Catalyst.jl Files

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)
• Bump julia-actions/cache from 1 to 2 (#1397) (@dependabot[bot])
• Bump actions/checkout from 4 to 6 (#1398) (@dependabot[bot])
• Update docstrings for V16 API changes (#1402) (@isaacsas)
• Update model creation docs for v16 (#1403) (@TorkelE)
• Update and slim doc dependencies (#1405) (@isaacsas)
• Fix some test_broken tests (#1406) (@isaacsas)
• Latex display of symbolics and System to ReactionSystem conversion (#1408) (@isaacsas)
• Add mapping system metadata and complete HISTORY.md (#1410) (@isaacsas)
• Update ODESystem/SDESystem/JumpSystem/NonlinearSystem references (#1411) (@isaacsas)
• Update OptimizationBase requirement from 4 to 4, 5.0 in /docs in the all-julia-packages group across 1 directory (#1412) (@dependabot[bot])
• Document SymbolicIndexingInterface.getname in API reference and tutorial (#1413) (@isaacsas)
• Use => instead of ~ in DSL syntax. (#1414) (@TorkelE)
• V16 spatial update (#1415) (@TorkelE)
• Add doc page init section (inverse problems, steady state analysis, and network analysis) (#1416) (@TorkelE)
• New start of doc page section (model creation and simualtion) (#1417) (@TorkelE)
• mark all module-level globals as const for type stability (#1418) (@isaacsas)
• Conservation law improvements (#1419) (@TorkelE)
• New bk fix (#1421) (@TorkelE)
• Add symbolic tstops (#1422) (@isaacsas)
• Enable symbolic tstops for SDEProblem, JumpProblem, and HybridProblem (#1425) (@isaacsas)
• Disable code coverage and remove badges (#1426) (@isaacsas)
• test for higher order MassActionJumps rate scaling (#1427) (@isaacsas)
• Add supports for bindings (#1428) (@TorkelE)
• Reenable oscillation parameter fitting example (#1429) (@TorkelE)
• Replace structural_simplify with mtkcompile (#1430) (@TorkelE)
• SDEProblem brownians fix (#1431) (@isaacsas)
• Proposed V16 README and index page updates (#1432) (@isaacsas)
• Fix LTS extension test failures (#1434) (@isaacsas)

Closed issues:

• Combinatoric rate law scaling (#311)
• events, constant and boundary condition species for SDEs and Jumps (#414)
• add some basic developer docs (#680)
• Check if ExprValues length might cause performance issues (#794)
• Special case of creating ODEProblem from ODESystem with conservation laws and default values takes very long time (#886)
• parameter dependencies (#909)
• Tracker of issues related to broken tests (#942)
• update unicode "₊" separator to use the default separator variable (#949)
• Summary of breakages when updating problems with conservation laws (#952)
• allow composing with SDESystems (#1000)
• Update doc discussion of parameter typing and check tests (#1011)
• non-SI units not working (#1037)
• fix broken DAE-related tests (#1049)
• switch from our findvars! to MTK's collect_vars! (#1061)
• Update for recent MTK namespacing changes (#1204)
• Tests failing for prerelease (#1235)
• Needed test updates (#1250)
• Catalyst V16 with MTK11 planning (#1274)
• species graph nodes incorrectly labeled with array species variables (#1284)
• Print helpful error if non-integer stoichiometry detected in network analysis functions (#1286)
• How to get the name of a species? (#1325)
• Continuous events dropped for jumps via ODEProblem (#1340)
• [Post V16] create a System to ReactionSystem converter (#1364)
• Move ParsedReactionNetwork struct to Catalyst (#1409)
• substoich=[2] ignored in Reaction generates wrong ODEs (#1438)