Perform invlinking in assume rather than implicitly in getindex (#360)

Currently, in `assume`, etc., `invlink` is called implicitly in `getindex` using the distribution extracted from `vi`.

This has a couple of drawbacks:
1. We can only use the distribution for a particular `vn` stored in `vi` obtained during the initial run. This means that we can't even run models where the distributions has dynamic domains, i.e. the domain of a particular random variable is dependent on the realizations of other random variables.
2. We have to store the distribution for each `vn` in `vi`. This was fine when we only had `VarInfo` because we also need it for other functionality, but this is not the case in `SimpleVarInfo` (nor will it be).

So. In this PR we introduce a `getindex_raw` which is `getindex` but without `invlink` if it's already linked, and uses this within `assume`, etc. where we now use the distributions that are passed to `assume` rather than those stored in `vi`.

E.g. the following now works:

``` julia
julia> @model demo() = x ~ InverseGamma(2, 3)
demo (generic function with 2 methods)

julia> vi = SimpleVarInfo((x = 10.0, ), true)
SimpleVarInfo((x = 10.0,), 0.0, true)

julia> _, vi = DynamicPPL.evaluate!!(model, vi, DefaultContext())
(22026.465794806718, SimpleVarInfo{NamedTuple{(:x,), Tuple{Float64}}, Float64}((x = 10.0,), -17.80291162245307, true))
```

Co-authored-by: Hong Ge <[email protected]>

Author: torfjelde

.github/workflows/CI.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         version:
-          - '1.3' # minimum supported version
+          - '1.6' # minimum supported version
           - '1' # current stable version
         os:
           - ubuntu-latest

.github/workflows/IntegrationTest.yml

@@ -40,7 +40,7 @@ jobs:
             # force it to use this PR's version of the package
             Pkg.develop(PackageSpec(path="."))  # resolver may fail with main deps
             Pkg.update()
-            Pkg.test()  # resolver may fail with test time deps
+            Pkg.test(julia_args=["--depwarn=no"])  # resolver may fail with test time deps
           catch err
             err isa Pkg.Resolve.ResolverError || rethrow()
             # If we can't resolve that means this is incompatible by SemVer and this is fine

Project.toml

@@ -1,14 +1,16 @@
 name = "DynamicPPL"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-version = "0.19.3"
+version = "0.20.0"
 
 [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"
+ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -22,8 +24,10 @@ AbstractPPL = "0.5.1"
 BangBang = "0.3"
 Bijectors = "0.5.2, 0.6, 0.7, 0.8, 0.9, 0.10"
 ChainRulesCore = "0.9.7, 0.10, 1"
+ConstructionBase = "1"
 Distributions = "0.23.8, 0.24, 0.25"
+DocStringExtensions = "0.8"
 MacroTools = "0.5.6"
 Setfield = "0.7.1, 0.8"
 ZygoteRules = "0.2"
-julia = "1.3"
+julia = "1.6"

docs/src/api.md

@@ -103,8 +103,14 @@ NamedDist
 DynamicPPL provides several demo models and helpers for testing samplers in the `DynamicPPL.TestUtils` submodule.
 
 ```@docs
-DynamicPPL.TestUtils.test_sampler_demo_models
+DynamicPPL.TestUtils.test_sampler
+DynamicPPL.TestUtils.test_sampler_on_demo_models
 DynamicPPL.TestUtils.test_sampler_continuous
+DynamicPPL.TestUtils.marginal_mean_of_samples
+```
+
+```@docs
+DynamicPPL.TestUtils.DEMO_MODELS
 ```
 
 For every demo model, one can define the true log prior, log likelihood, and log joint probabilities.
@@ -115,6 +121,20 @@ DynamicPPL.TestUtils.loglikelihood_true
 DynamicPPL.TestUtils.logjoint_true
 ```
 
+And in the case where the model includes constrained variables, it can also be useful to define
+
+```@docs
+DynamicPPL.TestUtils.logprior_true_with_logabsdet_jacobian
+DynamicPPL.TestUtils.logjoint_true_with_logabsdet_jacobian
+```
+
+Finally, the following methods can also be of use:
+
+```@docs
+DynamicPPL.TestUtils.varnames
+DynamicPPL.TestUtils.posterior_mean
+```
+
 ## Advanced
 
 ### Variable names

src/DynamicPPL.jl

@@ -12,6 +12,8 @@ using MacroTools: MacroTools
 using Setfield: Setfield
 using ZygoteRules: ZygoteRules
 
+using DocStringExtensions
+
 using Random: Random
 
 import Base:

src/context_implementations.jl

@@ -55,7 +55,7 @@ end
 function tilde_assume(context::PriorContext{<:NamedTuple}, right, vn, vi)
     if haskey(context.vars, getsym(vn))
         vi = setindex!!(vi, vectorize(right, get(context.vars, vn)), vn)
-        settrans!(vi, false, vn)
+        settrans!!(vi, false, vn)
     end
     return tilde_assume(PriorContext(), right, vn, vi)
 end
@@ -64,15 +64,15 @@ function tilde_assume(
 )
     if haskey(context.vars, getsym(vn))
         vi = setindex!!(vi, vectorize(right, get(context.vars, vn)), vn)
-        settrans!(vi, false, vn)
+        settrans!!(vi, false, vn)
     end
     return tilde_assume(rng, PriorContext(), sampler, right, vn, vi)
 end
 
 function tilde_assume(context::LikelihoodContext{<:NamedTuple}, right, vn, vi)
     if haskey(context.vars, getsym(vn))
         vi = setindex!!(vi, vectorize(right, get(context.vars, vn)), vn)
-        settrans!(vi, false, vn)
+        settrans!!(vi, false, vn)
     end
     return tilde_assume(LikelihoodContext(), right, vn, vi)
 end
@@ -86,7 +86,7 @@ function tilde_assume(
 )
     if haskey(context.vars, getsym(vn))
         vi = setindex!!(vi, vectorize(right, get(context.vars, vn)), vn)
-        settrans!(vi, false, vn)
+        settrans!!(vi, false, vn)
     end
     return tilde_assume(rng, LikelihoodContext(), sampler, right, vn, vi)
 end
@@ -194,7 +194,7 @@ end
 
 # fallback without sampler
 function assume(dist::Distribution, vn::VarName, vi)
-    r = vi[vn]
+    r = vi[vn, dist]
     return r, Bijectors.logpdf_with_trans(dist, r, istrans(vi, vn)), vi
 end
 
@@ -211,16 +211,21 @@ function assume(
         if sampler isa SampleFromUniform || is_flagged(vi, vn, "del")
             unset_flag!(vi, vn, "del")
             r = init(rng, dist, sampler)
-            vi[vn] = vectorize(dist, r)
-            settrans!(vi, false, vn)
+            vi[vn] = vectorize(dist, maybe_link(vi, vn, dist, r))
             setorder!(vi, vn, get_num_produce(vi))
         else
-            r = vi[vn]
+            # Otherwise we just extract it.
+            r = vi[vn, dist]
         end
     else
         r = init(rng, dist, sampler)
-        push!!(vi, vn, r, dist, sampler)
-        settrans!(vi, false, vn)
+        if istrans(vi)
+            push!!(vi, vn, link(dist, r), dist, sampler)
+            # By default `push!!` sets the transformed flag to `false`.
+            settrans!!(vi, true, vn)
+        else
+            push!!(vi, vn, r, dist, sampler)
+        end
     end
 
     return r, Bijectors.logpdf_with_trans(dist, r, istrans(vi, vn)), vi
@@ -286,7 +291,7 @@ function dot_tilde_assume(context::LikelihoodContext{<:NamedTuple}, right, left,
         var = get(context.vars, vn)
         _right, _left, _vns = unwrap_right_left_vns(right, var, vn)
         set_val!(vi, _vns, _right, _left)
-        settrans!.(Ref(vi), false, _vns)
+        settrans!!.((vi,), false, _vns)
         dot_tilde_assume(LikelihoodContext(), _right, _left, _vns, vi)
     else
         dot_tilde_assume(LikelihoodContext(), right, left, vn, vi)
@@ -305,19 +310,20 @@ function dot_tilde_assume(
         var = get(context.vars, vn)
         _right, _left, _vns = unwrap_right_left_vns(right, var, vn)
         set_val!(vi, _vns, _right, _left)
-        settrans!.(Ref(vi), false, _vns)
+        settrans!!.((vi,), false, _vns)
         dot_tilde_assume(rng, LikelihoodContext(), sampler, _right, _left, _vns, vi)
     else
         dot_tilde_assume(rng, LikelihoodContext(), sampler, right, left, vn, vi)
     end
 end
+
 function dot_tilde_assume(context::LikelihoodContext, right, left, vn, vi)
-    return dot_assume(NoDist.(right), left, vn, vi)
+    return dot_assume(nodist(right), left, vn, vi)
 end
 function dot_tilde_assume(
     rng::Random.AbstractRNG, context::LikelihoodContext, sampler, right, left, vn, vi
 )
-    return dot_assume(rng, sampler, NoDist.(right), vn, left, vi)
+    return dot_assume(rng, sampler, nodist(right), vn, left, vi)
 end
 
 # `PriorContext`
@@ -326,7 +332,7 @@ function dot_tilde_assume(context::PriorContext{<:NamedTuple}, right, left, vn,
         var = get(context.vars, vn)
         _right, _left, _vns = unwrap_right_left_vns(right, var, vn)
         set_val!(vi, _vns, _right, _left)
-        settrans!.(Ref(vi), false, _vns)
+        settrans!!.((vi,), false, _vns)
         dot_tilde_assume(PriorContext(), _right, _left, _vns, vi)
     else
         dot_tilde_assume(PriorContext(), right, left, vn, vi)
@@ -345,7 +351,7 @@ function dot_tilde_assume(
         var = get(context.vars, vn)
         _right, _left, _vns = unwrap_right_left_vns(right, var, vn)
         set_val!(vi, _vns, _right, _left)
-        settrans!.(Ref(vi), false, _vns)
+        settrans!!.((vi,), false, _vns)
         dot_tilde_assume(rng, PriorContext(), sampler, _right, _left, _vns, vi)
     else
         dot_tilde_assume(rng, PriorContext(), sampler, right, left, vn, vi)
@@ -383,14 +389,14 @@ function dot_assume(
     vns::AbstractVector{<:VarName},
     vi::AbstractVarInfo,
 )
-    @assert length(dist) == size(var, 1)
+    @assert length(dist) == size(var, 1) "dimensionality of `var` ($(size(var, 1))) is incompatible with dimensionality of `dist` $(length(dist))"
     # NOTE: We cannot work with `var` here because we might have a model of the form
     #
     #     m = Vector{Float64}(undef, n)
     #     m .~ Normal()
     #
     # in which case `var` will have `undef` elements, even if `m` is present in `vi`.
-    r = vi[vns]
+    r = vi[vns, dist]
     lp = sum(zip(vns, eachcol(r))) do (vn, ri)
         return Bijectors.logpdf_with_trans(dist, ri, istrans(vi, vn))
     end
@@ -412,19 +418,21 @@ function dot_assume(
 end
 
 function dot_assume(
-    dists::Union{Distribution,AbstractArray{<:Distribution}},
+    dist::Distribution, var::AbstractArray, vns::AbstractArray{<:VarName}, vi
+)
+    r = getindex.((vi,), vns, (dist,))
+    lp = sum(Bijectors.logpdf_with_trans.((dist,), r, istrans.((vi,), vns)))
+    return r, lp, vi
+end
+
+function dot_assume(
+    dists::AbstractArray{<:Distribution},
     var::AbstractArray,
     vns::AbstractArray{<:VarName},
     vi,
 )
-    # NOTE: We cannot work with `var` here because we might have a model of the form
-    #
-    #     m = Vector{Float64}(undef, n)
-    #     m .~ Normal()
-    #
-    # in which case `var` will have `undef` elements, even if `m` is present in `vi`.
-    r = reshape(vi[vec(vns)], size(vns))
-    lp = sum(Bijectors.logpdf_with_trans.(dists, r, istrans(vi, vns[1])))
+    r = getindex.((vi,), vns, dists)
+    lp = sum(Bijectors.logpdf_with_trans.(dists, r, istrans.((vi,), vns)))
     return r, lp, vi
 end
 
@@ -438,7 +446,7 @@ function dot_assume(
 )
     r = get_and_set_val!(rng, vi, vns, dists, spl)
     # Make sure `r` is not a matrix for multivariate distributions
-    lp = sum(Bijectors.logpdf_with_trans.(dists, r, istrans(vi, vns[1])))
+    lp = sum(Bijectors.logpdf_with_trans.(dists, r, istrans.((vi,), vns)))
     return r, lp, vi
 end
 function dot_assume(rng, spl::Sampler, ::Any, ::AbstractArray{<:VarName}, ::Any, ::Any)
@@ -462,19 +470,23 @@ function get_and_set_val!(
             r = init(rng, dist, spl, n)
             for i in 1:n
                 vn = vns[i]
-                vi[vn] = vectorize(dist, r[:, i])
-                settrans!(vi, false, vn)
+                vi[vn] = vectorize(dist, maybe_link(vi, vn, dist, r[:, i]))
                 setorder!(vi, vn, get_num_produce(vi))
             end
         else
-            r = vi[vns]
+            r = vi[vns, dist]
         end
     else
         r = init(rng, dist, spl, n)
         for i in 1:n
             vn = vns[i]
-            push!!(vi, vn, r[:, i], dist, spl)
-            settrans!(vi, false, vn)
+            if istrans(vi)
+                push!!(vi, vn, Bijectors.link(dist, r[:, i]), dist, spl)
+                # `push!!` sets the trans-flag to `false` by default.
+                settrans!!(vi, true, vn)
+            else
+                push!!(vi, vn, r[:, i], dist, spl)
+            end
         end
     end
     return r
@@ -496,12 +508,13 @@ function get_and_set_val!(
             for i in eachindex(vns)
                 vn = vns[i]
                 dist = dists isa AbstractArray ? dists[i] : dists
-                vi[vn] = vectorize(dist, r[i])
-                settrans!(vi, false, vn)
+                vi[vn] = vectorize(dist, maybe_link(vi, vn, dist, r[i]))
                 setorder!(vi, vn, get_num_produce(vi))
             end
         else
-            r = reshape(vi[vec(vns)], size(vns))
+            # r = reshape(vi[vec(vns)], size(vns))
+            r_raw = getindex_raw(vi, vec(vns))
+            r = maybe_invlink.((vi,), vns, dists, reshape(r_raw, size(vns)))
         end
     else
         f = (vn, dist) -> init(rng, dist, spl)
@@ -511,8 +524,13 @@ function get_and_set_val!(
         # 1. Figure out the broadcast size and use a `foreach`.
         # 2. Define an anonymous function which returns `nothing`, which
         #    we then broadcast. This will allocate a vector of `nothing` though.
-        push!!.(Ref(vi), vns, r, dists, Ref(spl))
-        settrans!.(Ref(vi), false, vns)
+        if istrans(vi)
+            push!!.((vi,), vns, link.((vi,), vns, dists, r), dists, (spl,))
+            # `push!!` sets the trans-flag to `false` by default.
+            settrans!!.((vi,), true, vns)
+        else
+            push!!.((vi,), vns, r, dists, (spl,))
+        end
     end
     return r
 end

src/distribution_wrappers.jl

@@ -13,6 +13,9 @@ end
 
 NamedDist(dist::Distribution, name::Symbol) = NamedDist(dist, VarName{name}())
 
+Base.length(dist::NamedDist) = Base.length(dist.dist)
+Base.size(dist::NamedDist) = Base.size(dist.dist)
+
 Distributions.logpdf(dist::NamedDist, x::Real) = Distributions.logpdf(dist.dist, x)
 function Distributions.logpdf(dist::NamedDist, x::AbstractArray{<:Real})
     return Distributions.logpdf(dist.dist, x)
@@ -24,12 +27,20 @@ function Distributions.loglikelihood(dist::NamedDist, x::AbstractArray{<:Real})
     return Distributions.loglikelihood(dist.dist, x)
 end
 
+Bijectors.bijector(d::NamedDist) = Bijectors.bijector(d.dist)
+
 struct NoDist{variate,support,Td<:Distribution{variate,support}} <:
        Distribution{variate,support}
     dist::Td
 end
 NoDist(dist::NamedDist) = NamedDist(NoDist(dist.dist), dist.name)
 
+nodist(dist::Distribution) = NoDist(dist)
+nodist(dists::AbstractArray) = nodist.(dists)
+
+Base.length(dist::NoDist) = Base.length(dist.dist)
+Base.size(dist::NoDist) = Base.size(dist.dist)
+
 Distributions.rand(rng::Random.AbstractRNG, d::NoDist) = rand(rng, d.dist)
 Distributions.logpdf(d::NoDist{<:Univariate}, ::Real) = 0
 Distributions.logpdf(d::NoDist{<:Multivariate}, ::AbstractVector{<:Real}) = 0
@@ -40,9 +51,21 @@ Distributions.logpdf(d::NoDist{<:Matrixvariate}, ::AbstractMatrix{<:Real}) = 0
 Distributions.minimum(d::NoDist) = minimum(d.dist)
 Distributions.maximum(d::NoDist) = maximum(d.dist)
 
-Bijectors.logpdf_with_trans(d::NoDist{<:Univariate}, ::Real) = 0
-Bijectors.logpdf_with_trans(d::NoDist{<:Multivariate}, ::AbstractVector{<:Real}) = 0
-function Bijectors.logpdf_with_trans(d::NoDist{<:Multivariate}, x::AbstractMatrix{<:Real})
+Bijectors.logpdf_with_trans(d::NoDist{<:Univariate}, ::Real, ::Bool) = 0
+function Bijectors.logpdf_with_trans(
+    d::NoDist{<:Multivariate}, ::AbstractVector{<:Real}, ::Bool
+)
+    return 0
+end
+function Bijectors.logpdf_with_trans(
+    d::NoDist{<:Multivariate}, x::AbstractMatrix{<:Real}, ::Bool
+)
     return zeros(Int, size(x, 2))
 end
-Bijectors.logpdf_with_trans(d::NoDist{<:Matrixvariate}, ::AbstractMatrix{<:Real}) = 0
+function Bijectors.logpdf_with_trans(
+    d::NoDist{<:Matrixvariate}, ::AbstractMatrix{<:Real}, ::Bool
+)
+    return 0
+end
+
+Bijectors.bijector(d::NoDist) = Bijectors.bijector(d.dist)