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)