Bump the all-julia-packages group across 3 directories with 3 updates

[dependabot]

Updates the requirements on AdvancedPS, Turing and TimerOutputs to permit the latest version.
Updates AdvancedPS to 0.8.0

Release notes

Sourced from AdvancedPS's releases.

v0.8.0

AdvancedPS v0.8.0

Diff since v0.7.2

Changelog: Dropped the Requires dependency. The Libtask extension now loads only through native package extensions, so Julia 1.10 or later is required (already the minimum).

Raised compat lower bounds: AbstractMCMC to 5, Distributions to 0.25, and StatsFuns to 1 (now also allowing 2).

This will most likely be the last release of AdvancedPS.jl before its deprecation!

Merged pull requests:

• Add Dependabot config (#122) (@​shravanngoswamii)
• Bump the all-github-actions-packages group with 3 updates (#123) (@​dependabot[bot])
• Dependency updates and maintenance (#125) (@​shravanngoswamii)

Changelog

Sourced from AdvancedPS's changelog.

0.8.0

Breaking changes

Dropped the Requires dependency. The Libtask extension now loads only through native package extensions, so Julia 1.10 or later is required (already the minimum).

Raised compat lower bounds: AbstractMCMC to 5, Distributions to 0.25, and StatsFuns to 1 (now also allowing 2).

Commits

• e6e615b Dependency updates and maintenance (#125)
• 1022556 Bump the all-github-actions-packages group with 3 updates (#123)
• 2b1e5d3 Add Dependabot config (#122)
• See full diff in compare view

Updates Turing to 0.46.1

Release notes

Sourced from Turing's releases.

v0.46.1

Turing v0.46.1

Diff since v0.46.0

Fixed a bug, present since v0.41.0, that biased PG / CSMC posteriors, whether sampled on their own or as a Gibbs component.

Merged pull requests:

• Bump the all-julia-packages group across 5 directories with 13 updates (#2849) (@​shravanngoswamii)
• docs: fix some typos (#2850) (@​jeis4wpi)

Changelog

Sourced from Turing's changelog.

0.46.1

Fixed a bug, present since v0.41.0, that biased PG / CSMC posteriors, whether sampled on their own or as a Gibbs component.

0.46.0

Breaking changes

DynamicPPL 0.42

Turing.jl v0.46 brings with it all the underlying changes in DynamicPPL 0.42. Most notably, gradient preparation and evaluation now go through AbstractPPL's prepare / value_and_gradient!! interface. This is an internal change and does not affect sampling results. Please see the DynamicPPL changelog for full details, and the AdvancedVI section below for the user-facing changes in this release.

AdvancedVI 0.7

Turing.jl v0.46 also brings in the changes in AdvancedVI 0.7. Please see the AdvancedVI changelog for full details; the changes most pertinent to users of vi are:

• AutoReverseDiff(; compile=true) is no longer supported for VI, and is rejected with an ArgumentError, as compiled tapes can silently produce incorrect gradients when reused across optimisation steps. Use AutoReverseDiff(; compile=false), or a different reverse-mode backend such as AutoMooncake(), instead.
• vi with KLMinScoreGradDescent now optimises in unconstrained (linked) space, making it consistent with the other KLMin... algorithms. If you use it with a model that has constrained parameters, results may differ slightly from previous releases.

Other changes

DifferentiationInterface removed as a direct dependency

informationmatrix (and hence vcov) now computes its Hessian through AbstractPPL's second-order interface instead of DifferentiationInterface. There is no change in behaviour for users.

Performance of nested submodels

DynamicPPL 0.42.1 fixes a type-inference failure that made nested submodels (a x ~ to_submodel(...) statement inside a model that is itself used as a submodel) many times slower to evaluate and differentiate; see TuringLang/Turing.jl#2844.

MCMCChains extension fix

Turing v0.45.0 was accidentally released without declaring the TuringMCMCChainsExt package extension, meaning that the extension did not load when MCMCChains was imported. This broke some MCMCChains-specific functionality, such as loadstate (for resuming sampling from a previous chain) and the post-sampling divergence warnings for Hamiltonian samplers; this is now fixed.

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.

... (truncated)

Commits

• 6575e24 Fix biased PG/CSMC posteriors: make delete_retained! mutate (#2855)
• 11f081b docs: fix some typos (#2850)
• 6ba5152 Bump the all-julia-packages group across 5 directories with 13 updates (#2849)
• 98e9773 Release 0.46.0 (#2846)
• cdded58 Bump actions/checkout from 6 to 7 in the all-github-actions-packages group (#...
• abde704 Bump codecov/codecov-action from 6 to 7 in the all-github-actions-packages gr...
• f6f9d13 skip codecov upload on Dependabot PRs (#2843)
• 56793a9 CompatHelper: bump compat for DynamicPPL to 0.42, (keep existing compat) (#2832)
• 00e8f1d Bump the all-github-actions-packages group with 4 updates (#2839)
• 602a69f Replace CompatHelper with Dependabot (#2838)
• Additional commits viewable in compare view

Updates AdvancedPS to 0.8.0

Release notes

Sourced from AdvancedPS's releases.

v0.8.0

AdvancedPS v0.8.0

Diff since v0.7.2

Changelog: Dropped the Requires dependency. The Libtask extension now loads only through native package extensions, so Julia 1.10 or later is required (already the minimum).

Raised compat lower bounds: AbstractMCMC to 5, Distributions to 0.25, and StatsFuns to 1 (now also allowing 2).

This will most likely be the last release of AdvancedPS.jl before its deprecation!

Merged pull requests:

• Add Dependabot config (#122) (@​shravanngoswamii)
• Bump the all-github-actions-packages group with 3 updates (#123) (@​dependabot[bot])
• Dependency updates and maintenance (#125) (@​shravanngoswamii)

Changelog

Sourced from AdvancedPS's changelog.

0.8.0

Breaking changes

Dropped the Requires dependency. The Libtask extension now loads only through native package extensions, so Julia 1.10 or later is required (already the minimum).

Raised compat lower bounds: AbstractMCMC to 5, Distributions to 0.25, and StatsFuns to 1 (now also allowing 2).

Commits

• e6e615b Dependency updates and maintenance (#125)
• 1022556 Bump the all-github-actions-packages group with 3 updates (#123)
• 2b1e5d3 Add Dependabot config (#122)
• See full diff in compare view

Updates TimerOutputs to 1.2.0

Release notes

Sourced from TimerOutputs's releases.

v1.2.0

TimerOutputs v1.2.0

Diff since v1.1.1

Merged pull requests:

• Forward pretty tables kwargs (#235) (@​JoshuaLampert)

Changelog

Sourced from TimerOutputs's changelog.

TimerOutputs changelog

Version 1.0.0

TimerOutputs 1.0.0 is a rewrite of the package internals with a number of new features. The documented API keeps working; code that relied on undocumented internals may need updating (see "Internal changes" below).

New features

• Zero-overhead timer disabling: the new NoTimerOutput is a dummy timer where all operations are no-ops. When its type is known to the compiler (a const, or a type parameter of the struct holding it), @timeit sections compile away entirely — a per-timer alternative to @timeit_debug. Runtime-disabled regular timers also became ~10x cheaper (~1.4 ns per section).
• Tables.jl interface: timers are tables — DataFrame(to), CSV.write("timings.csv", to) and any other Tables.jl consumer work directly, with one row per section holding the raw measurements (path, section, depth, ncalls, time_ns, gc_time_ns, allocated_bytes, firstexec_ns).
• New table layout (now built on PrettyTables.jl): tree guides (├─, └─) instead of plain indentation, and an optional %par column showing each section's share of its enclosing section (columns = [..., :time_par]).
• Heat bars: the default table shows a small bar per section visualizing its share of the total time / allocations, colored from blue (cheap) to red (expensive) in color-capable terminals. Displaying a subsection rescales the bars to that subsection's total. Hide them with bars = false (compact = true also drops them), or select them explicitly through the columns keyword (:time_bar, :allocs_bar).
• Column selection: print_timer(to; columns = [:ncalls, :time, :time_pct]) picks exactly which columns to show, in order; allocations and compact remain as shorthands.
• GC time column: print_timer(to; gc = true) (or the :gc_time column) adds a column with the time spent in garbage collection within each section. Off by default. Also available programmatically as TimerOutputs.gctime(to).
• Call shorthand: @timeit to foo(args) times the call under a label derived from the callee (here "foo"), a shorthand for @timeit to "foo" foo(args). Works with the default timer too (@timeit foo(args)). Qualified calls keep their qualification (Mod.foo → "Mod.foo"); operators and other non-name calls still need an explicit label.
• @timed_testset: a drop-in replacement for Test.@testset that times each set (nested sets nest in the timer), so print_timer() after the tests shows where the test time went. Test stays a non-dependency; the emitted @testset is resolved at the call site.
• Recursive debug timings: enable_debug_timings/disable_debug_timings now recurse into submodules by default, so one call on a package's top module instruments the whole package (#75). Pass recursive = false for the old single-module behavior.

... (truncated)

Commits

• 44c0121 Bump version from 1.1.1 to 1.2.0
• 278bb9f Forward pretty tables kwargs (#235)
• 1d315a4 Bump version from 1.1.0 to 1.1.1
• dd4d805 Fix precompilation of packages defining a named function in a timed body (#237)
• c313091 only truncate vertical display for huge tables (#236)
• 3b4336d fix @​label in a timed body (#228) (#230)
• 8c0d876 Bump version from 1.0.1 to 1.1.0
• 135cb7b add min max avg std (#227)
• fe50905 Bump version from 1.0.0 to 1.0.1
• 84ed9fd tweak printing of sections with 0 allocations (#226)
• Additional commits viewable in compare view

[github-actions]

Turing.jl documentation for PR #2852 is available at:
https://TuringLang.github.io/Turing.jl/previews/PR2852/

[shravanngoswamii]

I am holding this off because AdvancedPS work is being migrated here.