v13.5.0

Catalyst v13.5.0

Diff since v13.4.1

Merged pull requests:

• Update index.md (#671) (@ElisabethRoesch)
• Bump actions/checkout from 3 to 4 (#673) (@dependabot[bot])
• Documentation of initial conditions that depend on a parameter (#681) (@TorkelE)
• Test cleanup (#682) (@TorkelE)
• Homotopy Continuation extension and remake (#683) (@TorkelE)
• Bump Optimization bound (#688) (@ChrisRackauckas)
• CompatHelper: bump compat for NonlinearSolve to 2 for package docs, (keep existing compat) (#698) (@github-actions[bot])

Closed issues:

• Unable to interpolate parameters when using @parameters within DSL (#692)

v13.4.1

Catalyst v13.4.1

Diff since v13.4.0

Merged pull requests:

• fix hh docs (#669) (@isaacsas)

v13.4.0

Catalyst v13.4.0

Diff since v13.3.0

Closed issues:

• @parameters and @variables are malfunctioning (#646)
• Linear Interpolation as an algebraic function in a reaction network (#647)
• Species' order is not defined by @species (#649)

Merged pull requests:

• Tutorial for (mostly Symbol based) interfacing with problems, integrators, and solutions (#639) (@TorkelE)
• CompatHelper: add new compat entry for OrdinaryDiffEq at version 6 for package docs, (keep existing compat) (#642) (@github-actions[bot])
• CompatHelper: add new compat entry for StochasticDiffEq at version 6 for package docs, (keep existing compat) (#643) (@github-actions[bot])
• finish Hodgkin-Huxley tutorial (#645) (@isaacsas)
• Adds @Compound macro (#651) (@LalitChauhan56)
• adding discrete event to event doc (#652) (@tstrey)
• disable formatter on test files (#654) (@isaacsas)
• Fix namespacing (#666) (@YingboMa)
• Finish balancing PR (#667) (@isaacsas)
• update HISTORY for compounds (#668) (@isaacsas)

v13.3.0

Catalyst v13.3.0

Diff since v13.2.1

Merged pull requests:

• CompatHelper: bump compat for Latexify to 0.16, (keep existing compat) (#640) (@github-actions[bot])
• CompatHelper: bump compat for Latexify to 0.16 for package docs, (keep existing compat) (#641) (@github-actions[bot])

v13.2.1

Catalyst v13.2.1

Diff since v13.2.0

Closed issues:

• xrightleftharpoons not rendered in VSCode (#637)

Merged pull requests:

• enable dependabot for GitHub actions (#631) (@ranocha)
• Bump codecov/codecov-action from 1 to 3 (#632) (@dependabot[bot])
• Bump actions/cache from 1 to 3 (#633) (@dependabot[bot])
• Bump actions/checkout from 1 to 3 (#634) (@dependabot[bot])
• mathjax mhchem workaround (#638) (@isaacsas)

v13.2.0

Catalyst v13.2.0

Diff since v13.1.0

Merged pull requests:

• allow array variables in DSL (#630) (@isaacsas)

v13.1.0

Catalyst v13.1.0

Diff since v13.0.0

Closed issues:

• Tutorials to add (#222)
• Allowing units via the DSL (#382)
• Add back BifurcationKit tutorial (#604)
• add @variables to the DSL (#615)
• Allow setting independent variables in the DSL (#624)

Merged pull requests:

• Dynamic doc index (#621) (@isaacsas)
• Tests remake (#622) (@TorkelE)
• Variables in DSL (#623) (@isaacsas)
• Finalise test remake (#626) (@TorkelE)
• Doc updates (#627) (@isaacsas)
• Reorder symbols at beginning of home readme (#628) (@TorkelE)

v13.0.0

Catalyst v13.0.0

Diff since v12.3.2

Closed issues:

• @add_reactions macro issue (#249)
• TODO per discussion of 11/25 (#280)
• Create new model without declaring parameters (#333)
• steady-state of reaction system (#389)
• disallow repeated substrates or products in reactions (#516)
• consider ordering Reaction components (#547)
• Distinguishing species from normal variables and handling non-rx equations (#569)
• drop add_reactions! (#573)
• Change Docoument outline (#581)
• Enable symbolic manipulation of u0 and p vector (#582)
• drop mutating system extenders (#583)
• Catalyst 13 TODO (#584)
• Variable rate constants in programatically constructed ReactionSystems (#586)
• Parse error when defining reaction network in Jupyter notebook (#595)
• Forbidden symbols check in DSL no longer working (#597)
• Parameter optimization tutorial outdated (#603)

Merged pull requests:

• Redo dsl syntax (#572) (@TorkelE)
• add and use metadata for species (#585) (@isaacsas)
• Fix array printing (#587) (@isaacsas)
• Starting documentation reordering (#588) (@TorkelE)
• Add form option to latexify (#589) (@TorkelE)
• Add advanced simulation tutorial (#591) (@TorkelE)
• Various docs fixes (#592) (@TorkelE)
• Fix forbidden symbols (#605) (@TorkelE)
• Drop mhchem (#609) (@isaacsas)
• Update param est tutorial and fix advanced simulation tutorial figures (#611) (@isaacsas)
• add back homotopy continuation tutorial (#612) (@isaacsas)
• Event tests and continuous event bug fix (#613) (@isaacsas)
• constraint and event tutorial with latexify fixes (#614) (@isaacsas)
• Disallow repeated reactants and making hashing order independent (#616) (@isaacsas)
• tweak event tutorial (#617) (@isaacsas)
• doc tweak (#618) (@isaacsas)
• fix broken latex from Katex (#619) (@isaacsas)

v12.3.2

Catalyst v12.3.2

Diff since v12.3.1

Closed issues:

• bifurcation analysis support (#81)
• Reaction rates with greek letter is followed by a number cause latexify error (#566)
• Non-unicode alternative for overriding mass action kinetics (#574)
• Unable to remake large network ODEProblem for ensemble calculation (#575)

Merged pull requests:

• Remove unnecessary type parameter (#564) (@LilithHafner)
• Add tutorial for Catalyst and Julia for users inexperienced with Julia (#565) (@TorkelE)
• reproducible docs (#567) (@ArnoStrouwen)
• fix local doc builds, use joinpath, and tweak tutorial (#568) (@isaacsas)
• [skip ci] doc compat (#570) (@ArnoStrouwen)
• [skip ci] doc compats (#577) (@ArnoStrouwen)
• Enable => and <= to ignore law of mass action in DSL (#580) (@TorkelE)

v12.3.1

Catalyst v12.3.1

Diff since v12.3.0

Closed issues:

• support more general affects (#308)
• Matricial ts theory (#555)
• Unable to compute sparse jacobian (using SparseDiffTools) for reaction system (UndefVarError: m not defined) (#559)
• Unable to plot observables with vars=observed(rn) (#560)

Merged pull requests:

• update first few tutorials to be dynamic (#556) (@isaacsas)
• allow multivariable states (#557) (@isaacsas)
• PDE support doc updates (#561) (@isaacsas)
• canonize docs (#562) (@ArnoStrouwen)
• add logo (#563) (@ArnoStrouwen)