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Updates the requirements on LogDensityProblems, OrderedCollections, MetaGraphsNext, ADTypes, BridgeStan, JuliaBUGS, StanLogDensityProblems, DataFrames, Mooncake, PrettyTables, Chairmarks, AbstractPPL, AbstractMCMC, AdvancedHMC, MCMCChains, ForwardDiff, DifferentiationInterface, ReverseDiff, DocumenterMermaid, Distributions, LogExpFunctions, AbstractGPs, Lux, Plots, Functors, DifferentialEquations, SciMLSensitivity and FillArrays to permit the latest version.
Updates LogDensityProblems to 2.2.0

Release notes

Sourced from LogDensityProblems's releases.

v2.2.0

LogDensityProblems v2.2.0

Diff since v2.1.2

Merged pull requests:

Changelog

Sourced from LogDensityProblems's changelog.

Unreleased

  • test Zygote on all Julia branches #55

Major cleanup #54

  • remove support for ReverseDiff
  • replace Flux with Tracker
  • bump Documenter version, minor docs cleanup

0.9.2

  • follow API change in Zygote (#51, thanks @​scheidan)

  • add compat bounds (for automatic registration)

0.9.1

  • clarify constant shifts in log densities

  • test for inference issues, fix for Flux

0.9.0

Major, breaking API changes.

  1. Wrapper types Value and ValueGradient are removed. Interface functions return real numbers (logdensity), or a real number and a vector (logdensity_and_gradient). The calling convention of these types is simplified.

  2. Capabilities of log density objects are described by traits, see capabilities.

  3. dimension is now distinct from TransformVariables.dimension, as it is not really the same thing.

  4. Condition-based wrappers removed, as it was interfering with AD (mostly Zygote).

  5. Documentation significantly improved.

  6. Code organized into a single file (except for conditional loads), tests greatly simplified.

0.8.3

  • update to work with new Zygote interface

0.8.2

  • no code change, just a version bump to fix registoy problems

0.8.1

  • minor package and version fixes

... (truncated)

Commits

Updates OrderedCollections to 2.0.1

Release notes

Sourced from OrderedCollections's releases.

v2.0.1

OrderedCollections v2.0.1

Diff since v2.0.0

Merged pull requests:

Commits
  • ee78af1 Bump version from 2.0.0 to 2.0.1 (#170)
  • 304d5ed avoid rehashing in read-only operations (and fix some bugs) (#169)
  • d5d76c7 Merge pull request #164 from JuliaCollections/ox/v2
  • 68ab740 Remove depreacations for v2.0 release
  • 7bb0847 Bump version from 1.8.1 to 1.8.2
  • 6af78d8 OrderedDict: improve performance for non-concrete values and keys (#166)
  • 1eaa980 Bump actions/checkout from 5 to 6 (#157)
  • 7be2211 Bump actions/checkout from 4 to 5 (#156)
  • a25bffa Add Integer type annotation to sizehint! overloads (#155)
  • a64f186 issorted(ld; byvalue=true) for LittleDicts (#151)
  • Additional commits viewable in compare view

Updates MetaGraphsNext to 0.8.0

Release notes

Sourced from MetaGraphsNext's releases.

v0.8.0

MetaGraphsNext v0.8.0

Diff since v0.7.5

Breaking changes

  • JLD2.jl needs to be loaded by the user in order to use the loadgraph and savegraph functions and is no longer automatically loaded together with MetaGraphsNext.jl

Merged pull requests:

Commits

Updates ADTypes to 1.22.1

Release notes

Sourced from ADTypes's releases.

v1.22.1

Release v1.22.1 (tag created to match the registered version).

Commits
  • 6cbd3d8 Release v1.22.1 (#160)
  • 839efbb Use SciMLTesting v1.2 folder-based run_tests (#159)
  • b690050 Split tests into Core/QA groups; CI.yml -> grouped-tests.yml caller (#157)
  • d5b0a58 Canonical CI cleanup: TagBot thin-caller + downgrade-caller cleanup (#156)
  • 676f171 Drop allow-reresolve input from downgrade workflow(s) (#155)
  • 5ff806c ci: add standard centralized workflows (auto-format, dependabot-automerge, do...
  • 410f861 Merge pull request #153 from ChrisRackauckas-Claude/downgrade-ci-reenable
  • 4c94a00 Downgrade: drop Julia 'pre' from matrix (Resolver.jl --min fails on 1.13-rc1:...
  • ce2d236 Re-enable downgrade CI with genuine test-at-floor (allow_reresolve: false)
  • 61ada37 Merge pull request #152 from ChrisRackauckas-Claude/centralize-ci
  • Additional commits viewable in compare view

Updates BridgeStan to 2.9.0

Release notes

Sourced from BridgeStan's releases.

v2.9.0

BridgeStan v2.9.0

What's Changed

Features

Documentation

Other

Full Changelog: roualdes/bridgestan@v2.8.0...v2.9.0

Commits
  • 49e248f Release 2.9.0: updating version numbers
  • 9efbdd7 Bump actions/checkout from 6 to 7 (#328)
  • e804c10 Bump r-lib/actions from 2.12.0 to 2.12.1 (#326)
  • 543e8e1 Bump actions/cache from 5 to 6 (#327)
  • 80c9143 Allow NULL for json in bs_param_initialize (#325)
  • 88a3360 ci: use windows-2022 to un-hang Julia tests
  • 60ebbf1 ci: cache Stan off matrix.os, not runner.os
  • e05ed75 dependabot: disable on submodules until next Stan release
  • 1369e04 R: Fix doc build with roxygen2 v8.0.0 (#322)
  • 9898e2e Merge pull request #320 from roualdes/feature/bs_param_initialize
  • Additional commits viewable in compare view

Updates JuliaBUGS to 0.15.0

Release notes

Sourced from JuliaBUGS's releases.

JuliaBUGS-v0.15.0

JuliaBUGS JuliaBUGS-v0.15.0

Diff since JuliaBUGS-v0.14.1

Highlights

  • Generated quantities (#501). Every node now carries an explicit VariableType: Observation, ModelParameter, TransformedParameter, GeneratedQuantity, or FixedParameter. A generated quantity is an unobserved node (stochastic or deterministic) with no observed descendants, so it lies outside the log-density target. Generated quantities are excluded from the log density in all three evaluation modes (UseGraph, UseGeneratedLogDensityFunction, UseAutoMarginalization) and recovered after sampling by forward simulation instead of being sampled by MCMC. Under auto-marginalization, a generated quantity that depends on a marginalized discrete latent first recovers that latent from its conditional posterior p(z | θ, y). gen_chains applies this automatically, so reported generated quantities are genuine posterior(-predictive) draws.

  • AbstractPPL fix/unfix. BUGSModel now implements AbstractPPL.fix and AbstractPPL.unfix. Fixed stochastic variables are interventions: descendants see the fixed value, but the fixed variable's distribution is not scored and the variable is removed from the parameter vector. This is supported in graph, generated log-density, and auto-marginalized evaluation modes.

  • New functions, exported from the JuliaBUGS.Model submodule (like the existing parameters), so reachable as JuliaBUGS.model_parameters rather than via using JuliaBUGS: model_parameters, generated_quantities, fixed_parameters, variable_type, and the VariableType enum with its instances. forward_sample_generated_quantities!! is unexported, available as JuliaBUGS.Model.forward_sample_generated_quantities!!.

  • FlexiChains support (#483): Sampling can now collect results into a FlexiChains.FlexiChain{VarName} by passing chain_type=VNChain (after using FlexiChains). Chains are keyed by VarName, so array-valued variables are stored whole instead of being flattened into scalar columns, and sampler statistics are stored as FlexiChains.Extra entries. This is the chain format the rest of the TuringLang ecosystem is moving to (Turing 0.45 uses it by default); the docs now use it in examples. MCMCChains remains fully supported via chain_type=MCMCChains.Chains, and a FlexiChain can be converted with MCMCChains.Chains(chain).

  • Slice sampling (SliceSampling.jl): slice samplers can now sample BUGSModels once using SliceSampling. They work standalone — pass a sampler such as SliceSteppingOut directly to AbstractMCMC.sample — and as component samplers inside JuliaBUGS.Gibbs (in the sampler_map), where each single-site conditional is univariate. Being derivative-free, they need no AD backend. Both MCMCChains (chain_type=Chains) and FlexiChains (chain_type=VNChain) outputs are supported, with sampler statistics (lp, num_proposals) recorded. Shipped as three package extensions mirroring the existing HMC/MH split. See the Slice Sampling page in the docs.

  • Callable @bugs (#383). @bugs and @bugs"..." now return a callable BUGSModelDef instead of a bare Expr, so a model builds in one step — model = (@bugs begin … end)(data) — mirroring @model. This is primarily a syntax/ergonomics change: compile still accepts the wrapper (and raw Exprs), so existing compile(@bugs(...), data) code, serialization, and source generation keep working unchanged, and the underlying AST stays available via the .model_def field. It makes compile an implementation detail rather than a required step.

Breaking Changes

  • Unobserved stochastic nodes with no observed descendants (e.g. posterior-predictive draws, or priors unused by any likelihood) are now generated quantities: excluded from model_parameters, the parameter vector, and LogDensityProblems.dimension, and forward-sampled in post-processing instead of sampled by MCMC/Gibbs. The joint distribution is unchanged.
  • parameters(model) (all unobserved stochastic nodes) and model_parameters(model) (the MCMC target) can now differ, and dimension follows model_parameters. Use LogDensityProblems.dimension(model) (or length(model_parameters(model))) where you previously relied on length(parameters(model)) as the parameter-vector length.
  • Gibbs sampler maps that reference a reclassified variable now error, since it is no longer in model_parameters.
  • The return type of @bugs / @bugs"..." changed from Expr to BUGSModelDef (#383). This is a low-impact, largely syntactic change (see the Callable @bugs highlight): the usual compile(@bugs(...), data) path, serialization, and source generation are unaffected. Only code that introspected the macro result as an Expr (e.g. (@bugs ...).args) must switch to the .model_def field.

Closed issues:

  • Try out caucal inference with BUGS models (#178)
  • More model manipulation functionalities (#179)
  • Separating stochastic interpolation of missing data from the model (#327)
  • Support AdvancedMH and SliceSampling samplers in AbstractMCMC.sample. (#382)
  • Unify model construction workflow (#383)
  • DoodleBUGS: SSM plates notation (#411)
Commits
  • e1e3bd2 Merge pull request #512 from TuringLang/sunxd/slice-sampling-docs-changelog
  • 1351f85 Document slice sampling and consolidate 0.15.0 changelog
  • cfe567a Merge pull request #509 from TuringLang/sunxd/bugs-modeldef
  • 3e53c42 Address review: doc/convention polish for BUGSModelDef
  • 7eb1e1d Merge branch 'main' into sunxd/bugs-modeldef
  • 2cc9004 Merge pull request #510 from TuringLang/sunxd/abstractppl-fix
  • 27e59e8 Fix chained fix graph surgery
  • 01e1bb6 Merge branch 'main' into sunxd/abstractppl-fix
  • 0b5d1af Merge pull request #511 from TuringLang/sunxd/slice-sampling-support
  • c8f53e4 Add docs for fix/unfix with causal-intervention example
  • Additional commits viewable in compare view

Updates StanLogDensityProblems to 0.1.11

Release notes

Sourced from StanLogDensityProblems's releases.

v0.1.11

Features

  • feat: Support constructing a problem with log_density_kwargs (#32) (9dac5ff) - Penelope Yong

Chores

  • chore: Bump julia-actions/setup-julia from 2 to 3 (#33) (08bd18d) - dependabot[bot]
  • chore: Bump julia-actions/cache from 2 to 3 (#29) (9a108c9) - dependabot[bot]
  • chore: Bump codecov/codecov-action from 5 to 6 (#30) (950087e) - dependabot[bot]

Other Changes

  • Bump actions/checkout from 5 to 6 (#28) (f6cb373) - dependabot[bot]
  • Bump actions/checkout from 4 to 5 (#27) (dadb510) - dependabot[bot]
  • Bump julia-actions/julia-downgrade-compat from 1 to 2 (#24) (211388b) - dependabot[bot]

Full Changelog: sethaxen/StanLogDensityProblems.jl@v0.1.10...v0.1.11

Commits
  • 9dac5ff feat: Support constructing a problem with log_density_kwargs (#32)
  • 08bd18d chore: Bump julia-actions/setup-julia from 2 to 3 (#33)
  • 9a108c9 chore: Bump julia-actions/cache from 2 to 3 (#29)
  • 950087e chore: Bump codecov/codecov-action from 5 to 6 (#30)
  • f6cb373 Bump actions/checkout from 5 to 6 (#28)
  • dadb510 Bump actions/checkout from 4 to 5 (#27)
  • 211388b Bump julia-actions/julia-downgrade-compat from 1 to 2 (#24)
  • e64cd57 CompatHelper: bump compat for PosteriorDB in [weakdeps] to 0.6, (keep existin...
  • 6194bec Update CompatHelper.yml to recommended workflow (#25)
  • 28b69a2 Don't copy Stan file if it already exists (#22)
  • Additional commits viewable in compare view

Updates DataFrames to 1.8.2

Release notes

Sourced from DataFrames's releases.

v1.8.2

DataFrames v1.8.2

Diff since v1.8.1

Merged pull requests:

Closed issues:

  • stack wrong makeunique suggestion (#3487)
  • invalid index with SubDataFrame and copycols = false (#3515)
  • Link to "Data Wrangling with DataFrames.jl Cheat Sheet" is broken in the documentation (#3518)
Changelog

Sourced from DataFrames's changelog.

DataFrames.jl v1.8.2 Release Notes

Bug fixes

  • Fix a column selection bug when transforming SubDataFrame with copycols=false (#3503)

DataFrames.jl v1.8.0 Release Notes

Ecosystem compatibility changes

  • Make DataFrames.jl hashing consistent with Julia 1.13 and take into account column names when hashing AbstractDataFrame (#3507)
  • Require Julia 1.10 and add PrettyTables.jl v3 support (#3510)

DataFrames.jl v1.7.1 Release Notes

Julia compatibility change

  • Make DataFrames.jl support DataStructures.jl version 0.19 (#3503)

DataFrames.jl v1.7.0 Release Notes

New functionalities

  • Allow passing multiple values to add in push!, pushfirst!, append!, and prepend! (#3372)
  • rename and rename! now allow to apply a function transforming column names only to a subset of the columns specified by the cols keyword argument (#3380)
  • mapcols and mapcols! now allow to apply a function transforming columns only to a subset of the columns specified by the cols keyword argument (#3386)

Bug fixes

  • Correctly throw an error if negative number of rows is passed to first or last (#3402)
  • Always use the default thread pool for multithreaded operations, instead of using the interactive thread pool when Julia was started with -tM,N with N > 0 (#3385)
  • Correctly return Bool[] in the nonunique function applied to a data frame with a pulled column that has zero levels in the pool (#3393)

... (truncated)

Commits

Updates Mooncake to 0.5.37

Release notes

Sourced from Mooncake's releases.

v0.5.37

Mooncake v0.5.37

Diff since v0.5.36

Merged pull requests:

Closed issues:

  • TTFX compile time present also on second run (#1235)
Changelog

Sourced from Mooncake's changelog.

0.5.32

  • Fix forward-over-reverse Hessian-vector products on closures that capture a Ref wrapped in a NoTangent-typed aggregate, which previously threw UndefRefError. prepare_hvp_cache now eagerly compiles the inner rrule!! together with its forward-mode dual callables and routes the outer forward pass through a new DerivedFoRRule, so the inner IdDict constructor is no longer inlined past Mooncake's rule (#1193, #1202).
  • Fix the gradient of copysign(x, y) with respect to x: the derivative is sign(x) * sign(y), and the missing sign(x) factor previously gave the wrong gradient sign when x < 0 (#1196).
  • Handle mutation of non-const globals (setglobal!) in forward mode on Julia 1.12+ (#1194).
  • Version-bound the Core._call_latest(CoreLogging.handle_message, ...) rule (and its keyword-argument variant) to Julia below 1.12 (#1200).

0.5.31

  • Guard codual_type / fcodual_type against unbound TypeVars (#1191, #1192).

0.5.30

  • Bump the LogExpFunctions compat bound to 1 (#1186).

0.5.29

  • Add a max_fd_step keyword to TestUtils.test_rule that caps the finite-difference step sizes, keeping perturbations of domain-restricted functions (log, sqrt, cholesky) inside their domains (#1173).
  • Pre-allocate and reuse the Hessian, gradient, and basis-direction buffers in the Hessian cache so that repeated value_gradient_and_hessian!! calls avoid allocation (#1178).
  • Add consistency checks for rule reuse (#1172).
  • Mark CUDACore.cudaError_enum as having no tangent (#1175).

0.5.28

  • Throw a clear UnhandledLanguageFeatureException for try / catch blocks in reverse-mode AD instead of an opaque IR-verification failure (#1161).
  • Import the ChainRules svd rule via @from_rrule (#1163, closes #670).
  • Guard the friendly_tangent_cache array branch against NoTangent element types (e.g. SparseMatrixCSC{Int}) (#1150).

0.5.27

  • Add a cached value_and_jacobian!! interface for both forward-mode (chunked) and reverse-mode (row-by-row) caches (#1153).
  • Fix tangent_type for Union{NoRData, RData{...}} (#1133).
  • Add foreigncall zero-derivative rules for jl_get_world_counter and jl_matching_methods, supporting forward-over-reverse over those calls (#1143).
  • Handle Ptr in zero_tangent by delegating to uninit_tangent (#1139).
  • Update the CUDA extension for CUDA + cuDNN 6 (#1148).

0.5.26

  • Add Config(empty_cache=true) to free internal caches before rebuilding rules.
config = Mooncake.Config(empty_cache=true)
cache = Mooncake.prepare_gradient_cache(sin, 1.0; config)

0.5.25

  • Add nfwd: a new N-wide forward-mode implementation built around NDual, with Nfwd / NfwdMooncake internals and broad tests for scalar, array, and rule-building paths.
  • Expand Mooncake's forward-mode interface and caching around nfwd, including prepared derivative/gradient cache improvements and lower-allocation hot paths for repeated calls.
  • Route a broader scalar-math set through nfwd-backed direct primitive frule!! / rrule!! wrappers, reducing dependence on imported ChainRules rules for these cases.

... (truncated)

Commits

Updates PrettyTables to 3.4.0

Release notes

Sourced from PrettyTables's releases.

v3.4.0

PrettyTables v3.4.0

Diff since v3.3.2

  • Add the Excel back end as a package extension. (PR #298)
  • Add support for Vector{Int} in horizontal_lines_at_data_rows and vertical_lines_at_data_columns of the Excel back end.
  • Add helper macros for enabling/disabling all lines in the Excel back end.
  • Refactor the Excel back end to use the PrettyTables.jl printing iterator and consolidate the style and border API.
  • Revamp the ExcelFormatter API, moving column widths to keyword arguments and replacing border fields with ExcelTableBorders.
  • Apply behavioural and consistency cleanups, remove dead code, and tidy style issues in the Excel back end.
  • Fix border style semantics, defaults, and bottom line drawing in the Excel back end.
  • Fix the vertical line after data columns and horizontal lines at summary rows in the Excel back end.
  • Fix footnotes in title and subtitles.
  • Fix cell styling in the Excel back end.
  • Bump CI actions. (PRs #302, #305, #310 and #311)

Merged pull requests:

  • Add Excel Backend as Package Extension (#298) (@​TimG1964)
  • 👷 Bump codecov/codecov-action from 5 to 6 in the github-actions group (#302) (@​dependabot[bot])
  • 👷 Bump julia-actions/setup-julia from 2 to 3 in the github-actions group (#305) (@​dependabot[bot])
  • 👷 Bump codecov/codecov-action from 6 to 7 in the github-actions group (#310) (@​dependabot[bot])
  • 👷 Bump actions/checkout from 6 to 7 in the github-actions group (#311) (@​dependabot[bot])

Closed issues:

  • HtmlCell replacement? (#304)
  • Slow print with specific tables (#307)
Changelog

Sourced from PrettyTables's changelog.

Version 3.4.0

  • ![Feature][badge-feature] Add the Excel back end as a package extension. (PR #298[gh-pr-298])
  • ![Feature][badge-feature] Add support for Vector{Int} in horizontal_lines_at_data_rows and vertical_lines_at_data_columns of the Excel back end.
  • ![Feature][badge-feature] Add helper macros for enabling/disabling all lines in the Excel back end.
  • ![Enhancement][badge-enhancement] Refactor the Excel back end to use the PrettyTables.jl printing iterator and consolidate the style and border API.
  • ![Enhancement][badge-enhancement] Revamp the ExcelFormatter API, moving column widths to keyword arguments and replacing border fields with ExcelTableBorders.
  • ![Enhancement][badge-enhancement] Apply behavioural and consistency cleanups, remove dead code, and tidy style issues in the Excel back end.
  • ![Bugfix][badge-bugfix] Fix border style semantics, defaults, and bottom line drawing in the Excel back end.
  • ![Bugfix][badge-bugfix] Fix the vertical line after data columns and horizontal lines at summary rows in the Excel back end.
  • ![Bugfix][badge-bugfix] Fix footnotes in title and subtitles.
  • ![Bugfix][badge-bugfix] Fix cell styling in the Excel back end.
  • ![Info][badge-info] Bump CI actions. (PRs #302[gh-pr-302], #305[gh-pr-305], #310[gh-pr-310] and #311[gh-pr-311])

Version 3.3.2

  • Dummy release.

Version 3.3.1

  • ![Bugfix][badge-bugfix] We fixed the column width computation in the text back end when merged cells are present in the column labels.

Version 3.3.0

  • ![Feature][badge-feature] The Typst back end now has the option minify to reduce the number of lines in the output.
  • ![Feature][badge-feature] We added support for configuring table borders in the Typst back end.
  • ![Bugfix][badge-bugfix] We fixed a bug in which the remaining ANSI escape sequences in an AnsiCell were being ignored, leading to problems in some edge cases.

Version 3.2.3

  • ![Enhancement][badge-enhancement] We simplified the Typst back end to improve the

... (truncated)

Commits
  • 4c1ee4a 🔖 Version 3.4.0
  • 4a0665f 📚 Update CHANGELOG.md
  • b9adf5d 🔧 [Excel] Drop redundant post-loop row-label border draw
  • 75f1508 🚨 [Excel] Add tests for the back-end review fixes
  • 60b221d 🎨 [Excel] Tidy minor style issues in the Excel back end
  • bbe6a98 📚 [Excel] Fix docstring issues across the Excel back end
  • 4ba3821 🔧 [Excel] Apply behavioural and consistency cleanupsDescription has been truncated

@dependabot
Bump the all-julia-packages group across 4 directories with 28 updates
50ced6f 
Updates the requirements on [LogDensityProblems](https://github.com/tpapp/LogDensityProblems.jl), [OrderedCollections](https://github.com/JuliaCollections/OrderedCollections.jl), [MetaGraphsNext](https://github.com/JuliaGraphs/MetaGraphsNext.jl), [ADTypes](https://github.com/SciML/ADTypes.jl), [BridgeStan](https://github.com/roualdes/bridgestan), [JuliaBUGS](https://github.com/TuringLang/JuliaBUGS.jl), [StanLogDensityProblems](https://github.com/sethaxen/StanLogDensityProblems.jl), [DataFrames](https://github.com/JuliaData/DataFrames.jl), [Mooncake](https://github.com/chalk-lab/Mooncake.jl), [PrettyTables](https://github.com/ronisbr/PrettyTables.jl), [Chairmarks](https://github.com/LilithHafner/Chairmarks.jl), [AbstractPPL](https://github.com/TuringLang/AbstractPPL.jl), [AbstractMCMC](https://github.com/TuringLang/AbstractMCMC.jl), [AdvancedHMC](https://github.com/TuringLang/AdvancedHMC.jl), [MCMCChains](https://github.com/TuringLang/MCMCChains.jl), [ForwardDiff](https://github.com/JuliaDiff/ForwardDiff.jl), [DifferentiationInterface](https://github.com/JuliaDiff/DifferentiationInterface.jl), [ReverseDiff](https://github.com/JuliaDiff/ReverseDiff.jl), [DocumenterMermaid](https://github.com/JuliaDocs/DocumenterMermaid.jl), [Distributions](https://github.com/JuliaStats/Distributions.jl), [LogExpFunctions](https://github.com/JuliaStats/LogExpFunctions.jl), [AbstractGPs](https://github.com/JuliaGaussianProcesses/AbstractGPs.jl), [Lux](https://github.com/LuxDL/Lux.jl), [Plots](https://github.com/JuliaPlots/Plots.jl), [Functors](https://github.com/FluxML/Functors.jl), [DifferentialEquations](https://github.com/SciML/DifferentialEquations.jl), [SciMLSensitivity](https://github.com/SciML/SciMLSensitivity.jl) and [FillArrays](https://github.com/JuliaArrays/FillArrays.jl) to permit the latest version.

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 `OrderedCollections` to 2.0.1
- [Release notes](https://github.com/JuliaCollections/OrderedCollections.jl/releases)
- [Commits](JuliaCollections/OrderedCollections.jl@v0.1.0...v2.0.1)

Updates `MetaGraphsNext` to 0.8.0
- [Release notes](https://github.com/JuliaGraphs/MetaGraphsNext.jl/releases)
- [Commits](JuliaGraphs/MetaGraphsNext.jl@v0.1.0...v0.8.0)

Updates `ADTypes` to 1.22.1
- [Release notes](https://github.com/SciML/ADTypes.jl/releases)
- [Commits](SciML/ADTypes.jl@v0.1.0...v1.22.1)

Updates `BridgeStan` to 2.9.0
- [Release notes](https://github.com/roualdes/bridgestan/releases)
- [Commits](roualdes/bridgestan@v1.0.0...v2.9.0)

Updates `JuliaBUGS` to 0.15.0
- [Release notes](https://github.com/TuringLang/JuliaBUGS.jl/releases)
- [Commits](JuliaBUGS-v0.10.0...JuliaBUGS-v0.15.0)

Updates `StanLogDensityProblems` to 0.1.11
- [Release notes](https://github.com/sethaxen/StanLogDensityProblems.jl/releases)
- [Commits](sethaxen/StanLogDensityProblems.jl@v0.1.0...v0.1.11)

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 `Mooncake` to 0.5.37
- [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...v0.5.37)

Updates `PrettyTables` to 3.4.0
- [Release notes](https://github.com/ronisbr/PrettyTables.jl/releases)
- [Changelog](https://github.com/ronisbr/PrettyTables.jl/blob/master/CHANGELOG.md)
- [Commits](ronisbr/PrettyTables.jl@v0.1.0...v3.4.0)

Updates `Chairmarks` to 1.3.1
- [Release notes](https://github.com/LilithHafner/Chairmarks.jl/releases)
- [Commits](LilithHafner/Chairmarks.jl@v0.1.0...v1.3.1)

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 `MetaGraphsNext` to 0.8.0
- [Release notes](https://github.com/JuliaGraphs/MetaGraphsNext.jl/releases)
- [Commits](JuliaGraphs/MetaGraphsNext.jl@v0.1.0...v0.8.0)

Updates `AbstractPPL` to 0.15.3
- [Release notes](https://github.com/TuringLang/AbstractPPL.jl/releases)
- [Changelog](https://github.com/TuringLang/AbstractPPL.jl/blob/main/HISTORY.md)
- [Commits](TuringLang/AbstractPPL.jl@v0.1.0...v0.15.3)

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 `ADTypes` to 1.22.1
- [Release notes](https://github.com/SciML/ADTypes.jl/releases)
- [Commits](SciML/ADTypes.jl@v0.1.0...v1.22.1)

Updates `AdvancedHMC` to 0.8.6
- [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...v0.8.6)

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 `JuliaBUGS` to 0.15.0
- [Release notes](https://github.com/TuringLang/JuliaBUGS.jl/releases)
- [Commits](JuliaBUGS-v0.10.0...JuliaBUGS-v0.15.0)

Updates `Mooncake` to 0.5.37
- [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...v0.5.37)

Updates `ForwardDiff` to 1.4.1
- [Release notes](https://github.com/JuliaDiff/ForwardDiff.jl/releases)
- [Commits](JuliaDiff/ForwardDiff.jl@v0.0.2...v1.4.1)

Updates `DifferentiationInterface` to 0.7.19
- [Release notes](https://github.com/JuliaDiff/DifferentiationInterface.jl/releases)
- [Commits](JuliaDiff/DifferentiationInterface.jl@DifferentiationInterface-v0.1.0...DifferentiationInterface-v0.7.19)

Updates `ReverseDiff` to 1.17.0
- [Release notes](https://github.com/JuliaDiff/ReverseDiff.jl/releases)
- [Commits](JuliaDiff/ReverseDiff.jl@v0.0.1...v1.17.0)

Updates `DocumenterMermaid` to 0.2.0
- [Release notes](https://github.com/JuliaDocs/DocumenterMermaid.jl/releases)
- [Changelog](https://github.com/JuliaDocs/DocumenterMermaid.jl/blob/main/CHANGELOG.md)
- [Commits](JuliaDocs/DocumenterMermaid.jl@v0.1.0...v0.2.0)

Updates `Distributions` to 0.25.129
- [Release notes](https://github.com/JuliaStats/Distributions.jl/releases)
- [Commits](JuliaStats/Distributions.jl@0.2.2...v0.25.129)

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@v0.2.0...v1.0.1)

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 `ADTypes` to 1.22.1
- [Release notes](https://github.com/SciML/ADTypes.jl/releases)
- [Commits](SciML/ADTypes.jl@v0.1.0...v1.22.1)

Updates `AdvancedHMC` to 0.8.6
- [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...v0.8.6)

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 `JuliaBUGS` to 0.15.0
- [Release notes](https://github.com/TuringLang/JuliaBUGS.jl/releases)
- [Commits](JuliaBUGS-v0.10.0...JuliaBUGS-v0.15.0)

Updates `Mooncake` to 0.5.37
- [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...v0.5.37)

Updates `AbstractGPs` to 0.5.24
- [Release notes](https://github.com/JuliaGaussianProcesses/AbstractGPs.jl/releases)
- [Commits](JuliaGaussianProcesses/AbstractGPs.jl@v0.1.0...v0.5.24)

Updates `Lux` to 1.31.4
- [Release notes](https://github.com/LuxDL/Lux.jl/releases)
- [Commits](LuxDL/Lux.jl@LuxLib-v0.1.0...v1.31.4)

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 `Functors` to 0.5.2
- [Release notes](https://github.com/FluxML/Functors.jl/releases)
- [Commits](FluxML/Functors.jl@v0.1.0...v0.5.2)

Updates `DifferentialEquations` to 8.0.2
- [Release notes](https://github.com/SciML/DifferentialEquations.jl/releases)
- [Changelog](https://github.com/SciML/DifferentialEquations.jl/blob/master/NEWS.md)
- [Commits](https://github.com/SciML/DifferentialEquations.jl/commits)

Updates `SciMLSensitivity` to 7.113.0
- [Release notes](https://github.com/SciML/SciMLSensitivity.jl/releases)
- [Commits](https://github.com/SciML/SciMLSensitivity.jl/commits)

Updates `FillArrays` to 1.16.0
- [Release notes](https://github.com/JuliaArrays/FillArrays.jl/releases)
- [Commits](JuliaArrays/FillArrays.jl@v0.0.1...v1.16.0)

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@v0.2.0...v1.0.1)

Updates `OrderedCollections` to 2.0.1
- [Release notes](https://github.com/JuliaCollections/OrderedCollections.jl/releases)
- [Commits](JuliaCollections/OrderedCollections.jl@v0.1.0...v2.0.1)

Updates `JuliaBUGS` to 0.15.0
- [Release notes](https://github.com/TuringLang/JuliaBUGS.jl/releases)
- [Commits](JuliaBUGS-v0.10.0...JuliaBUGS-v0.15.0)

---
updated-dependencies:
- dependency-name: LogDensityProblems
  dependency-version: 2.2.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: OrderedCollections
  dependency-version: 2.0.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: MetaGraphsNext
  dependency-version: 0.8.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: ADTypes
  dependency-version: 1.22.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: BridgeStan
  dependency-version: 2.9.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: JuliaBUGS
  dependency-version: 0.15.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: StanLogDensityProblems
  dependency-version: 0.1.11
  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: Mooncake
  dependency-version: 0.5.37
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: PrettyTables
  dependency-version: 3.4.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Chairmarks
  dependency-version: 1.3.1
  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: MetaGraphsNext
  dependency-version: 0.8.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: AbstractPPL
  dependency-version: 0.15.3
  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: ADTypes
  dependency-version: 1.22.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: AdvancedHMC
  dependency-version: 0.8.6
  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: JuliaBUGS
  dependency-version: 0.15.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Mooncake
  dependency-version: 0.5.37
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: ForwardDiff
  dependency-version: 1.4.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: DifferentiationInterface
  dependency-version: 0.7.19
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: ReverseDiff
  dependency-version: 1.17.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: DocumenterMermaid
  dependency-version: 0.2.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Distributions
  dependency-version: 0.25.129
  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: 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: ADTypes
  dependency-version: 1.22.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: AdvancedHMC
  dependency-version: 0.8.6
  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: JuliaBUGS
  dependency-version: 0.15.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Mooncake
  dependency-version: 0.5.37
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: AbstractGPs
  dependency-version: 0.5.24
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Lux
  dependency-version: 1.31.4
  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: Functors
  dependency-version: 0.5.2
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: DifferentialEquations
  dependency-version: 8.0.2
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: SciMLSensitivity
  dependency-version: 7.113.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: FillArrays
  dependency-version: 1.16.0
  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: OrderedCollections
  dependency-version: 2.0.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: JuliaBUGS
  dependency-version: 0.15.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
...

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@dependabot dependabot Bot added dependencies Pull requests that update a dependency file julia Pull requests that update julia code labels Jul 9, 2026
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JuliaBUGS.jl documentation for PR #516 is available at:
https://TuringLang.github.io/JuliaBUGS.jl/previews/PR516/

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