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Updates the requirements on SciMLBase and FlexiChains to permit the latest version.
Updates SciMLBase to 3.3.0

Release notes

Sourced from SciMLBase's releases.

v3.3.0

SciMLBase v3.3.0

Diff since v3.2.0

Merged pull requests:

Closed issues:

  • Remaining Mooncake SymbolicIndexingInterface AD gaps (#1316)
Commits
  • a91f0e1 Update Project.toml
  • 556fd80 Merge pull request #1317 from ChrisRackauckas-Claude/mooncake-observable-foll...
  • 2aace14 Mooncake observable AD: NonlinearSolution, vector, DAE, init param-grad
  • dddf175 Merge pull request #1314 from ChrisRackauckas-Claude/mooncake-symbolic-indexi...
  • d8e49f5 Propagate parameter gradient through observable indexing rrule
  • 2a90d97 Enable Mooncake test for ODE observable autodiff
  • 480674f Add Mooncake rrules for symbolic indexing of solutions
  • 22ed166 Bump version from 3.1.0 to 3.2.0
  • 8569c5c Merge pull request #1214 from ChrisRackauckas-Claude/mooncake-tmap-responsibl...
  • 154b9dd Merge pull request #1315 from ChrisRackauckas-Claude/cc/unbreak-master-ci-aft...
  • Additional commits viewable in compare view

Updates FlexiChains to 0.4.9

Release notes

Sourced from FlexiChains's releases.

v0.4.9

FlexiChains v0.4.9

Diff since v0.4.8

Implemented MCMCDiagnosticTools.gelmandiag, MCMCDiagnosticTools.gelmandiag_multivariate, and MCMCDiagnosticTools.discretediag for FlexiChains.

Merged pull requests:

Closed issues:

  • Add gelmandiag (Gelman-Rubin-Brooks diagnostic) (#120)
  • Add discretediag (discrete parameter diagnostics) (#141)
  • begin and end don't work when indexing into chains (#153)
  • Test JLD2 serialisation (#157)
  • DynamicHMC wrapping (#158)
Changelog

Sourced from FlexiChains's changelog.

0.4.9

Implemented MCMCDiagnosticTools.gelmandiag, MCMCDiagnosticTools.gelmandiag_multivariate, and MCMCDiagnosticTools.discretediag for FlexiChains.

0.4.8

Adds a new function FlexiChains.from_stan_csv to parse Stan CSV files, plus a method FlexiChain{Symbol}(::StanSample.SampleModel) to convert from a SampleModel to FlexiChain (if sampling has already been run on the SampleModel).

0.4.7

Allow conversion of any FlexiChain{T} to MCMCChains.Chains, as long as Symbol(::T) is defined. Previously this conversion only worked for T <: VarName.

When indexing into a FlexiChain{Symbol} with a Symbol, FlexiChains now allows the symbol to resolve to an Extra, if such a key exists. Previously this would only look up parameters.

0.4.6

Adds a new function, FlexiChains.to_nt_and_stats, which samplers can overload in order to automatically bundle samples into FlexiChain{Symbol}.

Also implements the above for AdvancedHMC.jl, meaning that you can define a model that satisfies the LogDensityProblems interface, sample from it with AdvancedHMC, and collect the results in a FlexiChain{Symbol}.

See the integration docs page for more info.

0.4.5

Adds FlexiChains.Prefixed as a quick way to access VarNames that have an arbitrary prefix.

0.4.4

Added a new method FlexiChain{Symbol}(::MCMCChains.Chains) to convert a MCMCChains.Chains object into a FlexiChain{Symbol}. (Note that, if you are sampling with Turing, this is a poorer representation of the chain: you can sample directly into a VNChain instead, which is a FlexiChain{VarName}.)

Also improved the fidelity of the conversion to MCMCChains.Chains (previously metadata like sampling times and sampler states were dropped; they will now be included).

0.4.3

When using getindex on a chain or a summary, the returned DimArray now has the parameter as its name. Note that the name is stringified, so it is a lossy representation: this is because DimensionalData does not (publicly) allow the use of arbitrary types for array names (one can do it, but it requires overloading an internal method).

0.4.2

Added methods for FlexiChains.values_at and FlexiChains.parameters_at that take keyword arguments iter and chain instead of positional arguments. If unspecified, they default to :, i.e., all iterations and chains. This behaviour is designed to be consistent with that of getindex on FlexiChains.

The positional arguments are still supported, but will be removed in v0.5.

Fixed a few bugs in values_at and parameters_at where selectors or vectors of indices such as [1, 2] would fail.

... (truncated)

Commits

Updates SciMLBase to 3.3.0

Release notes

Sourced from SciMLBase's releases.

v3.3.0

SciMLBase v3.3.0

Diff since v3.2.0

Merged pull requests:

Closed issues:

  • Remaining Mooncake SymbolicIndexingInterface AD gaps (#1316)
Commits
  • a91f0e1 Update Project.toml
  • 556fd80 Merge pull request #1317 from ChrisRackauckas-Claude/mooncake-observable-foll...
  • 2aace14 Mooncake observable AD: NonlinearSolution, vector, DAE, init param-grad
  • dddf175 Merge pull request #1314 from ChrisRackauckas-Claude/mooncake-symbolic-indexi...
  • d8e49f5 Propagate parameter gradient through observable indexing rrule
  • 2a90d97 Enable Mooncake test for ODE observable autodiff
  • 480674f Add Mooncake rrules for symbolic indexing of solutions
  • 22ed166 Bump version from 3.1.0 to 3.2.0
  • 8569c5c Merge pull request #1214 from ChrisRackauckas-Claude/mooncake-tmap-responsibl...
  • 154b9dd Merge pull request #1315 from ChrisRackauckas-Claude/cc/unbreak-master-ci-aft...
  • Additional commits viewable in compare view

Updates FlexiChains to 0.4.9

Release notes

Sourced from FlexiChains's releases.

v0.4.9

FlexiChains v0.4.9

Diff since v0.4.8

Implemented MCMCDiagnosticTools.gelmandiag, MCMCDiagnosticTools.gelmandiag_multivariate, and MCMCDiagnosticTools.discretediag for FlexiChains.

Merged pull requests:

Closed issues:

  • Add gelmandiag (Gelman-Rubin-Brooks diagnostic) (#120)
  • Add discretediag (discrete parameter diagnostics) (#141)
  • begin and end don't work when indexing into chains (#153)
  • Test JLD2 serialisation (#157)
  • DynamicHMC wrapping (#158)
Changelog

Sourced from FlexiChains's changelog.

0.4.9

Implemented MCMCDiagnosticTools.gelmandiag, MCMCDiagnosticTools.gelmandiag_multivariate, and MCMCDiagnosticTools.discretediag for FlexiChains.

0.4.8

Adds a new function FlexiChains.from_stan_csv to parse Stan CSV files, plus a method FlexiChain{Symbol}(::StanSample.SampleModel) to convert from a SampleModel to FlexiChain (if sampling has already been run on the SampleModel).

0.4.7

Allow conversion of any FlexiChain{T} to MCMCChains.Chains, as long as Symbol(::T) is defined. Previously this conversion only worked for T <: VarName.

When indexing into a FlexiChain{Symbol} with a Symbol, FlexiChains now allows the symbol to resolve to an Extra, if such a key exists. Previously this would only look up parameters.

0.4.6

Adds a new function, FlexiChains.to_nt_and_stats, which samplers can overload in order to automatically bundle samples into FlexiChain{Symbol}.

Also implements the above for AdvancedHMC.jl, meaning that you can define a model that satisfies the LogDensityProblems interface, sample from it with AdvancedHMC, and collect the results in a FlexiChain{Symbol}.

See the integration docs page for more info.

0.4.5

Adds FlexiChains.Prefixed as a quick way to access VarNames that have an arbitrary prefix.

0.4.4

Added a new method FlexiChain{Symbol}(::MCMCChains.Chains) to convert a MCMCChains.Chains object into a FlexiChain{Symbol}. (Note that, if you are sampling with Turing, this is a poorer representation of the chain: you can sample directly into a VNChain instead, which is a FlexiChain{VarName}.)

Also improved the fidelity of the conversion to MCMCChains.Chains (previously metadata like sampling times and sampler states were dropped; they will now be included).

0.4.3

When using getindex on a chain or a summary, the returned DimArray now has the parameter as its name. Note that the name is stringified, so it is a lossy representation: this is because DimensionalData does not (publicly) allow the use of arbitrary types for array names (one can do it, but it requires overloading an internal method).

0.4.2

Added methods for FlexiChains.values_at and FlexiChains.parameters_at that take keyword arguments iter and chain instead of positional arguments. If unspecified, they default to :, i.e., all iterations and chains. This behaviour is designed to be consistent with that of getindex on FlexiChains.

The positional arguments are still supported, but will be removed in v0.5.

Fixed a few bugs in values_at and parameters_at where selectors or vectors of indices such as [1, 2] would fail.

... (truncated)

Commits

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@dependabot
chore: bump the all-julia-packages group across 4 directories with 2 …
9abe524 
…updates

Updates the requirements on [SciMLBase](https://github.com/SciML/SciMLBase.jl) and [FlexiChains](https://github.com/penelopeysm/FlexiChains.jl) to permit the latest version.

Updates `SciMLBase` to 3.3.0
- [Release notes](https://github.com/SciML/SciMLBase.jl/releases)
- [Commits](SciML/SciMLBase.jl@v2.30.0...v3.3.0)

Updates `FlexiChains` to 0.4.9
- [Release notes](https://github.com/penelopeysm/FlexiChains.jl/releases)
- [Changelog](https://github.com/penelopeysm/FlexiChains.jl/blob/main/HISTORY.md)
- [Commits](penelopeysm/FlexiChains.jl@v0.3.4...v0.4.9)

Updates `SciMLBase` to 3.3.0
- [Release notes](https://github.com/SciML/SciMLBase.jl/releases)
- [Commits](SciML/SciMLBase.jl@v2.30.0...v3.3.0)

Updates `FlexiChains` to 0.4.9
- [Release notes](https://github.com/penelopeysm/FlexiChains.jl/releases)
- [Changelog](https://github.com/penelopeysm/FlexiChains.jl/blob/main/HISTORY.md)
- [Commits](penelopeysm/FlexiChains.jl@v0.3.4...v0.4.9)

---
updated-dependencies:
- dependency-name: SciMLBase
  dependency-version: 3.3.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: FlexiChains
  dependency-version: 0.4.9
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: SciMLBase
  dependency-version: 3.3.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: FlexiChains
  dependency-version: 0.4.9
  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 Apr 13, 2026
@dependabot dependabot bot mentioned this pull request Apr 13, 2026
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