Remove `Sampler`, remove `InferenceAlgorithm`, transfer `initialstep`, `init_strategy`, and other functions from DynamicPPL to Turing #2689

penelopeysm · 2025-10-16T21:57:58Z

TuringLang/DynamicPPL.jl#1037 deletes DynamicPPL.Sampler and its interface. This PR makes the necessary upstream adjustments.

Once this PR and the DPPL counterpart are merged, all of the MCMC sampling behaviour will be self-contained in Turing: this means that we can easily refactor sampler code in Turing without being held back by interface code in DynamicPPL. This will finally pave the way for things like sampling with LogDensityFunction #2555 and allow long-standing things to be fixed like weird parameters to NUTS #2678. It's been a few months coming so I am very pleased with this!

Literally all of the actual code changes in this PR are perfunctory boilerplate, like copy-pastes from DynamicPPL, changing x::Sampler{<:X} to x::X, etc. However, there is one conceptual bit that I think is worth explaining:

Special behaviour when sampling from Turing models with Turing samplers

As discussed in, e.g. #2413, there are certain special behaviours that are enabled when somebody calls sample(model, NUTS(), 1000). For example:

check_model runs checks on the model,
initial_params is set to DynamicPPL.init_strategy(spl) (now Turing.Inference.init_strategy(spl)),
chain_type is set to MCMCChains.Chains, ...

Previously the way this was accomplished was by

declaring NUTS <: InferenceAlgorithm,
sample(rng, ::AbstractModel, ::InferenceAlgorithm, N) would then wrap NUTS in DynamicPPL.Sampler
sample(rng, ::AbstractModel, ::DynamicPPL.Sampler, N) would then do all the special behaviour

This PR changes it such that the special behaviour is triggered in sample(rng, ::DynamicPPL.Model, ::AbstractSampler), in src/mcmc/abstractmcmc.jl. That is to say, NUTS is no longer 'a special class of sampler'. If you write your own sampler that knows how to handle Turing models (i.e. if you define step(rng, ::DynamicPPL.Model, ::MySampler)), then you will get all the special behaviour when you call sample(model, MyNewSampler(), 1000).

This approach is a lot simpler than what came before, but as pointed out in #2413 there are some concerns with method ambiguities. For example, if somebody defines

sample(::AbstractModel, ::MyNewSampler, N) = ...

then calling sample(dynamicppl_model, MyNewSampler(), 1000) will lead to method ambiguities. However, it's been almost a year since then, and there are a number of reasons why I'm not really fussed about the ambiguities and why I no longer agree with the arguments in that thread (indeed I don't agree with my own comments from that thread).

I've gated the rest behind a details tag to avoid overwhelming. If you don't see a problem with the above, then feel free to ignore.

Method ambiguities

As explained in Remove (duplicate) samplers being defined explicitly in Turing.jl #2413 the only meaningful case where somebody might write such a sample method is if their sampler was a 'meta-sampler', i.e., it works with all models without knowing anything about the internal structure of said models. In practice this cannot be done because AbstractModel has no interface and if you don't know anything about the model, you can't do anything meaningful with it. For example, in principle Gibbs shouldn't need to know anything about the model because it just shuttles it between component samplers. In practice we have to specialise on the model type and include a ton of stuff like setparams_varinfo to make it even work.
Method ambiguities have a very straightforward solution which is to declaring an extra, more specific method. I think that is a perfectly fine price to pay if you are writing a (genuine) meta-sampler and want it to work with Turing models specifically. For example this is the case with RepeatSampler, it's just five extra lines of code to make it work.
Note that in the original proposal in Remove (duplicate) samplers being defined explicitly in Turing.jl #2413 the method ambiguities would be avoided but if somebody wrote a model and wanted to hook into the special behaviour, they would have to write the more specific method anyway! So IMO this is no worse.
I haven't exactly seen an explosion of activity in the Julia ecosystem around creating meta-samplers, so I'm quite unconvinced that in practice this will cause any problems

github-actions · 2025-10-16T22:02:41Z

Turing.jl documentation for PR #2689 is available at:
https://TuringLang.github.io/Turing.jl/previews/PR2689/

codecov · 2025-10-17T01:30:19Z

Codecov Report

❌ Patch coverage is 92.38095% with 8 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.15%. Comparing base (bbbde35) to head (aa49a80).

Files with missing lines	Patch %	Lines
src/mcmc/abstractmcmc.jl	90.90%	3 Missing ⚠️
src/mcmc/ess.jl	50.00%	2 Missing ⚠️
src/mcmc/gibbs.jl	84.61%	2 Missing ⚠️
src/mcmc/Inference.jl	0.00%	1 Missing ⚠️

Additional details and impacted files

@@                Coverage Diff                @@
##           py/dppl-0.38    #2689       +/-   ##
=================================================
+ Coverage         57.89%   85.15%   +27.26%     
=================================================
  Files                22       21        -1     
  Lines              1387     1415       +28     
=================================================
+ Hits                803     1205      +402     
+ Misses              584      210      -374

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penelopeysm · 2025-10-20T11:38:13Z

src/mcmc/abstractmcmc.jl

+# TODO(penelopeysm): Remove initialstep and generalise MCMC sampling procedures
+function initialstep end
+
+function AbstractMCMC.step(
+    rng::Random.AbstractRNG,
+    model::DynamicPPL.Model,
+    spl::AbstractSampler;
+    initial_params,
+    kwargs...,
+)
+    # Generate the default varinfo. Note that any parameters inside this varinfo
+    # will be immediately overwritten by the next call to `init!!`.
+    vi = default_varinfo(rng, model, spl)
+
+    # Fill it with initial parameters. Note that, if `InitFromParams` is used, the
+    # parameters provided must be in unlinked space (when inserted into the
+    # varinfo, they will be adjusted to match the linking status of the
+    # varinfo).
+    _, vi = DynamicPPL.init!!(rng, model, vi, initial_params)
+
+    # Call the actual function that does the first step.
+    return initialstep(rng, model, spl, vi; initial_params, kwargs...)
+end


This method of step is actually a little bit evil. It used to be less bad because it only applied to Sampler{<:InferenceAlgorithm}, but now it applies to all AbstractSampler, which actually does cause some method ambiguities (which I've pointed out in my other comments).

On top of that, this is just generally a bit inflexible when it comes to warmup steps since it's only defined as a method for step and not step_warmup.

I think that in the next version of Turing this method should be removed. However, I've opted to preserve it for now because I don't want to make too many conceptual changes in this PR (the diff is already too large).

penelopeysm · 2025-10-20T11:38:52Z

src/mcmc/ess.jl

+# Needed for method ambiguity resolution, even though this method is never going to be
+# called in practice. This just shuts Aqua up.
+# TODO(penelopeysm): Remove this when the default `step(rng, ::DynamicPPL.Model,
+# ::AbstractSampler) method in `src/mcmc/abstractmcmc.jl` is removed.
+function AbstractMCMC.step(
+    rng::AbstractRNG,
+    model::DynamicPPL.Model,
+    sampler::EllipticalSliceSampling.ESS;
+    kwargs...,
+)
+    return error(
+        "This method is not implemented! If you want to use the ESS sampler in Turing.jl, please use `Turing.ESS()` instead. If you want the default behaviour in EllipticalSliceSampling.jl, wrap your model in a different subtype of `AbstractMCMC.AbstractModel`, and then implement the necessary EllipticalSliceSampling.jl methods on it.",
+    )
+end


This is the first method ambiguity caused by step. This needs to exist because of https://github.com/TuringLang/EllipticalSliceSampling.jl/blob/6b8fc40e9568122331ef705a2f668d854b692538/src/abstractmcmc.jl#L20-L27

penelopeysm · 2025-10-20T11:39:05Z

src/mcmc/repeat_sampler.jl

+# The following method needed for method ambiguity resolution.
+# TODO(penelopeysm): Remove this method once the default `AbstractMCMC.step(rng,
+# ::DynamicPPL.Model, ::AbstractSampler)` method in `src/mcmc/abstractmcmc.jl` is removed.
+function AbstractMCMC.step(
+    rng::Random.AbstractRNG, model::DynamicPPL.Model, sampler::RepeatSampler; kwargs...
+)
+    return AbstractMCMC.step(rng, model, sampler.sampler; kwargs...)
+end


This is the second method ambiguity caused by step.

I'm confused as to why this is a method ambiguity. RepeatSampler is a subtype of AbstractSampler and should thus take precedence given the other positional arguments are the same. Kwargs don't do dispatch. I think I'm missing something.

Errr, sorry, I was very unclear. It's the method above this that used AbstractModel was the problem. This one is the solution.

My bad for not reading the PR properly. If you just need the two methods to disambiguate, and the plan is to remove the offending method soonish (a plan I like, initialstep is confusing), then I'm not too offended.

penelopeysm · 2025-10-20T11:42:51Z

@mhauru pinging you also for thoughts on the method ambiguity thing, if you have any

sunxd3

I am not too bothered with the method ambiguity.

sunxd3 · 2025-10-20T18:25:03Z

src/mcmc/external_sampler.jl

+    sampler_wrapper::ExternalSampler;
    initial_state=nothing,
-    initial_params=DynamicPPL.init_strategy(sampler_wrapper.alg.sampler),
+    initial_params=DynamicPPL.init_strategy(sampler_wrapper.sampler),


Suggested change

initial_params=DynamicPPL.init_strategy(sampler_wrapper.sampler),

initial_params=Turing.Inference.init_strategy(sampler_wrapper.sampler),

perhaps?

That's quite awkward, this implies that it wasn't tested lol

Oh, actually, it seems that the default value just wasn't needed, because sample() always passes initial_params through to step(), and sample() already has a default value. Removed now.

sunxd3 · 2025-10-20T18:34:04Z

src/mcmc/gibbs.jl

-    spl::DynamicPPL.Sampler{<:Gibbs};
-    initial_params::DynamicPPL.AbstractInitStrategy=DynamicPPL.init_strategy(spl),
+    spl::Gibbs;
+    initial_params=Turing.Inference.init_strategy(spl),


slightly tricky, this would technically override the init_strategy behavior for the component samplers, right? for instance HMC, when used for a component will default to sampling from prior instead of uniform?

Yup indeed. I think this was already the case prior to this, because initial_params would be generated as a single vector (using initialsampler(::Sampler{Gibbs}), which would be SampleFromPrior) and then just split up between the components. I'm actually not sure how to fix this, but I can open an issue to track it.

Most likely the solution would be to implement a custom InitStrategy for Gibbs

Co-authored-by: Xianda Sun <5433119+sunxd3@users.noreply.github.com>

sunxd3

It looks great, thanks!

* Import `varname_leaves` etc from AbstractPPL instead * [no ci] initial updates for InitContext * [no ci] More fixes * [no ci] Fix pMCMC * [no ci] Fix Gibbs * [no ci] More fixes, reexport InitFrom * Fix a bunch of tests; I'll let CI tell me what's still broken... * Remove comment * Fix more tests * More test fixes * Fix more tests * fix GeneralizedExtremeValue numerical test * fix sample method * fix ESS reproducibility * Fix externalsampler test correctly * Fix everything (I _think_) * Add changelog * Fix remaining tests (for real this time) * Specify default chain type in Turing * fix DPPL revision * Fix changelog to mention unwrapped NT / Dict for initial_params * Remove references to islinked, set_flag, unset_flag * use `setleafcontext(::Model, ::AbstractContext)` * Fix for upstream removal of default_chain_type * Add clarifying comment for IS test * Revert ESS test (and add some numerical accuracy checks) * istrans -> is_transformed * Remove `loadstate` and `resume_from` * Remove a Sampler test * Paper over one crack * fix `resume_from` * remove a `Sampler` test * Update HISTORY.md Co-authored-by: Markus Hauru <markus@mhauru.org> * Remove `Sampler`, remove `InferenceAlgorithm`, transfer `initialstep`, `init_strategy`, and other functions from DynamicPPL to Turing (#2689) * Remove `Sampler` and move its interface to Turing * Test fixes (this is admittedly quite tiring) * Fix a couple of Gibbs tests (no doubt there are more) * actually fix the Gibbs ones * actually fix it this time * fix typo * point to breaking * Improve loadstate implementation * Re-add tests that were removed from DynamicPPL * Fix qualifier in src/mcmc/external_sampler.jl Co-authored-by: Xianda Sun <5433119+sunxd3@users.noreply.github.com> * Remove the default argument for initial_params * [skip ci] Remove DynamicPPL sources --------- Co-authored-by: Xianda Sun <5433119+sunxd3@users.noreply.github.com> * Fix a word in changelog * Improve changelog * Add PNTDist to changelog --------- Co-authored-by: Markus Hauru <markus@mhauru.org> Co-authored-by: Xianda Sun <5433119+sunxd3@users.noreply.github.com>

* Bump minor version * Do not take an initial step before starting the chain in HMC (#2674) * Do not take an initial step before starting the chain in HMC * Fix some tests * update changelog * Compatibility with DynamicPPL 0.38 + InitContext (#2676) * Import `varname_leaves` etc from AbstractPPL instead * initial updates for InitContext * More fixes * Fix pMCMC * Fix Gibbs * More fixes, reexport InitFrom * Fix a bunch of tests; I'll let CI tell me what's still broken... * Remove comment * Fix more tests * More test fixes * Fix more tests * fix GeneralizedExtremeValue numerical test * fix sample method * fix ESS reproducibility * Fix externalsampler test correctly * Fix everything (I _think_) * Add changelog * Fix remaining tests (for real this time) * Specify default chain type in Turing * fix DPPL revision * Fix changelog to mention unwrapped NT / Dict for initial_params * Remove references to islinked, set_flag, unset_flag * use `setleafcontext(::Model, ::AbstractContext)` * Fix for upstream removal of default_chain_type * Add clarifying comment for IS test * Revert ESS test (and add some numerical accuracy checks) * istrans -> is_transformed * Remove `loadstate` and `resume_from` * Remove a Sampler test * Paper over one crack * fix `resume_from` * remove a `Sampler` test * Update HISTORY.md Co-authored-by: Markus Hauru <markus@mhauru.org> * Remove `Sampler`, remove `InferenceAlgorithm`, transfer `initialstep`, `init_strategy`, and other functions from DynamicPPL to Turing (#2689) * Remove `Sampler` and move its interface to Turing * Test fixes (this is admittedly quite tiring) * Fix a couple of Gibbs tests (no doubt there are more) * actually fix the Gibbs ones * actually fix it this time * fix typo * point to breaking * Improve loadstate implementation * Re-add tests that were removed from DynamicPPL * Fix qualifier in src/mcmc/external_sampler.jl Co-authored-by: Xianda Sun <5433119+sunxd3@users.noreply.github.com> * Remove the default argument for initial_params * Remove DynamicPPL sources --------- Co-authored-by: Xianda Sun <5433119+sunxd3@users.noreply.github.com> * Fix a word in changelog * Improve changelog * Add PNTDist to changelog --------- Co-authored-by: Markus Hauru <markus@mhauru.org> Co-authored-by: Xianda Sun <5433119+sunxd3@users.noreply.github.com> * Fix all docs warnings --------- Co-authored-by: Markus Hauru <mhauru@turing.ac.uk> Co-authored-by: Markus Hauru <markus@mhauru.org> Co-authored-by: Xianda Sun <5433119+sunxd3@users.noreply.github.com>

github-actions bot assigned penelopeysm Oct 16, 2025

penelopeysm changed the title ~~Remove Sampler, transfer initialstep, init_strategy, and other functions from DynamicPPL to Turing~~ Remove Sampler, remove InferenceAlgorithm, transfer initialstep, init_strategy, and other functions from DynamicPPL to Turing Oct 16, 2025

Remove Sampler and move its interface to Turing

42bfc8a

penelopeysm force-pushed the py/sampler-fixes branch from b6de6ae to 42bfc8a Compare October 16, 2025 22:33

Test fixes (this is admittedly quite tiring)

b8fed72

penelopeysm added 4 commits October 17, 2025 02:52

Fix a couple of Gibbs tests (no doubt there are more)

d9aa377

actually fix the Gibbs ones

90c3ed6

actually fix it this time

b5e0760

fix typo

593af43

penelopeysm marked this pull request as ready for review October 17, 2025 16:16

This was referenced Oct 17, 2025

Compatibility with DynamicPPL 0.38 + InitContext #2676

Merged

Do we need resume_from now that we have initial_state? #2171

Closed

penelopeysm added 3 commits October 20, 2025 11:13

point to breaking

58b2ea9

Merge branch 'py/dppl-0.38' into py/sampler-fixes

39e4d28

Improve loadstate implementation

e9a4f1f

penelopeysm force-pushed the py/sampler-fixes branch from ebe0661 to e9a4f1f Compare October 20, 2025 10:19

Re-add tests that were removed from DynamicPPL

992b05a

penelopeysm commented Oct 20, 2025

View reviewed changes

penelopeysm requested a review from sunxd3 October 20, 2025 11:42

penelopeysm mentioned this pull request Oct 20, 2025

ProductNamedTupleDistribution compatibility TuringLang/DynamicPPL.jl#1079

Merged

4 tasks

sunxd3 reviewed Oct 20, 2025

View reviewed changes

Fix qualifier in src/mcmc/external_sampler.jl

205704b

Co-authored-by: Xianda Sun <5433119+sunxd3@users.noreply.github.com>

penelopeysm mentioned this pull request Oct 21, 2025

Gibbs does not use initialisation strategies for component samplers #2693

Open

Remove the default argument for initial_params

aa49a80

penelopeysm requested a review from sunxd3 October 21, 2025 10:19

sunxd3 approved these changes Oct 21, 2025

View reviewed changes

[skip ci] Remove DynamicPPL sources

230a4b6

penelopeysm merged commit f927308 into py/dppl-0.38 Oct 21, 2025

penelopeysm deleted the py/sampler-fixes branch October 21, 2025 17:37

penelopeysm mentioned this pull request Oct 25, 2025

Better support for AbstractSampler #2011

Closed

	initial_params=DynamicPPL.init_strategy(sampler_wrapper.sampler),
	initial_params=Turing.Inference.init_strategy(sampler_wrapper.sampler),

Remove Sampler, remove InferenceAlgorithm, transfer initialstep, init_strategy, and other functions from DynamicPPL to Turing #2689

Remove Sampler, remove InferenceAlgorithm, transfer initialstep, init_strategy, and other functions from DynamicPPL to Turing #2689

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Special behaviour when sampling from Turing models with Turing samplers

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Remove `Sampler`, remove `InferenceAlgorithm`, transfer `initialstep`, `init_strategy`, and other functions from DynamicPPL to Turing #2689

Remove `Sampler`, remove `InferenceAlgorithm`, transfer `initialstep`, `init_strategy`, and other functions from DynamicPPL to Turing #2689

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