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)

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• CalibrateEmulateSample.jl is using an outdated buildkite pipeline (#289)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)

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)

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)

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)

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(phi_c) && isfinite(dphi_c) (#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)

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)
• find_mcmc_step! modifies MCMCObj (#61)
• Insanely long precompile times. (#65)
• EKI.construct_initial_ensemble 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', 'plot_fit'; 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/eks_imlplementation 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)