more test fixes (#2491)

* Remove LogDensityProblemsAD, part 1

* update Optimisation code to not use LogDensityProblemsAD

* Fix field name change

* Don't put chunksize=0

* Remove LogDensityProblemsAD dep

* Improve OptimLogDensity docstring

* Remove unneeded model argument to _optimize

* Fix more tests

* Remove essential/ad from the list of CI groups

* Fix HMC function

* More test fixes

Author: penelopeysm

src/mcmc/gibbs.jl

@@ -438,7 +438,9 @@ function setparams_varinfo!!(
     state::TuringState,
     params::AbstractVarInfo,
 )
-    logdensity = DynamicPPL.setmodel(state.ldf, model, sampler.alg.adtype)
+    logdensity = DynamicPPL.LogDensityFunction(
+        model, state.ldf.varinfo, state.ldf.context; adtype=sampler.alg.adtype
+    )
     new_inner_state = setparams_varinfo!!(
         AbstractMCMC.LogDensityModel(logdensity), sampler, state.state, params
     )

src/mcmc/sghmc.jl

@@ -72,7 +72,7 @@ function DynamicPPL.initialstep(
         DynamicPPL.SamplingContext(spl, DynamicPPL.DefaultContext());
         adtype=spl.alg.adtype,
     )
-    state = SGHMCState(ℓ, vi, zero(vi[spl]))
+    state = SGHMCState(ℓ, vi, zero(vi[:]))
 
     return sample, state
 end
@@ -87,7 +87,7 @@ function AbstractMCMC.step(
     # Compute gradient of log density.
     ℓ = state.logdensity
     vi = state.vi
-    θ = vi[spl]
+    θ = vi[:]
     grad = last(LogDensityProblems.logdensity_and_gradient(ℓ, θ))
 
     # Update latent variables and velocity according to
@@ -246,7 +246,7 @@ function AbstractMCMC.step(
     # Perform gradient step.
     ℓ = state.logdensity
     vi = state.vi
-    θ = vi[spl]
+    θ = vi[:]
     grad = last(LogDensityProblems.logdensity_and_gradient(ℓ, θ))
     step = state.step
     stepsize = spl.alg.stepsize(step)

test/mcmc/Inference.jl

@@ -512,7 +512,7 @@ using Turing
 
         @model function vdemo2(x)
             μ ~ MvNormal(zeros(size(x, 1)), I)
-            return x .~ MvNormal(μ, I)
+            return x ~ filldist(MvNormal(μ, I), size(x, 2))
         end
 
         D = 2
@@ -560,7 +560,7 @@ using Turing
 
         @model function vdemo7()
             x = Array{Real}(undef, N, N)
-            return x .~ [InverseGamma(2, 3) for i in 1:N]
+            return x ~ filldist(InverseGamma(2, 3), N, N)
         end
 
         sample(StableRNG(seed), vdemo7(), alg, 10)

test/mcmc/hmc.jl

@@ -218,7 +218,7 @@ using Turing
         # https://github.com/TuringLang/Turing.jl/issues/1308
         @model function mwe3(::Type{T}=Array{Float64}) where {T}
             m = T(undef, 2, 3)
-            return m .~ MvNormal(zeros(2), I)
+            return m ~ filldist(MvNormal(zeros(2), I), 3)
         end
         @test sample(StableRNG(seed), mwe3(), HMC(0.2, 4; adtype=adbackend), 100) isa Chains
     end

test/mcmc/mh.jl

@@ -238,7 +238,7 @@ GKernel(var) = (x) -> Normal(x, sqrt.(var))
 
         # Link if proposal is `AdvancedHM.RandomWalkProposal`
         vi = deepcopy(vi_base)
-        d = length(vi_base[DynamicPPL.SampleFromPrior()])
+        d = length(vi_base[:])
         alg = MH(AdvancedMH.RandomWalkProposal(MvNormal(zeros(d), I)))
         spl = DynamicPPL.Sampler(alg)
         vi = Turing.Inference.maybe_link!!(vi, spl, alg.proposals, gdemo_default)