Bump the all-julia-packages group across 1 directory with 6 updates

[dependabot]

Updates the requirements on SBMLImporter, ReactionNetworkImporters, NonlinearSolveFirstOrder, Turing, StatsPlots and SciMLBase to permit the latest version.
Updates SBMLImporter to 4.0.0

Release notes

Sourced from SBMLImporter's releases.

v4.0.0

SBMLImporter v4.0.0

Diff since v3.2.3

SBMLImporter 4.0 is a breaking release triggered by the Catalyst.jl v16 update.

Breaking changes

• Updated Catalyst to v16. Since Catalyst now uses a more flexible metadata interface, load_SBML now returns a ReactionSystem (rather than a ParsedReactionSystem). The initial value map and parameter map are stored as metadata on the returned system. See below for how to import a model with load_SBML. For more information, see the HISTORY file

Merged pull requests:

• Update to Catalyst v16 (#129) (@​sebapersson)

Changelog

Sourced from SBMLImporter's changelog.

Breaking updates and feature summaries across releases

SBMLImporter 4.0

SBMLImporter 4.0 is a breaking release triggered by the Catalyst.jl v16 update. Major changes are:

• Updated Catalyst to v16. Since Catalyst now uses a more flexible metadata interface, load_SBML now returns a ReactionSystem (rather than a ParsedReactionSystem). The initial value map and parameter map are stored as metadata on the returned system. See below for how to import a model with load_SBML.
• Dropped ModelingToolkit as a direct dependency and switched to ModelingToolkitBase. Since ModelingToolkit v11+ is AGPL-licensed, ModelingToolkit is no longer a direct dependency in order to keep SBMLImporter.jl and its dependencies permissively licensed.

Updated load_SBML return type and usage

Models are now imported as a ReactionSystem, where the initial value map (u0_map) and parameter value map (parameter_map) are stored as metadata. Importing as an ODEProblem now looks like:

# New syntax
using SBMLImporter, ModelingToolkitBase, OrdinaryDiffEq
rn, cb = load_SBML(path_sbml)
u0 = get_u0_map(rn)
ps = get_parameter_map(rn)
sys = mtkcompile(ode_model(rn))
tspan = (0.0, 10.0)
oprob = ODEProblem(sys, merge(Dict(u0), Dict(ps)), tspan; jac = true)
Old syntax
using SBMLImporter, ModelingToolkit, OrdinaryDiffEq
prn, cb = load_SBML(path_sbml)
sys = structural_simplify(convert(ODESystem, prn.rn))
tspan = (0.0, 10.0)
oprob = ODEProblem(sys, prn.u0, tspan, prn.p; jac = true)

Examples for importing into a JumpProblem or an SDEProblem are available in the online documentation.

ModelingToolkitBase and licensing

Since ModelingToolkit v11+ is AGPL-licensed (see discussion here), SBMLImporter.jl now depends on the MIT-licensed ModelingToolkitBase instead. SBMLImporter.jl aims to remain permissively licensed, and with this update none of its direct dependencies are AGPL-licensed (or more restrictive).

... (truncated)

Commits

• 70e6205 Merge pull request #129 from sebapersson/catalyst_v16
• 69f893c Add 1506 to FBDF tests
• ca50084 Format
• 0ff2016 Update contribution guide
• 54e6beb Add HISTORY file
• f308829 Use FBDF for hard-to-simulate tests
• 47ad7fd Use FBDF for hard-to-simulate tests
• 396feaf Refactor semantic tests
• eb3588f Use FBDF for hard-to-simulate tests
• 40e105d Update to Catalyst v16
• Additional commits viewable in compare view

Updates ReactionNetworkImporters to 1.1.0

Release notes

Sourced from ReactionNetworkImporters's releases.

v1.1.0

ReactionNetworkImporters v1.1.0

Diff since v1.0.0

Merged pull requests:

• Add more complete BioNetGen .net file support (#161) (@​isaacsas)

Changelog

Sourced from ReactionNetworkImporters's changelog.

History

v1.0.0

Breaking release for compatibility with Catalyst.jl v16.

Breaking changes

• loadrxnetwork now returns a ReactionSystem directly instead of a ParsedReactionNetwork. The ParsedReactionNetwork type has been removed.
• Initial conditions and parameter values from BNG files are stored as initial_conditions on the ReactionSystem, and are also available via the Catalyst metadata accessors Catalyst.get_u0_map(rn) and Catalyst.get_parameter_map(rn).
• BNG species name mappings and group symbols are stored as system metadata, accessible via the new exported accessors get_varstonames(rn) and get_groupstosyms(rn).
• ModelingToolkit is no longer a dependency; replaced by ModelingToolkitBase.
• Test dependency CSVFiles replaced by CSV.jl.
• Requires Catalyst.jl v16+.

Migration guide

Before (v0.x)	After (v1.0)
prn = loadrxnetwork(BNGNetwork(), file)	rn = loadrxnetwork(BNGNetwork(), file)
prn.rn	rn (the return value itself)
prn.u0	Catalyst.get_u0_map(rn)
prn.p	Catalyst.get_parameter_map(rn)
prn.varstonames	get_varstonames(rn)
prn.groupstosyms	get_groupstosyms(rn)
rs == prn.rn	Catalyst.isequivalent(rs, rn)
prn = loadrxnetwork(mn); prn.rn	rn = loadrxnetwork(mn)

Commits

• 36481af Bump version from 1.0.0 to 1.1.0
• 72a383f Merge pull request #161 from isaacsas/add_netfile_function_block
• fb68b15 Add time grid check to ODE validation, remove duplicate test
• ceddb49 Exclude data files from typos spell checker
• 237f212 Add 11 ODE validation tests against BNG reference data
• 405e3c7 Fix optional groups block and group-parameter name collisions
• 1c8af42 Fix Aqua stale-deps: add explicit HypergeometricFunctions import to module
• 7df0f0d Add complete BioNetGen .net file support: function blocks, fixed species, Sat...
• 999ff93 Merge pull request #159 from isaacsas/catalyst_v16
• df5cf56 Address PR review: restore commented-out blocks, use defmap
• Additional commits viewable in compare view

Updates NonlinearSolveFirstOrder to 2.1.0

Release notes

Sourced from NonlinearSolveFirstOrder's releases.

NonlinearSolveFirstOrder-v2.1.0

NonlinearSolveFirstOrder NonlinearSolveFirstOrder-v2.1.0

Diff since NonlinearSolveFirstOrder-v2.0.0

Merged pull requests:

• CompatHelper: bump compat for NonlinearSolveFirstOrder to 2, (keep existing compat) (#822) (@​github-actions[bot])
• CompatHelper: bump compat for NonlinearSolveFirstOrder to 2 for package docs, (keep existing compat) (#823) (@​github-actions[bot])
• CompatHelper: bump compat for NonlinearSolveFirstOrder in [extras] to 2 for package SCCNonlinearSolve, (keep existing compat) (#824) (@​github-actions[bot])
• Fix Jacobian diagonal calculation in LM when using StaticArrays (#825) (@​JamesWrigley)
• fix modAB typos (#826) (@​oscardssmith)
• switch default bracketing solver to ModAB (#828) (@​oscardssmith)
• Fix Runic CI workflow and formatting (#830) (@​ChrisRackauckas-Claude)
• Refactor ModAB constructor and update method name (#831) (@​Just-A-Random-Geek)
• Add ModAB method to bracketing nonlinear solve documentation (#833) (@​Just-A-Random-Geek)
• fix: remove closure in vector SCC branch, well-type sols vector (#834) (@​ChrisRackauckas-Claude)
• feat: AutoSpecialize norecompile infrastructure for NonlinearSolveBase (#838) (@​ChrisRackauckas-Claude)
• Fix ForwardDiff through bracketing solvers when Duals are in tspan (#840) (@​ChrisRackauckas-Claude)
• Handle mixed case in tspan-Dual ForwardDiff extension (#841) (@​ChrisRackauckas-Claude)
• Handle null u0 in SimpleNonlinearSolve for NonlinearLeastSquaresProblem (#843) (@​ChrisRackauckas-Claude)
• Fix tspan-Dual ForwardDiff ext: secant step instead of foreign Dual tag (#844) (@​ChrisRackauckas-Claude)
• Handle MixedDuplicated in Enzyme custom rules for solve_up (#845) (@​ChrisRackauckas-Claude)
• Fix support for bounds when using init() (#848) (@​JamesWrigley)
• Revise recommended methods for bracketing solvers (#849) (@​Just-A-Random-Geek)
• Update convergence rate in ModAB method description (#850) (@​Just-A-Random-Geek)
• Improved ModAB with adaptive k factor and threshold for bisection fallback (#852) (@​Just-A-Random-Geek)
• Update symmetry factor and deviation factor calculations (#853) (@​Just-A-Random-Geek)
• Fix SimpleNonlinearSolve GPU compat without unnecessary @​generated (#854) (@​ChrisRackauckas-Claude)
• Update LinearSolve compat to 3.48 (#856) (@​JamesWrigley)
• Apply runic formatting to fix CI (#857) (@​JamesWrigley)
• Add precompile workload for Dual and SubArray broadcast operations (#858) (@​ChrisRackauckas-Claude)
• Make ModAB iteration always shrink the bracket even if there's numerical noise (#861) (@​DaniGlez)
• fix warning messages for reverse diff backends (#863) (@​hexaeder)
• Bump julia-actions/cache from 2 to 3 (#864) (@​dependabot[bot])
• Remove @​test_broken for LevenbergMarquardt Zygote+SVector (#866) (@​AdityaPandeyCN)
• Replace Buildkite CI with GitHub Actions self-hosted runners (#867) (@​ChrisRackauckas-Claude)
• Fix CUDA V100 compatibility with LocalPreferences.toml (#868) (@​ChrisRackauckas-Claude)
• Fix type inference for polyalgorithm solve!() (#870) (@​ChrisRackauckas-Claude)
• Avoid MArrays for out-of-place problems with SciMLJacobianOperators (#871) (@​dingraha)
• Remove V100 CUDA compatibility workarounds (#873) (@​ChrisRackauckas-Claude)
• Fix Enzyme reverse rule NamedTuple broadcasting with MTKParameters (#879) (@​ChrisRackauckas-Claude)
• remove-redundant-var (#881) (@​oscardssmith)
• Fix incorrect termination mode names and maxiters default in docs (#882) (@​ChrisRackauckas-Claude)
• Simplify _scc_solve for Enzyme compatibility (#884) (@​ChrisRackauckas-Claude)
• Fix Enzyme rule to handle DuplicatedNoNeed and other annotation types (#885) (@​ChrisRackauckas-Claude)
• Bump codecov/codecov-action from 5 to 6 (#886) (@​dependabot[bot])
• Bump minor versions for NonlinearSolve and NonlinearSolveBase (#888) (@​ChrisRackauckas-Claude)
• Accept any parameter type in AutoSpecialize wrapping (#891) (@​ChrisRackauckas-Claude)

... (truncated)

Commits

• 8843054 bump minor versions for release
• 958ce24 Accept any parameter type in AutoSpecialize wrapping
• 3865118 bump minor versions for release
• f47d870 bump SciMLBase lower bound to 2.154 for FWW v1 compat
• 2444ffd move OrdinaryDiffEqTsit5 to downstream test group
• c0abd50 bump DiffEqBase compat to 6.213 in test/trim
• 4ba7560 require FunctionWrappersWrappers v1+ (drop 0.1 compat)
• 1027190 bump FunctionWrappersWrappers compat to include v1.0
• 7bdfecc Remove stale remake imports from extension files
• d3e1692 Unwrap AutoSpecialize in AD-over-solve paths and external wrapper extensions
• Additional commits viewable in compare view

Updates Turing to 0.43.5

Release notes

Sourced from Turing's releases.

v0.43.5

Turing v0.43.5

Diff since v0.43.4

Fix incorrect handling of VarNamedTuple templates inside submodels when sampling with Gibbs.

Merged pull requests:

• Fix Gibbs/submodel/template handling bug (#2799) (@​penelopeysm)

Closed issues:

• Gibbs / submodel bug (#2797)
• Broken interaction between Gibbs Sampler and Submodels with Vector assignment (#2798)

Changelog

Sourced from Turing's changelog.

0.43.5

Fix incorrect handling of VarNamedTuple templates inside submodels when sampling with Gibbs.

0.43.4

Fix some missing Base.copy implementations on internal structs.

0.43.3

Unify parameter initialisation for HMC and external samplers. External samplers (like HMC) now attempt multiple times to generate valid initial parameters, instead of just taking the first set of parameters.

Re-exports set_logprob_type! from DynamicPPL to allow users to control the base log-probability type used when evaluating Turing models. For example, calling set_logprob_type!(Float32) will mean that Turing will use Float32 for log-probability calculations, only promoting if there is something in the model that causes it to be (e.g. a distribution that returns Float64 log-probabilities). Note that this is a compile-time preference: for it to take effect you will have to restart your Julia session after calling set_logprob_type!.

Furthermore, note that sampler support for non-Float64 log-probabilities is currently limited. Although DynamicPPL promises not promote float types unnecessarily, many samplers, including HMC and NUTS, still use Float64 internally and thus will cause log-probabilities and parameters to be promoted to Float64, even if the model itself uses Float32.

0.43.2

Throw an ArgumentError when a Gibbs sampler is missing component samplers for any variable in the model. This check can be bypassed by passing check_model=false to sample.

0.43.1

Ignore discard_initial and thinning for SMC samplers to prevent a BoundsError when these arguments are provided.

0.43.0

DynamicPPL 0.40 and VarNamedTuple

DynamicPPL v0.40 includes a major overhaul of Turing's internal data structures. Most notably, cases where we might once have used Dict{VarName} or NamedTuple have all been replaced with a single data structure, called VarNamedTuple.

This provides substantial benefits in terms of robustness and performance.

However, it does place some constraints on Turing models, and introduces some breaking changes to the user interface. Specifically, the types of containers that can include random variables are now more limited: if x[i] ~ dist is a random variable, then x must obey the following criteria:

• They must be AbstractArrays. Dicts and other containers are currently unsupported (we have an issue to track this). If you really need this functionality, please open an issue and let us know; we can try to make it a priority.

  @model function f()
      # Allowed
      x = Array{Float64}(undef, 1)
      x[1] ~ Normal()

... (truncated)

Commits

• ab29465 Fix Gibbs/submodel/template handling bug (#2799)
• 8410b09 Fix some missing Base.copy implementations (#2796)
• f86999b Unify HMC + externalsampler + DynamicHMC parameter initialisation; re-export ...
• 838ae6a Throw an error when Gibbs sampler is missing components for any variable (#2788)
• 33e1a22 Ignore discard_initial and thinning for SMC (#2784)
• 2211373 Twiddle API docs
• 26c0b49 Fix docs
• 94ec347 JuliaRegistrator really wants me to say 'breaking'
• 84ad63a Remove temporary optim doc in anticipation of releasing
• 158b2a0 breaking - v0.43 (#2733)
• Additional commits viewable in compare view

Updates StatsPlots to 0.15.8

Changelog

Sourced from StatsPlots's changelog.

StatsPlots.jl NEWS

0.10

• Rename package from StatPlots to StatsPlots

0.7 current version

0.7.3

• fixed out of bound error with violin and boxplot
• fixed title location in corrplot
• better handling of NaN and Inf
• recipe for hclust dendrogram (clustering visualization)
• dataviewer recipe for interactive GUIs

0.7.2

• fix stack overflow with @df and begin ... end blocks
• avoid recomputing data unnecessarily in @df

0.7.1

• remove Loess dependency
• fix hygien macro issue in @df
• add curly bracket syntax for automatic naming of groups
• add cols() to select all columns

0.7.0

• remove DataFrames dependency
• improve tick handling in correlation plots
• add support for discrete distributions
• add automatic legend with @df
• allow passing columns of a data table programmatically with cols

0.6.0

• deprecate the plot(df, :x, :y) syntax
• complete the removal of groupederror
• remove shadederror
• suppress axis labels in marginalhist

0.5.1

• remove groupederror, as that is now in it's own package
• add qqnorm and qqplot
• fix 2d density plots

0.5.0

• major reconfiguring of the support for tables:
  • change the syntax to @df mydataframe plot(:a, :b)
  • allows using DataFrames automatically in user recipes

... (truncated)

Commits

• 9db7d09 bump DS and Interp compat, + StatsPlots version (#569)
• 44200aa Merge pull request #564 from Jonas-a-Zimmermann/PermuteInsteadOfOrientation
• 1ef19e9 Update README.md
• 1c80878 Changed Orientation to Permute
• 7cfe9c1 Update README.md
• e34f65e Bump codecov/codecov-action from 3 to 4 (#548)
• bb65b7c bump Project.toml
• b1311cc Merge pull request #546 from JuliaPlots/compathelper/new_version/2023-11-25-0...
• 710d428 CompatHelper: bump compat for Interpolations to 0.15, (keep existing compat)
• 15fc66b Bump actions/checkout from 3 to 4 (#542)
• 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

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Superseded by #1459.