Recent Releases of JumpProcesses
JumpProcesses - v9.17.0
JumpProcesses v9.17.0
Merged pull requests:
- Kernels for SimpleTauLeaping (#490) (@sivasathyaseeelan)
- CompatHelper: add new compat entry for Adapt in [weakdeps] at version 4, (keep existing compat) (#496) (@github-actions[bot])
- CompatHelper: add new compat entry for KernelAbstractions in [weakdeps] at version 0.9, (keep existing compat) (#497) (@github-actions[bot])
- Add spell checking configuration (#501) (@ChrisRackauckas)
- Add downgrade CI workflow (#502) (@ChrisRackauckas)
- Update CI to properly use Julia version matrix (#503) (@ChrisRackauckas)
- Update code formatting with JuliaFormatter (#504) (@ChrisRackauckas)
- Fix unnecessary line splits following Catalyst.jl PR #1306 (#507) (@ChrisRackauckas)
- Update DataStructures.jl compatibility to v0.19 (#508) (@ChrisRackauckas)
- Fix documentation bloat by forcing PNG plots (#509) (@ChrisRackauckas)
- Fix autodiff Bool parameter deprecation warnings (#510) (@ChrisRackauckas)
- Fix downgrade (#511) (@ChrisRackauckas)
- GPU-compatible Poisson sampling (#512) (@sivasathyaseeelan)
- Remove undocumented arguments from JumpProcess solve dispatch (#514) (@ChrisRackauckas)
Closed issues: - drop RandomNumbers dependency (#492) - rand(hawkes) fails in advanced point processes tutorial (#494) - poisson_rand optimization in GPU enhanced SimpleTauLeaping (#498) - Remove the generation of animations from the documentation (#505)
- Julia
Published by github-actions[bot] 10 months ago
JumpProcesses - v9.16.1
JumpProcesses v9.16.1
Merged pull requests: - Bug fixed in vr_agg (#489) (@sivasathyaseeelan) - Add buildkite runner (#491) (@ChrisRackauckas) - drop RandomNumbers.jl (#493) (@isaacsas)
- Julia
Published by github-actions[bot] 11 months ago
JumpProcesses - v9.16.0
JumpProcesses v9.16.0
Merged pull requests: - VR_DirectFW aggregator (#488) (@sivasathyaseeelan)
- Julia
Published by github-actions[bot] 12 months ago
JumpProcesses - v9.15.0
JumpProcesses v9.15.0
Merged pull requests: - feat: Introducing vraggregator with VRDirectCB and VRFRMODE (#477) (@sivasathyaseeelan) - removed VariableRateJumps from VRDirectEventCache (#486) (@sivasathyaseeelan) - cached u for DirectEventCache (#487) (@isaacsas)
- Julia
Published by github-actions[bot] about 1 year ago
JumpProcesses - v9.14.3
JumpProcesses v9.14.3
Merged pull requests: - add test initial variable rate propensities are unique in ensembles (#475) (@isaacsas) - fix neg mass action rates with FP types (#480) (@isaacsas)
Closed issues:
- DiscreteProblems do not accept Int64 tspans (or rather, simulations of these errors) (#478)
- Potential issue with FRM solver (#479)
- Julia
Published by github-actions[bot] about 1 year ago
JumpProcesses - v9.14.2
JumpProcesses v9.14.2
Merged pull requests: - don't access callbacks till checking they exist (#473) (@isaacsas)
Closed issues: - update VariableRateJump plots to show how to only plot variables (#452) - Can't access component array field in continuous callback with variable rate jump (#471) - Crash when using EnsembleThreads and variable rate jump (#472)
- Julia
Published by github-actions[bot] over 1 year ago
JumpProcesses - v9.14.1
JumpProcesses v9.14.1
Merged pull requests: - plottable_indices dispatch (#461) (@isaacsas) - add implicit solver VariableRateJump test (#462) (@isaacsas) - make affects wrapping vrjs return nothing (#463) (@isaacsas) - Bump codecov/codecov-action from 4 to 5 (#467) (@dependabot[bot]) - fix: remove ambiguous methods (#469) (@AayushSabharwal)
Closed issues: - ODE-jump models with implicit solvers not working (#459)
- Julia
Published by github-actions[bot] over 1 year ago
JumpProcesses - v9.14.0
JumpProcesses v9.14.0
Merged pull requests:
- add more vrj correctness tests (#453) (@isaacsas)
- tweak RegularJump doc string (#454) (@isaacsas)
- [Ready for Review] - Constant-complexity NRM implementation (#455) (@vyudu)
- ci: test with 1, lts and pre versions of julia (#457) (@thazhemadam)
- Julia
Published by github-actions[bot] over 1 year ago
JumpProcesses - v9.13.7
JumpProcesses v9.13.7
Merged pull requests: - Document regular jumps (#449) (@isaacsas) - fix vrj reinitialization bug (#450) (@isaacsas) - make terminate! really terminate (#451) (@isaacsas)
Closed issues: - Tracking issue for Documenter and design of docstrings and new tutorials. (#238) - VariableRateJump - Jumps don't match expected distribution for birth-death process (#320)
- Julia
Published by github-actions[bot] over 1 year ago
JumpProcesses - v9.13.6
JumpProcesses v9.13.6
Merged pull requests: - Document regular jumps (#449) (@isaacsas) - fix vrj reinitialization bug (#450) (@isaacsas)
Closed issues: - Tracking issue for Documenter and design of docstrings and new tutorials. (#238) - VariableRateJump - Jumps don't match expected distribution for birth-death process (#320)
- Julia
Published by github-actions[bot] over 1 year ago
JumpProcesses - v9.13.5
JumpProcesses v9.13.5
Merged pull requests: - periodic callback and tstop aliasing fixes (#443) (@isaacsas) - ExtendedJumpArray remake fixes II (#448) (@isaacsas)
Closed issues: - Use FunctionWranglers.jl (#172) - Discrete events with repeated dosage fails for JumpSystems (fine ofr e.g. ODEs) (#417) - don't alias user tstops when modifying it in SSAStepper (#442)
- Julia
Published by github-actions[bot] almost 2 years ago
JumpProcesses - v9.13.4
JumpProcesses v9.13.4
Merged pull requests: - ExtendedJumpArrays remake fix (#447) (@isaacsas)
Closed issues: - Issue with remaking a variable rate jump problem (#446)
- Julia
Published by github-actions[bot] almost 2 years ago
JumpProcesses - v9.13.3
JumpProcesses v9.13.3
Merged pull requests: - Make RSSA methods work with floating point u (#440) (@isaacsas)
Closed issues:
- Make trunc in bracketing work with Float64 us (#439)
- Julia
Published by github-actions[bot] almost 2 years ago
JumpProcesses - v9.13.2
JumpProcesses v9.13.2
Merged pull requests: - preserve observed and sys when extending functions (#438) (@isaacsas)
- Julia
Published by github-actions[bot] almost 2 years ago
JumpProcesses - v9.13.1
JumpProcesses v9.13.1
Merged pull requests: - create variables for the various auto-alg thresholds (#437) (@isaacsas)
- Julia
Published by github-actions[bot] almost 2 years ago
JumpProcesses - v9.13.0
JumpProcesses v9.13.0
Merged pull requests:
- Choose an SSA if no SSA is passed in JumpProblem. (#351) (@Vilin97)
- Help wanted (#432) (@Vilin97)
- update docs for Catalyst 14 and new saveat behavior (#433) (@isaacsas)
Closed issues:
- Interface for Jump simulations seems non-ideally messy? (#360)
- Certain Continuous Callbacks does not work for JumpProcessess (#390)
- Automatic selection of solver method (e.g. SSAStepper()) (#419)
- Julia
Published by github-actions[bot] almost 2 years ago
JumpProcesses - v9.12.0
JumpProcesses v9.12.0
Merged pull requests: - CompatHelper: bump compat for PointProcesses to 0.5 for package docs, (keep existing compat) (#394) (@github-actions[bot]) - Bump julia-actions/setup-julia from 1 to 2 (#414) (@dependabot[bot]) - ci: standardise workflows using SciML's reusable workflows (#418) (@thazhemadam) - CompatHelper: add new compat entry for FastBroadcast in [weakdeps] at version 0.3, (keep existing compat) (#422) (@github-actions[bot]) - restrict FastBroadcast to 0.3 and delete the extension (#425) (@oscardssmith) - remove support for unsuported julia versions (#426) (@oscardssmith) - Fix saveat plotting (#430) (@isaacsas)
Closed issues:
- Plotting is misleading when not saving all jumps (#206)
- FunctionMap not defined (#423)
- Julia
Published by github-actions[bot] almost 2 years ago
JumpProcesses - v9.11.1
JumpProcesses v9.11.1
Merged pull requests: - use SII.finalizeparametershook! when updating problems (#409) (@isaacsas) - Fix test warnings (#411) (@isaacsas)
Closed issues: - figure out why CI is now taking a ridiculous amount of time (#410)
- Julia
Published by github-actions[bot] about 2 years ago
JumpProcesses - v9.11.0
JumpProcesses v9.11.0
Merged pull requests: - Juliacon2023 Revisions (#373) (@gzagatti) - Ambiguity fix (#385) (@isaacsas) - Juliacon2023 Latex Dependencies (#391) (@gzagatti) - Bump crate-ci/typos from 1.16.23 to 1.17.0 (#393) (@dependabot[bot]) - add references to other Julia libraries (#395) (@gzagatti) - Bump actions/cache from 3 to 4 (#396) (@dependabot[bot]) - Bump crate-ci/typos from 1.17.0 to 1.18.0 (#397) (@dependabot[bot]) - Bump codecov/codecov-action from 3 to 4 (#398) (@dependabot[bot]) - [skip ci] Update dependabot.yml (#399) (@ArnoStrouwen) - ci: explicitly specify token for codecov (#400) (@thazhemadam) - reapply formatter (#403) (@ArnoStrouwen) - Complete 2nd rebuttal, fix #402 (#404) (@gzagatti) - Print version Juliacon 2023 paper (#406) (@gzagatti) - Add new reference to the JumpProcesses.jl version used for benchmark (#407) (@gzagatti) - Indexing fixes (#408) (@isaacsas)
Closed issues: - possible interpolation bug in hybrid systems (#361) - Remarks about paper JuliaCon Proceedings review - Remarks about package JuliaCon Proceedings review - Remarks about paper - episode 2 JuliaCon Proceedings review
- Julia
Published by github-actions[bot] about 2 years ago
JumpProcesses - v9.10.1
JumpProcesses v9.10.1
Merged pull requests: - Update JumpProcesses documentation (#372) (@gzagatti) - Doc update v5 (#381) (@gzagatti)
Closed issues: - Remarks about docs JuliaCon Proceedings review
- Julia
Published by github-actions[bot] over 2 years ago
JumpProcesses - v9.10.0
JumpProcesses v9.10.0
Merged pull requests: - chore: bump RecursiveArrayTools compat (#363) (@AayushSabharwal) - typos CI (#377) (@ArnoStrouwen) - Bump actions/checkout from 3 to 4 (#378) (@dependabot[bot])
- Julia
Published by github-actions[bot] over 2 years ago
JumpProcesses - v9.9.0
JumpProcesses v9.9.0
Merged pull requests: - Documenter 1.0 upgrade (#352) (@ArnoStrouwen) - Update FormatCheck.yml (#354) (@ArnoStrouwen) - Revert "Documenter 1.0 upgrade" (#357) (@isaacsas) - Update documenter attempt 2 (#358) (@isaacsas) - Fix typos in docs (#366) (@gdalle) - Change typeof(x) <: y to x isa y (#371) (@pepijndevos) - Remove TreeViews (#375) (@sathvikbhagavan)
- Julia
Published by github-actions[bot] over 2 years ago
JumpProcesses - v9.8.0
JumpProcesses v9.8.0
Merged pull requests: - Refactor internal functions in spatial SSAs. (#342) (@Vilin97) - Bracketing unit tests (#344) (@Vilin97) - Set up bracketing for spatial solvers. (#345) (@Vilin97) - Bump actions/checkout from 3 to 4 (#347) (@dependabot[bot]) - Improve spatial tests (#348) (@Vilin97) - CompatHelper: bump compat for SciMLBase to 2, (keep existing compat) (#350) (@github-actions[bot])
- Julia
Published by github-actions[bot] over 2 years ago
JumpProcesses - v9.7.3
JumpProcesses v9.7.3
Closed issues:
- Error when simulating variable rate jump problem with OOP ODEProblem (#321)
- Coevolve can call urate with a time beyond the time span (#330)
- Efficency of ExtendedJumpArray broadcasting in ode_interpolant (#335)
Merged pull requests: - Juliacon2023 Revision (#319) (@gzagatti) - Add test for Coevolve calling user-provided funcs with t beyond tspan (#331) (@gaurav-arya) - removes stackengine dependency (#336) (@gzagatti) - Adds subfig.sty (#337) (@gzagatti) - Juliacon2023 (#338) (@gzagatti) - Juliacon2023 (#339) (@gzagatti) - Add non-default broadcasting of ExtendedJumpArray's. (#340) (@meson800)
- Julia
Published by github-actions[bot] almost 3 years ago
JumpProcesses - v9.7.2
JumpProcesses v9.7.2
Merged pull requests: - Added ExtendedJumpArray dispatch for ODEDEFAULTNORM (#334) (@meson800)
- Julia
Published by github-actions[bot] almost 3 years ago
JumpProcesses - v9.7.1
JumpProcesses v9.7.1
Merged pull requests: - Docstring tweak (#332) (@isaacsas)
- Julia
Published by github-actions[bot] almost 3 years ago
JumpProcesses - v9.7.0
JumpProcesses v9.7.0
Merged pull requests: - CoevolveSynced (#315) (@gzagatti) - Allocations test fix (#328) (@isaacsas)
- Julia
Published by github-actions[bot] almost 3 years ago
JumpProcesses - v9.6.4
JumpProcesses v9.6.4
Closed issues:
- Callback broken with Coevolve (#324)
Merged pull requests: - fix reinit of existing function wrapped affects! vector (#326) (@isaacsas)
- Julia
Published by github-actions[bot] almost 3 years ago
JumpProcesses - v9.6.3
JumpProcesses v9.6.3
Closed issues: - Eliminate small allocations in RSSA/RSSACR (#317)
Merged pull requests: - Fix rssa allocations (#318) (@isaacsas)
- Julia
Published by github-actions[bot] about 3 years ago
JumpProcesses - v9.6.2
JumpProcesses v9.6.2
Closed issues: - Memory allocations when calling FunctionWrapped Symbolic affect functions (#308)
Merged pull requests: - JuliaCon 2023 Paper (#304) (@gzagatti) - function wrapper type instability fix (#309) (@isaacsas) - Setfields for jump problems (#310) (@TorkelE) - Juliacon2023: Adds missing pdf assets (#313) (@gzagatti)
- Julia
Published by github-actions[bot] about 3 years ago
JumpProcesses - v9.6.1
JumpProcesses v9.6.1
Closed issues:
- allocations with updatestates! for Direct (#305)
- Cannot set `saveeverystepkeyword argument onsolveorinit` (#306)
Merged pull requests: - Direct method allocations fix (#307) (@isaacsas)
- Julia
Published by github-actions[bot] about 3 years ago
JumpProcesses - v9.6.0
JumpProcesses v9.6.0
Merged pull requests: - enable dependabot for GitHub actions (#299) (@ranocha) - Bump actions/checkout from 1 to 3 (#300) (@dependabot[bot]) - Bump codecov/codecov-action from 1 to 3 (#301) (@dependabot[bot]) - Bump actions/cache from 1 to 3 (#302) (@dependabot[bot]) - destats -> stats (#303) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] about 3 years ago
JumpProcesses - v9.5.1
JumpProcesses v9.5.1
Merged pull requests: - Update for catalyst13 (#297) (@isaacsas)
- Julia
Published by github-actions[bot] over 3 years ago
JumpProcesses - v9.5.0
JumpProcesses v9.5.0
- Julia
Published by github-actions[bot] over 3 years ago
JumpProcesses - v9.4.0
JumpProcesses v9.4.0
Merged pull requests: - update ArrayInterface to v7 (#294) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] over 3 years ago
JumpProcesses - v9.3.2
JumpProcesses v9.3.2
Closed issues:
- Ambiguity of ldiv! in 1.9 (#289)
Merged pull requests: - [skip ci] docstring spelling (#285) (@ArnoStrouwen) - format markdown (#286) (@ArnoStrouwen) - Fix ldiv! ambiguity on v1.9 (#290) (@ChrisRackauckas) - Return success (#293) (@isaacsas)
- Julia
Published by github-actions[bot] over 3 years ago
JumpProcesses - v9.3.1
JumpProcesses v9.3.1
Merged pull requests:
- [skip ci] LanguageTool (#281) (@ArnoStrouwen)
- Tiny fix of Coevolve() with the dependency graph check (#282) (@palmtree2013)
- Out of place variable rate jump extensions (#283) (@ChrisRackauckas)
- Spatial JumpProblem validation check fix (#284) (@isaacsas)
- Julia
Published by github-actions[bot] over 3 years ago
JumpProcesses - v9.3.0
JumpProcesses v9.3.0
Merged pull requests:
- Coevolve aggregator for VariableRateJump (#276) (@gzagatti)
- Move spatial tutorial from SciMLTutorials (#277) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] over 3 years ago
JumpProcesses - v9.2.3
JumpProcesses v9.2.3
Merged pull requests: - reproducible docs (#272) (@ArnoStrouwen) - [skip ci] doc compat (#273) (@ArnoStrouwen) - Update return codes (#274) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] over 3 years ago
JumpProcesses - v9.2.2
JumpProcesses v9.2.2
Merged pull requests: - add logo (#271) (@ArnoStrouwen)
- Julia
Published by github-actions[bot] over 3 years ago
JumpProcesses - v9.2.1
JumpProcesses v9.2.1
Closed issues: - Needs type constraint (#269)
Merged pull requests: - Change Int64 to Int8 in nums_neighbors (#259) (@Vilin97) - badges (#261) (@ArnoStrouwen) - doc cov (#262) (@ArnoStrouwen) - Remove CartesianGridIter. (#264) (@Vilin97) - MassInstallAction: Install the Invalidations workflow on this repository (#265) (@devmotion) - drop fastmaths (#266) (@isaacsas) - remove unbound type parameters (#267) (@nsajko) - canonify docs (#268) (@ArnoStrouwen) - constrain DiffEqBase.solve! (#270) (@isaacsas)
- Julia
Published by github-actions[bot] over 3 years ago
JumpProcesses - v9.2.0
JumpProcesses v9.2.0
Merged pull requests: - update SciMLBase bound for function unwrapping (#260) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] almost 4 years ago
JumpProcesses - v9.1.3
JumpProcesses v9.1.3
- Julia
Published by github-actions[bot] almost 4 years ago
JumpProcesses - v9.1.2
JumpProcesses v9.1.2
- Julia
Published by github-actions[bot] almost 4 years ago
JumpProcesses - v9.1.1
JumpProcesses v9.1.1
Closed issues:
- [likely a bug] Using nth_potantial_nbr instead of nth_nbr in hop_rates.jl (#251)
Merged pull requests: - Refactor spatial unit tests. (#255) (@Vilin97) - doc unification (#256) (@ArnoStrouwen) - Make the diffusion test a bit faster and less flaky. (#257) (@Vilin97)
- Julia
Published by github-actions[bot] almost 4 years ago
JumpProcesses - v9.1.0
JumpProcesses v9.1.0
Closed issues: - Error in tutorial in JumpProcesses.jl (#253)
Merged pull requests: - Allow passing callbacks via JumpProblem (#254) (@isaacsas)
- Julia
Published by github-actions[bot] almost 4 years ago
JumpProcesses - v9.0.1
JumpProcesses v9.0.1
- Julia
Published by github-actions[bot] almost 4 years ago
JumpProcesses - v9.0.0
JumpProcesses v9.0.0
Closed issues: - Consider a rename (#242)
Merged pull requests: - update package name to JumpProcesses.jl (#250) (@isaacsas)
- Julia
Published by github-actions[bot] almost 4 years ago
JumpProcesses - v8.6.3
DiffEqJump v8.6.3
Closed issues: - Accessing previous values of the SSAIntegrator (#214)
Merged pull requests: - Clean README and docs (#243) (@pitmonticone) - Make sure to use SciML Style format (#245) (@ChrisRackauckas) - cleanup from formatter (#246) (@isaacsas) - update docs more (#247) (@isaacsas) - fix doc dependencies (#249) (@isaacsas)
- Julia
Published by github-actions[bot] almost 4 years ago
JumpProcesses - v8.6.2
DiffEqJump v8.6.2
- Julia
Published by github-actions[bot] almost 4 years ago
JumpProcesses - v8.6.1
DiffEqJump v8.6.1
Closed issues: - SSAIntegrator not playing nice with PresetTimeCallback -- ERROR: type SSAIntegrator has no field tdir (#239)
Merged pull requests:
- Added basic Documenter.jl configuration. (#237) (@00krishna)
- Add tdir (#240) (@isaacsas)
- bring docs over from DifferentialEquations.jl (#241) (@isaacsas)
- Julia
Published by github-actions[bot] almost 4 years ago
JumpProcesses - v8.6.0
DiffEqJump v8.6.0
Merged pull requests: - CompatHelper: bump compat for DocStringExtensions to 0.9, (keep existing compat) (#235) (@github-actions[bot])
- Julia
Published by github-actions[bot] almost 4 years ago
JumpProcesses - v8.5.0
DiffEqJump v8.5.0
Merged pull requests: - Remove Compat.jl (#232) (@ChrisRackauckas) - Switch to ArrayInterfaceCore (#234) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] about 4 years ago
JumpProcesses - v8.4.2
DiffEqJump v8.4.2
Merged pull requests: - Docs for extendedjumps (#230) (@isaacsas)
- Julia
Published by github-actions[bot] about 4 years ago
JumpProcesses - v8.4.1
DiffEqJump v8.4.1
Merged pull requests: - Call user VariableRateJumps with unpacked ExtendedJumpArray (#228) (@isaacsas)
- Julia
Published by github-actions[bot] about 4 years ago
JumpProcesses - v8.4.0
DiffEqJump v8.4.0
Closed issues: - using complex states with VariableRateJumps (#226)
Merged pull requests: - Attempt to fix complex states with VariableRateJumps (#225) (@isaacsas)
- Julia
Published by github-actions[bot] about 4 years ago
JumpProcesses - v8.3.1
DiffEqJump v8.3.1
Merged pull requests: - Doc strings (#224) (@isaacsas)
- Julia
Published by github-actions[bot] about 4 years ago
JumpProcesses - v8.3.0
DiffEqJump v8.3.0
Merged pull requests: - CompatHelper: bump compat for ArrayInterface to 5, (keep existing compat) (#223) (@github-actions[bot])
- Julia
Published by github-actions[bot] about 4 years ago
JumpProcesses - v8.2.1
DiffEqJump v8.2.1
Closed issues: - Strange Crash for SortingDirect under obscure circumstances (#221)
Merged pull requests: - fix bug in not registering new tspan[2] values (#222) (@isaacsas)
- Julia
Published by github-actions[bot] over 4 years ago
JumpProcesses - v8.2.0
DiffEqJump v8.2.0
Closed issues: - RNG on 1.7 (#212)
Merged pull requests: - working on spatially varying reaction rates, WIP (#219) (@Vilin97) - Change default rng on 1.7 up (#220) (@isaacsas)
- Julia
Published by github-actions[bot] over 4 years ago
JumpProcesses - v8.1.0
DiffEqJump v8.1.0
Closed issues: - Jump problem with ensemble dies after large number of iterations in Approximate Bayes computation (#217)
Merged pull requests: - CI for LTS (#216) (@ChrisRackauckas) - CompatHelper: bump compat for ArrayInterface to 4, (keep existing compat) (#218) (@github-actions[bot])
- Julia
Published by github-actions[bot] over 4 years ago
JumpProcesses - v8.0.0
DiffEqJump v8.0.0
Closed issues: - Precompiling of DifferentialEquations.jl fails due to LoadError in DiffEqJump.jl (#213)
Merged pull requests: - LightGraphs to Graphs (#215) (@jaakkor2)
- Julia
Published by github-actions[bot] over 4 years ago
JumpProcesses - v7.3.1
DiffEqJump v7.3.1
Closed issues: - Tutorial for resetting and reinitializing jumps, docs for parameter-based MassActionJumps (#160) - BenchmarkTools + DiffEqJump Bug (#205)
Merged pull requests: - Rename file (#204) (@Vilin97) - added hopping rates of form D_s (#209) (@Vilin97)
- Julia
Published by github-actions[bot] over 4 years ago
JumpProcesses - v7.3.0
DiffEqJump v7.3.0
Merged pull requests: - Cosmetic improvements (#201) (@Vilin97) - Now the general form of hopping rates with a cartesian grid is faster (#202) (@Vilin97) - Two more forms of hopping rates: Ds * L{i,j} and D{s,i} * L{i,j} (#203) (@Vilin97)
- Julia
Published by github-actions[bot] almost 5 years ago
JumpProcesses - v7.2.0
DiffEqJump v7.2.0
Merged pull requests:
- made tstops type-stable in SSAStepper (#199) (@Vilin97)
- Import initialize! (#200) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] almost 5 years ago
JumpProcesses - v7.1.0
DiffEqJump v7.1.0
Merged pull requests:
- Spatial TODOs (#192) (@Vilin97)
- added reset! for PriorityTable (#195) (@Vilin97)
- [WIP] DirectCRonDirect (#197) (@Vilin97)
- Improved HopRatesGeneral (#198) (@Vilin97)
- Julia
Published by github-actions[bot] almost 5 years ago
JumpProcesses - v7.0.0
DiffEqJump v7.0.0
Merged pull requests: - MassActionJump param update functor (#193) (@isaacsas)
- Julia
Published by github-actions[bot] almost 5 years ago
JumpProcesses - v6.15.1
DiffEqJump v6.15.1
Closed issues: - Allow changing reaction rate in MassActionJumps (#35) - Interface for spatial problems (#130) - Mass-action jumps and event handling (#185)
Merged pull requests: - Next Subvolume Method on Graphs (#183) (@Vilin97) - Allow MassActionJumps to use standard parameter vectors (#190) (@isaacsas) - Pass kwargs when resetting aggregators (#191) (@isaacsas)
- Julia
Published by github-actions[bot] almost 5 years ago
JumpProcesses - v6.15.0
DiffEqJump v6.15.0
Closed issues: - JumpProblem with large number of jumps crashes (#180) - document resetaggregatedjumps (#182)
Merged pull requests: - Fix reversible test (#187) (@isaacsas) - reexport DiffEqBase (#188) (@isaacsas)
- Julia
Published by github-actions[bot] almost 5 years ago
JumpProcesses - v6.14.2
DiffEqJump v6.14.2
Merged pull requests: - add kwarg-based JumpSet constructor (#181) (@isaacsas)
- Julia
Published by github-actions[bot] about 5 years ago
JumpProcesses - v6.14.1
DiffEqJump v6.14.1
Merged pull requests: - update SSAStepper to allow multiple events per step (#178) (@isaacsas)
- Julia
Published by github-actions[bot] about 5 years ago
JumpProcesses - v6.14.0
DiffEqJump v6.14.0
Closed issues: - VariableRateJump documentation fails (#169) - Fix tests to use a stable RNG (#174)
Merged pull requests: - reactivate coveralls (#171) (@isaacsas) - add stable rng and safetestsets (#175) (@isaacsas) - Fix summary IO (#176) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] about 5 years ago
JumpProcesses - v6.13.0
DiffEqJump v6.13.0
Merged pull requests: - add informative error for DiscreteProblem + VariableRateJumps (#167) (@ChrisRackauckas) - fix jump array show (#168) (@ChrisRackauckas) - CompatHelper: bump compat for "ArrayInterface" to "3.0" (#170) (@github-actions[bot])
- Julia
Published by github-actions[bot] over 5 years ago
JumpProcesses - v6.12.2
DiffEqJump v6.12.2
Merged pull requests: - Call initializer and finalizer for user callback in SSAIntegrator (#166) (@manuel-rhdt)
- Julia
Published by github-actions[bot] over 5 years ago
JumpProcesses - v6.12.1
DiffEqJump v6.12.1
Closed issues:
- Broken interpolation when solving with save_idxs (#92)
Merged pull requests: - Fix double init val (#165) (@isaacsas)
- Julia
Published by github-actions[bot] over 5 years ago
JumpProcesses - v6.12.0
DiffEqJump v6.12.0
Closed issues: - Improve typing on tstops kwarg (#1) - JumpArray Typing (#2) - Jump DDEs error (#71) - remake for JumpProblems (#97)
Merged pull requests: - Fix out of bounds error for SSAStepper's DiffEqBase.__init (#163) (@manuel-rhdt) - remake for JumpProblems (#164) (@isaacsas)
- Julia
Published by github-actions[bot] over 5 years ago
JumpProcesses - v6.11.1
DiffEqJump v6.11.1
Merged pull requests: - Fix resetaggregatedjumps! which is currently a no-op on SSAIntegrator (#161) (@ChrisRackauckas) - SSAIntegrator callback test (#162) (@manuel-rhdt)
- Julia
Published by github-actions[bot] over 5 years ago
JumpProcesses - v6.11.0
DiffEqJump v6.11.0
Closed issues:
- Allocations from sizehint! show up in profiles (#152)
- Length of solution does not match expected length with saveat (#157)
Merged pull requests: - MassInstallAction: Install the TagBot workflow on this repository (#153) (@christopher-dG) - add kwarg for SSAStepper sizehint! and reduce default (#154) (@isaacsas) - CompatHelper: bump compat for "StaticArrays" to "1.0" (#155) (@github-actions[bot]) - MassInstallAction: Install the GitHubActionsCI workflow on this repository (#156) (@christopher-dG)
- Julia
Published by github-actions[bot] over 5 years ago
JumpProcesses - v6.10.1
DiffEqJump v6.10.1
Closed issues: - Bump DataStructures to v0.18 after other dependencies update (#145)
Merged pull requests: - Make dependency graphs more flexible (#151) (@isaacsas)
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.10.0
DiffEqJump v6.10.0
Merged pull requests: - CompatHelper: bump compat for "DataStructures" to "0.18" (#143) (@github-actions[bot]) - Revert "CompatHelper: bump compat for "DataStructures" to "0.18"" (#144) (@isaacsas) - Autogenerate dependency graphs for mass action jumps (#147) (@isaacsas) - Crashing extinction test (#149) (@isaacsas) - Enable DataStructures 0.18 (#150) (@devmotion)
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.9.5
DiffEqJump v6.9.5
Closed issues: - Optimization of RejectionDirect (#123) - terminating SSAStepper for exit time problems and such (#137) - A bug? (#138)
Merged pull requests: - Update ssajump.jl (#136) (@Vilin97) - Test of A+B <-> C (#139) (@Vilin97) - Rejection direct optimization (#140) (@Vilin97) - update rxs to spec dep graph to vector of vector (#141) (@isaacsas) - Terminator (#142) (@isaacsas)
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.9.4
DiffEqJump v6.9.4
Closed issues: - Memory allocation in RSSACR (#126) - Keep track of tprev and uprev in SSAStepper (for use in callbacks) (#132)
Merged pull requests: - add option for MassActionJumps to modify inputs (#129) (@isaacsas) - Add tprev field to SSAIntegrator (#133) (@manuel-rhdt) - some cleanup, fixes and extensions (#134) (@isaacsas)
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.9.3
DiffEqJump v6.9.3
Merged pull requests: - Strictly type RSSACRJumpAggregation (#127) (@ChrisRackauckas) - Force type stability in truncations (#128) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.9.2
DiffEqJump v6.9.2
Closed issues: - saveat not working (#124)
Merged pull requests: - Rejection direct (#118) (@Vilin97) - add citations to algorithms (#122) (@ChrisRackauckas) - fix SSAStepper saveat (#125) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.9.1
DiffEqJump v6.9.1
Merged pull requests: - patch callback resetting when not used from SSAStepper (#121) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.9.0
DiffEqJump v6.9.0
Closed issues: - Add discrete callbacks and tstops to SSAStepper (#78) - Aggregated jump callback resetting (#119)
Merged pull requests: - Cleaning SSA code (#115) (@Vilin97) - implement callback resets and DiscreteCallbacks in SSAStepper (#120) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.8.3
DiffEqJump v6.8.3
Merged pull requests: - fix variable rate jump broadcast sizing (#117) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.8.2
DiffEqJump v6.8.2
Merged pull requests: - add useiszero to MassActionJumps for MT to use (#116) (@isaacsas)
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.8.1
DiffEqJump v6.8.1
Closed issues: - VariableRateJumps cause a broadcast error with certain types of solvers (#59)
Merged pull requests: - Refactor some reused code (#114) (@isaacsas)
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.8.0
DiffEqJump v6.8.0
Merged pull requests: - Variable rate jumps with stiff ODEs (#94) (@ChrisRackauckas) - proper recursion in ExtendedJumpArray broadcast (#112) (@ChrisRackauckas) - CompatHelper: add new compat entry for "ArrayInterface" at version "2.8" (#113) (@github-actions[bot])
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.7.7
DiffEqJump v6.7.7
Merged pull requests: - RSSACR (#110) (@Vilin97) - save last saveat point too (#111) (@isaacsas)
- Julia
Published by github-actions[bot] almost 6 years ago
JumpProcesses - v6.7.6
DiffEqJump v6.7.6
Closed issues: - Tau-Leaping and beyond (#8) - Broken tests related to seeding and EnsembleProblems (#108)
Merged pull requests: - Fix tests (#109) (@isaacsas)
- Julia
Published by github-actions[bot] about 6 years ago
JumpProcesses - v6.7.5
DiffEqJump v6.7.5
Merged pull requests: - Alias jumps by default in single threaded use (#104) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] about 6 years ago
JumpProcesses - v6.7.3
DiffEqJump v6.7.3
Closed issues: - some SSAs giving segmentation faults (#101) - Variable rate tests failing (#103)
Merged pull requests: - Replace eps(x) with eps(typeof(x)) (#102) (@isaacsas)
- Julia
Published by github-actions[bot] about 6 years ago
JumpProcesses - v6.6.3
DiffEqJump v6.6.3
Merged pull requests: - Make SimpleTauLeaping safer (#99) (@ChrisRackauckas) - Allow static arrays in mass rate jumps (#100) (@ChrisRackauckas)
- Julia
Published by github-actions[bot] about 6 years ago
JumpProcesses - v6.6.2
DiffEqJump v6.6.2
Merged pull requests: - MT needs iszero instead of == (#98) (@isaacsas)
- Julia
Published by github-actions[bot] about 6 years ago