Update to Turing 0.40 (#636)

* Update to Turing 0.40

* Update version in _quarto.yml

* Fix DPPL 0.37 run_ad change

* Fix VI tutorial

* Fix model-manual's use of contexts

* Fix references to __context__

* Fix use of addlogprob for log prior

* Fix typo

* Regenerate manifest

* Remove version pin of DelayDiffEq and update Manifest

* Fix call to evaluate

* Add note about contexts tutorial being out of date

* Apply suggestions from code review

Co-authored-by: Penelope Yong <penelopeysm@gmail.com>

---------

Co-authored-by: Penelope Yong <penelopeysm@gmail.com>

Author: mhauru

Manifest.toml

@@ -1,8 +1,8 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.11.6"
+julia_version = "1.11.7"
 manifest_format = "2.0"
-project_hash = "2db94c909342da49eb3ff313436b75e25977ace6"
+project_hash = "6ed163b5c6c108dfaae31b757b21ff71e297872f"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "27cecae79e5cc9935255f90c53bb831cc3c870d7"
@@ -39,10 +39,14 @@ uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
 version = "5.8.0"
 
 [[deps.AbstractPPL]]
-deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random", "StatsBase"]
-git-tree-sha1 = "478b0b6176125cf0a5e6e9fd69fdd0923754531c"
+deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "LinearAlgebra", "Random", "StatsBase"]
+git-tree-sha1 = "3a9c1e6e7418494454260b0c8efd7b00fca251bc"
 uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf"
-version = "0.12.0"
+version = "0.13.1"
+weakdeps = ["Distributions"]
+
+    [deps.AbstractPPL.extensions]
+    AbstractPPLDistributionsExt = ["Distributions"]
 
 [[deps.AbstractTrees]]
 git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"
@@ -686,9 +690,9 @@ version = "0.1.2"
 
 [[deps.DelayDiffEq]]
 deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "FastBroadcast", "ForwardDiff", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqRosenbrock", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack", "SymbolicIndexingInterface"]
-git-tree-sha1 = "c50981fb5b6441a1213debb1423385a462e88032"
+git-tree-sha1 = "bb84c7ab3de56ada66430b5671db3b3cdaadcd61"
 uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
-version = "5.56.0"
+version = "5.61.0"
 
 [[deps.DelimitedFiles]]
 deps = ["Mmap"]
@@ -894,10 +898,10 @@ uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb"
 version = "3.5.1"
 
 [[deps.DynamicPPL]]
-deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Requires", "Statistics", "Test"]
-git-tree-sha1 = "07218fc45d4f1abc9de4498e8cf966b6672c84f0"
+deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Printf", "Random", "Requires", "Statistics", "Test"]
+git-tree-sha1 = "65649377104973412c10fb00ebc2f8430dcf8b93"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-version = "0.36.15"
+version = "0.37.2"
 
     [deps.DynamicPPL.extensions]
     DynamicPPLChainRulesCoreExt = ["ChainRulesCore"]
@@ -1752,7 +1756,6 @@ version = "3.40.1"
     LinearSolveCUDAExt = "CUDA"
     LinearSolveCUDSSExt = "CUDSS"
     LinearSolveCUSOLVERRFExt = ["CUSOLVERRF", "SparseArrays"]
-    LinearSolveCliqueTreesExt = ["CliqueTrees", "SparseArrays"]
     LinearSolveEnzymeExt = "EnzymeCore"
     LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices"
     LinearSolveFastLapackInterfaceExt = "FastLapackInterface"
@@ -1774,7 +1777,6 @@ version = "3.40.1"
     CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
     CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e"
     CUSOLVERRF = "a8cc9031-bad2-4722-94f5-40deabb4245c"
-    CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8"
     EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
     FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e"
     FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641"
@@ -3655,9 +3657,9 @@ version = "1.6.0"
 
 [[deps.Turing]]
 deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "58ad6cfe65311dc4ddc0e13e6747f3fad26f1034"
+git-tree-sha1 = "8e1e790cfdffd15524575b84c4709033d1ea9550"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.39.10"
+version = "0.40.3"
 weakdeps = ["DynamicHMC", "Optim"]
 
     [deps.Turing.extensions]

Project.toml

@@ -56,5 +56,4 @@ Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [compat]
-Turing = "0.39"
-DelayDiffEq = "~5.56"
+Turing = "0.40"

_quarto.yml

@@ -43,7 +43,7 @@ website:
         href: https://turinglang.org/team/
     right:
       # Current version
-      - text: "v0.39"
+      - text: "v0.40"
         menu:
           - text: Changelog
             href: https://turinglang.org/docs/changelog.html

developers/compiler/minituring-contexts/index.qmd

@@ -14,6 +14,10 @@ Pkg.instantiate();
 
 In the [Mini Turing]({{< meta minituring >}}) tutorial we developed a miniature version of the Turing language, to illustrate its core design. A passing mention was made of contexts. In this tutorial we develop that aspect of our mini Turing language further to demonstrate how and why contexts are an important part of Turing's design.
 
+::: {.callout-important}
+Note: The way Turing actually uses contexts changed somewhat in releases 0.39 and 0.40. The content of this page remains relevant, the principles of how contexts operate remain the same, and concepts like leaf and parent contexts still exist. However, we've moved away from using contexts for quite as many things as we used to. Most importantly, whether to accumulate the log joint, log prior, or log likelihood is no longer done using different contexts. Please keep this in mind as you read this page: The principles remain, but the details have changed. We will update this page once the refactoring of internals that is happening around releases like 0.39 and 0.40 is done.
+:::
+
 # Mini Turing expanded, now with more contexts
 
 If you haven't read [Mini Turing]({{< meta minituring >}}) yet, you should do that first. We start by repeating verbatim much of the code from there. Define the type for holding values for variables:

developers/compiler/model-manual/index.qmd

@@ -33,21 +33,21 @@ Taking the `gdemo` model above as an example, the macro-based definition can be
 using DynamicPPL
 
 # Create the model function.
-function gdemo2(model, varinfo, context, x)
+function gdemo2(model, varinfo, x)
     # Assume s² has an InverseGamma distribution.
     s², varinfo = DynamicPPL.tilde_assume!!(
-        context, InverseGamma(2, 3), @varname(s²), varinfo
+        model.context, InverseGamma(2, 3), @varname(s²), varinfo
     )
 
     # Assume m has a Normal distribution.
     m, varinfo = DynamicPPL.tilde_assume!!(
-        context, Normal(0, sqrt(s²)), @varname(m), varinfo
+        model.context, Normal(0, sqrt(s²)), @varname(m), varinfo
     )
 
     # Observe each value of x[i] according to a Normal distribution.
     for i in eachindex(x)
         _retval, varinfo = DynamicPPL.tilde_observe!!(
-            context, Normal(m, sqrt(s²)), x[i], @varname(x[i]), varinfo
+            model.context, Normal(m, sqrt(s²)), x[i], @varname(x[i]), varinfo
         )
     end
 

developers/contexts/submodel-condition/index.qmd

@@ -108,13 +108,13 @@ unwrap_sampling_context(ctx::DynamicPPL.SamplingContext) = ctx.context
 unwrap_sampling_context(ctx::DynamicPPL.AbstractContext) = ctx
 
 @model function inner()
-    println("inner context: $(unwrap_sampling_context(__context__))")
+    println("inner context: $(unwrap_sampling_context(__model__.context))")
     x ~ Normal()
     return y ~ Normal()
 end
 
 @model function outer()
-    println("outer context: $(unwrap_sampling_context(__context__))")
+    println("outer context: $(unwrap_sampling_context(__model__.context))")
     return a ~ to_submodel(inner())
 end
 
@@ -124,7 +124,7 @@ with_outer_cond = outer() | (@varname(a.x) => 1.0)
 # 'Inner conditioning'
 inner_cond = inner() | (@varname(x) => 1.0)
 @model function outer2()
-    println("outer context: $(unwrap_sampling_context(__context__))")
+    println("outer context: $(unwrap_sampling_context(__model__.context))")
     return a ~ to_submodel(inner_cond)
 end
 with_inner_cond = outer2()

developers/transforms/dynamicppl/index.qmd

@@ -351,7 +351,7 @@ Hence, one might expect that if we try to evaluate the model using this `VarInfo
 Here, `evaluate!!` returns two things: the model's return value itself (which we defined above to be a `NamedTuple`), and the resulting `VarInfo` post-evaluation.
 
 ```{julia}
-retval, ret_varinfo = DynamicPPL.evaluate!!(model, vi_linked, DefaultContext())
+retval, ret_varinfo = DynamicPPL.evaluate!!(model, vi_linked)
 getlogp(ret_varinfo)
 ```
 

tutorials/variational-inference/index.qmd

@@ -182,8 +182,8 @@ Usually, `q_avg` will perform better than the last-iterate `q_last`.
 For instance, we can compare the ELBO of the two:
 ```{julia}
 @info("Objective of q_avg and q_last",
-    ELBO_q_avg = estimate_objective(AdvancedVI.RepGradELBO(32), q_avg, Turing.Variational.make_logdensity(m)),
-    ELBO_q_last = estimate_objective(AdvancedVI.RepGradELBO(32), q_last, Turing.Variational.make_logdensity(m)) 
+    ELBO_q_avg = estimate_objective(AdvancedVI.RepGradELBO(32), q_avg, LogDensityFunction(m)),
+    ELBO_q_last = estimate_objective(AdvancedVI.RepGradELBO(32), q_last, LogDensityFunction(m))
 )
 ```
 We can see that `ELBO_q_avg` is slightly more optimal.
@@ -205,9 +205,9 @@ For example, the following callback function estimates the ELBO on `q_avg` every
 ```{julia}
 function callback(; stat, averaged_params, restructure, kwargs...)
     if mod(stat.iteration, 10) == 1
-        q_avg    = restructure(averaged_params)
-        obj      = AdvancedVI.RepGradELBO(128)
-        elbo_avg = estimate_objective(obj, q_avg, Turing.Variational.make_logdensity(m))
+        q_avg = restructure(averaged_params)
+        obj = AdvancedVI.RepGradELBO(128)
+        elbo_avg = estimate_objective(obj, q_avg, LogDensityFunction(m))
         (elbo_avg = elbo_avg,)
     else
         nothing
@@ -223,7 +223,7 @@ q_mf, _, info_mf, _ = vi(m, q_init, n_iters; show_progress=false, callback=callb
 
 Let's plot the result:
 ```{julia}
-iters   = 1:10:length(info_mf)
+iters = 1:10:length(info_mf)
 elbo_mf = [i.elbo_avg for i in info_mf[iters]]
 Plots.plot!(iters, elbo_mf, xlabel="Iterations", ylabel="ELBO", label="callback", ylims=(-200,Inf))
 ```
@@ -247,7 +247,7 @@ _, _, info_adam, _ = vi(m, q_init, n_iters; show_progress=false, callback=callba
 ```
 
 ```{julia}
-iters     = 1:10:length(info_mf)
+iters = 1:10:length(info_mf)
 elbo_adam = [i.elbo_avg for i in info_adam[iters]]
 Plots.plot(iters, elbo_mf, xlabel="Iterations", ylabel="ELBO", label="DoWG")
 Plots.plot!(iters, elbo_adam, xlabel="Iterations", ylabel="ELBO", label="Adam")

usage/automatic-differentiation/index.qmd

@@ -91,7 +91,7 @@ model = gdemo(1.5, 2)
 
 for adtype in [AutoForwardDiff(), AutoReverseDiff()]
     result = run_ad(model, adtype; benchmark=true)
-    @show result.time_vs_primal
+    @show result.grad_time / result.primal_time
 end
 ```
 

usage/modifying-logprob/index.qmd

@@ -47,13 +47,10 @@ using LinearAlgebra
 end
 ```
 
-Note that `@addlogprob!` always increases the accumulated log probability, regardless of the provided
-sampling context.
-For instance, if you do not want to apply `@addlogprob!` when evaluating the prior of your model but only when computing the log likelihood and the log joint probability, then you should [check the type of the internal variable `__context_`](https://github.com/TuringLang/DynamicPPL.jl/issues/154), as in the following example:
+Note that `@addlogprob! (p::Float64)` adds `p` to the log likelihood.
+If instead you want to add to the log prior, you can use
 
 ```{julia}
 #| eval: false
-if DynamicPPL.leafcontext(__context__) !== Turing.PriorContext()
-    @addlogprob! myloglikelihood(x, μ)
-end
+@addlogprob! (; logprior=value_goes_here)
 ```