CalibrateEmulateSample.jl - v0.7.0

CalibrateEmulateSample v0.7.0

Diff since v0.6.1

Breaking Changes

• Added compatability to EKP >2
• New Autodiff compatable emulators and gradient-based MCMC (Barker Sampling) NB AbstractGP.jl has no training API, currently use other GP packages to find appropriate hyperparameters and provide them in :(
• Bugfix of shrinkage estimator (where estimator was overly regularizing matrices in RandomFeature training)
• Bugfix of multithreading issue using threadid()

Merged pull requests: - Add Autodiff compatable emulator and Barker gradient-based sampler (#339) (@odunbar) - WIP: Enable (naive) minibatching within MCMC. (#349) (@odunbar) - Update README.md (#350) (@odunbar) - CompatHelper: bump compat for ForwardDiff to 1, (keep existing compat) (#353) (@github-actions[bot]) - Fixing multithreading with chunks (#355) (@odunbar) - Bugfix shrinkage estimator (#357) (@odunbar) - Update Project.toml v0.7.0 (#358) (@odunbar)

Closed issues: - Implement the Barker Gradient-based sampler in src/ using ForwardDiff (#341) - Implement the useful diagnostics of the chains in src/ which are able to differentiate different methodologies performance (e.g. ESS, ESJD). (#342) - Add modularity in the choice of autodiff package for the samplers (#343) - Add an end-to-end unit test with CES and autodiff emulators (#344) - Implement the AbstractGP + forward-diff emulator object from provided GP hyperparameters (#345) - Likely erroneous use of Threads.nthreads and Threads.threadid (#351) - Extra minus in shrinkage cov (#356)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] 10 months ago

CalibrateEmulateSample.jl - v0.6.1

CalibrateEmulateSample v0.6.1

Diff since v0.6.0

Merged pull requests: - Fix windows test failures (#262) (@odunbar) - Create dependabot.yml and codecov.yml (#332) (@odunbar) - Combine dependabot PRs (#338) (@odunbar) - Compat with EKP 2.1.0 (#347) (@odunbar) - Update Project.toml v0.6.1 (#348) (@odunbar)

Closed issues: - Add deps update manager for github actions (#331)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] about 1 year ago

CalibrateEmulateSample.jl - v0.6.0

CalibrateEmulateSample v0.6.0

Diff since v0.5.3

Merged pull requests: - Function Parameters within CES & Darcy example (#316) (@odunbar) - CompatHelper: bump compat for EnsembleKalmanProcesses to 2, (keep existing compat) (#318) (@github-actions[bot]) - Fix python dependency issues with Python 3.12 and add to docs (#319) (@odunbar) - [WIP] Experiment updates and more flexible cross-validation for Paper revisions (#321) (@odunbar) - Update Project.toml to v0.6.0 (#326) (@odunbar) - Orad/compat update (#328) (@odunbar) - fix python versions for default conda installation (#329) (@odunbar)

Closed issues: - Installation instructions - add common error (#317) - Add any remaining functionality to handle function parameter types (#323) - Add an example inverse problem (Darcy?) (#324)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 1 year ago

CalibrateEmulateSample.jl - v0.5.3

CalibrateEmulateSample v0.5.3

Diff since v0.5.2

Merged pull requests: - Convergence plots for Emulator examples & a bugfix (#279) (@odunbar) - New GSA example for emulator testing. Sobol G function (#292) (@odunbar) - Repair compatability with EnsembleKalmanProcesses v1.1.7 (#312) (@odunbar) - Update version v0.5.3 (#315) (@odunbar)

Closed issues: - repeated index i in nested loop (#278) - Problems installing the package (#311)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 1 year ago

CalibrateEmulateSample.jl - v0.5.2

CalibrateEmulateSample v0.5.2

Diff since v0.5.1

Merged pull requests: - JOSS address editor comments (#305) (@odunbar) - Fixing DOI issue (#307) (@arfon) - Update README.md with JOSS badges (#308) (@odunbar) - v0.5.2 update Project.toml post JOSS (#309) (@odunbar)

Closed issues: - Role of random phase in sinusoid example unclear (#285)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] almost 2 years ago

CalibrateEmulateSample.jl - v0.5.1

CalibrateEmulateSample v0.5.1

Diff since v0.5.0

Merged pull requests: - Bugfix parameter name bug for MV distributions, cap mac-os tests to julia v1.9.0 (#277) (@odunbar) - Orad/fix emulator bug repeat call (#281) (@odunbar) - de souza to nogueira de souza (#286) (@sandreza) - Sinusoidal example (#287) (@lm2612) - added link to examples/ dir to docs (#290) (@odunbar) - update buildkite to new-central (#291) (@odunbar) - added note to sinusoid docs about phase shift (#295) (@odunbar) - JOSS docs updates (#296) (@odunbar) - JOSS paper corrections (#297) (@odunbar) - JOSS review: sinusoid examples and plots in paper (#298) (@lm2612) - JOSS: Emulator docstring and warning (#299) (@odunbar) - JOSS Emulator docstring (#300) (@odunbar) - JOSS add author (#301) (@odunbar) - JOSS fix typos (#302) (@odunbar) - update version v0.5.1 for JOSS release (#304) (@odunbar)

Closed issues: - O3.1.2 JOSS paper for CalibrateEmulateSample (#240) - Duplicate emulators when repeating emulator = Emulator(); optimize_hyperparameters!(emulator) (#280) - Sinusoid example not fully reproducible (#283) - Author list on JOSS paper (#284) - CalibrateEmulateSample.jl is using an outdated buildkite pipeline (#289) - Minor suggestions of improvement to JOSS paper (#293) - Suggestions for improving the docs (#294)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] almost 2 years ago

CalibrateEmulateSample.jl - v0.5.0

CalibrateEmulateSample v0.5.0

Diff since v0.4.0

Merged pull requests: - ProgressBars bugfix removal (#237) (@odunbar) - add ishigami example & compatible with new EKP (#238) (@odunbar) - Add some repeats, and plotting of marginal CDFs for validation (#239) (@odunbar) - CompatHelper: bump compat for AbstractMCMC to 5, (keep existing compat) (#241) (@github-actions[bot]) - Joss paper (#242) (@odunbar) - CompatHelper: add new compat entry for Statistics at version 1, (keep existing compat) (#243) (@github-actions[bot]) - CompatHelper: bump compat for AdvancedMH to 0.8, (keep existing compat) (#244) (@github-actions[bot]) - Update [compat] with new requirements (#246) (@odunbar) - Sinusoidal example (#248) (@lm2612) - Update to new EKP (remove local posdef_correct) & typo fix (#249) (@odunbar) - CES Lorenz example for JOSS paper (#250) (@mhowlan3) - update workflows to rm bors (#252) (@odunbar) - Resuscitate the Cloudy example and add Documentation (#253) (@bielim) - Consolidate emulator comparison examples, and add docs pages for them. (#257) (@odunbar) - fix badges on readme (#263) (@odunbar) - Add vector RF case to Cloudy example (#265) (@bielim) - Various docs tasks for consistency (#271) (@odunbar) - Add figures to EDMF example (#272) (@odunbar) - add buildkite pipeline (#275) (@odunbar) - update to v0.5.0, add pdf of paper for JOSS (#276) (@odunbar)

Closed issues: - Add the necessary compile tools / markdowns for the JOSS paper in a new branch (#245) - Add a simple transparent example to aid the user understanding (#247) - Write consistent docs pages for Emulator comparison examples (#254) - Write consistent docs page for Lorenz (#255) - Write consistent docs page for Cloudy (#256) - Remove strict = true to build docs (#259) - finish JOSS paper Markdown file (#261) - Reproducible Emulator training (#266) - Make MCMC docs more consistent with GP and EKP docs (#270) - add figures to EDMF examples, adjust for JLD2 updates (#273) - Write "Recommended configuration for GP/RF" at top of docs pages and improve defaults (#274)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] about 2 years ago

CalibrateEmulateSample.jl - v0.4.0

CalibrateEmulateSample v0.4.0

Diff since v0.3.0

Merged pull requests: - Refactor and extend RF interface for more flexible kernels. (#220) (@odunbar) - Low rank normalization (#227) (@odunbar) - RF emulator documentation (#232) (@odunbar) - added RF to buildkite (#235) (@odunbar)

Closed issues: - Input normalization fails when ensemble size in EKI less than number of parameters (#225) - interface for defining user-priors (#228) - SVD truncation for vector RF (#229) - Sample stage for GCM application (#230) - ignore.. (#231) - Documentation (beyond API) and uncomment docs API (#233) - add new examples/tests into buildkite pipeline (#234)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 2 years ago

CalibrateEmulateSample.jl - v0.3.0

CalibrateEmulateSample v0.3.0

Diff since v0.2.0

Closed issues: - Inconsistent precompiliation errors from Cloudy example's dependencies (#131) - New Documentation pages request (#136) - Rename master to main (#146) - Random Feature development (#164) - LineSearches not in GaussianProcesses dependencies (#195) - Import statements to remove warnings (#201) - bug in examples from GP.mcmc (#204) - update license (#210) - Type piracy breaks Turing/AbstractMCMC sampling in external code (#221)

Merged pull requests: - CES applied to EDMF for parametric uncertainty (#170) (@odunbar) - Add DOI badge (#193) (@odunbar) - Random Feature-based CES (#194) (@odunbar) - Delete old Manifest affecting local docs build (#196) (@odunbar) - CompatHelper: bump compat for EnsembleKalmanProcesses to 0.14, (keep existing compat) (#197) (@github-actions[bot]) - CompatHelper: bump compat for AdvancedMH to 0.7, (keep existing compat) (#198) (@github-actions[bot]) - Modify how to load prior distributions from edmf data (#199) (@szy21) - remove redefinition warnings (#202) (@odunbar) - Orad/remove gp (#205) (@odunbar) - fix testing bugs (#208) (@odunbar) - condensed compat changes (#209) (@odunbar) - Update LICENSE (#211) (@odunbar) - Rename LICENSE to NOTICE (#212) (@odunbar) - Create LICENSE (#213) (@odunbar) - CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat) (#214) (@github-actions[bot]) - Compatibility with new EKP, version and updated Lorenz example (#218) (@odunbar) - Extend AdvancedMH.transition to CES types only (#223) (@odunbar)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 2 years ago

CalibrateEmulateSample.jl - v0.2.0

CalibrateEmulateSample v0.2.0

Diff since v0.1.0

Closed issues: - Log posterior calculation (#105) - Any tagged releases like v0.1.0 planned? (#110) - ERROR: LoadError: AssertionError: isfinite(phic) && isfinite(dphic) (#168) - Seperable matrix-valued random features (#173) - Some packages in Manifest are outdated (#174) - SciKitLearn python backend update breaks GH testing (#176) - typos in installation instructions (#180) - stepsize bug in MCMC (#182) - Performance Hit for MCMC on updating Manifest? (#184)

Merged pull requests: - Docsgp (#145) (@lm2612) - CompatHelper: bump compat for DocStringExtensions to 0.9, (keep existing compat) (#165) (@github-actions[bot]) - CompatHelper: bump compat for EnsembleKalmanProcesses to 0.9, (keep existing compat) (#167) (@github-actions[bot]) - Add args/kwargs to optimize_hyperparameters!() (#172) (@odunbar) - Resolve scikit-learn conflict (#177) (@tsj5) - CompatHelper: bump compat for EnsembleKalmanProcesses to 0.11, (keep existing compat) (#179) (@github-actions[bot]) - Installation docs typos (#181) (@odunbar) - Update TagBot.yml (#186) (@odunbar) - remove manifest, fix mcmc performance (#188) (@odunbar) - Update to v0.2.0 (#189) (@odunbar) - Update README.md (#190) (@odunbar) - Update README.md (#191) (@odunbar)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

CalibrateEmulateSample.jl - v0.1.0

CalibrateEmulateSample v0.1.0

Closed issues: - Tolerance for test (#1) - Add Windows 32-bit build back in (#25) - master is currently broken (#29) - Remove Pkg.build() in GModel (#36) - Improve the build (#39) - Timestep for EKI (#56) - SVD decomposition (#57) - Noise learning bug in GP (#58) - A series of Examples (#59) - findmcmcstep! modifies MCMCObj (#61) - Insanely long precompile times. (#65) - EKI.constructinitialensemble only accepts univariate priors (#66) - Add Scikit-learn install into a build script for the Project (#68) - Observations constructor modified given observation covariance (#71) - Avoid unnecessary matrix inversions (#73) - Use of JLD vs JLD2 (#75) - API Documentation (#77) - Docs link in "about"? (#80) - Docs mention module EKI.jl but there's only EKP.jl (#81) - Use EnsembleKalmanProcess rather than EKObj? (#82) - Consistency in Rows/Columns/1d-arrays (#90) - Sampler should infer a mean and covariance from EKP prior (#91) - Incorrect instantiation of posterior ParameterDistribution in get_posterior (#93) - Add documentation for adding unit-test, integration tests / examples, and documentation to package (#98) - Add lorenz96 CES example (#99) - Add End to End ClimateMachine.jl example (#100) - How should examples track the CES package? (#103) - Dealing with constraints (#104) - LaTeX equation in documentation homepage isn't properly rendered (#116) - Modular emulator interface (#119) - Unit tests broken under Julia 1.7 due to RNG change (#121) - Buildkite CI broken on staging branch (#125) - EnsembleKalmanProcesses.jl v0.5 dependency breaks for me (#138) - Add compat entries for all dependencies to main Project.toml (#152)

Merged pull requests: - rename to Solus.jl, add NEKI (#2) (@simonbyrne) - Add Lorenz 96 model to examples (#4) (@simonbyrne) - Fix NEKI (#5) (@simonbyrne) - Create .gitignore, ignore vim *.swp files (#6) (@dburov190) - GPRWrap (#7) (@dburov190) - Lorenz96 (#8) (@dburov190) - Implement 'mmstd', 'plotfit'; add tests (#9) (@dburov190) - Histograms (#10) (@dburov190) - Histograms (#11) (@dburov190) - Fix package name (#12) (@charleskawczynski) - Add Melanie's CES code - EKI, GPEmulator, MCMC, and Truth (#14) (@bielim) - Add notebook demonstrating CES on Cloudy (#15) (@bielim) - Update README, add bors.toml (#16) (@charleskawczynski) - Switch to Travis and AppVeyor (#17) (@charleskawczynski) - Try to fix CodeCov, config docs (#19) (@charleskawczynski) - Try to fix docs (#20) (@charleskawczynski) - Try to fix Bors (#21) (@charleskawczynski) - Add Cloudy example to test (#22) (@charleskawczynski) - Update index.md (#27) (@bielim) - Dev CES.jl to docs (#28) (@charleskawczynski) - Fix build (#31) (@charleskawczynski) - Separate cloudy and improve CES (#32) (@bielim) - Fix GPR example (#33) (@charleskawczynski) - Remove GModel dependence on Cloudy (#35) (@charleskawczynski) - Improve memory management & flow control with dispatch (#37) (@charleskawczynski) - Normalize GP input (#42) (@bielim) - Try to fix build (#43) (@charleskawczynski) - Update Cloudy test and Cloudy notebook (#44) (@bielim) - Add Dockerfile (#47) (@charleskawczynski) - Switch to Github Action docker-based CI (#48) (@charleskawczynski) - Fix org name (#50) (@charleskawczynski) - Add unit tests (#51) (@bielim) - Unit-tests with CI Update (#53) (@jakebolewski) - Update README.md (#54) (@jakebolewski) - Replace FreeParameters.jl with Priors.jl - 2nd Attempt (#55) (@bielim) - Add timestep for EKI, and timestep finder function. (#60) (@ilopezgp) - Extend tests for GPEmulator.jl and Observations.jl (#62) (@bielim) - Add SVD functionality (#63) (@odunbar) - Clean up CalibrateEmulateSample (#67) (@bielim) - Update index.md (#69) (@bielim) - WIP: Add Ensemble Kalman Sampler (#70) (@bielim) - Substitute unnecessary matrix inversion, use linear solve instead. (#74) (@ilopezgp) - Change code infrastructure to accommodate both EKI and EKS (#76) (@bielim) - add mindmap link to README.md (#79) (@odunbar) - Corrected EKS implementation (#83) (@agarbuno) - Merge duplicate Ag/eksimlplementation into original ag/eks-implementation (with new commits) (#84) (@odunbar) - Update Tests.yml (#85) (@jakebolewski) - Refactor: Parameter Distributions (#88) (@odunbar) - WIP: replace Prior and posterior samples with ParameterDistributions (#89) (@odunbar) - Update examples to work with the latest CES code (#94) (@bielim) - More verbose naming (#95) (@odunbar) - Adds LossMinimization folder and two examples (#96) (@sandreza) - Adding L96 example (#101) (@mhowlan3) - Data storage objects (#102) (@odunbar) - CalibrateEmulateSample dependence on EnsembleKalmanProcesses (#106) (@odunbar) - Create README.md (#108) (@odunbar) - add buildkite setup to build examples (#109) (@jakebolewski) - Regularization & standardization (#111) (@mhowlan3) - build and deploy docs (#112) (@jakebolewski) - build and deploy docs against master / bors branch (#113) (@jakebolewski) - update julia to 1.5.4, check if precompilation issues are fixed (#114) (@jakebolewski) - Update bors.toml (#117) (@odunbar) - Modular emulator interface (#120) (@odunbar) - Use EKP.jl 0.2.0 & pass explicit RNG object where used (#122) (@tsj5) - Miscellaneous cleanup of warnings; formatting (#123) (@tsj5) - Add preconditioned Crank-Nicholson method for MCMC sampling (#124) (@tsj5) - Standardize on julia 1.6.x (#126) (@tsj5) - Standardize on Julia 1.6.2 (#127) (@tsj5) - Update examples to use Emulator interface (#129) (@tsj5) - [WIP] Modular Sampler interface (#130) (@tsj5) - Substitute types with abstractions (#132) (@tsj5) - Use EKP.jl 0.5.x (#135) (@tsj5) - Update README.md (#137) (@odunbar) - Update docs: initial page updates (#139) (@odunbar) - Fix CI (#140) (@charleskawczynski) - Update to EKP 0.8 - CI checks (#142) (@odunbar) - GP bug for noise_learn = false underprediction of uncertainty (#143) (@odunbar) - Emulator/Data processing docs (#144) (@odunbar) - Standardize notation with EKP, add Glossary (#147) (@ilopezgp) - Clean docs, examples and docstrings (#148) (@pitmonticone) - Add calibration docs. (#149) (@ilopezgp) - Add JuliaFormatter, up to 1.7.3 (#150) (@ilopezgp) - Add compat helper, tag bot (#151) (@ilopezgp) - Add compat entries for dependencies (#153) (@ilopezgp) - Move workflows to their directory (#154) (@ilopezgp) - Add missing compatibilities (#155) (@ilopezgp) - LICENSE (#156) (@odunbar) - julia ^1.6, EKP ^0.8 (#157) (@odunbar) - Add python dependencies (#162) (@ilopezgp)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago