v10.4.0

Catalyst v10.4.0

Diff since v10.3.1

Closed issues:

• on reactionparammap function (#449)
• Changes to parameter orders (#453)
• provide defaults using @reaction_network (#464)

Merged pull requests:

• fix DSL annoyances (#468) (@isaacsas)
• Use symmaps in Problems and explain in the docs (#469) (@isaacsas)

v10.3.1

Catalyst v10.3.1

Diff since v10.3.0

Closed issues:

• Moving functions to sub package (#355)
• Variables added with addparam! or addspecies! are not accessible with getproperty (#461)

Merged pull requests:

• CompatHelper: bump compat for AbstractAlgebra to 0.23, (keep existing compat) (#459) (@github-actions[bot])
• Update reaction_network.jl (#460) (@rpmuller)
• Fix access to variables added with addparam! or addspecies! (#462) (@lgrozinger)
• Update bifurcation_diagram.md (#463) (@rveltz)
• Interpolate make_ReactionSystem_internal (#465) (@andreasnoack)

v10.3.0

Catalyst v10.3.0

Diff since v10.2.0

Closed issues:

• Error in tutorial "Generating ReactionSystems Programmatically" (#450)

Merged pull requests:

• CI for LTS (#451) (@ChrisRackauckas)
• Fix parameter ordering (#452) (@TorkelE)
• Add history entry for paraemter order change. (#455) (@TorkelE)
• CompatHelper: bump compat for "ModelingToolkit" to "8.0" (#457) (@github-actions[bot])

v10.2.0

Catalyst v10.2.0

Diff since v10.1.0

Merged pull requests:

• CompatHelper: bump compat for "DiffEqJump" to "8.0" (#448) (@github-actions[bot])

v10.1.0

Catalyst v10.1.0

Diff since v10.0.0

Closed issues:

• Move ReactionSystem definition over to Catalyst (#218)
• Allow nonlinear eqs and ODEs attached to ReactionSystems (#328)
• Merging more than one subnetworks using merge! (#439)
• Graph and complexgraph results in following error (#440)

Merged pull requests:

• switch LightGraphs to Graphs (#437) (@isaacsas)
• typo in reactionrates function description for docs (#438) (@yewalenikhil65)
• Add var_to_name field (#442) (@isaacsas)
• forward observed when converting systems (#443) (@isaacsas)
• Update README.md for adding an old talk of diffeqbiological from JuliaCon 2018 (#444) (@yewalenikhil65)
• CompatHelper: bump compat for "ModelingToolkit" to "7.0" (#445) (@github-actions[bot])
• V10.1 (#447) (@isaacsas)

v10.0.0

Catalyst v10.0.0

Diff since v9.0.0

Closed issues:

• WARNING: both Catalyst and Flux export "params"; uses of it in module Main must be qualified (#260)
• Sparse stoichmat dispatches? (#386)
• Linkage classes, deficiency, Part 1 (#390)
• conservation law analysis (#393)
• [WIP]- subnetworks, linkagedeficiency (#395)
• Constraints in for weak acids and pH equilibrium (#398)
• reversibility and weak reversibility of CRNs (#401)
• Settling time of CRN (i.e. time taken for each species to reach steadystate) (#403)
• update API functions to work properly with mixed subsystems (#405)
• add back @add_constraints (#408)
• Solution of SteadyStateProblem is extremely slow (#409)
• weird (?) behaviour of get_variables in Reaction (#422)
• simple constructor ReactionSystem(rxns) (#425)
• always flatten in converting ReactionSystems to other types (#428)

Merged pull requests:

• [WIP] linkageclasses and deficiency of reaction network (#394) (@yewalenikhil65)
• subnetworks and linkagedeficieny (#396) (@yewalenikhil65)
• Use Flint via Nemo for integer matrix calculations (#397) (@isaacsas)
• fix networkapi.jl example typo (#399) (@isaacsas)
• docs for subnetworks and linkagedeficiencies (#400) (@yewalenikhil65)
• fixing spaces for docs of subnetworks and linkagedeficieny (#402) (@yewalenikhil65)
• Add subsystem support to enable constraints and composition of ODE/Nonlinear sys (#404) (@isaacsas)
• on reversibility and weak reversibility of reaction networks (#406) (@yewalenikhil65)
• Update API and docs for subsystems (#407) (@isaacsas)
• attempt 2 at naming for compositional systems (#411) (@isaacsas)
• Update using_catalyst.md (#412) (@pitmonticone)
• Change ReactionNetworkImportes link (#415) (@TorkelE)
• Fix reaction equality in sets and add upconversion to ODESystems in convert (#419) (@isaacsas)
• tweak docs (#420) (@isaacsas)
• CompatHelper: bump compat for "AbstractAlgebra" to "0.22" (#421) (@github-actions[bot])
• Constraints, flattening, and extending for ReactionSystems (#423) (@isaacsas)
• Simplified ReactionSystem constructor (#426) (@isaacsas)
• Make undefined variables in DSL become species (#427) (@isaacsas)
• Always flatten before converting (#429) (@isaacsas)
• add smap as a karg for convert to ODESystem (#430) (@LauraBMo)
• Fix JumpSystem conversion bug (#431) (@isaacsas)
• allow interpolation of species and parameters in the DSL (#432) (@isaacsas)
• Doc updates for v10.0 (#434) (@isaacsas)
• fix namespacing for reactions (#435) (@isaacsas)
• update history for 10 (#436) (@isaacsas)

v9.0.0

Catalyst v9.0.0

Diff since v8.3.0

Closed issues:

• Error while asignning units as shown in Catalyst readme.md (#385)
• equations(rs::ReactionSystem) returns Vector{Reaction} (#388)

Merged pull requests:

• Sparse representation of stoichiometric matrices functions and matrices in complex-based functions (#387) (@yewalenikhil65)
• Create history file (#391) (@isaacsas)
• fix docstrings (#392) (@isaacsas)

v8.3.0

Catalyst v8.3.0

Diff since v8.2.0

Closed issues:

• Support Array Symbolics in ReactionSystem (#336)
• plotting reaction complex network.. (#374)
• Catalyst/DifferentialEquations: Gillespie simulation not working for large chemical reaction networks (#378)

Merged pull requests:

• ReactionComplexesGraph using existing Graphviz code in graphs.jl (#380) (@yewalenikhil65)
• Unit validation and tests (#381) (@isaacsas)
• add test for new complex graph (#383) (@isaacsas)
• update docs and README for 8.3 (#384) (@isaacsas)

v8.2.0

Catalyst v8.2.0

Diff since v8.1.0

Closed issues:

• Feature request for Representing reactions with focus on intermediate complexes (#318)
• still stuck at [email protected] (#375)

Merged pull requests:

• update doc action (#376) (@isaacsas)
• ModelingToolkit unit validation logic (#377) (@lamorton)

v8.1.0

Catalyst v8.1.0

Diff since v8.0.1

Merged pull requests:

• Reaction complexes v2 (#373) (@isaacsas)