Release v0.1.0 · SciML/SciMLBenchmarks.jl

SciMLBenchmarks v0.1.0

Closed issues:

Pictures (#1)
Benchmarks for Dynamical ODEs (#2)
Benchmarks for DDEs (#3)
Benchmarks for stiff SDEs (#5)
Issue with DiffEqBase in LorenzParameter Estimation (#13)
Benchmarks for SSA/jump systems (#25)
Convert benchmarks to use Weave.jl (#29)
Benchmarks for ExpRK methods (#30)
Wheldon, Kirk, and Finlay (#33)
Regressions from v1.0 upgrade (#37)
Weak SDE estimation is currently broken (#40)
DiffEqBayesLorenz and DiffEqBayesLotkaVolterra need to be re-ran (#41)
Filament needs to be fixed (#42)
Jump equations need to run (#43)
Oval2 Timings need an update (#46)
BCR import location (#55)
Pleiades (#95)
Precompilation broken on julia 1.5 beta1 (#105)
Build log (#116)
Re-run stiff ODE benchmarks (#128)
Re-run DynamicalODE benchmarks (#131)
update BCR benchmark for Catalyst (#169)

Merged pull requests:

Add benchmarks of constant delay DDEs (#4) (@devmotion)
Add DynamicalODE (#7) (@SebastianM-C)
Update DDE benchmarks (#8) (@devmotion)
Fix DDE interpolation and add Rodas5 to QS (#9) (@devmotion)
Update DynamicalODE (#10) (@SebastianM-C)
Added notebooks for DiffEqBayes benchmarking (#11) (@Vaibhavdixit02)
Modifications to summary and update to new syntax (#12) (@Vaibhavdixit02)
DiffEqBayes Benchmarks for LV and Lorenz equation (#16) (@Vaibhavdixit02)
Use plot_chain for turing_inference (#18) (@Vaibhavdixit02)
Notebook for Lotka Volterra parameter estimation with optimisation methods (#19) (@Vaibhavdixit02)
Update the Readme summary and typo in Lorenz notebook (#20) (@Vaibhavdixit02)
FitzHugh-Nagumo Parameter estimation using optimization methods. (#21) (@Vaibhavdixit02)
Updates to Readme and some changes in LV notebook (#22) (@Vaibhavdixit02)
Added QuadDIRECT to the optimization methods benchmarks for parameter estimation (#23) (@Vaibhavdixit02)
jump benchmarks (#26) (@isaacsas)
RFC: Restructure benchmarks to use Weave instead of notebooks (#32) (@ChrisRackauckas)
Update parameter estimation benchmarks (#36) (@Vaibhavdixit02)
Add Project.toml (#38) (@asinghvi17)
Benchmark jmd files for ROCK2 and ROCK4 (#39) (@deeepeshthakur)
Updated the filament benchmark (#44) (@dextorious)
added four differential equations (#45) (@HH3117)
created the PDE folder (#48) (@HH3117)
add extrapolation methods (#49) (@saurabhkgp21)
Update DiffEqBayesLotkaVolterra.jl for breaking uncertainity/uncertainty typo (#50) (@jamesjscully)
BCR chemical reaction system benchmarks (#52) (@ChrisRackauckas)
Update jump benchmarks (#54) (@isaacsas)
CompatHelper: add new compat entry for "DataFrames" at version "0.19" (#57) (@github-actions[bot])
CompatHelper: add new compat entry for "RecursiveFactorization" at version "0.1" (#58) (@github-actions[bot])
CompatHelper: add new compat entry for "ReactionNetworkImporters" at version "0.1" (#59) (@github-actions[bot])
CompatHelper: add new compat entry for "IJulia" at version "1.20" (#60) (@github-actions[bot])
CompatHelper: add new compat entry for "BlackBoxOptim" at version "0.5" (#61) (@github-actions[bot])
CompatHelper: add new compat entry for "DiffEqDevTools" at version "2.15" (#62) (@github-actions[bot])
CompatHelper: add new compat entry for "ParameterizedFunctions" at version "4.2" (#63) (@github-actions[bot])
CompatHelper: add new compat entry for "DiffEqJump" at version "6.2" (#64) (@github-actions[bot])
CompatHelper: add new compat entry for "Weave" at version "0.9" (#65) (@github-actions[bot])
CompatHelper: add new compat entry for "ApproxFun" at version "0.11" (#66) (@github-actions[bot])
CompatHelper: add new compat entry for "ODEInterfaceDiffEq" at version "3.4" (#67) (@github-actions[bot])
CompatHelper: add new compat entry for "OrdinaryDiffEq" at version "5.23" (#68) (@github-actions[bot])
CompatHelper: add new compat entry for "ODEInterface" at version "0.4" (#69) (@github-actions[bot])
CompatHelper: add new compat entry for "ODE" at version "2.5" (#70) (@github-actions[bot])
CompatHelper: add new compat entry for "DiffEqProblemLibrary" at version "4.5" (#71) (@github-actions[bot])
CompatHelper: add new compat entry for "DiffEqUncertainty" at version "1.3" (#72) (@github-actions[bot])
CompatHelper: add new compat entry for "LSODA" at version "0.6" (#73) (@github-actions[bot])
CompatHelper: add new compat entry for "DiffEqBiological" at version "4.0" (#74) (@github-actions[bot])
CompatHelper: add new compat entry for "SteadyStateDiffEq" at version "1.5" (#75) (@github-actions[bot])
CompatHelper: add new compat entry for "Sundials" at version "3.8" (#76) (@github-actions[bot])
CompatHelper: add new compat entry for "NLopt" at version "0.5" (#77) (@github-actions[bot])
CompatHelper: add new compat entry for "DiffEqParamEstim" at version "1.8" (#78) (@github-actions[bot])
CompatHelper: add new compat entry for "Plots" at version "0.27" (#79) (@github-actions[bot])
CompatHelper: add new compat entry for "NLopt" at version "0.5" (#80) (@github-actions[bot])
Save all figures as SVG (#81) (@asinghvi17)
Default html to svg (#82) (@ChrisRackauckas)
CompatHelper: bump compat for "Plots" to "0.28" (#83) (@github-actions[bot])
CompatHelper: bump compat for "DataFrames" to "0.20" (#84) (@github-actions[bot])
Update BCR benchmark to use correct path (#85) (@isaacsas)
CompatHelper: add new compat entry for "DiffEqBase" at version "6.7" (#86) (@github-actions[bot])
CompatHelper: add new compat entry for "DifferentialEquations" at version "6.9" (#87) (@github-actions[bot])
CompatHelper: add new compat entry for "ParallelDataTransfer" at version "0.5" (#88) (@github-actions[bot])
Myb/noauto (#89) (@ChrisRackauckas)
CompatHelper: bump compat for "Plots" to "0.29" (#92) (@github-actions[bot])
Install TagBot as a GitHub Action (#93) (@JuliaTagBot)
CompatHelper: bump compat for "ParameterizedFunctions" to "5.0" (#94) (@github-actions[bot])
CompatHelper: bump compat for "Plots" to "1.0" (#96) (@github-actions[bot])
CompatHelper: bump compat for "Sundials" to "4.0" (#97) (@github-actions[bot])
Update DiffEqBayes benchmarks (#98) (@Vaibhavdixit02)
CompatHelper: add new compat entry for "DiffEqBayes" at version "2.9" (#99) (@github-actions[bot])
CompatHelper: bump compat for "DataFrames" to "0.21" (#100) (@github-actions[bot])
Use truncated instead of Truncated (#101) (@devmotion)
CompatHelper: bump compat for "NLopt" to "0.6" (#102) (@github-actions[bot])
Add NBodySimulator benchmarks (#106) (@SebastianM-C)
Rebuild benchmarks (#108) (@christopher-dG)
Move to separate projects (#109) (@christopher-dG)
CompatHelper: bump compat for "DiffEqNoiseProcess" to "5.0" for package AdaptiveSDE (#110) (@github-actions[bot])
CompatHelper: bump compat for "DiffEqMonteCarlo" to "1.0" for package AdaptiveSDE (#111) (@github-actions[bot])
CompatHelper: bump compat for "DiffEqNoiseProcess" to "5.0" for package StiffSDE (#112) (@github-actions[bot])
Rebuild StiffSDE/QuadraticStiffness.jmd (#114) (@github-actions[bot])
Activate project env (#115) (@christopher-dG)
Rebuild NonStiffODE/FitzhughNagumo_wpd.jmd, NonStiffODE/LotkaVolterra_wpd.jmd, NonStiffODE/Pleiades_wpd.jmd, NonStiffODE/RigidBody_wpd.jmd, NonStiffODE/ThreeBody_wpd.jmd, NonStiffODE/linear_wpd.jmd (#117) (@github-actions[bot])
Rebuild Jumps/Diffusion_CTRW.jmd, Jumps/Mendes_multistate_example.jmd, Jumps/NegFeedback_GeneExpr.jmd, Jumps/NegFeedback_GeneExpr_Marchetti.jmd (#119) (@github-actions[bot])
Rebuild StiffSDE/Oval2LongRun.jmd, StiffSDE/Oval2LongTimes.jmd, StiffSDE/Oval2Timings.jmd, StiffSDE/QuadraticStiffness.jmd, StiffSDE/StochasticHeat.jmd (#123) (@github-actions[bot])
Rebuild NonStiffDDE/Mackey_Glass_wpd.jmd, NonStiffDDE/Wheldon_Kirk_Finlay_wpd.jmd (#125) (@github-actions[bot])
Rebuild StiffDDE/QuorumSensing.jmd (#127) (@github-actions[bot])
Rebuild StiffSDE/StochasticHeat.jmd (#133) (@github-actions[bot])
Rebuild Jumps/Mendes_multistate_example.jmd (#134) (@github-actions[bot])
Rebuild NonStiffDDE/Mackey_Glass_wpd.jmd (#135) (@github-actions[bot])
Avoid module usage (#136) (@SebastianM-C)
Add missing package (#139) (@SebastianM-C)
CompatHelper: add new compat entry for "StatsPlots" at version "0.14" for package NBodySimulator (#140) (@github-actions[bot])
CompatHelper: add new compat entry for "StaticArrays" at version "0.12" for package NBodySimulator (#141) (@github-actions[bot])
CompatHelper: add new compat entry for "Plots" at version "1.5" for package NBodySimulator (#142) (@github-actions[bot])
CompatHelper: add new compat entry for "OrdinaryDiffEq" at version "5.41" for package NBodySimulator (#143) (@github-actions[bot])
CompatHelper: add new compat entry for "ProgressLogging" at version "0.1" for package NBodySimulator (#144) (@github-actions[bot])
CompatHelper: add new compat entry for "DataFrames" at version "0.21" for package NBodySimulator (#145) (@github-actions[bot])
CompatHelper: add new compat entry for "NBodySimulator" at version "1.3" for package NBodySimulator (#146) (@github-actions[bot])
CompatHelper: add new compat entry for "BenchmarkTools" at version "0.5" for package NBodySimulator (#147) (@github-actions[bot])
Rebuild NonStiffODE/ThreeBody_wpd.jmd (#149) (@github-actions[bot])
Finish renaming DiffEqBenchmarks -> SciMLBenchmarks (#150) (@christopher-dG)
Rebuild MOLPDE/ks_spectral_wpd.jmd (#153) (@github-actions[bot])
Rebuild MOLPDE/burgers_spectral_wpd.jmd (#154) (@github-actions[bot])
Rebuild StiffDDE/QuorumSensing.jmd (#156) (@github-actions[bot])
Special case for TaylorIntegration (#157) (@SebastianM-C)
Rebuild NonStiffODE/LotkaVolterra_wpd.jmd (#159) (@github-actions[bot])
CompatHelper: bump compat for "ReactionNetworkImporters" to "0.2" for package StiffODE (#161) (@github-actions[bot])
CompatHelper: bump compat for "ApproxFun" to "0.12" for package MOLPDE (#162) (@github-actions[bot])
CompatHelper: bump compat for "Distributions" to "0.24" for package ParameterEstimation (#165) (@github-actions[bot])
MassInstallAction: Install the TagBot workflow on this repository (#166) (@christopher-dG)
CompatHelper: bump compat for "DataFrames" to "0.22" for package Jumps (#167) (@github-actions[bot])
CompatHelper: bump compat for "DataFrames" to "0.22" for package NBodySimulator (#168) (@github-actions[bot])
CompatHelper: bump compat for "StaticArrays" to "1.0" for package DynamicalODE (#170) (@github-actions[bot])
CompatHelper: bump compat for "StaticArrays" to "1.0" for package NBodySimulator (#171) (@github-actions[bot])
CompatHelper: bump compat for "ReactionNetworkImporters" to "0.3" for package StiffODE (#172) (@github-actions[bot])
CompatHelper: bump compat for "GeometricIntegratorsDiffEq" to "0.2" for package StiffODE (#174) (@github-actions[bot])
Update BCR benchmark to Catalyst and MT (#175) (@isaacsas)
Remove ReactionNetworkImporters dep for StiffOdes (#177) (@isaacsas)
CompatHelper: add new compat entry for "OrdinaryDiffEq" at version "5.47" for package Bio (#178) (@github-actions[bot])
CompatHelper: bump compat for "ReactionNetworkImporters" to "0.5" for package Bio (#180) (@github-actions[bot])
CompatHelper: bump compat for "ODEInterface" to "0.5" for package Bio (#182) (@github-actions[bot])
CompatHelper: bump compat for "ODEInterface" to "0.5" for package MultiLanguage (#183) (@github-actions[bot])
CompatHelper: bump compat for "ODEInterface" to "0.5" for package NonStiffODE (#184) (@github-actions[bot])
CompatHelper: bump compat for "ReactionNetworkImporters" to "0.6" for package Bio (#186) (@github-actions[bot])
CompatHelper: bump compat for "MATLABDiffEq" to "1.0" for package MultiLanguage (#187) (@github-actions[bot])
CompatHelper: bump compat for "ReactionNetworkImporters" to "0.7" for package Bio (#188) (@github-actions[bot])
CompatHelper: bump compat for "BenchmarkTools" to "0.6" for package NBodySimulator (#189) (@github-actions[bot])
CompatHelper: bump compat for "BenchmarkTools" to "0.6" for package ParameterEstimation (#190) (@github-actions[bot])
CompatHelper: bump compat for "BenchmarkTools" to "0.7" for package NBodySimulator (#191) (@github-actions[bot])
CompatHelper: bump compat for "BenchmarkTools" to "0.7" for package ParameterEstimation (#192) (@github-actions[bot])
[WIP] This adds the buildkite setup (#193) (@ven-k)
CompatHelper: bump compat for "LSODA" to "0.7" for package Bio (#194) (@github-actions[bot])
CompatHelper: bump compat for "LSODA" to "0.7" for package MOLPDE (#195) (@github-actions[bot])
CompatHelper: bump compat for "LSODA" to "0.7" for package NonStiffODE (#196) (@github-actions[bot])
CompatHelper: bump compat for "LSODA" to "0.7" for package StiffODE (#197) (@github-actions[bot])
This adds files to weekly update all the directories. (#199) (@ven-k)
CompatHelper: bump compat for "DataFrames" to "1.0" for package Jumps (#200) (@github-actions[bot])
CompatHelper: bump compat for "DataFrames" to "1.0" for package NBodySimulator (#201) (@github-actions[bot])
Fix some grammar in linear wpd (#202) (@ChrisRackauckas)
CompatHelper: add new compat entry for "Git" at version "1.2" (#204) (@github-actions[bot])
use the exclusive tag with the buildkite pipeline (#205) (@ChrisRackauckas)
Registry is General (#206) (@ven-k)
Set timeout to 4 hrs and update only changed artifacts (#207) (@ven-k)
Watch Project.toml and upload the specific artifacts (#208) (@ven-k)
Setup project/manifest for nonstiff ODE (#209) (@ChrisRackauckas)
Add "watch toml" in pipeline.yml (#210) (@ven-k)
update nonstiff ode manifest (#212) (@ChrisRackauckas)
[WIP] A separate watcher for each file (#213) (@ven-k)
Update rebuild_models.jl (#214) (@staticfloat)
update for Weave's silent mega breaking change (#215) (@ChrisRackauckas)
Update linear_wpd.jmd (#216) (@ChrisRackauckas)
CompatHelper: bump compat for "Distributions" to "0.25" for package ParameterEstimation (#218) (@github-actions[bot])
Split SciMLBenchmarks into two repositories (#219) (@staticfloat)
Fix activation (#220) (@staticfloat)
Update Sundials version for NonStiffODE (#221) (@ChrisRackauckas)
Manual S3 uploading (#222) (@staticfloat)
Updated AdaptiveSDE for benchmarks (#223) (@github-actions[bot])
Remove extra /html or /pdf or etc. (#224) (@ChrisRackauckas)
CompatHelper: add new compat entry for "Plots" at version "1.13" for package Testing (#225) (@github-actions[bot])
bump nonstiff ODE packages for FastBroadcast.jl (#226) (@ChrisRackauckas)
Setup and run stiff ODE benchmarks (#227) (@ChrisRackauckas)
update Bio benchmarks (#228) (@ChrisRackauckas)
remove threads setting in StiffODE (#231) (@ChrisRackauckas)
update NBodySimulator benchmarks (#232) (@ChrisRackauckas)
update NonStiffDDE benchmarks (#233) (@ChrisRackauckas)
update NonStiffSDE benchmarks (#234) (@ChrisRackauckas)
update StiffDDE benchmarks (#235) (@ChrisRackauckas)
update StiffSDE benchmarks (#236) (@ChrisRackauckas)
update ParameterEstimation benchmarks (#237) (@ChrisRackauckas)
CompatHelper: bump compat for "DynamicHMC" to "3.1" for package ParameterEstimation (#238) (@github-actions[bot])
re-run stiff ODE on AMDCI (#239) (@ChrisRackauckas)
rerun NonStiffODE on AMDCI (#240) (@ChrisRackauckas)
CompatHelper: add new compat entry for "ModelingToolkit" at version "5.17" for package Bio (#241) (@github-actions[bot])

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v0.1.0

SciMLBenchmarks v0.1.0