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Bump the all-julia-packages group across 5 directories with 6 updates - #2916

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Bump the all-julia-packages group across 5 directories with 6 updates#2916
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Note

This update adds <0.0.1 to standard library compat entries. Before Julia 1.10, Pkg.test() gave standard libraries version 0.0.0, so while the julia compat entry admits those releases, a stdlib compat entry needs <0.0.1 for tests to resolve. Raising the julia compat entry to 1.10 or later removes the need for it. See the stdlib compat PSA.

Updates the requirements on FlexiChains, DocStringExtensions, MCMCChains, Turing, Test and Logging to permit the latest version.
Updates FlexiChains to 0.7.2

Release notes

Sourced from FlexiChains's releases.

v0.7.2

FlexiChains v0.7.2

Diff since v0.7.1

Add compatibility with DocStringExtensions@0.10.

Merged pull requests:

Changelog

Sourced from FlexiChains's changelog.

0.7.2

Add compatibility with DocStringExtensions@0.10.

0.7.1

Fixes a bug in pushforward_discrete so that this function now applies custom settings for alpha_limits instead of always using the default. The default setting for alpha_limits is now listed in the docstrings of all three pushforward_ functions.

0.7

v0.7 is a fairly large release of FlexiChains containing breaking changes.

Changes to core types

Extra is no longer parametric. Its name must be a Symbol, regardless of the chain's parameter key type.

FlexiChains now uses the VarName, VarNamedTuple, and Draw types defined in VarNames.jl, instead of the versions previously defined in AbstractPPL and DynamicPPL. This allows for a good amount of code simplification as previously any VarNamedTuple-specific functionality had to rely on DynamicPPL, which was an unnecessarily large dependency.

In order to not completely break users, the old code based on AbstractPPL and DynamicPPL types has been retained for compatibility. However, please note that VNChain is now aliased to the new type, i.e., FlexiChain{VarNames.VarName}. Until and unless Turing itself updates its codebase (please see this issue), Turing users should stick to FlexiChains 0.6 where possible (this will be enforced by compatibility bounds).

If you are only using Turing, it is unlikely that you will have FlexiChains v0.7 in your environment. However, if for some reason you need to use FlexiChains 0.7, please:

  • update your code to use FlexiChain{AbstractPPL.VarName} instead of VNChain
  • if you need to convert to/from the new VNChain, you can use the FlexiChains.upgrade and FlexiChains.downgrade conversion functions

Apart from this one change, everything else should still work seamlessly. If/when Turing migrates to using VarNames.jl, the two aliases can be unified.

Pushforward plot functions

The keyword arguments of the plotting functions to create pushforward visualisations (pushforward_hist, pushforward_continuous, pushforward_discrete) have been changed:

  • the baseline keyword argument has been deleted from pushforward_continuous and pushforward_discrete. As an alternative, we recommend using lines! or scatter! to overlay baseline values on the pushforward plot.
  • the residual keyword argument has been deleted from pushforward_continuous and pushforward_discrete. As an alternative, we recommend using transform_values to calculate residuals inside the FlexiChain and to then plot this new parameter using the respective pushforward_ function.
  • quantiles keyword argument has been renamed to levels across all pushforward functions and matches how forestplot's levels keyword argument works.

Stacking of array-valued parameters

Previously, if you had a parameter whose value was a DimArray, accessing its data (i.e., chain[key]) would automatically stack the parameter's dimensions with the iteration and chain dimensions. This behaviour has been removed now; you must explicitly request stacking by passing stack=true to getindex, i.e., chain[key, stack=true].

Removal of deprecated functions

The deprecated top-level plotting functions have been removed. Please use the versions in the FlexiChains.Plots and FlexiChains.Makie submodules instead:

... (truncated)

Commits

Updates DocStringExtensions to 0.10.2

Release notes

Sourced from DocStringExtensions's releases.

v0.10.2

DocStringExtensions v0.10.2

Diff since v0.10.1

See https://github.com/JuliaDocs/DocStringExtensions.jl/blob/master/CHANGELOG.md for a list of changes.

Merged pull requests:

Closed issues:

  • Precompile workload slows loading of every dependent package (#313)
Changelog

Sourced from DocStringExtensions's changelog.

v0.10.2 - 2026-10-21

Changed

  • Remove the precompilation workload and the PrecompileTools dependency, which made every package depending on DocStringExtensions slower to precompile and load. On Julia 1.6 and later the package runs interpreted, with inference on. Rendering the first docstring of a session takes about 0.2 s, against 1 s in v0.10.0 (#313, #314)

v0.10.1 - 2026-10-20

Changed

  • Improved the TTFX of the package by reducing specializations and adding a precompilation workload (#309).

v0.10.0 - 2026-10-14

Breaking

  • @template rejects a category no docstring belongs to, such as a misspelled name, with an ArgumentError. It used to store a template that never applied, so a package with such a category now fails to precompile until the category is corrected or removed (#223)
  • @template throws an ArgumentError for a template string without $(DOCSTRING), including a plain string literal, when the template is defined. Some of these templates used to load and fail with a MethodError only when Julia displayed a docstring. A package that defines one now fails to precompile (#151)
  • More docstrings get a template, and some get a different one. A docstring now gets its template when it sits in the same begin block as the @template (#288), documents a bare existing name such as "..." f (#291), or documents a parametric type's constructor (#226). A method defined through a const alias gets METHODS where it got CONSTANTS (#289). A function named like a macro, such as var"@f", no longer gets MACROS (#263). Bindings documented together each get their own category's template (#210). Where a docstring repeats by hand what its template prints, the text now appears twice

Added

  • Add TYPEDMETHODLIST, which lists methods like METHODLIST but with argument and return types. TypedMethodList(returns = false) leaves out the return types (#150, #197)
  • Add TypedMethodSignatures(returns = false), which renders typed signatures without return types (#159, #179)
  • Add a returns option to MethodSignatures and MethodList that follows each signature with its inferred return type. MethodSignatures and TypedMethodSignatures also take a string, such as returns = "success::Bool", which they print after -> in place of the inferred type (#206, #246)
  • Add the DOCSTRINGEXTENSIONS_RETURN_ARROW and DOCSTRINGEXTENSIONS_SIGNATURE_WIDTH environment variables. A reader sets them to change the arrow before return types, such as to →, and the width at which a signature wraps to one argument per line, 60 by default (#252, #267)
  • Add a defaults = true option to MethodSignatures and TypedMethodSignatures that prints default argument values, with the methods generated for positional defaults collapsed into one signature (#19, #107, #194)
  • Add a defaults = :brackets option to MethodSignatures and TypedMethodSignatures. It prints the collapsed signature without default values. Each optional positional argument appears in brackets. Any other symbol passed as defaults throws an ArgumentError (#206, #247)
  • Add PUBLIC to list a module's public names, both exported and declared public (#190)
  • Add INSTANCES to list the instances of an enum with their values. It supports @enum and EnumX.jl's @enumx (#171)
  • Add SUBTYPES to list the direct subtypes of a type as links. It lists only subtypes defined in the type's own module or a module inside it (#47, #154, #227)
  • Add BODY to print the body of the documented method definition as a Julia code block (#54, #237)
  • Add NOTEMPLATE, which stops a module's @template applying to the docstring it appears in. TemplateOverride(category) applies the template for another category instead (#158, #240)
  • Add the ABSTRACTTYPES template category for abstract types. A module without one documents abstract types with its TYPES template, as before (#147, #241)
  • SIGNATURES and TYPEDSIGNATURES in the docstring of a macro print it as its caller writes it, such as @m a b. The __source__ and __module__ arguments and the inferred return type are left out. They printed nothing before. METHODLIST and TYPEDMETHODLIST list a macro the same way. For a vararg macro they printed its hidden arguments, and for any other macro nothing (#262)
  • SIGNATURES and TYPEDSIGNATURES in the docstring of a struct list the constructors its definition creates. They printed nothing before (#71, #245)
  • Declare the interface for writing an abbreviation public on Julia 1.11 and later: Abbreviation, format and interpolation. A new guide covers it (#86, #303)
  • Declare the types that take abbreviation options public on Julia 1.11 and later, such as MethodSignatures and TypeFields. Each one appears on its topic's reference page (#303)
  • Add TypeFields(; types, defaults), whose keywords match the other option types (#303)

Changed

  • Signatures leave out a return type inferred as Any, as they already did for Nothing. -> Any says only that inference could not work out the type (#301, #298)
  • The manual splits into Examples and Reference sections with one page per topic. Each example page prints its source above the rendered docstrings, and new pages cover PUBLIC, INSTANCES, and @template with DOCSTRING. The package docstring is rewritten. A Setup page covers adding the package, templates, and Documenter. The docstrings of the package, @template and every abbreviation except README and LICENSE carry examples as doctests, which the docs build checks against the real output. They replace hand-written samples that had drifted from it (#122, #215)
  • SIGNATURES prints an unnamed argument with a declared type as ::T, as TYPEDSIGNATURES does, so foo(::Val{N}) no longer prints as foo(_). An untyped unnamed argument still prints as _ (#161, #235)
  • TYPEDSIGNATURES and TYPEDMETHODLIST print the declared type of each keyword argument, such as f(x; n::Int64). An untyped keyword and a kwargs... keyword print without one (#97, #244)
  • FIELDS and TYPEDFIELDS print each field's default value, such as retries::Int64 = 3, for structs defined with Base.@kwdef or a macro that uses the same syntax. TypeFields(defaults = false) hides them (#182, #245)
  • @template applies a template when its docstring is defined, not when it is displayed, so a templated docstring no longer stores the documented expression in the package image. A docstring for a binding that does not exist yet keeps its template until display. Bindings documented together, such as @doc "..." (f, T), each get the template for their own category, where they all used the last binding's (#210)

... (truncated)

Commits

Updates MCMCChains to 8.0.0

Release notes

Sourced from MCMCChains's releases.

v8.0.0

MCMCChains v8.0.0

Diff since v7.8.1

Added

  • describe accepts digits to set the decimal places in its summary and quantile tables.
  • hcat now adds scalar or vector values by name, including matrices of named tuples, while preserving iteration labels and chain metadata.
  • var and std, with one estimate per parameter.
  • cov, with parameter names on both axes of the covariance matrix.

Breaking Changes

  • corner, corner! and seriestype=:corner were replaced by StatsPlots.cornerplot and StatsPlots.cornerplot!.

Fixed

  • StatsPlots.cornerplot and StatsPlots.cornerplot! threw when given a Chains object.
  • hcat failed to add named-tuple draws stored in an Any-typed matrix and could return a plain matrix for one draw.
  • ChainDataFrame summaries could not be converted with Array, and convert(Array, summary) failed for a single statistic.
  • get returned numeric array parameters in stored column order instead of array index order.
  • Chains selection by a vector of parameter names returned columns in stored order instead of requested order.
  • Chains assignment by a vector of parameter names placed values in stored order instead of requested order.
  • get and get_params with flatten=true lost draws, while get also threw for section selections or included names from other sections.

Merged pull requests:

Closed issues:

  • Add unit tests for diagnostics (#9)
  • Add model selection tools (#83)
  • Describe method keyword arguments (#106)
  • Estimating marginal likelihoods using thermodynamic integral (#134)
  • Support for short chains? (#226)
  • Mean of grouped variables as array (#231)
  • [RFC] MCMCChains Goals (#246)
  • Handle weighted samples (#253)
  • Adding Parameters to an Existing Chain (#298)
  • Order of Array Parameters is not Preserved by get (#311)
  • section=:parameters cannot be combined with flatten=true (#380)

... (truncated)

Changelog

Sourced from MCMCChains's changelog.

8.0.0

Added

  • describe accepts digits to set the decimal places in its summary and quantile tables.
  • hcat now adds scalar or vector values by name, including matrices of named tuples, while preserving iteration labels and chain metadata.
  • var and std, with one estimate per parameter.
  • cov, with parameter names on both axes of the covariance matrix.

Changed

  • corner, corner! and seriestype=:corner were replaced by StatsPlots.cornerplot and StatsPlots.cornerplot!.

Fixed

  • StatsPlots.cornerplot and StatsPlots.cornerplot! threw when given a Chains object.
  • hcat failed to add named-tuple draws stored in an Any-typed matrix and could return a plain matrix for one draw.
  • ChainDataFrame summaries could not be converted with Array, and convert(Array, summary) failed for a single statistic.
  • get returned numeric array parameters in stored column order instead of array index order.
  • Chains selection by a vector of parameter names returned columns in stored order instead of requested order.
  • Chains assignment by a vector of parameter names placed values in stored order instead of requested order.
  • get and get_params with flatten=true lost draws, while get also threw for section selections or included names from other sections.

7.8.1

  • countplot, which counts distinct sampled values on a categorical axis.
  • histogram placed empty bars between a parameter's few sampled values and now bins on those values under bins = :auto when the edges fit.

7.8.0

Added

  • diagnosticsplot, which puts every convergence diagnostic for every parameter in one coloured grid.
  • essplot, rhatplot and mcseplot, one dot per parameter for the diagnostics the package already reports.
  • evolutionplot, which recomputes a diagnostic on growing prefixes of the chain.
  • parallelplot, which draws every draw across all parameters and picks out the divergent ones.
  • nutsplot, for the acceptance rate, step size, tree depth and divergence count an HMC sampler records.
  • rankplot.
  • The :ecdfplot series type.
  • plot_style! and reset_plot_style!, which set the palette, the grid, the background, the frame, the font, and where a multi-panel plot names its chains.

Changed

  • Plots drop the grid, the top and right spines, and the legend box, and draw chains from the Okabe-Ito palette.
  • Multi-panel plots name the chains in one panel, instead of leaving the lines unlabelled.
  • Histograms choose their bin count from the draws rather than always using 25.

Fixed

  • ridgelineplot and forestplot threw when given no parameter list, though the docstring said they would plot every parameter.

... (truncated)

Commits

Updates Turing to 0.49.0

Release notes

Sourced from Turing's releases.

v0.49.0

Turing v0.49.0

Diff since v0.48.0

DynamicPPL 0.42.13 is now the minimum, so that SMC, PG and CSMC build a TapedTask again (#2895).

Breaking changes

NamedDist is no longer re-exported, following its removal from DynamicPPL. Replace x ~ NamedDist(dist, :y) with y ~ dist, followed by x = y if a local alias is needed (#2895).

Merged pull requests:

Changelog

Sourced from Turing's changelog.

0.49.0

DynamicPPL 0.42.13 is now the minimum, so that SMC, PG and CSMC build a TapedTask again (#2895).

Breaking changes

NamedDist is no longer re-exported, following its removal from DynamicPPL. Replace x ~ NamedDist(dist, :y) with y ~ dist, followed by x = y if a local alias is needed (#2895).

0.48.0

Breaking changes

The SGLD and SGHMC samplers, which did not support minibatching, have been removed along with PolynomialStepsize (#2890).

MH(var => proposal, ...) and LinkedRW have been removed. Use MH() for prior proposals, or MH(cov_matrix) for a Gaussian random walk over the complete linked parameter vector. In Gibbs, assign MH(cov_matrix) to the target variable block (#2883).

Gibbs now conditions its components with DynamicPPL.condition. GibbsContext and Turing.Inference.make_conditional are removed. Rename isgibbscomponent to supports_gibbs and gibbs_get_raw_values to gibbs_get_parameter_values; the old names are deprecated. Gibbs no longer supports model arguments containing missing: declare the latent variable inside the model and condition on observations instead (#2863).

Every variable reached by a Gibbs model must belong to a component. A component may not change the dimension or existence of a variable owned only by another component; put the variable and whatever decides its shape in one block. Changes to another block's support or distributional form remain unchecked and can make the chain reducible; see the Gibbs docstring (#2863).

Other changes

ESS Gibbs components now use the current conditional prior after another component changes its parameters (#2885).

Gibbs chains now include component-sampler statistics (#2863).

NUTS and HMCDA now accept a NamedTuple or Dict{VarName} initial_params, which HMC already did (#2878).

Emcee now honours chain_type=MCMCChains.Chains, and refuses walkers that start in different parameter layouts instead of failing inside the decode or the stretch proposal (#2879).

estimate_mode now represents indexed bounds using the model's parameter shapes, avoiding growable-array warnings during optimisation (#2888).

estimate_mode now throws on a bound that does not cover a whole variable, where it previously either dropped it and returned the unconstrained mode or failed with a bare DimensionMismatch, and warns on a bound no variable can use rather than ignoring it in silence (#2880).

Prior() now warns that initial_params has no effect instead of discarding it silently (#2881).

... (truncated)

Commits
  • 9d78370 Drop the NamedDist re-export and require DynamicPPL 0.42.13 (#2895)
  • b8af3d0 Fix Gibbs handling of wrapped external samplers and conditional sites (#2891)
  • 8e6474e Remove SGLD and SGHMC (#2890)
  • 0427d59 docs: clarify README (#2889)
  • 230890a Gibbs: condition components instead of GibbsContext (#2863)
  • 9c52f65 optimisation: eliminate growable constraint warnings (#2888)
  • afeec14 mh: remove per-variable proposals (#2883)
  • 41a8c37 optimisation: Stop silently discarding lb/ub bounds (#2880)
  • b1f8d57 emcee: Honour chain_type and refuse walkers in different parameter layouts ...
  • 4528262 prior: Warn that initial_params has no effect (#2881)
  • Additional commits viewable in compare view

Updates FlexiChains to 0.7.2

Release notes

Sourced from FlexiChains's releases.

v0.7.2

FlexiChains v0.7.2

Diff since v0.7.1

Add compatibility with DocStringExtensions@0.10.

Merged pull requests:

Changelog

Sourced from FlexiChains's changelog.

0.7.2

Add compatibility with DocStringExtensions@0.10.

0.7.1

Fixes a bug in pushforward_discrete so that this function now applies custom settings for alpha_limits instead of always using the default. The default setting for alpha_limits is now listed in the docstrings of all three pushforward_ functions.

0.7

v0.7 is a fairly large release of FlexiChains containing breaking changes.

Changes to core types

Extra is no longer parametric. Its name must be a Symbol, regardless of the chain's parameter key type.

FlexiChains now uses the VarName, VarNamedTuple, and Draw types defined in VarNames.jl, instead of the versions previously defined in AbstractPPL and DynamicPPL. This allows for a good amount of code simplification as previously any VarNamedTuple-specific functionality had to rely on DynamicPPL, which was an unnecessarily large dependency.

In order to not completely break users, the old code based on AbstractPPL and DynamicPPL types has been retained for compatibility. However, please note that VNChain is now aliased to the new type, i.e., FlexiChain{VarNames.VarName}. Until and unless Turing itself updates its codebase (please see this issue), Turing users should stick to FlexiChains 0.6 where possible (this will be enforced by compatibility bounds).

If you are only using Turing, it is unlikely that you will have FlexiChains v0.7 in your environment. However, if for some reason you need to use FlexiChains 0.7, please:

  • update your code to use FlexiChain{AbstractPPL.VarName} instead of VNChain
  • if you need to convert to/from the new VNChain, you can use the FlexiChains.upgrade and FlexiChains.downgrade conversion functions

Apart from this one change, everything else should still work seamlessly. If/when Turing migrates to using VarNames.jl, the two aliases can be unified.

Pushforward plot functions

The keyword arguments of the plotting functions to create pushforward visualisations (pushforward_hist, pushforward_continuous, pushforward_discrete) have been changed:

  • the baseline keyword argument has been deleted from pushforward_continuous and pushforward_discrete. As an alternative, we recommend using lines! or scatter! to overlay baseline values on the pushforward plot.
  • the residual keyword argument has been deleted from pushforward_continuous and pushforward_discrete. As an alternative, we recommend using transform_values to calculate residuals inside the FlexiChain and to then plot this new parameter using the respective pushforward_ function.
  • quantiles keyword argument has been renamed to levels across all pushforward functions and matches how forestplot's levels keyword argument works.

Stacking of array-valued parameters

Previously, if you had a parameter whose value was a DimArray, accessing its data (i.e., chain[key]) would automatically stack the parameter's dimensions with the iteration and chain dimensions. This behaviour has been removed now; you must explicitly request stacking by passing stack=true to getindex, i.e., chain[key, stack=true].

Removal of deprecated functions

The deprecated top-level plotting functions have been removed. Please use the versions in the FlexiChains.Plots and FlexiChains.Makie submodules instead:

... (truncated)

Commits

Updates MCMCChains to 8.0.0

Release notes

Sourced from MCMCChains's releases.

v8.0.0

MCMCChains v8.0.0

Diff since v7.8.1

Added

  • describe accepts digits to set the decimal places in its summary and quantile tables.
  • hcat now adds scalar or vector values by name, including matrices of named tuples, while preserving iteration labels and chain metadata.
  • var and std, with one estimate per parameter.
  • cov, with parameter names on both axes of the covariance matrix.

Breaking Changes

  • corner, corner! and seriestype=:corner were replaced by StatsPlots.cornerplot and StatsPlots.cornerplot!.

Fixed

  • StatsPlots.cornerplot and StatsPlots.cornerplot! threw when given a Chains object.
  • hcat failed to add named-tuple draws stored in an Any-typed matrix and could return a plain matrix for one draw.
  • ChainDataFrame summaries could not be converted with Array, and convert(Array, summary) failed for a single statistic.
  • get returned numeric array parameters in stored column order instead of array index order.
  • Chains selection by a vector of parameter names returned columns in stored order instead of requested order.
  • Chains assignment by a vector of parameter names placed values in stored order instead of requested order.
  • get and get_params with flatten=true lost draws, while get also threw for section selections or included names from other sections.

Merged pull requests:

Closed issues:

  • Add unit tests for diagnostics (#9)
  • Add model selection tools (#83)
  • Describe method keyword arguments (#106)
  • Estimating marginal likelihoods using thermodynamic integral (#134)
  • Support for short chains? (#226)
  • Mean of grouped variables as array (#231)
  • [RFC] MCMCChains Goals (#246)
  • Handle weighted samples (#253)
  • Adding Parameters to an Existing Chain (#298)
  • Order of Array Parameters is not Preserved by get (#311)
  • section=:parameters cannot be combined with flatten=true (#380)

... (truncated)

Changelog

Sourced from MCMCChains's changelog.

8.0.0

Added

  • describe accepts digits to set the decimal places in its summary and quantile tables.
  • hcat now adds scalar or vector values by name, including matrices of named tuples, while preserving iteration labels and chain metadata.
  • var and std, with one estimate per parameter.
  • cov, with parameter names on both axes of the covariance matrix.

Changed

  • corner, corner! and seriestype=:corner were replaced by StatsPlots.cornerplot and StatsPlots.cornerplot!.

Fixed

  • StatsPlots.cornerplot and StatsPlots.cornerplot! threw when given a Chains object.
  • hcat failed to add named-tuple draws stored in an Any-typed matrix and could return a plain matrix for one draw.
  • ChainDataFrame summaries could not be converted with Array, and convert(Array, summary) failed for a single statistic.
  • get returned numeric array parameters in stored column order instead of array index order.
  • Chains selection by a vector of parameter names returned columns in stored order instead of requested order.
  • Chains assignment by a vector of parameter names placed values in stored order instead of requested order.
  • get and get_params with flatten=true lost draws, while get also threw for section selections or included names from other sections.

7.8.1

  • countplot, which counts distinct sampled values on a categorical axis.
  • histogram placed empty bars between a parameter's few sampled values and now bins on those values under bins = :auto when the edges fit.

7.8.0

Added

  • diagnosticsplot, which puts every convergence diagnostic for every parameter in one coloured grid.
  • essplot, rhatplot and mcseplot, one dot per parameter for the diagnostics the package already reports.
  • evolutionplot, which recomputes a diagnostic on growing prefixes of the chain.
  • parallelplot, which draws every draw across all parameters and picks out the divergent ones.
  • nutsplot, for the acceptance rate, step size, tree depth and divergence count an HMC sampler records.
  • rankplot.
  • The :ecdfplot series type.
  • plot_style! and reset_plot_style!, which set the palette, the grid, the background, the frame, the font, and where a multi-panel plot names its chains.

Changed

  • Plots drop the grid, the top and right spines, and the legend box, and draw chains from the Okabe-Ito palette.
  • Multi-panel plots name the chains in one panel, instead of leaving the lines unlabelled.
  • Histograms choose their bin count from the draws rather than always using 25.

Fixed

  • ridgelineplot and forestplot threw when given no parameter list, though the docstring said they would plot every parameter.

... (truncated)

Commits

Updates Test to 1.10.0

Updates Logging to 1.10.0

Updates FlexiChains to 0.7.2

Release notes

Sourced from FlexiChains's releases.

v0.7.2

FlexiChains v0.7.2

Diff since v0.7.1

Add compatibility with DocStringExtensions@0.10.

Merged pull requests:

Changelog

Sourced from FlexiChains's changelog.

0.7.2

Add compatibility with DocStringExtensions@0.10.

0.7.1

Fixes a bug in pushforward_discrete so that this function now applies custom settings for alpha_limits instead of always using the default. The default setting for alpha_limits is now listed in the docstrings of all three pushforward_ functions.

0.7

v0.7 is a fairly large release of FlexiChains containing breaking changes.

Changes to core types

Extra is no longer parametric. Its name must be a Symbol, regardless of the chain's parameter key type.

FlexiChains now uses the VarName, VarNamedTuple, and Draw types defined in VarNames.jl, instead of the versions previously defined in AbstractPPL and DynamicPPL. This allows for a good amount of code simplification as previously any VarNamedTuple-specific functionality had to rely on DynamicPPL, which was an unnecessarily large dependency.

In order to not completely break users, the old code based on AbstractPPL and DynamicPPL types has been retained for compatibility. However, please note that VNChain is now aliased to the new type, i.e., FlexiChain{VarNames.VarName}. Until and unless Turing itself updates its codebase (please see this issue), Turing users should stick to FlexiChains 0.6 where possible (this will be enforced by compatibility bounds).

If you are only using Turing, it is unlikely that you will have FlexiChains v0.7 in your environment. However, if for some reason you need to use FlexiChains 0.7, please:

  • update your code to use FlexiChain{AbstractPPL.VarName} instead of VNChain
  • if you need to convert to/from the new VNChain, you can use the FlexiChains.upgrade and FlexiChains.downgrade conversion functions

Apart from this one change, everything else should still work seamlessly. If/when Turing migrates to using VarNames.jl, the two aliases can be unified.

Pushforward plot functions

The keyword arguments of the plotting functions to create pushforward visualisations (pushforward_hist, pushforward_continuous, pushforward_discrete) have been changed:

  • the baseline keyword argument has been deleted from pushforward_continuous and pushforward_discrete. As an alternative, we recommend using lines! or scatter! to overlay baseline values on the pushforward plot.
  • the residual keyword argument has been deleted from pushforward_continuous and pushforward_discrete. As an alternative, we recommend using transform_values to calculate residuals inside the FlexiChain and to then plot ...

    Description has been truncated

@dependabot
Bump the all-julia-packages group across 5 directories with 6 updates
01e23cd 
Updates the requirements on [FlexiChains](https://github.com/JuliaBayes/FlexiChains.jl), [DocStringExtensions](https://github.com/JuliaDocs/DocStringExtensions.jl), [MCMCChains](https://github.com/TuringLang/MCMCChains.jl), [Turing](https://github.com/TuringLang/Turing.jl), Test and Logging to permit the latest version.

Updates `FlexiChains` to 0.7.2
- [Release notes](https://github.com/JuliaBayes/FlexiChains.jl/releases)
- [Changelog](https://github.com/JuliaBayes/FlexiChains.jl/blob/main/HISTORY.md)
- [Commits](JuliaBayes/FlexiChains.jl@v0.6.0...v0.7.2)

Updates `DocStringExtensions` to 0.10.2
- [Release notes](https://github.com/JuliaDocs/DocStringExtensions.jl/releases)
- [Changelog](https://github.com/JuliaDocs/DocStringExtensions.jl/blob/master/CHANGELOG.md)
- [Commits](https://github.com/JuliaDocs/DocStringExtensions.jl/commits/v0.10.2)

Updates `MCMCChains` to 8.0.0
- [Release notes](https://github.com/TuringLang/MCMCChains.jl/releases)
- [Changelog](https://github.com/TuringLang/MCMCChains.jl/blob/main/HISTORY.md)
- [Commits](https://github.com/TuringLang/MCMCChains.jl/commits/v8.0.0)

Updates `Turing` to 0.49.0
- [Release notes](https://github.com/TuringLang/Turing.jl/releases)
- [Changelog](https://github.com/TuringLang/Turing.jl/blob/main/HISTORY.md)
- [Commits](v0.0.1...v0.49.0)

Updates `FlexiChains` to 0.7.2
- [Release notes](https://github.com/JuliaBayes/FlexiChains.jl/releases)
- [Changelog](https://github.com/JuliaBayes/FlexiChains.jl/blob/main/HISTORY.md)
- [Commits](JuliaBayes/FlexiChains.jl@v0.6.0...v0.7.2)

Updates `MCMCChains` to 8.0.0
- [Release notes](https://github.com/TuringLang/MCMCChains.jl/releases)
- [Changelog](https://github.com/TuringLang/MCMCChains.jl/blob/main/HISTORY.md)
- [Commits](https://github.com/TuringLang/MCMCChains.jl/commits/v8.0.0)

Updates `Test` to 1.10.0

Updates `Logging` to 1.10.0

Updates `FlexiChains` to 0.7.2
- [Release notes](https://github.com/JuliaBayes/FlexiChains.jl/releases)
- [Changelog](https://github.com/JuliaBayes/FlexiChains.jl/blob/main/HISTORY.md)
- [Commits](JuliaBayes/FlexiChains.jl@v0.6.0...v0.7.2)

Updates `Test` to 1.0.0

Updates `Test` to 1.0.0

---
updated-dependencies:
- dependency-name: FlexiChains
  dependency-version: 0.7.2
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: DocStringExtensions
  dependency-version: 0.10.2
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: MCMCChains
  dependency-version: 8.0.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Turing
  dependency-version: 0.49.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: FlexiChains
  dependency-version: 0.7.2
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: MCMCChains
  dependency-version: 8.0.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Test
  dependency-version: 1.10.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Logging
  dependency-version: 1.10.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: FlexiChains
  dependency-version: 0.7.2
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Test
  dependency-version: 1.0.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Test
  dependency-version: 1.0.0
  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 Nov 9, 2026

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