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Bump the all-julia-packages group across 1 directory with 3 updates#72

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Bump the all-julia-packages group across 1 directory with 3 updates#72
ChrisRackauckas merged 1 commit into
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dependabot/julia/docs/all-julia-packages-e3ab09974d

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Updates the requirements on Catalyst, Documenter and Example to permit the latest version.
Updates Catalyst to 16.2.0

Release notes

Sourced from Catalyst's releases.

v16.2.0

Catalyst v16.2.0

Diff since v16.1.2

Merged pull requests:

Changelog

Sourced from Catalyst's changelog.

Breaking updates and feature summaries across releases

Unreleased (on master)

Catalyst 16.1

  • Added use_jump_ratelaws keyword argument to ode_model, sde_model, hybrid_model, ODEProblem, SDEProblem, and HybridProblem. When set to true, both drift and diffusion terms use the jump/stochastic rate law (binomial propensities) instead of the ODE rate law (power-based). This gives the mathematically correct CLE derived from the CME when species populations are integers. Defaults to false for backward compatibility.

Catalyst 16.0

Catalyst 16 is a major release that transitions from ModelingToolkit (MT) v9 to ModelingToolkitBase (the base for ModelingToolkit v11); introduces unified hybrid model support for mixed ODE/SDE/Jump systems; supports user-provided coupled ODEs, SDEs, jump processes, and jump-diffusions; and modernizes the conversion and problem-creation API.

Please also see the ModelingToolkit NEWS.md for all the changes that have occurred in ModelingToolkit as part of v10 and v11, and which are now relevant for Catalyst users.

BREAKING: ModelingToolkitBase replaces ModelingToolkit

  • Catalyst now depends on and re-exports ModelingToolkitBase instead of ModelingToolkit. This ensures Catalyst remains fully MIT-licensed after the library split that occurred in ModelingToolkit v11. ModelingToolkitBase provides the core symbolic system infrastructure (types, accessors, problem construction) that Catalyst needs. With this update, Catalyst moves from ModelingToolkit v9 to ModelingToolkitBase 1.12+ (part of ModelingToolkit v11).

    Most commonly used functions (unknowns, parameters, equations, @mtkcompile, etc.) are available through ModelingToolkitBase. However, if you relied on structural_simplify, now part of mtkcompile, for reducing models with algebraic equations, you may need to explicitly load ModelingToolkit to obtain equivalent levels of model reduction and optimization:

    using Catalyst
using ModelingToolkit  # only if you need MTK-specific features not in MTKBase

    The version of mtkcompile in ModelingToolkitBase is less feature filled than in ModelingToolkit, but please be aware that the latter version now loads AGPL-licensed libraries that may impose additional restrictions on your code.

BREAKING: Conversion functions renamed

... (truncated)

Commits
  • 3c24a17 Update Project.toml
  • 08e33b1 Merge pull request #1479 from SciML/dependabot/julia/all-julia-packages-08a47...
  • 2466e1f Merge branch 'master' into dependabot/julia/all-julia-packages-08a474db6d
  • dc25874 Merge pull request #1453 from SciML/dependabot/github_actions/codecov/codecov...
  • 52df5c4 Bump the all-julia-packages group across 3 directories with 18 updates
  • a61242f Merge pull request #1477 from ChrisRackauckas-Claude/dependabot-turing-0.45-d...
  • 7040da1 Merge branch 'master' into dependabot-turing-0.45-doc-compat
  • 5111190 Merge pull request #1478 from ChrisRackauckas-Claude/centralize-ci
  • 2c03cb7 Drop Runic reformatting and check from this PR
  • 64c8b0e Centralize CI on SciML reusable workflows; apply Runic + fix typos
  • Additional commits viewable in compare view

Updates Documenter to 1.17.0

Release notes

Sourced from Documenter's releases.

v1.17.0

Added

  • The version selector now also preserves the anchor (hash) when switching between documentation versions. Additionally, the outdated/dev version warning banner now also tries to keep you on the same page (and position) when linking to the latest stable release. (#2880)
  • Added Remotes.Forgejo for specifying a Remote hosted on a Forgejo instance (such as codeberg.org). (#2857)
  • Doctests now default to the parser_for_module of the module that the docstring appears in, allowing modules that set their syntax version via Base.Experimental.@set_syntax_version to have their doctests parsed with the correct syntax automatically. Also added support for DocTestSyntax metadata and per-block syntax= attributes to explicitly specify a syntax version. (#2874)
  • Added a show_log keyword for Documenter.LaTeX to print LaTeX compiler logs to stdout when PDF compilation fails, and support for forcing this via DOCUMENTER_LATEX_SHOW_LOGS in CI environments. (#1697)
  • Added support for new features of the Markdown stdlib introduced in Julia 1.14, namely strike through, HTML blocks and inline HTML (this requires Julia 1.14+ and MarkdownAST 0.1.3).

Changed

  • reduced time complexity from O(n^2) to O(n) to improve the initial load time for search (#2875)
  • Git no longer displays a message about the default branch name when calling deploydocs(). (#2854)
  • Don't escape characters (such as ~) in URLs when writing LaTeX. (#2210)
  • Tweak the layout of the table of contents in LaTeX / PDF output so that for a document with 8 or more parts, the part number (VIII) does not overlap with the part title. (#2871)

Fixed

  • Fixed rendering of operator docstring bindings such as Base.:(:) and Base.:(==) in doc headers and indices. (#2844)

The changes are documented in the CHANGELOG.md file.

Diff since v1.16.1

Changelog

Sourced from Documenter's changelog.

Version [v1.17.0] - 2026-02-20

Added

  • The version selector now also preserves the anchor (hash) when switching between documentation versions. Additionally, the outdated/dev version warning banner now also tries to keep you on the same page (and position) when linking to the latest stable release. (#2880)
  • Added Remotes.Forgejo for specifying a Remote hosted on a Forgejo instance (such as codeberg.org). (#2857)
  • Doctests now default to the parser_for_module of the module that the docstring appears in, allowing modules that set their syntax version via Base.Experimental.@set_syntax_version to have their doctests parsed with the correct syntax automatically. Also added support for DocTestSyntax metadata and per-block syntax= attributes to explicitly specify a syntax version. (#2874)
  • Added a show_log keyword for Documenter.LaTeX to print LaTeX compiler logs to stdout when PDF compilation fails, and support for forcing this via DOCUMENTER_LATEX_SHOW_LOGS in CI environments. (#1697)
  • Added support for new features of the Markdown stdlib introduced in Julia 1.14, namely strike through, HTML blocks and inline HTML (this requires Julia 1.14+ and MarkdownAST 0.1.3).

Changed

  • reduced time complexity from O(n^2) to O(n) to improve the initial load time for search (#2875)
  • Git no longer displays a message about the default branch name when calling deploydocs(). (#2854)
  • Don't escape characters (such as ~) in URLs when writing LaTeX. (#2210)
  • Tweak the layout of the table of contents in LaTeX / PDF output so that for a document with 8 or more parts, the part number (VIII) does not overlap with the part title. (#2871)

Fixed

  • During cross-referencing find_object correctly locates the Documenter.Object associated with UnionAll method signatures. (#2836, #2889)
  • Fixed rendering of operator docstring bindings such as Base.:(:) and Base.:(==) in doc headers and indices. (#2844)

Version [v1.16.1] - 2025-11-21

Fixed

  • The -g is now passed to curl when checking links, to disable globbing, which could cause undesirable behavior when checking links containing characters like for example [, {, & or ?. (#2839, #2842)
  • Fixed insufficient paragraph spacing in HTML output for @docs blocks. ([#2845, #2847])
  • Don't expand details admonition by default. ([#2846, #2847])
  • Removed superfluous vertical space at end of @docs blocks. (#2849)

Version [v1.16.0] - 2025-11-14

Added

  • Added option treat_markdown_warnings_as_error which throws an error when encountering a markdown/interpolation warning (#2792, #2751)
  • Footnotes can now be previewed by hovering over the link. (#2080)
  • The version selector now attempts to stay on the same page when switching between documentation versions. If the page doesn't exist in the target version, it falls back to the version homepage. (#2801)
  • Allow named @eval blocks: such a block shares its execution context with all other @eval, @example, @repl and @setup blocks on the same page which use the same name. (#2074, #2812)

Changed

  • Page category is removed from the search index and now everything is in section category. (#2762, #2413)
  • Changed the docstring block accordions from a custom implementation to HTML details+summary tag. (#2772, #2773)
  • Improved the search tokenizer and custom trimmer to improve search results. (#1457, #2114, #2744)
  • Improved several warning/error messages to (more accurately) report the location (filename, line range) in which the warning/error originated. (#2426, #2752, #2793, #2803, #2809)
  • Warn/error if jldoctest starts with an empty line; or lacks empty line between two REPL prompts. (#2031, #2083, #2679, #2808)
  • The forcepush=true option to deploydocs now uses --force-with-lease instead of --force. (#2817)
  • Improved the generation of anchors for admonitions in HTML output to be more stable and e.g. not change due to changes of the internal representation across different Julia versions. (#2710)

... (truncated)

Commits

Updates Example to 0.5.5

Release notes

Sourced from Example's releases.

v0.5.5

Example v0.5.5

Diff since v0.5.4

Commits

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@dependabot
Bump the all-julia-packages group across 1 directory with 3 updates
1bb7818 
Updates the requirements on [Catalyst](https://github.com/SciML/Catalyst.jl), [Documenter](https://github.com/JuliaDocs/Documenter.jl) and [Example](https://github.com/JuliaLang/Example.jl) to permit the latest version.

Updates `Catalyst` to 16.2.0
- [Release notes](https://github.com/SciML/Catalyst.jl/releases)
- [Changelog](https://github.com/SciML/Catalyst.jl/blob/master/HISTORY.md)
- [Commits](SciML/Catalyst.jl@v0.0.1...v16.2.0)

Updates `Documenter` to 1.17.0
- [Release notes](https://github.com/JuliaDocs/Documenter.jl/releases)
- [Changelog](https://github.com/JuliaDocs/Documenter.jl/blob/master/CHANGELOG.md)
- [Commits](JuliaDocs/Documenter.jl@v0.1.0...v1.17.0)

Updates `Example` to 0.5.5
- [Release notes](https://github.com/JuliaLang/Example.jl/releases)
- [Commits](JuliaLang/Example.jl@v0.0.1...v0.5.5)

---
updated-dependencies:
- dependency-name: Catalyst
  dependency-version: 16.2.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Documenter
  dependency-version: 1.17.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Example
  dependency-version: 0.5.5
  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 Jun 10, 2026
@ChrisRackauckas ChrisRackauckas merged commit 313a34e into main Jun 10, 2026
4 of 6 checks passed
@dependabot dependabot Bot deleted the dependabot/julia/docs/all-julia-packages-e3ab09974d branch June 10, 2026 20:52
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