Merge branch 'master' into py/cherry-pick-0.28.5

ext/DynamicPPLMCMCChainsExt.jl

@@ -108,86 +108,14 @@ function DynamicPPL.generated_quantities(
     varinfo = DynamicPPL.VarInfo(model)
     iters = Iterators.product(1:size(chain, 1), 1:size(chain, 3))
     return map(iters) do (sample_idx, chain_idx)
-        if DynamicPPL.supports_varname_indexing(chain)
-            varname_pairs = _varname_pairs_with_varname_indexing(
-                chain, varinfo, sample_idx, chain_idx
-            )
-        else
-            varname_pairs = _varname_pairs_without_varname_indexing(
-                chain, varinfo, sample_idx, chain_idx
-            )
-        end
-        fixed_model = DynamicPPL.fix(model, Dict(varname_pairs))
-        return fixed_model()
+        # TODO: Use `fix` once we've addressed https://github.com/TuringLang/DynamicPPL.jl/issues/702.
+        # Update the varinfo with the current sample and make variables not present in `chain`
+        # to be sampled.
+        DynamicPPL.setval_and_resample!(varinfo, chain, sample_idx, chain_idx)
+        # NOTE: Some of the varialbes can be a view into the `varinfo`, so we need to
+        # `deepcopy` the `varinfo` before passing it to the `model`.
+        model(deepcopy(varinfo))
     end
 end
 
-"""
-    _varname_pairs_with_varname_indexing(
-        chain::MCMCChains.Chains, varinfo, sample_idx, chain_idx
-    )
-
-Get pairs of `VarName => value` for all the variables in the `varinfo`, picking the values
-from the chain.
-
-This implementation assumes `chain` can be indexed using variable names, and is the
-preffered implementation.
-"""
-function _varname_pairs_with_varname_indexing(
-    chain::MCMCChains.Chains, varinfo, sample_idx, chain_idx
-)
-    vns = DynamicPPL.varnames(chain)
-    vn_parents = Iterators.map(vns) do vn
-        # The call nested_setindex_maybe! is used to handle cases where vn is not
-        # the variable name used in the model, but rather subsumed by one. Except
-        # for the subsumption part, this could be
-        # vn => getindex_varname(chain, sample_idx, vn, chain_idx)
-        # TODO(mhauru) This call to nested_setindex_maybe! is unintuitive.
-        DynamicPPL.nested_setindex_maybe!(
-            varinfo, DynamicPPL.getindex_varname(chain, sample_idx, vn, chain_idx), vn
-        )
-    end
-    varname_pairs = Iterators.map(Iterators.filter(!isnothing, vn_parents)) do vn_parent
-        vn_parent => varinfo[vn_parent]
-    end
-    return varname_pairs
-end
-
-"""
-Check which keys in `key_strings` are subsumed by `vn_string` and return the their values.
-
-The subsumption check is done with `DynamicPPL.subsumes_string`, which is quite weak, and
-won't catch all cases. We should get rid of this if we can.
-"""
-# TODO(mhauru) See docstring above.
-function _vcat_subsumed_values(vn_string, values, key_strings)
-    indices = findall(Base.Fix1(DynamicPPL.subsumes_string, vn_string), key_strings)
-    return !isempty(indices) ? reduce(vcat, values[indices]) : nothing
-end
-
-"""
-    _varname_pairs_without_varname_indexing(
-        chain::MCMCChains.Chains, varinfo, sample_idx, chain_idx
-    )
-
-Get pairs of `VarName => value` for all the variables in the `varinfo`, picking the values
-from the chain.
-
-This implementation does not assume that `chain` can be indexed using variable names. It is
-thus not guaranteed to work in cases where the variable names have complex subsumption
-patterns, such as if the model has a variable `x` but the chain stores `x.a[1]`.
-"""
-function _varname_pairs_without_varname_indexing(
-    chain::MCMCChains.Chains, varinfo, sample_idx, chain_idx
-)
-    values = chain.value[sample_idx, :, chain_idx]
-    keys = Base.keys(chain)
-    keys_strings = map(string, keys)
-    varname_pairs = [
-        vn => _vcat_subsumed_values(string(vn), values, keys_strings) for
-        vn in Base.keys(varinfo)
-    ]
-    return varname_pairs
-end
-
 end