chore: Bump the all-julia-packages group across 4 directories with 8 updates

[dependabot]

Updates the requirements on LogExpFunctions, PlutoStaticHTML, DimensionalData, Turing, MCMCChains, ArviZ, SampleChains and SampleChainsDynamicHMC 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:

• Add source path for LogExpFunctions in docs/Project.toml (#114) (@​devmotion)
• Replace CompatHelper with dependabot (#115) (@​devmotion)
• Don't add/update LogExpFunctions compat entries (#117) (@​devmotion)
• Bump the all-julia-packages group across 1 directory with 9 updates (#118) (@​dependabot[bot])
• expand version bounds for ForwardDiff (#119) (@​tpapp)

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 PlutoStaticHTML to 8.0.0

Release notes

Sourced from PlutoStaticHTML's releases.

v8.0.0

PlutoStaticHTML v8.0.0

Diff since v7.0.11

Breaking changes

• Dependency on Pluto 1.0

Merged pull requests:

• Update Pluto to 1.0.1 (#221) (@​rikhuijzer)

Commits

• See full diff in compare view

Updates DimensionalData to 0.30.1

Release notes

Sourced from DimensionalData's releases.

v0.30.1

DimensionalData v0.30.1

Diff since v0.30.0

Merged pull requests:

• move DimensionalPlot back to the main package (#1178) (@​rafaqz)

Closed issues:

• What is the replacement for LookupArrays? (#1176)

Commits

• See full diff in compare view

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:

• Make FlexiChains the default chain type (#2743) (@​penelopeysm)
• add Claude stuff (#2822) (@​penelopeysm)

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

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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:

• fix prettytables version check (#500) (@​penelopeysm)

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 viewable in compare view

Updates ArviZ to 0.14.2

Release notes

Sourced from ArviZ's releases.

v0.14.2

ArviZ v0.14.2

Diff since v0.14.1

Commits

• f233782 docs: update for ArviZPythonPlots v0.2 (#435)
• 8303053 chore: Update README.md reference to CoC (#434)
• 40053eb chore: Have Code of Conduct default to org level file (#429)
• 2d884c0 chore: Bump actions/checkout from 6 to 7 (#432)
• ad37e97 chore: Bump codecov/codecov-action from 6 to 7 (#431)
• e286a41 chore: remove stale Travis-era coverage script (#430)
• 864c648 ci: replace CompatHelper with dependabot for Julia deps (#427)
• 86e8518 ci: remove invalidations workflow (#428)
• c7a9abd chore: Bump actions/github-script from 8 to 9 (#422)
• c5ebf7b chore: Bump julia-actions/setup-julia from 2 to 3 (#423)
• Additional commits viewable in compare view

Updates DimensionalData to 0.30.1

Release notes

Sourced from DimensionalData's releases.

v0.30.1

DimensionalData v0.30.1

Diff since v0.30.0

Merged pull requests:

• move DimensionalPlot back to the main package (#1178) (@​rafaqz)

Closed issues:

• What is the replacement for LookupArrays? (#1176)

Commits

• See full diff in compare view

Updates SampleChains to 0.5.1

Release notes

Sourced from SampleChains's releases.

v0.5.1

SampleChains v0.5.1

Diff since v0.5.0

Commits

• a08442f Update Project.toml
• 3963d52 Update Project.toml
• 3c49617 Merge pull request #4 from cscherrer/kwargs
• 384a1a0 fixing imports
• e0247ba drop some extra dependencies
• 1239655 initialize! => newchain
• 80363d0 export ChainConfig
• feba0c1 drawsamples! => sample!
• 0883ecb buigfix
• 455f385 chainconfig
• Additional commits viewable in compare view

Updates SampleChainsDynamicHMC to 0.3.5

Release notes

Sourced from SampleChainsDynamicHMC's releases.

v0.3.5

SampleChainsDynamicHMC v0.3.5

Diff since v0.3.4

Commits

• a87cbe9 update dependencies
• 03c7b92 Merge branch 'master' of github.com:cscherrer/SampleChainsDynamicHMC.jl
• 96402cf Reporter (#18)
• 3de62d4 Update Project.toml
• cb997e8 mutable struct
• 866a0fb Use a Ref instead
• c087be4 Update Project.toml
• 3e3a771 bugfix
• d4129f6 divergences WIP
• da702e2 Delete Manifest.toml
• Additional commits viewable in compare view

Updates ArviZ to 0.14.2

Release notes

Sourced from ArviZ's releases.

v0.14.2

ArviZ v0.14.2

Diff since v0.14.1

Commits

• f233782 docs: update for ArviZPythonPlots v0.2 (#435)
• 8303053 chore: Update README.md reference to CoC (#434)
• 40053eb chore: Have Code of Conduct default to org level file (#429)
• 2d884c0 chore: Bump actions/checkout from 6 to 7 (#432)
• ad37e97 chore: Bump codecov/codecov-action from 6 to 7 (#431)
• e286a41 chore: remove stale Travis-era coverage script (#430)
• 864c648 ci: replace CompatHelper with dependabot for Julia deps (#427)
• 86e8518 ci: remove invalidations workflow (#428)
• c7a9abd chore: Bump actions/github-script from 8 to 9 (#422)
• c5ebf7b chore: Bump julia-actions/setup-julia from 2 to 3 (#423)
• Additional commits viewable in compare view

Updates DimensionalData to 0.30.1

Release notes

Sourced from DimensionalData's releases.

v0.30.1

DimensionalData v0.30.1

Diff since v0.30.0

Merged pull requests:

• move DimensionalPlot back to the main package (#1178) (@​rafaqz)

Closed issues:

• What is the replacement for LookupArrays? (#1176)

Commits

• See full diff in compare view

Updates SampleChains to 0.5.1

Release notes

Sourced from SampleChains's releases.

v0.5.1

SampleChains v0.5.1

Diff since v0.5.0

Commits

• a08442f Update Project.toml
• 3963d52 Update Project.toml
• 3c49617 Merge pull request #4 from cscherrer/kwargs
• 384a1a0 fixing imports
• e0247ba drop some extra dependencies
• 1239655 initialize! => newchain
• 80363d0 export ChainConfig
• feba0c1 drawsamples! => sample!
• 0883ecb buigfix
• 455f385 chainconfig
• Additional commits viewable in compare view

Updates ArviZ to 0.14.2

Release notes

Sourced from ArviZ's releases.

v0.14.2

ArviZ v0.14.2

Diff since v0.14.1

Commits

• f233782 docs: update for ArviZPythonPlots v0.2 (#435)
• 8303053 chore: Update README.md reference to CoC (#434)
• 40053eb chore: Have Code of Conduct default to org level file (#429)
• 2d884c0 chore: Bump actions/checkout from 6 to 7 (#432)
• ad37e97 chore: Bump codecov/codecov-action from 6 to 7 (#431)
• e286a41 chore: remove stale Travis-era coverage script (#430)
• 864c648 ci: replace CompatHelper with dependabot for Julia deps (#427)
• 86e8518 ci: remove invalidations workflow (#428)
• c7a9abd chore: Bump actions/github-script from 8 to 9 (#422)
• c5ebf7b chore: Bump julia-actions/setup-julia from 2 to 3 (#423)
• Additional commits viewable in compare view

Updates DimensionalData to 0.30.1

Release notes

Sourced from DimensionalData's releases.

v0.30.1

DimensionalData v0.30.1

Diff since v0.30.0

Merged pull requests:

• move DimensionalPlot back to the main package (#1178) (@​rafaqz)

Closed issues:

• What is the replacement for LookupArrays? (#1176)

Commits

• See full diff in compare view

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[dependabot]

Looks like these dependencies are updatable in another way, so this is no longer needed.