into torfjelde/subset-and-merge

Project.toml

@@ -1,13 +1,14 @@
 name = "DynamicPPL"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-version = "0.23.18"
+version = "0.23.19"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
 AbstractPPL = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf"
 BangBang = "198e06fe-97b7-11e9-32a5-e1d131e6ad66"
 Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
 ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
@@ -21,13 +22,20 @@ Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"
 
+[weakdeps]
+MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
+
+[extensions]
+DynamicPPLMCMCChainsExt = ["MCMCChains"]
+
 [compat]
 AbstractMCMC = "2, 3.0, 4"
 AbstractPPL = "0.6"
 BangBang = "0.3"
 Bijectors = "0.13"
 ChainRulesCore = "0.9.7, 0.10, 1"
 ConstructionBase = "1.5.4"
+Compat = "4"
 Distributions = "0.23.8, 0.24, 0.25"
 DocStringExtensions = "0.8, 0.9"
 LogDensityProblems = "2"
@@ -39,11 +47,5 @@ Setfield = "0.7.1, 0.8, 1"
 ZygoteRules = "0.2"
 julia = "1.6"
 
-[extensions]
-DynamicPPLMCMCChainsExt = ["MCMCChains"]
-
 [extras]
 MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
-
-[weakdeps]
-MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"

docs/Project.toml

@@ -12,7 +12,7 @@ StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 [compat]
 DataStructures = "0.18"
 Distributions = "0.25"
-Documenter = "0.27"
+Documenter = "1"
 FillArrays = "0.13, 1"
 LogDensityProblems = "2"
 MCMCChains = "5, 6"

docs/make.jl

@@ -21,7 +21,6 @@ makedocs(;
         "API" => "api.md",
         "Tutorials" => ["tutorials/prob-interface.md"],
     ],
-    strict=true,
     checkdocs=:exports,
 )
 

src/DynamicPPL.jl

@@ -3,6 +3,7 @@ module DynamicPPL
 using AbstractMCMC: AbstractSampler, AbstractChains
 using AbstractPPL
 using Bijectors
+using Compat
 using Distributions
 using OrderedCollections: OrderedDict
 

src/varinfo.jl

@@ -1116,33 +1116,59 @@ function _inner_transform!(vi::VarInfo, vn::VarName, dist, f)
     return vi
 end
 
+# HACK: We need `SampleFromPrior` to result in ALL values which are in need
+# of a transformation to be transformed. `_getvns` will by default return
+# an empty iterable for `SampleFromPrior`, so we need to override it here.
+# This is quite hacky, but seems safer than changing the behavior of `_getvns`.
+_getvns_link(varinfo::VarInfo, spl::AbstractSampler) = _getvns(varinfo, spl)
+_getvns_link(varinfo::UntypedVarInfo, spl::SampleFromPrior) = nothing
+function _getvns_link(varinfo::TypedVarInfo, spl::SampleFromPrior)
+    return map(Returns(nothing), varinfo.metadata)
+end
+
 function link(::DynamicTransformation, varinfo::VarInfo, spl::AbstractSampler, model::Model)
-    return _link(varinfo)
+    return _link(varinfo, spl)
 end
 
-function _link(varinfo::UntypedVarInfo)
+function _link(varinfo::UntypedVarInfo, spl::AbstractSampler)
     varinfo = deepcopy(varinfo)
     return VarInfo(
-        _link_metadata!(varinfo, varinfo.metadata),
+        _link_metadata!(varinfo, varinfo.metadata, _getvns_link(varinfo, spl)),
         Base.Ref(getlogp(varinfo)),
         Ref(get_num_produce(varinfo)),
     )
 end
 
-function _link(varinfo::TypedVarInfo)
+function _link(varinfo::TypedVarInfo, spl::AbstractSampler)
     varinfo = deepcopy(varinfo)
-    md = map(Base.Fix1(_link_metadata!, varinfo), varinfo.metadata)
-    # TODO: Update logp, etc.
+    md = _link_metadata_namedtuple!(
+        varinfo, varinfo.metadata, _getvns_link(varinfo, spl), Val(getspace(spl))
+    )
     return VarInfo(md, Base.Ref(getlogp(varinfo)), Ref(get_num_produce(varinfo)))
 end
 
-function _link_metadata!(varinfo::VarInfo, metadata::Metadata)
+@generated function _link_metadata_namedtuple!(
+    varinfo::VarInfo, metadata::NamedTuple{names}, vns::NamedTuple, ::Val{space}
+) where {names,space}
+    vals = Expr(:tuple)
+    for f in names
+        if inspace(f, space) || length(space) == 0
+            push!(vals.args, :(_link_metadata!(varinfo, metadata.$f, vns.$f)))
+        else
+            push!(vals.args, :(metadata.$f))
+        end
+    end
+
+    return :(NamedTuple{$names}($vals))
+end
+function _link_metadata!(varinfo::VarInfo, metadata::Metadata, target_vns)
     vns = metadata.vns
 
     # Construct the new transformed values, and keep track of their lengths.
     vals_new = map(vns) do vn
         # Return early if we're already in unconstrained space.
-        if istrans(varinfo, vn)
+        # HACK: if `target_vns` is `nothing`, we ignore the `target_vns` check.
+        if istrans(varinfo, vn) || (target_vns !== nothing && vn ∉ target_vns)
             return metadata.vals[getrange(metadata, vn)]
         end
 
@@ -1186,32 +1212,49 @@ end
 function invlink(
     ::DynamicTransformation, varinfo::VarInfo, spl::AbstractSampler, model::Model
 )
-    return _invlink(varinfo)
+    return _invlink(varinfo, spl)
 end
 
-function _invlink(varinfo::UntypedVarInfo)
+function _invlink(varinfo::UntypedVarInfo, spl::AbstractSampler)
     varinfo = deepcopy(varinfo)
     return VarInfo(
-        _invlink_metadata!(varinfo, varinfo.metadata),
+        _invlink_metadata!(varinfo, varinfo.metadata, _getvns_link(varinfo, spl)),
         Base.Ref(getlogp(varinfo)),
         Ref(get_num_produce(varinfo)),
     )
 end
 
-function _invlink(varinfo::TypedVarInfo)
+function _invlink(varinfo::TypedVarInfo, spl::AbstractSampler)
     varinfo = deepcopy(varinfo)
-    md = map(Base.Fix1(_invlink_metadata!, varinfo), varinfo.metadata)
-    # TODO: Update logp, etc.
+    md = _invlink_metadata_namedtuple!(
+        varinfo, varinfo.metadata, _getvns_link(varinfo, spl), Val(getspace(spl))
+    )
     return VarInfo(md, Base.Ref(getlogp(varinfo)), Ref(get_num_produce(varinfo)))
 end
 
-function _invlink_metadata!(varinfo::VarInfo, metadata::Metadata)
+@generated function _invlink_metadata_namedtuple!(
+    varinfo::VarInfo, metadata::NamedTuple{names}, vns::NamedTuple, ::Val{space}
+) where {names,space}
+    vals = Expr(:tuple)
+    for f in names
+        if inspace(f, space) || length(space) == 0
+            push!(vals.args, :(_invlink_metadata!(varinfo, metadata.$f, vns.$f)))
+        else
+            push!(vals.args, :(metadata.$f))
+        end
+    end
+
+    return :(NamedTuple{$names}($vals))
+end
+function _invlink_metadata!(varinfo::VarInfo, metadata::Metadata, target_vns)
     vns = metadata.vns
 
     # Construct the new transformed values, and keep track of their lengths.
     vals_new = map(vns) do vn
-        # Return early if we're already in constrained space.
-        if !istrans(varinfo, vn)
+        # Return early if we're already in constrained space OR if we're not
+        # supposed to touch this `vn`, e.g. when `vn` does not belong to the current sampler. 
+        # HACK: if `target_vns` is `nothing`, we ignore the `target_vns` check.
+        if !istrans(varinfo, vn) || (target_vns !== nothing && vn ∉ target_vns)
             return metadata.vals[getrange(metadata, vn)]
         end
 

test/Project.toml

@@ -28,7 +28,7 @@ Bijectors = "0.13"
 Compat = "4.3.0"
 Distributions = "0.25"
 DistributionsAD = "0.6.3"
-Documenter = "0.26.1, 0.27"
+Documenter = "0.26.1, 0.27, 1"
 ForwardDiff = "0.10.12"
 LogDensityProblems = "2"
 MCMCChains = "4.0.4, 5, 6"

test/varinfo.jl

@@ -14,6 +14,10 @@ function check_varinfo_keys(varinfo, vns)
     end
 end
 
+# A simple "algorithm" which only has `s` variables in its space.
+struct MySAlg end
+DynamicPPL.getspace(::DynamicPPL.Sampler{MySAlg}) = (:s,)
+
 @testset "varinfo.jl" begin
     @testset "TypedVarInfo" begin
         @model gdemo(x, y) = begin
@@ -539,4 +543,42 @@ end
             end
         end
     end
+
+    @testset "VarInfo with selectors" begin
+        @testset "$(model.f)" for model in DynamicPPL.TestUtils.DEMO_MODELS
+            varinfo = VarInfo(model)
+            selector = DynamicPPL.Selector()
+            spl = Sampler(MySAlg(), model, selector)
+
+            vns = DynamicPPL.TestUtils.varnames(model)
+            vns_s = filter(vn -> DynamicPPL.getsym(vn) === :s, vns)
+            vns_m = filter(vn -> DynamicPPL.getsym(vn) === :m, vns)
+            for vn in vns_s
+                DynamicPPL.updategid!(varinfo, vn, spl)
+            end
+
+            # Should only get the variables subsumed by `@varname(s)`.
+            @test varinfo[spl] ==
+                mapreduce(Base.Fix1(DynamicPPL.getval, varinfo), vcat, vns_s)
+
+            # `link`
+            varinfo_linked = DynamicPPL.link(varinfo, spl, model)
+            # `s` variables should be linked
+            @test any(Base.Fix1(DynamicPPL.istrans, varinfo_linked), vns_s)
+            # `m` variables should NOT be linked
+            @test any(!Base.Fix1(DynamicPPL.istrans, varinfo_linked), vns_m)
+            # And `varinfo` should be unchanged
+            @test all(!Base.Fix1(DynamicPPL.istrans, varinfo), vns)
+
+            # `invlink`
+            varinfo_invlinked = DynamicPPL.invlink(varinfo_linked, spl, model)
+            # `s` variables should no longer be linked
+            @test all(!Base.Fix1(DynamicPPL.istrans, varinfo_invlinked), vns_s)
+            # `m` variables should still not be linked
+            @test all(!Base.Fix1(DynamicPPL.istrans, varinfo_invlinked), vns_m)
+            # And `varinfo_linked` should be unchanged
+            @test any(Base.Fix1(DynamicPPL.istrans, varinfo_linked), vns_s)
+            @test any(!Base.Fix1(DynamicPPL.istrans, varinfo_linked), vns_m)
+        end
+    end
 end