v0.1.2

SciMLBenchmarks v0.1.2

Diff since v0.1.1

Closed issues:

• PDE notebooks need to be rerun or re-linked (#53)
• No recompilation of Stan models in Bayesian benchmarks (#103)
• Make a Brusselator benchmark (#107)
• Re-run parameter estimation benchmarks (#129)
• Fix automated notebooks (#310)
• PINN solver benchmarks are broken (#353)
• Dynamical ODE benchmark HTML is too big (#455)
• Errors in precompilation (#469)
• Fixing the Stan binary for the Bayesian estimation (#484)
• Ensure Stan defaults used in benchmarks (#489)
• Stan and Turing.jl don't use the same HMC parameters (#492)
• Stan and Turing.jl don't sample from the same posteriors for the Bayesian parameter estimation benchmarks (#493)
• Newly added Gupta (bio) benchmarks links not working in the Readme (#498)

Merged pull requests:

• update parameter_estimation (#362) (@ChrisRackauckas)
• Jump benchmarks (#408) (@isaacsas)
• Add MethodOfLines Benchmark (#425) (@xtalax)
• bump nbody (#450) (@ChrisRackauckas)
• bump adaptive sde (#451) (@ChrisRackauckas)
• Use default names for algorithms in DDE benchmarks (#468) (@devmotion)
• bump DynamicalODE (#470) (@ChrisRackauckas)
• bump non-stiff SDE (#471) (@ChrisRackauckas)
• change sigmoid to tanh in PINNs' benchmarks (#473) (@YichengDWu)
• Bump Lotka-Volterra SDE (#474) (@ChrisRackauckas)
• CompatHelper: add new compat entry for StanSample at version 6 for package BayesianInference, (keep existing compat) (#476) (@github-actions[bot])
• CompatHelper: add new compat entry for DiffEqCallbacks at version 2 for package BayesianInference, (keep existing compat) (#477) (@github-actions[bot])
• CompatHelper: add new compat entry for Turing at version 0.21 for package BayesianInference, (keep existing compat) (#478) (@github-actions[bot])
• Attempt another Bayesian inference build (#485) (@ChrisRackauckas)
• Fix PDE definition for Nernst-Planck (#486) (@ChrisRackauckas)
• Add Gupta model benchmarks (#487) (@TorkelE)
• badges (#488) (@ArnoStrouwen)
• MassInstallAction: Install the Invalidations workflow on this repository (#490) (@devmotion)
• Add extrapolation benchmarks to new bio models (#491) (@utkarsh530)
• Try using a static direct Turing.jl version (#495) (@ChrisRackauckas)
• change adapt_delta to fit with Turing.jl (#497) (@EvoArt)
• bump a few packages (#499) (@ChrisRackauckas)
• Fix the Stan delta choice to match Turing (#500) (@ChrisRackauckas)
• CompatHelper: add new compat entry for StaticArrays at version 1 for package BayesianInference, (keep existing compat) (#501) (@github-actions[bot])
• Update gupta benchmarks (#502) (@TorkelE)
• update to v1.8 and update Bio to have nonstiff stuff (#504) (@ChrisRackauckas)
• Update stiff ODE benchmarks for Rodas5P and specializations (#505) (@ChrisRackauckas)
• update non-stiff ODEs to have static arrays and full specialization (#506) (@ChrisRackauckas)
• CompatHelper: add new compat entry for StaticArrays at version 1 for package NonStiffODE, (keep existing compat) (#507) (@github-actions[bot])
• Fix up Brusselator benchmark (#508) (@ChrisRackauckas)
• Create static versions of the problems for small stiff (#509) (@ChrisRackauckas)
• simplify static stiff (#510) (@ChrisRackauckas)
• Expand bruss benchmarks (#511) (@ChrisRackauckas)
• CompatHelper: add new compat entry for AlgebraicMultigrid at version 0.5 for package StiffODE, (keep existing compat) (#512) (@github-actions[bot])
• CompatHelper: add new compat entry for Symbolics at version 4 for package StiffODE, (keep existing compat) (#513) (@github-actions[bot])
• CompatHelper: add new compat entry for IncompleteLU at version 0.2 for package StiffODE, (keep existing compat) (#514) (@github-actions[bot])
• CompatHelper: add new compat entry for ModelingToolkit at version 8 for package StiffODE, (keep existing compat) (#515) (@github-actions[bot])
• Update problem library for StiffSDE (#516) (@ChrisRackauckas)
• update stiff dde (#517) (@ChrisRackauckas)
• update nonstiff sde (#518) (@ChrisRackauckas)
• update nonstiff dde (#519) (@ChrisRackauckas)
• update to jump problem library (#520) (@ChrisRackauckas)
• bump pde (#521) (@ChrisRackauckas)
• add fast bruss implemenation (#522) (@ChrisRackauckas)
• bump multisite and multistate (#523) (@ChrisRackauckas)
• Bump fceri (#524) (@ChrisRackauckas)
• CompatHelper: add new compat entry for LinearSolve at version 1 for package Bio, (keep existing compat) (#525) (@github-actions[bot])
• Adjust some of the new bio benchmarks to stop around steady state time (#526) (@ChrisRackauckas)
• Update Bio WP diagrams (#527) (@TorkelE)
• .buildkite: run_benchmark: use v1 of coppermind plugin (#529) (@thazhemadam)
• Try new Bio build (#533) (@ChrisRackauckas)
• Fix typo in BCR (#534) (@ChrisRackauckas)
• full specialize in Bidkhori2012 (#535) (@ChrisRackauckas)
• remove extrapolation from sparse (#536) (@ChrisRackauckas)
• Fix preconditioner definitions (#537) (@ChrisRackauckas)
• Bump DynamicalODE (#539) (@ChrisRackauckas)
• Bump Bayes (#540) (@ChrisRackauckas)
• MOL move to analytic errors for burgers (#541) (@xtalax)
• CompatHelper: add new compat entry for MethodOfLines at version 0.7 for package MOLPDE, (keep existing compat) (#542) (@github-actions[bot])
• CompatHelper: add new compat entry for ModelingToolkit at version 8 for package MOLPDE, (keep existing compat) (#543) (@github-actions[bot])
• CompatHelper: add new compat entry for DomainSets at version 0.6 for package MOLPDE, (keep existing compat) (#544) (@github-actions[bot])
• CompatHelper: add new compat entry for Sundials at version 4 for package MethodOfLinesPDE, (keep existing compat) (#545) (@github-actions[bot])
• CompatHelper: add new compat entry for OrdinaryDiffEq at version 6 for package MethodOfLinesPDE, (keep existing compat) (#546) (@github-actions[bot])
• CompatHelper: add new compat entry for LinearSolve at version 1 for package MethodOfLinesPDE, (keep existing compat) (#547) (@github-actions[bot])
• CompatHelper: add new compat entry for MethodOfLines at version 0.7 for package StiffODE, (keep existing compat) (#553) (@github-actions[bot])
• CompatHelper: add new compat entry for DomainSets at version 0.6 for package StiffODE, (keep existing compat) (#554) (@github-actions[bot])
• Bump stiff Bio models (#558) (@ChrisRackauckas)
• Update buildkite tags and re-sign treehashes (#559) (@thazhemadam)
• Adds Coevolve aggregator to the Jumps benchmark suite (#565) (@gzagatti)
• ci: fix encrypted repo_key and sign treehashes (#568) (@thazhemadam)
• Disable test checking for .html (#569) (@ChrisRackauckas)
• Fullspecialize on the Bio benchmarks (#572) (@ChrisRackauckas)
• update burgers mol package versions (should be working now) (#574) (@xtalax)
• add BCR benchmark summary figure (#577) (@TorkelE)
• improve Bio benchmarks (#581) (@TorkelE)
• Automatic benchmarking of various MOL discretizations across all of PDESystemLibrary (#583) (@xtalax)
• Adds Multivariate Hawkes benchmark. (#584) (@gzagatti)
• MultivariateHawkes: Do not run Python benchmark in the cloud (#585) (@gzagatti)
• enable dependabot for GitHub actions (#591) (@ranocha)
• Bump actions/checkout from 2 to 3 (#592) (@dependabot[bot])
• CompatHelper: bump compat for LinearSolve to 2 for package Bio, (keep existing compat) (#600) (@github-actions[bot])
• CompatHelper: bump compat for LinearSolve to 2 for package MethodOfLinesPDE, (keep existing compat) (#601) (@github-actions[bot])
• CompatHelper: bump compat for LinearSolve to 2 for package StiffODE, (keep existing compat) (#602) (@github-actions[bot])