chore: bump the all-julia-packages group across 4 directories with 2 updates

[dependabot]

Updates the requirements on SciMLBase and FlexiChains to permit the latest version.
Updates SciMLBase to 3.0.0

Release notes

Sourced from SciMLBase's releases.

v3.0.0

SciMLBase v3.0.0

Diff since v2.154.0

SciMLBase v3.0.0 — Breaking Release

RecursiveArrayTools v4: Solution types are now AbstractArrays (#1297)

Most impactful change. AbstractVectorOfArray (and thus ODESolution, DDESolution, RODESolution, DAESolution) now subtypes AbstractArray:

• sol[i] returns the ith scalar element (column-major), not the ith timestep. Use sol.u[i] or sol[:, i] for timesteps.
• length(sol) returns total elements (prod(size(sol))). Use length(sol.u) for number of timesteps.
• iterate(sol) iterates scalar elements. Use sol.u for timestep iteration.
• map(f, sol) maps over elements. Use map(f, sol.u) for timesteps.

Ensemble RNG redesign (#1252)

• prob_func(prob, i, repeat) → prob_func(prob, ctx) where ctx::EnsembleContext
• output_func(sol, i) → output_func(sol, ctx)
• EnsembleContext includes sim_id, repeat, rng, sim_seed, worker_id, master_rng
• New seed/rng/rng_func kwargs on solve() for deterministic, thread-count-independent ensemble solves

Removed deprecated APIs

• u_modified! renamed to derivative_discontinuity! (#1289)
• Removed deprecated.jl: old type aliases (DEAlgorithm, DEProblem, DESolution, etc.), constructors, deprecated accessors (#1291)
• Removed backward compat shims in remake.jl and MLStyle extension (#1292)
• Removed old iterators: tuples, intervals, TimeChoiceIterator (#1290)

Simplified getproperty

• Removed redundant getproperty overloads on solution abstract types (#1293)
• Removed deprecated getproperty aliases (.destats, .x, .lb/.ub, .minimizer, .minimum) (#1294)

Other breaking changes

• Replaced Moshi with plain Julia structs for Clocks — 23% precompilation improvement (#1295)
• ODEFunction uses DEFAULT_SPECIALIZATION (AutoSpecialize) for convenience constructors (#1300)
• Propagate interp/dense to DiffEqArrays from solution callables (#1297)
• is_discrete_time_domain(nothing) now returns false (#1306)

Migration Guide

Old (v2)	New (v3)
sol[i] (timestep)	sol.u[i] or sol[:, i]
length(sol) (timesteps)	length(sol.u)
for u in sol	for u in sol.u
u_modified!(integrator, true)	derivative_discontinuity!(integrator, true)
prob_func(prob, i, repeat)	prob_func(prob, ctx) — use ctx.sim_id, ctx.repeat
output_func(sol, i)	output_func(sol, ctx)
sol.destats	sol.stats

... (truncated)

Commits

• 014e294 Document v3.0 breaking changes and migration guide
• 83ba080 Update Project.toml
• 6aadd3b Merge pull request #1310 from ChrisRackauckas-Claude/remove-redundant-zygote-...
• a3d3838 Remove redundant Zygote integer-indexing adjoints for ODESolution
• 70ff4b8 Merge pull request #1304 from SciML/v3
• 9790e8e Merge pull request #1252 from isaacsas/ensemble_rng_redesign
• e833b03 Merge pull request #1309 from SciML/as/fix-ci
• c5a1764 Remove backwards-compatible 5-arg solve_batch shims for DiffEqGPU
• e0a6dd0 Merge origin/v3 into ensemble_rng_redesign
• 2da04cb test: disable SDDE tests
• Additional commits viewable in compare view

Updates FlexiChains to 0.4.8

Release notes

Sourced from FlexiChains's releases.

v0.4.8

FlexiChains v0.4.8

Diff since v0.4.7

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).

Merged pull requests:

• Parse StanCSV (#154) (@​penelopeysm)

Changelog

Sourced from FlexiChains's changelog.

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.

0.4.1

Added the method Base.rand([rng,] chn, [dims...]) to sample from a FlexiChain.

... (truncated)

Commits

• 7a82f93 Parse StanCSV (#154)
• 8ffda63 Broaden MCMCChains conversion (#159)
• e534fdc Conversions to NamedTuple for FlexiChain{Symbol} (#156)
• 68791e3 Revert "Conversions"
• 680f8b9 Conversions
• 8a3a7f3 Prefixed VarNames (#119)
• 4dc0929 Slightly improve _split_varnames (#151)
• 50b30f3 MCMCChains -> FlexiChain{Symbol} conversion (#117)
• 06a4ea4 Add names to DimArrays (#116)
• 77e4980 Switch to Runic (#115)
• Additional commits viewable in compare view

Updates SciMLBase to 3.0.0

Release notes

Sourced from SciMLBase's releases.

v3.0.0

SciMLBase v3.0.0

Diff since v2.154.0

SciMLBase v3.0.0 — Breaking Release

RecursiveArrayTools v4: Solution types are now AbstractArrays (#1297)

Most impactful change. AbstractVectorOfArray (and thus ODESolution, DDESolution, RODESolution, DAESolution) now subtypes AbstractArray:

• sol[i] returns the ith scalar element (column-major), not the ith timestep. Use sol.u[i] or sol[:, i] for timesteps.
• length(sol) returns total elements (prod(size(sol))). Use length(sol.u) for number of timesteps.
• iterate(sol) iterates scalar elements. Use sol.u for timestep iteration.
• map(f, sol) maps over elements. Use map(f, sol.u) for timesteps.

Ensemble RNG redesign (#1252)

• prob_func(prob, i, repeat) → prob_func(prob, ctx) where ctx::EnsembleContext
• output_func(sol, i) → output_func(sol, ctx)
• EnsembleContext includes sim_id, repeat, rng, sim_seed, worker_id, master_rng
• New seed/rng/rng_func kwargs on solve() for deterministic, thread-count-independent ensemble solves

Removed deprecated APIs

• u_modified! renamed to derivative_discontinuity! (#1289)
• Removed deprecated.jl: old type aliases (DEAlgorithm, DEProblem, DESolution, etc.), constructors, deprecated accessors (#1291)
• Removed backward compat shims in remake.jl and MLStyle extension (#1292)
• Removed old iterators: tuples, intervals, TimeChoiceIterator (#1290)

Simplified getproperty

• Removed redundant getproperty overloads on solution abstract types (#1293)
• Removed deprecated getproperty aliases (.destats, .x, .lb/.ub, .minimizer, .minimum) (#1294)

Other breaking changes

• Replaced Moshi with plain Julia structs for Clocks — 23% precompilation improvement (#1295)
• ODEFunction uses DEFAULT_SPECIALIZATION (AutoSpecialize) for convenience constructors (#1300)
• Propagate interp/dense to DiffEqArrays from solution callables (#1297)
• is_discrete_time_domain(nothing) now returns false (#1306)

Migration Guide

Old (v2)	New (v3)
sol[i] (timestep)	sol.u[i] or sol[:, i]
length(sol) (timesteps)	length(sol.u)
for u in sol	for u in sol.u
u_modified!(integrator, true)	derivative_discontinuity!(integrator, true)
prob_func(prob, i, repeat)	prob_func(prob, ctx) — use ctx.sim_id, ctx.repeat
output_func(sol, i)	output_func(sol, ctx)
sol.destats	sol.stats

... (truncated)

Commits

• 014e294 Document v3.0 breaking changes and migration guide
• 83ba080 Update Project.toml
• 6aadd3b Merge pull request #1310 from ChrisRackauckas-Claude/remove-redundant-zygote-...
• a3d3838 Remove redundant Zygote integer-indexing adjoints for ODESolution
• 70ff4b8 Merge pull request #1304 from SciML/v3
• 9790e8e Merge pull request #1252 from isaacsas/ensemble_rng_redesign
• e833b03 Merge pull request #1309 from SciML/as/fix-ci
• c5a1764 Remove backwards-compatible 5-arg solve_batch shims for DiffEqGPU
• e0a6dd0 Merge origin/v3 into ensemble_rng_redesign
• 2da04cb test: disable SDDE tests
• Additional commits viewable in compare view

Updates FlexiChains to 0.4.8

Release notes

Sourced from FlexiChains's releases.

v0.4.8

FlexiChains v0.4.8

Diff since v0.4.7

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).

Merged pull requests:

• Parse StanCSV (#154) (@​penelopeysm)

Changelog

Sourced from FlexiChains's changelog.

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.

0.4.1

Added the method Base.rand([rng,] chn, [dims...]) to sample from a FlexiChain.

... (truncated)

Commits

• 7a82f93 Parse StanCSV (#154)
• 8ffda63 Broaden MCMCChains conversion (#159)
• e534fdc Conversions to NamedTuple for FlexiChain{Symbol} (#156)
• 68791e3 Revert "Conversions"
• 680f8b9 Conversions
• 8a3a7f3 Prefixed VarNames (#119)
• 4dc0929 Slightly improve _split_varnames (#151)
• 50b30f3 MCMCChains -> FlexiChain{Symbol} conversion (#117)
• 06a4ea4 Add names to DimArrays (#116)
• 77e4980 Switch to Runic (#115)
• Additional commits viewable in compare view

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[dependabot]

Superseded by #332.