Tags: andreasnoack/Catalyst.jl
Tags
[Diff since v10.2.0](SciML/Catalyst.jl@v10.2.0...v10.3.0) **Closed issues:** - Error in tutorial "Generating ReactionSystems Programmatically" (SciML#450) **Merged pull requests:** - CI for LTS (SciML#451) (@ChrisRackauckas) - Fix parameter ordering (SciML#452) (@TorkelE) - Add history entry for paraemter order change. (SciML#455) (@TorkelE) - CompatHelper: bump compat for "ModelingToolkit" to "8.0" (SciML#457) (@github-actions[bot])
[Diff since v10.0.0](SciML/Catalyst.jl@v10.0.0...v10.1.0) **Closed issues:** - Move ReactionSystem definition over to Catalyst (SciML#218) - Allow nonlinear eqs and ODEs attached to ReactionSystems (SciML#328) - Merging more than one `subnetworks` using merge! (SciML#439) - `Graph` and `complexgraph` results in following error (SciML#440) **Merged pull requests:** - switch LightGraphs to Graphs (SciML#437) (@isaacsas) - typo in `reactionrates` function description for docs (SciML#438) (@yewalenikhil65) - Add var_to_name field (SciML#442) (@isaacsas) - forward observed when converting systems (SciML#443) (@isaacsas) - Update README.md for adding an old talk of diffeqbiological from JuliaCon 2018 (SciML#444) (@yewalenikhil65) - CompatHelper: bump compat for "ModelingToolkit" to "7.0" (SciML#445) (@github-actions[bot]) - V10.1 (SciML#447) (@isaacsas)
[Diff since v9.0.0](SciML/Catalyst.jl@v9.0.0...v10.0.0) **Closed issues:** - WARNING: both Catalyst and Flux export "params"; uses of it in module Main must be qualified (SciML#260) - Sparse `stoichmat` dispatches? (SciML#386) - `Linkage classes`, `deficiency`, Part 1 (SciML#390) - conservation law analysis (SciML#393) - [WIP]- `subnetworks`, `linkagedeficiency` (SciML#395) - Constraints in for weak acids and pH equilibrium (SciML#398) - reversibility and weak reversibility of CRNs (SciML#401) - Settling time of CRN (i.e. time taken for each species to reach steadystate) (SciML#403) - update API functions to work properly with mixed subsystems (SciML#405) - add back @add_constraints (SciML#408) - Solution of SteadyStateProblem is extremely slow (SciML#409) - weird (?) behaviour of get_variables in `Reaction` (SciML#422) - simple constructor `ReactionSystem(rxns)` (SciML#425) - always flatten in converting ReactionSystems to other types (SciML#428) **Merged pull requests:** - [WIP] `linkageclasses` and `deficiency` of reaction network (SciML#394) (@yewalenikhil65) - `subnetworks` and `linkagedeficieny` (SciML#396) (@yewalenikhil65) - Use Flint via Nemo for integer matrix calculations (SciML#397) (@isaacsas) - fix networkapi.jl example typo (SciML#399) (@isaacsas) - docs for `subnetworks` and `linkagedeficiencies` (SciML#400) (@yewalenikhil65) - fixing spaces for docs of subnetworks and linkagedeficieny (SciML#402) (@yewalenikhil65) - Add subsystem support to enable constraints and composition of ODE/Nonlinear sys (SciML#404) (@isaacsas) - on reversibility and weak reversibility of reaction networks (SciML#406) (@yewalenikhil65) - Update API and docs for subsystems (SciML#407) (@isaacsas) - attempt 2 at naming for compositional systems (SciML#411) (@isaacsas) - Update using_catalyst.md (SciML#412) (@pitmonticone) - Change ReactionNetworkImportes link (SciML#415) (@TorkelE) - Fix reaction equality in sets and add upconversion to ODESystems in convert (SciML#419) (@isaacsas) - tweak docs (SciML#420) (@isaacsas) - CompatHelper: bump compat for "AbstractAlgebra" to "0.22" (SciML#421) (@github-actions[bot]) - Constraints, flattening, and extending for ReactionSystems (SciML#423) (@isaacsas) - Simplified ReactionSystem constructor (SciML#426) (@isaacsas) - Make undefined variables in DSL become species (SciML#427) (@isaacsas) - Always flatten before converting (SciML#429) (@isaacsas) - add smap as a karg for convert to ODESystem (SciML#430) (@LauraBMo) - Fix JumpSystem conversion bug (SciML#431) (@isaacsas) - allow interpolation of species and parameters in the DSL (SciML#432) (@isaacsas) - Doc updates for v10.0 (SciML#434) (@isaacsas) - fix namespacing for reactions (SciML#435) (@isaacsas) - update history for 10 (SciML#436) (@isaacsas)
[Diff since v8.3.0](SciML/Catalyst.jl@v8.3.0...v9.0.0) **Closed issues:** - Error while asignning units as shown in Catalyst readme.md (SciML#385) - `equations(rs::ReactionSystem)` returns `Vector{Reaction}` (SciML#388) **Merged pull requests:** - Sparse representation of `stoichiometric matrices` functions and matrices in complex-based functions (SciML#387) (@yewalenikhil65) - Create history file (SciML#391) (@isaacsas) - fix docstrings (SciML#392) (@isaacsas)
[Diff since v8.2.0](SciML/Catalyst.jl@v8.2.0...v8.3.0) **Closed issues:** - Support Array Symbolics in ReactionSystem (SciML#336) - plotting reaction complex network.. (SciML#374) - Catalyst/DifferentialEquations: Gillespie simulation not working for large chemical reaction networks (SciML#378) **Merged pull requests:** - ReactionComplexesGraph using existing Graphviz code in graphs.jl (SciML#380) (@yewalenikhil65) - Unit validation and tests (SciML#381) (@isaacsas) - add test for new complex graph (SciML#383) (@isaacsas) - update docs and README for 8.3 (SciML#384) (@isaacsas)
[Diff since v8.1.0](SciML/Catalyst.jl@v8.1.0...v8.2.0) **Closed issues:** - Feature request for Representing reactions with focus on intermediate complexes (SciML#318) - still stuck at [email protected] (SciML#375) **Merged pull requests:** - update doc action (SciML#376) (@isaacsas) - ModelingToolkit unit validation logic (SciML#377) (@lamorton)
[Diff since v7.0.0](SciML/Catalyst.jl@v7.0.0...v8.0.0) **Closed issues:** - How to add tests for an array of reaction systems (SciML#358) - query on conservationlaws returned matrix (SciML#360) - KeyErrors running models in parallel with Distributed (SciML#361) **Merged pull requests:** - Test AbstractAlgebra v0.21 (SciML#363) (@ChrisRackauckas) - Add reactionsystems (SciML#370) (@isaacsas)
PreviousNext