chore: bump the all-julia-packages group across 3 directories with 1 update

[dependabot]

Updates the requirements on and DynamicPPL to permit the latest version.
Updates DynamicPPL to 0.40.6

Release notes

Sourced from DynamicPPL's releases.

v0.40.6

DynamicPPL v0.40.6

Diff since v0.40.5

Add an extra constructor for LogDensityFunction(::Model, logdensity_function, ::AbstractTransformStrategy[, accs; adtype]), which is a shorthand for generating the vectorised values according to the given transform strategy, and then calling the existing constructor with those values. This allows you to conveniently construct a linked LogDensityFunction in one line via

ldf = LogDensityFunction(model, logdensity_function, LinkAll())

instead of the old route where you had to create a VarInfo or VectorValueAccumulator first.

Added a method rand([rng,] ::LogDensityFunction[, init_strategy]) which allows you to sample new parameter vectors from a LogDensityFunction directly.

Added a transform_strategy keyword argument to DynamicPPL.TestUtils.run_ad. It is intended to (eventually) replace the varinfo keyword argument; however, for now both are still supported for backwards compatibility. If both varinfo and transform_strategy are passed, then varinfo takes precedence.

Added a small precompilation workload to DynamicPPLMooncakeExt, which should reduce the time to first gradient down on Turing models.

Merged pull requests:

• Add convenient constructors for LDF, plus rand(::LogDensityFunction), plus run_ad (#1307) (@​penelopeysm)

Closed issues:

• Pass VarInfo and islinked to LogDensityFunction (#863)

Changelog

Sourced from DynamicPPL's changelog.

0.40.6

Add an extra constructor for LogDensityFunction(::Model, logdensity_function, ::AbstractTransformStrategy[, accs; adtype]), which is a shorthand for generating the vectorised values according to the given transform strategy, and then calling the existing constructor with those values. This allows you to conveniently construct a linked LogDensityFunction in one line via

ldf = LogDensityFunction(model, logdensity_function, LinkAll())

instead of the old route where you had to create a VarInfo or VectorValueAccumulator first.

Added a method rand([rng,] ::LogDensityFunction[, init_strategy]) which allows you to sample new parameter vectors from a LogDensityFunction directly.

Added a transform_strategy keyword argument to DynamicPPL.TestUtils.run_ad. It is intended to (eventually) replace the varinfo keyword argument; however, for now both are still supported for backwards compatibility. If both varinfo and transform_strategy are passed, then varinfo takes precedence.

Added a small precompilation workload to DynamicPPLMooncakeExt, which should reduce the time to first gradient down on Turing models.

0.40.5

Remove DynamicPPL's internal variable transformation code and replace it directly with the new Bijectors.VectorBijectors module. There should be no difference for end-users, apart from increased performance in many cases.

If you were extending the internal from_vec_transform, to_vec_transform, from_linked_vec_transform, to_linked_vec_transform, or tovec methods, please note that these have been removed. In place of this, you should implement the Bijectors.VectorBijectors interface, which is public and is guaranteed to be semver-compliant now onwards. Please see the Bijectors documentation for more information.

0.40.4

Moved filldist and arraydist from DistributionsAD.jl to DynamicPPL.jl (with greatly simplified definitions).

0.40.3

Added a convenience function, get_priors(::AbstractVarInfo), which extracts the VarNamedTuple of prior distributions from a VarInfo that contains a PriorDistributionAccumulator.

0.40.2

Fix a bug where DebugAccumulator was being improperly mutated during model checks.

0.40.1

Fix AD performance with ReverseDiff (v0.39.9 inadvertently introduced a bug that did not cause any correctness issues, but did cause severe slowdowns with ReverseDiff -- this patch reverts that).

0.40

v0.40 of DynamicPPL brings with it a complete rewrite of DynamicPPL's core data structure, VarInfo.

The main breaking change for users here is the removal of non-array indexing in random variables of DynamicPPL models, and the stipulation that arrays of random variables do not change size during model execution. Other breaking changes relate to the function signatures of some core DynamicPPL functions, and will not affect you unless you are developing against DynamicPPL.

... (truncated)

Commits

• See full diff in compare view

Updates DynamicPPL to 0.40.6

Release notes

Sourced from DynamicPPL's releases.

v0.40.6

DynamicPPL v0.40.6

Diff since v0.40.5

Add an extra constructor for LogDensityFunction(::Model, logdensity_function, ::AbstractTransformStrategy[, accs; adtype]), which is a shorthand for generating the vectorised values according to the given transform strategy, and then calling the existing constructor with those values. This allows you to conveniently construct a linked LogDensityFunction in one line via

ldf = LogDensityFunction(model, logdensity_function, LinkAll())

instead of the old route where you had to create a VarInfo or VectorValueAccumulator first.

Added a method rand([rng,] ::LogDensityFunction[, init_strategy]) which allows you to sample new parameter vectors from a LogDensityFunction directly.

Added a transform_strategy keyword argument to DynamicPPL.TestUtils.run_ad. It is intended to (eventually) replace the varinfo keyword argument; however, for now both are still supported for backwards compatibility. If both varinfo and transform_strategy are passed, then varinfo takes precedence.

Added a small precompilation workload to DynamicPPLMooncakeExt, which should reduce the time to first gradient down on Turing models.

Merged pull requests:

• Add convenient constructors for LDF, plus rand(::LogDensityFunction), plus run_ad (#1307) (@​penelopeysm)

Closed issues:

• Pass VarInfo and islinked to LogDensityFunction (#863)

Changelog

Sourced from DynamicPPL's changelog.

0.40.6

Add an extra constructor for LogDensityFunction(::Model, logdensity_function, ::AbstractTransformStrategy[, accs; adtype]), which is a shorthand for generating the vectorised values according to the given transform strategy, and then calling the existing constructor with those values. This allows you to conveniently construct a linked LogDensityFunction in one line via

ldf = LogDensityFunction(model, logdensity_function, LinkAll())

instead of the old route where you had to create a VarInfo or VectorValueAccumulator first.

Added a method rand([rng,] ::LogDensityFunction[, init_strategy]) which allows you to sample new parameter vectors from a LogDensityFunction directly.

Added a transform_strategy keyword argument to DynamicPPL.TestUtils.run_ad. It is intended to (eventually) replace the varinfo keyword argument; however, for now both are still supported for backwards compatibility. If both varinfo and transform_strategy are passed, then varinfo takes precedence.

Added a small precompilation workload to DynamicPPLMooncakeExt, which should reduce the time to first gradient down on Turing models.

0.40.5

Remove DynamicPPL's internal variable transformation code and replace it directly with the new Bijectors.VectorBijectors module. There should be no difference for end-users, apart from increased performance in many cases.

If you were extending the internal from_vec_transform, to_vec_transform, from_linked_vec_transform, to_linked_vec_transform, or tovec methods, please note that these have been removed. In place of this, you should implement the Bijectors.VectorBijectors interface, which is public and is guaranteed to be semver-compliant now onwards. Please see the Bijectors documentation for more information.

0.40.4

Moved filldist and arraydist from DistributionsAD.jl to DynamicPPL.jl (with greatly simplified definitions).

0.40.3

Added a convenience function, get_priors(::AbstractVarInfo), which extracts the VarNamedTuple of prior distributions from a VarInfo that contains a PriorDistributionAccumulator.

0.40.2

Fix a bug where DebugAccumulator was being improperly mutated during model checks.

0.40.1

Fix AD performance with ReverseDiff (v0.39.9 inadvertently introduced a bug that did not cause any correctness issues, but did cause severe slowdowns with ReverseDiff -- this patch reverts that).

0.40

v0.40 of DynamicPPL brings with it a complete rewrite of DynamicPPL's core data structure, VarInfo.

The main breaking change for users here is the removal of non-array indexing in random variables of DynamicPPL models, and the stipulation that arrays of random variables do not change size during model execution. Other breaking changes relate to the function signatures of some core DynamicPPL functions, and will not affect you unless you are developing against DynamicPPL.

... (truncated)

Commits

• See full diff in compare view

Updates DynamicPPL to 0.40.6

Release notes

Sourced from DynamicPPL's releases.

v0.40.6

DynamicPPL v0.40.6

Diff since v0.40.5

Add an extra constructor for LogDensityFunction(::Model, logdensity_function, ::AbstractTransformStrategy[, accs; adtype]), which is a shorthand for generating the vectorised values according to the given transform strategy, and then calling the existing constructor with those values. This allows you to conveniently construct a linked LogDensityFunction in one line via

ldf = LogDensityFunction(model, logdensity_function, LinkAll())

instead of the old route where you had to create a VarInfo or VectorValueAccumulator first.

Added a method rand([rng,] ::LogDensityFunction[, init_strategy]) which allows you to sample new parameter vectors from a LogDensityFunction directly.

Added a transform_strategy keyword argument to DynamicPPL.TestUtils.run_ad. It is intended to (eventually) replace the varinfo keyword argument; however, for now both are still supported for backwards compatibility. If both varinfo and transform_strategy are passed, then varinfo takes precedence.

Added a small precompilation workload to DynamicPPLMooncakeExt, which should reduce the time to first gradient down on Turing models.

Merged pull requests:

• Add convenient constructors for LDF, plus rand(::LogDensityFunction), plus run_ad (#1307) (@​penelopeysm)

Closed issues:

• Pass VarInfo and islinked to LogDensityFunction (#863)

Changelog

Sourced from DynamicPPL's changelog.

0.40.6

Add an extra constructor for LogDensityFunction(::Model, logdensity_function, ::AbstractTransformStrategy[, accs; adtype]), which is a shorthand for generating the vectorised values according to the given transform strategy, and then calling the existing constructor with those values. This allows you to conveniently construct a linked LogDensityFunction in one line via

ldf = LogDensityFunction(model, logdensity_function, LinkAll())

instead of the old route where you had to create a VarInfo or VectorValueAccumulator first.

Added a method rand([rng,] ::LogDensityFunction[, init_strategy]) which allows you to sample new parameter vectors from a LogDensityFunction directly.

Added a transform_strategy keyword argument to DynamicPPL.TestUtils.run_ad. It is intended to (eventually) replace the varinfo keyword argument; however, for now both are still supported for backwards compatibility. If both varinfo and transform_strategy are passed, then varinfo takes precedence.

Added a small precompilation workload to DynamicPPLMooncakeExt, which should reduce the time to first gradient down on Turing models.

0.40.5

Remove DynamicPPL's internal variable transformation code and replace it directly with the new Bijectors.VectorBijectors module. There should be no difference for end-users, apart from increased performance in many cases.

If you were extending the internal from_vec_transform, to_vec_transform, from_linked_vec_transform, to_linked_vec_transform, or tovec methods, please note that these have been removed. In place of this, you should implement the Bijectors.VectorBijectors interface, which is public and is guaranteed to be semver-compliant now onwards. Please see the Bijectors documentation for more information.

0.40.4

Moved filldist and arraydist from DistributionsAD.jl to DynamicPPL.jl (with greatly simplified definitions).

0.40.3

Added a convenience function, get_priors(::AbstractVarInfo), which extracts the VarNamedTuple of prior distributions from a VarInfo that contains a PriorDistributionAccumulator.

0.40.2

Fix a bug where DebugAccumulator was being improperly mutated during model checks.

0.40.1

Fix AD performance with ReverseDiff (v0.39.9 inadvertently introduced a bug that did not cause any correctness issues, but did cause severe slowdowns with ReverseDiff -- this patch reverts that).

0.40

v0.40 of DynamicPPL brings with it a complete rewrite of DynamicPPL's core data structure, VarInfo.

The main breaking change for users here is the removal of non-array indexing in random variables of DynamicPPL models, and the stipulation that arrays of random variables do not change size during model execution. Other breaking changes relate to the function signatures of some core DynamicPPL functions, and will not affect you unless you are developing against DynamicPPL.

... (truncated)

Commits

• See full diff in compare view

Most Recent Ignore Conditions Applied to This Pull Request

Dependency Name	Ignore Conditions
DynamicPPL	[>= 0.39.a, < 0.40]

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