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Bump the all-julia-packages group across 6 directories with 27 updates#168

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Bump the all-julia-packages group across 6 directories with 27 updates#168
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Updates the requirements on LogExpFunctions, CUDA, Bijectors, Turing, DynamicPPL, Documenter, Literate, MCMCChains, Statistics, PDMats, Distributions, LogDensityProblems, AbstractMCMC, StaticArrays, ADTypes, SSMProblems, Mooncake, AdvancedMH, AdvancedHMC, Plots, Zygote, GeneralisedFilters, StatsBase, CSV, CairoMakie, DataFrames and UnPack to permit the latest version.
Updates LogExpFunctions to 1.0.1

Release notes

Sourced from LogExpFunctions's releases.

v1.0.1

LogExpFunctions v1.0.1

Diff since v1.0.0

expand compat bounds

Merged pull requests:

Closed issues:

  • ready for 1.0.0? (#90)
Changelog

Sourced from LogExpFunctions's changelog.

1.0.1

Changed

  • compat bounds

1.0.0

Added

  • add logabstanh

Changed

  • improve log1pmx, add Float32 implementation
  • make tests have their own environment, use JET.jl and Aqua.jl
  • improve _log1pmx_ker internal documentation on the polynomial
  • improve accuracy of logit, logcosh
  • more detailed testing (ULPError.jl)
  • relax the doc string of log2mexp to promise just "careful evaluation", technically breaking

0.3.29

A changelog is not available up to this version.

Commits
  • fa7d47b expand compat bounds
  • f06c2c1 Merge pull request #119 from JuliaStats/tp/fix-version-bounds
  • 66fec94 expand version bounds for ForwardDiff
  • 6df17ad Merge pull request #118 from JuliaStats/dependabot/julia/test/all-julia-packa...
  • 84c0be2 Apply suggestion from @​tpapp
  • b13baed Bump the all-julia-packages group across 1 directory with 9 updates
  • d8cdf25 Don't add/update LogExpFunctions compat entries (#117)
  • 11dd07c Replace CompatHelper with dependabot (#115)
  • 6a94534 Add source path for LogExpFunctions in docs/Project.toml (#114)
  • 34f13bb remove 'pre' from CI
  • Additional commits viewable in compare view

Updates CUDA to 6.1.0

Release notes

Sourced from CUDA's releases.

v6.1.0

CUDA v6.1.0

Diff since v6.0.0

Merged pull requests:

Closed issues:

  • CUFFT: support for arbitrary dims (#119)
  • LLVM 20: Adapt to LDG removal (#2531)
  • Julia 1.11: Views can return CPU SubArray (#2551)
  • 1-element view not recognized as contiguous (#2653)
  • Can't compare Float32 with Rational on CUDA (#2681)
  • Memory leak with unified memory? (#3013)
  • Stack overflow on sparse(::Symmetric) (#3042)
  • Scalar indexing on +(::Symmetric, ::Symmetric) (#3043)
  • Performance improvement ideas for randn! Float32 (#3056)
  • Base.FastMath.pow_fast fails to compile with integer exponent (#3065)
  • normalize on CuArray fails due to scalar indexing (#3097)
  • [cuSPARSE] Incorrect indexing for COO-formatted sparse arrays (#3100)
Commits

Updates Bijectors to 0.16.0

Release notes

Sourced from Bijectors's releases.

v0.16.0

Bijectors v0.16.0

Diff since v0.15.24

Breaking changes

ChainRulesCore and EnzymeCore have been moved from direct dependencies to weak dependencies. Their integration code, including the find_alpha Enzyme rule and the rrules previously defined in src/chainrules.jl, now lives in the new BijectorsChainRulesCoreExt and BijectorsEnzymeCoreExt package extensions. These extensions are only loaded when the user also loads ChainRulesCore or EnzymeCore themselves, so downstream packages that relied on Bijectors to pull in these packages transitively must now load them directly.

DifferentiationInterface has been removed from the package's direct dependencies. It is no longer used at runtime.

Merged pull requests:

Closed issues:

  • LKJCholesky Unconstrained Parameterization is Rather "Stiff" (#468)
Changelog

Sourced from Bijectors's changelog.

0.16.0

Breaking changes

ChainRulesCore and EnzymeCore have been moved from direct dependencies to weak dependencies. Their integration code, including the find_alpha Enzyme rule and the rrules previously defined in src/chainrules.jl, now lives in the new BijectorsChainRulesCoreExt and BijectorsEnzymeCoreExt package extensions. These extensions are only loaded when the user also loads ChainRulesCore or EnzymeCore themselves, so downstream packages that relied on Bijectors to pull in these packages transitively must now load them directly.

DifferentiationInterface has been removed from the package's direct dependencies. It is no longer used at runtime.

0.15.24

Export a few more functions from Bijectors.VectorBijectors, namely scalar_to_scalar_bijector, TypedIdentity, Log, and Untruncate.

0.15.23

Implement vector bijectors for Distributions.MvTDist.

0.15.22

Implement vector bijectors for Bijectors.TransformedDistribution.

0.15.21

Add compatibility with Roots.jl v3.

0.15.20

Export Bijectors.VectorBijectors.has_constant_vec_bijector to allow downstream packages to overload it.

0.15.19

Optimise performance of vector bijectors for products of univariate distributions.

0.15.18

Implemented vector bijectors for Bijectors.OrderedDistribution.

0.15.17

Adds a new module, Bijectors.VectorBijectors. This module implements bijectors that always return vectors as the output of a linking operation. This provides additional guarantees over the existing Bijectors interface, which in general will return some collection of values that are in Euclidean space, but whose shape is not generally a vector (it could be a scalar or a multidimensional array). The intention is to make it easier to implement bijectors that are compatible with libraries that use vector inputs, such as LogDensityProblems.jl (which is in turn heavily used in the Turing ecosystem).

Please see the documentation for further information.

0.15.16

Added compatibility with Mooncake.jl v0.5.

0.15.15

... (truncated)

Commits

Updates Turing to 0.45.0

Release notes

Sourced from Turing's releases.

v0.45.0

Turing v0.45.0

Diff since v0.44.5

Breaking changes

Make FlexiChains the default chain type for MCMC sampling.

MCMCChains is still fully supported: you can specify chain_type=MCMCChains.Chains in the sample function to use it instead. However, it is no longer loaded as a dependency of Turing and re-exported (it is now an extension). That means that if you were previously importing MCMCChains via Turing, you will now have to import it directly.

Merged pull requests:

Closed issues:

  • Rework sample() call stack to use LogDensityFunction (#2555)
Changelog

Sourced from Turing's changelog.

0.45.0

Breaking changes

Make FlexiChains the default chain type for MCMC sampling.

MCMCChains is still fully supported: you can specify chain_type=MCMCChains.Chains in the sample function to use it instead. However, it is no longer loaded as a dependency of Turing and re-exported (it is now an extension). That means that if you were previously importing MCMCChains via Turing, you will now have to import it directly.

0.44.5

Allow users to disable the post-sample hook by passing verbose=false keyword argument to sample.

0.44.4

Add post-sampling warning message when there are divergent transitions with HMC, NUTS or HMCDA.

0.44.3

Add compatibility with SciMLBase v3.

0.44.2

Fix a bug in v0.44 where extra keyword arguments passed to vi (e.g. callback) would cause Turing to error.

0.44.1

Re-export pointwise_logdensities and pointwise_prior_logdensities from DynamicPPL.

0.44.0

Breaking changes

Variational inference interface

The VI interface in Turing has been modified to make it more interoperable with the rest of Turing.

  • The arguments to vi(...) are slightly different: instead of specifying a q_init argument (the initial variational approximation), you now directly pass a function that constructs this for you. For example, instead of

    q_init = q_meanfield_gaussian(model)
vi(model, q_init, n_iters)

    you would now do

    vi(model, q_meanfield_gaussian, n_iters)

... (truncated)

Commits

Updates DynamicPPL to 0.42.0

Release notes

Sourced from DynamicPPL's releases.

v0.42.0

DynamicPPL v0.42.0

Diff since v0.41.8

LogDensityFunction now performs AD preparation through AbstractPPL's prepare / value_and_gradient!! interface instead of calling DifferentiationInterface directly. Internally this removes the _use_closure heuristic and the explicit DI.Constant plumbing; the choice between closure and constants now lives in AbstractPPL.

logdensity_at has been renamed to logdensity_internal. The old name is kept as a const alias so external callers do not break.

LogDensityAt is now a deprecation shim that emits a warning and returns an AbstractPPL.Evaluators.VectorEvaluator whose call forwards to logdensity_internal. New code should call AbstractPPL.prepare(logdensity_internal, x; context=...) directly.

Breaking changes

DifferentiationInterface is no longer a hard dependency of DynamicPPL. With AbstractPPL 0.15.2, the following backends now have native AbstractPPL extensions and only need the concrete AD package loaded:

  • AutoForwardDiff — load ForwardDiff
  • AutoMooncake, AutoMooncakeForward — load Mooncake

For other DI-routed backends like AutoReverseDiff, users must load DifferentiationInterface together with the concrete AD package:

using DynamicPPL, ADTypes, DifferentiationInterface, ReverseDiff
ldf = LogDensityFunction(model; adtype=AutoReverseDiff())

For distributed sampling the same packages must be loaded on every worker.

Compatibility bounds bumped:

  • AbstractPPL 0.14 → 0.15
  • Bijectors 0.15.17 → 0.16

The integration test suites for MarginalLogDensities, ReverseDiff, and Enzyme now live in their own environments under test/ext/DynamicPPL*Ext/ and run as separate CI jobs.

Merged pull requests:

Closed issues:

  • Improve DynamicPPL benchmarks (#1374)
Changelog

Sourced from DynamicPPL's changelog.

0.42.0

LogDensityFunction now performs AD preparation through AbstractPPL's prepare / value_and_gradient!! interface instead of calling DifferentiationInterface directly. Internally this removes the _use_closure heuristic and the explicit DI.Constant plumbing; the choice between closure and constants now lives in AbstractPPL.

logdensity_at has been renamed to logdensity_internal. The old name is kept as a const alias so external callers do not break.

LogDensityAt is now a deprecation shim that emits a warning and returns an AbstractPPL.Evaluators.VectorEvaluator whose call forwards to logdensity_internal. New code should call AbstractPPL.prepare(logdensity_internal, x; context=...) directly.

Breaking changes

DifferentiationInterface is no longer a hard dependency of DynamicPPL. With AbstractPPL 0.15.2, the following backends now have native AbstractPPL extensions and only need the concrete AD package loaded:

  • AutoForwardDiff — load ForwardDiff
  • AutoMooncake, AutoMooncakeForward — load Mooncake

For other DI-routed backends like AutoReverseDiff, users must load DifferentiationInterface together with the concrete AD package:

using DynamicPPL, ADTypes, DifferentiationInterface, ReverseDiff
ldf = LogDensityFunction(model; adtype=AutoReverseDiff())

For distributed sampling the same packages must be loaded on every worker.

Compatibility bounds bumped:

  • AbstractPPL 0.14 → 0.15
  • Bijectors 0.15.17 → 0.16

The integration test suites for MarginalLogDensities, ReverseDiff, and Enzyme now live in their own environments under test/ext/DynamicPPL*Ext/ and run as separate CI jobs.

0.41.8

Override MarginalLogDensities.optimize_marginal! for LogDensityFunctionWrapper so the underlying OptimizationProblem is rebuilt with the current non-marginalised parameters on each call, rather than reusing a stale problem.

0.41.7

Enable usage of ComponentVectors on the left-hand side of tilde-statements.

Accessing a nonexistent variable in a VarNamedTuple now throws a KeyError with the original VarName, instead of an opaque type NamedTuple has no field ... error.

0.41.6

Add a factorize::Bool keyword argument for pointwise_logdensities(model, values), which controls whether pointwise logdensities for factorisable distributions (e.g. MvNormal, product_distribution, etc.) are returned as a single log-density for the whole distribution, or as an array of log-densities for each factor. The same argument is also added to pointwise_loglikelihoods and pointwise_prior_logdensities.

0.41.5

Make sure that DynamicPPL.TestUtils.AD.run_ad(...; verbose=false) truly silences all messages.

... (truncated)

Commits

Updates Documenter to 1.17.0

Release notes

Sourced from Documenter's releases.

v1.17.0

Added

  • The version selector now also preserves the anchor (hash) when switching between documentation versions. Additionally, the outdated/dev version warning banner now also tries to keep you on the same page (and position) when linking to the latest stable release. (#2880)
  • Added Remotes.Forgejo for specifying a Remote hosted on a Forgejo instance (such as codeberg.org). (#2857)
  • Doctests now default to the parser_for_module of the module that the docstring appears in, allowing modules that set their syntax version via Base.Experimental.@set_syntax_version to have their doctests parsed with the correct syntax automatically. Also added support for DocTestSyntax metadata and per-block syntax= attributes to explicitly specify a syntax version. (#2874)
  • Added a show_log keyword for Documenter.LaTeX to print LaTeX compiler logs to stdout when PDF compilation fails, and support for forcing this via DOCUMENTER_LATEX_SHOW_LOGS in CI environments. (#1697)
  • Added support for new features of the Markdown stdlib introduced in Julia 1.14, namely strike through, HTML blocks and inline HTML (this requires Julia 1.14+ and MarkdownAST 0.1.3).

Changed

  • reduced time complexity from O(n^2) to O(n) to improve the initial load time for search (#2875)
  • Git no longer displays a message about the default branch name when calling deploydocs(). (#2854)
  • Don't escape characters (such as ~) in URLs when writing LaTeX. (#2210)
  • Tweak the layout of the table of contents in LaTeX / PDF output so that for a document with 8 or more parts, the part number (VIII) does not overlap with the part title. (#2871)

Fixed

  • Fixed rendering of operator docstring bindings such as Base.:(:) and Base.:(==) in doc headers and indices. (#2844)

The changes are documented in the CHANGELOG.md file.

Diff since v1.16.1

Changelog

Sourced from Documenter's changelog.

Version [v1.17.0] - 2026-02-20

Added

  • The version selector now also preserves the anchor (hash) when switching between documentation versions. Additionally, the outdated/dev version warning banner now also tries to keep you on the same page (and position) when linking to the latest stable release. (#2880)
  • Added Remotes.Forgejo for specifying a Remote hosted on a Forgejo instance (such as codeberg.org). (#2857)
  • Doctests now default to the parser_for_module of the module that the docstring appears in, allowing modules that set their syntax version via Base.Experimental.@set_syntax_version to have their doctests parsed with the correct syntax automatically. Also added support for DocTestSyntax metadata and per-block syntax= attributes to explicitly specify a syntax version. (#2874)
  • Added a show_log keyword for Documenter.LaTeX to print LaTeX compiler logs to stdout when PDF compilation fails, and support for forcing this via DOCUMENTER_LATEX_SHOW_LOGS in CI environments. (#1697)
  • Added support for new features of the Markdown stdlib introduced in Julia 1.14, namely strike through, HTML blocks and inline HTML (this requires Julia 1.14+ and MarkdownAST 0.1.3).

Changed

  • reduced time complexity from O(n^2) to O(n) to improve the initial load time for search (#2875)
  • Git no longer displays a message about the default branch name when calling deploydocs(). (#2854)
  • Don't escape characters (such as ~) in URLs when writing LaTeX. (#2210)
  • Tweak the layout of the table of contents in LaTeX / PDF output so that for a document with 8 or more parts, the part number (VIII) does not overlap with the part title. (#2871)

Fixed

  • During cross-referencing find_object correctly locates the Documenter.Object associated with UnionAll method signatures. (#2836, #2889)
  • Fixed rendering of operator docstring bindings such as Base.:(:) and Base.:(==) in doc headers and indices. (#2844)

Version [v1.16.1] - 2025-11-21

Fixed

  • The -g is now passed to curl when checking links, to disable globbing, which could cause undesirable behavior when checking links containing characters like for example [, {, & or ?. (#2839, #2842)
  • Fixed insufficient paragraph spacing in HTML output for @docs blocks. ([#2845, #2847])
  • Don't expand details admonition by default. ([#2846, #2847])
  • Removed superfluous vertical space at end of @docs blocks. (#2849)

Version [v1.16.0] - 2025-11-14

Added

  • Added option treat_markdown_warnings_as_error which throws an error when encountering a markdown/interpolation warning (#2792, #2751)
  • Footnotes can now be previewed by hovering over the link. (#2080)
  • The version selector now attempts to stay on the same page when switching between documentation versions. If the page doesn't exist in the target version, it falls back to the version homepage. (#2801)
  • Allow named @eval blocks: such a block shares its execution context with all other @eval, @example, @repl and @setup blocks on the same page which use the same name. (#2074, #2812)

Changed

  • Page category is removed from the search index and now everything is in section category. (#2762, #2413)
  • Changed the docstring block accordions from a custom implementation to HTML details+summary tag. (#2772, #2773)
  • Improved the search tokenizer and custom trimmer to improve search results. (#1457, #2114, #2744)
  • Improved several warning/error messages to (more accurately) report the location (filename, line range) in which the warning/error originated. (#2426, #2752, #2793, #2803, #2809)
  • Warn/error if jldoctest starts with an empty line; or lacks empty line between two REPL prompts. (#2031, #2083, #2679, #2808)
  • The forcepush=true option to deploydocs now uses --force-with-lease instead of --force. (#2817)
  • Improved the generation of anchors for admonitions in HTML output to be more stable and e.g. not change due to changes of the internal representation across different Julia versions. (#2710)

... (truncated)

Commits

Updates Literate to 2.21.0

Release notes

Sourced from Literate's releases.

v2.21.0

See CHANGELOG.md for notable changes.

See CHANGELOG.md for notable changes.

Diff since v2.20.1

Changelog

Sourced from Literate's changelog.

[v2.21.0] - 2025-11-19

Changed

  • Allow IOCapture version 1. (#280)

[v2.20.1] - 2024-10-17

Fixed

  • Errors from code evaluation (with continue_on_error = true) are now properly displayed with showerror. (#261)

[v2.20.0] - 2024-10-16

Added

  • A new keyword argument configuration continue_on_error::Bool = false has been added which controls the behavior of code execution errors. By default (continue_on_error = false) execution errors are re-thrown by Literate (as before). If continue_on_error = true is set the error is used as the block result and execution continues with following blocks. (#201, #257)
  • Literate now replaces Documenter-style admonitions when generating notebook output (#259). Concretely, 
    # !!! note
#     A note.

    !!! warn "Warning title text"
    

    A warning.
    is replaced with

    # > **Note**
# >
# > A note.

    > Warning title text
    

    >
    

    > A warning.

[v2.19.1] - 2024-09-13

Fixed

  • Set :SOURCE_PATH in the task local storage to the output file when executing code so that recursive include works as expected. (#251, #252)

[v2.19.0] - 2024-07-11

Changed

  • Literate.markdown, Literate.notebook, and Literate.script are marked as public in Julia version that support the public keyword. (#248)

[v2.18.0] - 2024-04-17

Added

... (truncated)

Commits

Updates MCMCChains to 7.7.0

Release notes

Sourced from MCMCChains's releases.

v7.7.0

MCMCChains v7.7.0

Diff since v7.6.0

Remove support for PrettyTables.jl versions prior to 3.0.

Merged pull requests:

Closed issues:

  • Chains internals shouldn't use (undocumented) reserved names (#469)
  • Chains shouldn't (really) be indexed by Symbols (#470)
Changelog

Sourced from MCMCChains's changelog.

7.7.0

Remove support for PrettyTables.jl versions prior to 3.0.

7.6.0

Compatibility for PrettyTables@3.

Minimum Julia version bumped to 1.10.

7.5.0

Add a method for MCMCDiagnosticTools.bfmi(::Chains). This computes the Bayesian Fraction of Missing Information for a chain or set of chains. Previously one had to extract a raw Array from the Chains object and pass that to bfmi.

Commits
  • a95a0ee fix prettytables version check (#500)
  • 9ba5d43 Add compatibility with PrettyTable v3.0 (#498)
  • 7f54270 Bump version to 7.5.0, start HISTORY.md (#496)
  • da56d52 BFMI function (#494)
  • 2bce4e9 no coveralls, some other CI updates
  • 8b5388d Prior/posterior predictive check plots (#319)
  • 6909f74 Make chainsstack([c]) put info fields into vectors (#492)
  • 1a03a99 Revert PrettyTables=3 compat, add a test (#490)
  • de2d3ec concatenate sampler states from chains (#488)
  • a45c09e CompatHelper: bump compat for PrettyTables to 3, (keep existing compat) (#485)
  • Additional commits viewa...

    Description has been truncated

@dependabot
Bump the all-julia-packages group across 6 directories with 27 updates
dd06af0 
Updates the requirements on [LogExpFunctions](https://github.com/JuliaStats/LogExpFunctions.jl), [CUDA](https://github.com/JuliaGPU/CUDA.jl), [Bijectors](https://github.com/TuringLang/Bijectors.jl), [Turing](https://github.com/TuringLang/Turing.jl), [DynamicPPL](https://github.com/TuringLang/DynamicPPL.jl), [Documenter](https://github.com/JuliaDocs/Documenter.jl), [Literate](https://github.com/fredrikekre/Literate.jl), [MCMCChains](https://github.com/TuringLang/MCMCChains.jl), [Statistics](https://github.com/JuliaStats/Statistics.jl), [PDMats](https://github.com/JuliaStats/PDMats.jl), [Distributions](https://github.com/JuliaStats/Distributions.jl), [LogDensityProblems](https://github.com/tpapp/LogDensityProblems.jl), [AbstractMCMC](https://github.com/TuringLang/AbstractMCMC.jl), [StaticArrays](https://github.com/JuliaArrays/StaticArrays.jl), [ADTypes](https://github.com/SciML/ADTypes.jl), [SSMProblems](https://github.com/TuringLang/SSMProblems.jl), [Mooncake](https://github.com/chalk-lab/Mooncake.jl), [AdvancedMH](https://github.com/TuringLang/AdvancedMH.jl), [AdvancedHMC](https://github.com/TuringLang/AdvancedHMC.jl), [Plots](https://github.com/JuliaPlots/Plots.jl), [Zygote](https://github.com/FluxML/Zygote.jl), [GeneralisedFilters](https://github.com/TuringLang/SSMProblems.jl), [StatsBase](https://github.com/JuliaStats/StatsBase.jl), [CSV](https://github.com/JuliaData/CSV.jl), [CairoMakie](https://github.com/MakieOrg/Makie.jl), [DataFrames](https://github.com/JuliaData/DataFrames.jl) and [UnPack](https://github.com/mauro3/UnPack.jl) to permit the latest version.

Updates `LogExpFunctions` to 1.0.1
- [Release notes](https://github.com/JuliaStats/LogExpFunctions.jl/releases)
- [Changelog](https://github.com/JuliaStats/LogExpFunctions.jl/blob/master/CHANGELOG.md)
- [Commits](JuliaStats/LogExpFunctions.jl@v0.3.0...v1.0.1)

Updates `CUDA` to 6.1.0
- [Release notes](https://github.com/JuliaGPU/CUDA.jl/releases)
- [Commits](JuliaGPU/CUDA.jl@v5.0.0...v6.1.0)

Updates `Bijectors` to 0.16.0
- [Release notes](https://github.com/TuringLang/Bijectors.jl/releases)
- [Changelog](https://github.com/TuringLang/Bijectors.jl/blob/main/HISTORY.md)
- [Commits](TuringLang/Bijectors.jl@v0.15.20...v0.16.0)

Updates `Turing` to 0.45.0
- [Release notes](https://github.com/TuringLang/Turing.jl/releases)
- [Changelog](https://github.com/TuringLang/Turing.jl/blob/main/HISTORY.md)
- [Commits](TuringLang/Turing.jl@v0.43.0...v0.45.0)

Updates `DynamicPPL` to 0.42.0
- [Release notes](https://github.com/TuringLang/DynamicPPL.jl/releases)
- [Changelog](https://github.com/TuringLang/DynamicPPL.jl/blob/main/HISTORY.md)
- [Commits](TuringLang/DynamicPPL.jl@v0.40.0...v0.42.0)

Updates `Documenter` to 1.17.0
- [Release notes](https://github.com/JuliaDocs/Documenter.jl/releases)
- [Changelog](https://github.com/JuliaDocs/Documenter.jl/blob/master/CHANGELOG.md)
- [Commits](JuliaDocs/Documenter.jl@v0.1.0...v1.17.0)

Updates `Literate` to 2.21.0
- [Release notes](https://github.com/fredrikekre/Literate.jl/releases)
- [Changelog](https://github.com/fredrikekre/Literate.jl/blob/master/CHANGELOG.md)
- [Commits](fredrikekre/Literate.jl@v0.1.0...v2.21.0)

Updates `MCMCChains` to 7.7.0
- [Release notes](https://github.com/TuringLang/MCMCChains.jl/releases)
- [Changelog](https://github.com/TuringLang/MCMCChains.jl/blob/main/HISTORY.md)
- [Commits](TuringLang/MCMCChains.jl@v0.1.0...v7.7.0)

Updates `Statistics` to 1.11.1
- [Release notes](https://github.com/JuliaStats/Statistics.jl/releases)
- [Commits](JuliaStats/Statistics.jl@v1.4.0...v1.11.1)

Updates `PDMats` to 0.11.37
- [Release notes](https://github.com/JuliaStats/PDMats.jl/releases)
- [Commits](JuliaStats/PDMats.jl@v0.1.1...v0.11.37)

Updates `Distributions` to 0.25.126
- [Release notes](https://github.com/JuliaStats/Distributions.jl/releases)
- [Commits](JuliaStats/Distributions.jl@0.2.2...v0.25.126)

Updates `LogDensityProblems` to 2.2.0
- [Release notes](https://github.com/tpapp/LogDensityProblems.jl/releases)
- [Changelog](https://github.com/tpapp/LogDensityProblems.jl/blob/master/CHANGELOG.md)
- [Commits](tpapp/LogDensityProblems.jl@v0.1.0...v2.2.0)

Updates `AbstractMCMC` to 5.15.1
- [Release notes](https://github.com/TuringLang/AbstractMCMC.jl/releases)
- [Commits](TuringLang/AbstractMCMC.jl@v0.1.0...v5.15.1)

Updates `StaticArrays` to 1.9.18
- [Release notes](https://github.com/JuliaArrays/StaticArrays.jl/releases)
- [Commits](JuliaArrays/StaticArrays.jl@v0.0.1...v1.9.18)

Updates `ADTypes` to 1.22.0
- [Release notes](https://github.com/SciML/ADTypes.jl/releases)
- [Commits](SciML/ADTypes.jl@v0.1.0...v1.22.0)

Updates `SSMProblems` to 0.6.1
- [Release notes](https://github.com/TuringLang/SSMProblems.jl/releases)
- [Commits](SSMProblems-v0.5.0...SSMProblems-v0.6.1)

Updates `Mooncake` to 0.5.31
- [Release notes](https://github.com/chalk-lab/Mooncake.jl/releases)
- [Changelog](https://github.com/chalk-lab/Mooncake.jl/blob/main/HISTORY.md)
- [Commits](chalk-lab/Mooncake.jl@v0.1.0...v0.5.31)

Updates `Turing` to 0.45.0
- [Release notes](https://github.com/TuringLang/Turing.jl/releases)
- [Changelog](https://github.com/TuringLang/Turing.jl/blob/main/HISTORY.md)
- [Commits](TuringLang/Turing.jl@v0.43.0...v0.45.0)

Updates `DynamicPPL` to 0.42.0
- [Release notes](https://github.com/TuringLang/DynamicPPL.jl/releases)
- [Changelog](https://github.com/TuringLang/DynamicPPL.jl/blob/main/HISTORY.md)
- [Commits](TuringLang/DynamicPPL.jl@v0.40.0...v0.42.0)

Updates `AdvancedMH` to 0.8.10
- [Release notes](https://github.com/TuringLang/AdvancedMH.jl/releases)
- [Commits](TuringLang/AdvancedMH.jl@v0.1.0...v0.8.10)

Updates `AdvancedHMC` to 0.8.5
- [Release notes](https://github.com/TuringLang/AdvancedHMC.jl/releases)
- [Changelog](https://github.com/TuringLang/AdvancedHMC.jl/blob/main/HISTORY.md)
- [Commits](TuringLang/AdvancedHMC.jl@v0.1.0...v0.8.5)

Updates `Plots` to 1.41.6
- [Release notes](https://github.com/JuliaPlots/Plots.jl/releases)
- [Changelog](https://github.com/JuliaPlots/Plots.jl/blob/v2/NEWS.md)
- [Commits](JuliaPlots/Plots.jl@Plots-v1.41.5+docs...Plots-v1.41.6)

Updates `Zygote` to 0.7.10
- [Release notes](https://github.com/FluxML/Zygote.jl/releases)
- [Commits](FluxML/Zygote.jl@v0.2.0...v0.7.10)

Updates `GeneralisedFilters` to 0.4.2
- [Release notes](https://github.com/TuringLang/SSMProblems.jl/releases)
- [Commits](GeneralisedFilters-v0.2.1...GeneralisedFilters-v0.4.2)

Updates `PDMats` to 0.11.37
- [Release notes](https://github.com/JuliaStats/PDMats.jl/releases)
- [Commits](JuliaStats/PDMats.jl@v0.1.1...v0.11.37)

Updates `Distributions` to 0.25.126
- [Release notes](https://github.com/JuliaStats/Distributions.jl/releases)
- [Commits](JuliaStats/Distributions.jl@0.2.2...v0.25.126)

Updates `LogExpFunctions` to 1.0.1
- [Release notes](https://github.com/JuliaStats/LogExpFunctions.jl/releases)
- [Changelog](https://github.com/JuliaStats/LogExpFunctions.jl/blob/master/CHANGELOG.md)
- [Commits](JuliaStats/LogExpFunctions.jl@v0.3.0...v1.0.1)

Updates `StatsBase` to 0.34.11
- [Release notes](https://github.com/JuliaStats/StatsBase.jl/releases)
- [Commits](JuliaStats/StatsBase.jl@0.2.3...v0.34.11)

Updates `SSMProblems` to 0.6.1
- [Release notes](https://github.com/TuringLang/SSMProblems.jl/releases)
- [Commits](SSMProblems-v0.5.0...SSMProblems-v0.6.1)

Updates `Literate` to 2.21.0
- [Release notes](https://github.com/fredrikekre/Literate.jl/releases)
- [Changelog](https://github.com/fredrikekre/Literate.jl/blob/master/CHANGELOG.md)
- [Commits](fredrikekre/Literate.jl@v0.1.0...v2.21.0)

Updates `GeneralisedFilters` to 0.4.2
- [Release notes](https://github.com/TuringLang/SSMProblems.jl/releases)
- [Commits](GeneralisedFilters-v0.2.1...GeneralisedFilters-v0.4.2)

Updates `CSV` to 0.10.16
- [Release notes](https://github.com/JuliaData/CSV.jl/releases)
- [Commits](JuliaData/CSV.jl@v0.0.1...v0.10.16)

Updates `CairoMakie` to 0.15.11
- [Release notes](https://github.com/MakieOrg/Makie.jl/releases)
- [Changelog](https://github.com/MakieOrg/Makie.jl/blob/master/CHANGELOG.md)
- [Commits](https://github.com/MakieOrg/Makie.jl/commits)

Updates `DataFrames` to 1.8.2
- [Release notes](https://github.com/JuliaData/DataFrames.jl/releases)
- [Changelog](https://github.com/JuliaData/DataFrames.jl/blob/main/NEWS.md)
- [Commits](JuliaData/DataFrames.jl@v0.0.0...v1.8.2)

Updates `Documenter` to 1.17.0
- [Release notes](https://github.com/JuliaDocs/Documenter.jl/releases)
- [Changelog](https://github.com/JuliaDocs/Documenter.jl/blob/master/CHANGELOG.md)
- [Commits](JuliaDocs/Documenter.jl@v0.1.0...v1.17.0)

Updates `Literate` to 2.21.0
- [Release notes](https://github.com/fredrikekre/Literate.jl/releases)
- [Changelog](https://github.com/fredrikekre/Literate.jl/blob/master/CHANGELOG.md)
- [Commits](fredrikekre/Literate.jl@v0.1.0...v2.21.0)

Updates `Distributions` to 0.25.126
- [Release notes](https://github.com/JuliaStats/Distributions.jl/releases)
- [Commits](JuliaStats/Distributions.jl@0.2.2...v0.25.126)

Updates `AbstractMCMC` to 5.15.1
- [Release notes](https://github.com/TuringLang/AbstractMCMC.jl/releases)
- [Commits](TuringLang/AbstractMCMC.jl@v0.1.0...v5.15.1)

Updates `SSMProblems` to 0.6.1
- [Release notes](https://github.com/TuringLang/SSMProblems.jl/releases)
- [Commits](SSMProblems-v0.5.0...SSMProblems-v0.6.1)

Updates `Literate` to 2.21.0
- [Release notes](https://github.com/fredrikekre/Literate.jl/releases)
- [Changelog](https://github.com/fredrikekre/Literate.jl/blob/master/CHANGELOG.md)
- [Commits](fredrikekre/Literate.jl@v0.1.0...v2.21.0)

Updates `Plots` to 1.41.6
- [Release notes](https://github.com/JuliaPlots/Plots.jl/releases)
- [Changelog](https://github.com/JuliaPlots/Plots.jl/blob/v2/NEWS.md)
- [Commits](JuliaPlots/Plots.jl@Plots-v1.41.5+docs...Plots-v1.41.6)

Updates `UnPack` to 1.0.2
- [Release notes](https://github.com/mauro3/UnPack.jl/releases)
- [Commits](mauro3/UnPack.jl@v0.1.0...v1.0.2)

---
updated-dependencies:
- dependency-name: LogExpFunctions
  dependency-version: 1.0.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: CUDA
  dependency-version: 6.1.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Bijectors
  dependency-version: 0.16.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Turing
  dependency-version: 0.45.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: DynamicPPL
  dependency-version: 0.42.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Documenter
  dependency-version: 1.17.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Literate
  dependency-version: 2.21.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: MCMCChains
  dependency-version: 7.7.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Statistics
  dependency-version: 1.11.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: PDMats
  dependency-version: 0.11.37
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Distributions
  dependency-version: 0.25.126
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: LogDensityProblems
  dependency-version: 2.2.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: AbstractMCMC
  dependency-version: 5.15.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: StaticArrays
  dependency-version: 1.9.18
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: ADTypes
  dependency-version: 1.22.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: SSMProblems
  dependency-version: 0.6.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Mooncake
  dependency-version: 0.5.31
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Turing
  dependency-version: 0.45.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: DynamicPPL
  dependency-version: 0.42.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: AdvancedMH
  dependency-version: 0.8.10
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: AdvancedHMC
  dependency-version: 0.8.5
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Plots
  dependency-version: 1.41.6
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Zygote
  dependency-version: 0.7.10
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: GeneralisedFilters
  dependency-version: 0.4.2
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: PDMats
  dependency-version: 0.11.37
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Distributions
  dependency-version: 0.25.126
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: LogExpFunctions
  dependency-version: 1.0.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: StatsBase
  dependency-version: 0.34.11
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: SSMProblems
  dependency-version: 0.6.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Literate
  dependency-version: 2.21.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: GeneralisedFilters
  dependency-version: 0.4.2
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: CSV
  dependency-version: 0.10.16
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: CairoMakie
  dependency-version: 0.15.11
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: DataFrames
  dependency-version: 1.8.2
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Documenter
  dependency-version: 1.17.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Literate
  dependency-version: 2.21.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Distributions
  dependency-version: 0.25.126
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: AbstractMCMC
  dependency-version: 5.15.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: SSMProblems
  dependency-version: 0.6.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Literate
  dependency-version: 2.21.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Plots
  dependency-version: 1.41.6
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: UnPack
  dependency-version: 1.0.2
  dependency-type: direct:production
  dependency-group: all-julia-packages
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file julia Pull requests that update julia code labels Jun 7, 2026
@github-actions

github-actions Bot commented Jun 7, 2026

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SSMProblems.jl/SSMProblems documentation for PR #168 is available at:
https://TuringLang.github.io/SSMProblems.jl/SSMProblems/previews/PR168/

@dependabot @github

dependabot Bot commented on behalf of github Jun 14, 2026

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Superseded by #173.

@dependabot dependabot Bot closed this Jun 14, 2026
@dependabot dependabot Bot deleted the dependabot/julia/GeneralisedFilters/all-julia-packages-d60ae4efb0 branch June 14, 2026 08:26
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