Sourced from Catalyst's releases.

v16.0.0

Catalyst v16.0.0

Diff since v15.0.11

See HISTORY.md for breaking changes.

Merged pull requests:

• [WIP] v16 changes to get tests passing (#1322) (@​TorkelE)
• Add Julia ecosystem to Dependabot configuration (#1346) (@​ChrisRackauckas-Claude)
• Bump actions/upload-artifact from 5 to 6 (#1348) (@​dependabot[bot])
• Version 16 jump fixes (#1354) (@​isaacsas)
• Ensure docs build on v16 (#1356) (@​TorkelE)
• Unify System creation during conversion (#1357) (@​isaacsas)
• remove performance benchmark tests (#1358) (@​TorkelE)
• init (#1359) (@​TorkelE)
• Minor: slight code reorder and error message addition (#1360) (@​isaacsas)
• Designate stoich ps as int in dsl (#1361) (@​TorkelE)
• Reduce symmap_to_varmap usage (#1362) (@​TorkelE)
• support user provided brownians and jumps for ReactionSystems (#1363) (@​isaacsas)
• CI updates (#1365) (@​isaacsas)
• ensure that serialization throws warning for new types (#1366) (@​TorkelE)
• Support @brownians in DSL (#1367) (@​TorkelE)
• Try initialization fix for Julia 1.10 with HC and MTKBase (#1368) (@​isaacsas)
• try using new Pre (#1369) (@​isaacsas)
• Hybrid SDE plus jump support in ReactionSystem (#1370) (@​isaacsas)
• Split out events from constraint equations docs (#1371) (@​TorkelE)
• Auto jump vars discovery and improve concrete typing (#1372) (@​isaacsas)
• drop unneeded accessor (#1374) (@​isaacsas)
• Constructor cleanup (#1375) (@​isaacsas)
• fix isdetailedbalanced tol issue (#1376) (@​isaacsas)
• Version 16 new (#1377) (@​isaacsas)
• Add save_positions tests for ConstantRateJump and SDE+Jump systems (#1379) (@​isaacsas)
• Hybrid tests remake (#1380) (@​isaacsas)
• merge symmap_to_varmap into master (#1381) (@​isaacsas)
• Add remake tests for hybrid problems and update JumpProcesses compat (#1382) (@​isaacsas)
• Jump int promotion fix (#1383) (@​isaacsas)
• rename conversion functions (#1384) (@​isaacsas)
• ExplictImports, ss_ode_model, and update HISTORY (#1385) (@​isaacsas)
• add Poisonnians support (#1386) (@​isaacsas)
• Fix spatial tests (#1387) (@​TorkelE)
• Add @​poissonians DSL option for @​reaction_network and @​network_component (#1388) (@​isaacsas)
• Bk/improve error for non integer stoichiometry (#1389) (@​calebjubal)
• Overhaul Catalyst's unit validation system (#1390) (@​isaacsas)
• Doc updates: README, Home, FAW, and API (#1391) (@​TorkelE)
• Update simulation doc section for v16 (#1392) (@​TorkelE)
• Update Catalyst Introduction doc pages (#1393) (@​TorkelE)
• Remove dead deps (Requires, DynamicPolynomials), clean up extension checks (#1394) (@​isaacsas)
• Fix deprecation warnings from ModelingToolkitBase (#1395) (@​ChrisRackauckas-Claude)
• Graph array fixes and some dep cleanup (#1396) (@​isaacsas)

... (truncated)

Sourced from Catalyst's changelog.

Breaking updates and feature summaries across releases

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

• convert(ODESystem, rs) is replaced by ode_model(rs).

• convert(SDESystem, rs) is replaced by sde_model(rs).

• convert(JumpSystem, rs) is replaced by jump_model(rs).

• convert(NonlinearSystem, rs) is replaced by ss_ode_model(rs).

  The old Base.convert methods have been removed since ModelingToolkit now has one, unified, system type, System. The new functions accept the same keyword arguments as before.

  Before:

... (truncated)

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