v5.1.0

Catalyst v5.1.0

Diff since v5.0.6

Merged pull requests:

• CompatHelper: bump compat for "Catlab" to "0.8" (#255) (@github-actions[bot])

v5.0.6

Catalyst v5.0.6

Diff since v5.0.5

Closed issues:

• reversible reaction (#198)

Merged pull requests:

• Switch Catlab to imports (#251) (@isaacsas)
• CompatHelper: bump compat for "Latexify" to "0.14" (#252) (@github-actions[bot])
• don't run Latexify tests (#257) (@isaacsas)

v5.0.5

Catalyst v5.0.5

Diff since v5.0.4

Closed issues:

• Error when trying to plot graph (#245)
• Error in Latexify (#246)

Merged pull requests:

• always check if rate is an Operation (#247) (@isaacsas)

v5.0.4

Catalyst v5.0.4

Diff since v5.0.3

Closed issues:

• Documentation to add (#227)
• Reaction rates as functions of time? (#238)
• Problems seem to require a parameter tuple/vector (#239)

Merged pull requests:

• Use numspecies and numparams in API tests (#236) (@zdroid)
• Add no parameter tests (#241) (@TorkelE)
• Fix Usage of ModelingToolkit Accessor Functions (#242) (@isaacsas)
• Add dependants test (#244) (@zdroid)

v5.0.3

Catalyst v5.0.3

Diff since v5.0.2

Closed issues:

• The first tutorial (#221)

Merged pull requests:

• Add noise scaling tests. (#232) (@TorkelE)
• Add edges for rate deps (#233) (@isaacsas)
• add a first tutorial (#234) (@isaacsas)
• Add :⇌, :⇋ to double_arrows (#235) (@zdroid)

v5.0.2

Catalyst v5.0.2

Diff since v5.0.1

Closed issues:

• Latexify for arrays of chemical reactions (#210)
• ReactionSystem graph plotting / generation (#216)

Merged pull requests:

• Generation of graphviz graphs (#228) (@isaacsas)
• add documentation for graphs (#230) (@isaacsas)
• disable checks for adding an exisiting variable (#231) (@isaacsas)

v5.0.1

Catalyst v5.0.1

Diff since v5.0.0

v5.0.0

Catalyst v5.0.0

Diff since v4.3.0

Closed issues:

• Obligate Production terms in stochastic differential equations. (#21)
• Automatic Linear Noise Approximation (#23)
• Proposal: new ReactionDSL based on SciCompDSL (#27)
• Diversify @reaction_network input options (#31)
• Feature request: automatic graph generation. (#33)
• Enable creation of problems with AffineNoise (#61)
• cache network dependency info (#66)
• rhs f and Jacobian representation for larger systems (#93)
• SymEngine changing species names to mathematical constants (#129)
• Relax type requirements of the equilibration functionality. (#134)
• @add_constraints gives error when ODEs verified conservation classes are correct (#150)
• Predefine reaction network structure outside macro (#158)
• stability does not return correct answer. (#163)
• Warnings on 1.4.1 (#192)
• remake issue with JumpProblem (#193)
• renaming discussion (#196)
• Rename the package (#197)
• SteadyState tests failing (at least some times) (#203)

Merged pull requests:

• Transfer internals to ModelingToolkit (#194) (@TorkelE)
• Update api for new MT-based DEBio (#199) (@isaacsas)
• Enable network expansion macros (#200) (@TorkelE)
• update more API functions (#202) (@isaacsas)
• Update docstrings for new docs (#204) (@isaacsas)
• Time for Catalyst (#205) (@isaacsas)
• Allow I as a variable and remove unneeded imports (#206) (@isaacsas)
• New UUID for name change (#208) (@ChrisRackauckas)

v4.3.0

DiffEqBiological v4.3.0

Diff since v4.2.0

Merged pull requests:

• CompatHelper: bump compat for "Latexify" to "0.13" (#187) (@github-actions[bot])
• CompatHelper: bump compat for "SymEngine" to "0.8" (#189) (@github-actions[bot])
• CompatHelper: bump compat for "RecipesBase" to "1.0" (#190) (@github-actions[bot])

v4.2.0

DiffEqBiological v4.2.0

Diff since v4.1.0

Closed issues:

• Not possible to save reaction network solutions with JLD2 (#73)
• Parallelise tests (#157)
• Fix Latexify tests (#180)
• HomotopyContinuation bound (#183)

Merged pull requests:

• Restructure and Parallelize tests (#181) (@ChrisRackauckas)
• Update README.md (#182) (@matbesancon)
• CompatHelper: bump compat for "RecipesBase" to "0.8" (#184) (@github-actions[bot])
• Install TagBot as a GitHub Action (#185) (@JuliaTagBot)
• Fix Latexify tests (#186) (@ChrisRackauckas)