Releases · bat/BAT.jl

09 Jul 13:50

github-actions

v3.0.0

01321f2

v3.0.0

BAT v3.0.0

Diff since v2.0.5

Closed issues:

Doesn't seem to work with Julia 1.6.2? (#319)
Pullback of DistributionTransform (#322)
Handling periodic parameters (#340)
MLE best-fit parameter disagreeing with pyhf (#345)
Order of Samples not preserved in IO via HDF5.jl (#355)
too strong version req. of dependencies (#400)

Merged pull requests:

Tests for sampling with hmc (#310) (@sthayashi)
CompatHelper: add new compat entry for PrettyTables at version 1, (keep existing compat) (#315) (@github-actions[bot])
Added test for bridge sampling, corrected error in bridge sampler (#316) (@celaue)
fixed bug in error estimate (#317) (@celaue)
Use DensityInterface (#320) (@oschulz)
Add tests for BAT.cov2pdmat() in test_distribution_functions.jl (#323) (@Micki-D)
extended test coverage for log_uniform.jl (#326) (@Micki-D)
Support DensityInterface v0.4 (#327) (@oschulz)
CompatHelper: bump compat for SpecialFunctions to 2, (keep existing compat) (#329) (@github-actions[bot])
Adapt to changes in ValueShapes API (#330) (@oschulz)
Replace dist_samples_pvalue with test_dist_samples (#332) (@oschulz)
Infer NamedTupleShape in bat_read (#333) (@oschulz)
CompatHelper: bump compat for FillArrays to 0.13, (keep existing compat) (#334) (@github-actions[bot])
Fix bat_read for samples without info (#335) (@oschulz)
CompatHelper: bump compat for IntervalSets to 0.6, (keep existing compat) (#339) (@github-actions[bot])
Overhaul vjp_algorithm and jvp_algorithm concept (#341) (@oschulz)
Fix Error in debug message (#342) (@lmh91)
Add internal function showhist_unicode (#343) (@oschulz)
Add RNG argument to bat_findmode (#347) (@Cornelius-G)
Store optim traces (#348) (@oschulz)
Import inverse-Hessian and WoodburyPDMat code from Pathfinder.jl (#349) (@oschulz)
Move AHMI and PartitionedSampling to separate packages (#350) (@oschulz)
fix ReadMe typo (#353) (@briochemc)
Fix apply_dist_trafo for ArrayLikeVariate (#354) (@oschulz)
Use track_order = true in IO via HDF5.jl (#356) (@lmh91)
CompatHelper: bump compat for DocStringExtensions to 0.9, (keep existing compat) (#358) (@github-actions[bot])
CompatHelper: bump compat for IntervalSets to 0.7, (keep existing compat) (#359) (@github-actions[bot])
Add bat_marginalize() and adjust plotting backend to use it (#361) (@Micki-D)
Use measure terminology (#365) (@oschulz)
Fix sample overview plots (cornelius' fix) (#366) (@Micki-D)
CompatHelper: add new compat entry for MacroTools at version 0.5, (keep existing compat) (#367) (@github-actions[bot])
CompatHelper: add new compat entry for Documenter at version 0.27, (keep existing compat) (#368) (@github-actions[bot])
unshape result_trafo and add initval_alg to MCMCChainPoolInit (#369) (@Cornelius-G)
Specialize broadcast of ComposedFunction over DensitySampleVector) (#370) (@oschulz)
Clean docs (#371) (@pitmonticone)
Add bat_report, refactor SampledMeasure (#372) (@oschulz)
Update deps (#373) (@oschulz)
Fix plotting and make bat_marginalize() consistent with BAT API (#375) (@Micki-D)
Temporary: Limit Distributions.jl to max version 0.25.64 (#376) (@oschulz)
Add smallest_credible_intervals for shaped samples (#377) (@oschulz)
Improved std normal pdf calc and cholesky for var trafo with diag matrices (#379) (@oschulz)
Add flat index support for bat_marginalize() (#380) (@Micki-D)
CompatHelper: bump compat for MeasureBase to 0.13, (keep existing compat) (#382) (@github-actions[bot])
Add bat_transform support for samples (#383) (@oschulz)
Update to HDF5 release v0.16.11 (#384) (@lmh91)
Improve error log (#387) (@oschulz)
CompatHelper: bump compat for PrettyTables to 2, (keep existing compat) (#388) (@github-actions[bot])
Add bat_convergence (#389) (@oschulz)
CompatHelper: bump compat for MeasureBase to 0.14, (keep existing compat) (#390) (@github-actions[bot])
Add Dirichlet to uniform transform (#391) (@oschulz)
Replace _all_exprs by _all_active_exprs in prior overview (#392) (@oschulz)
CompatHelper: bump compat for Functors to 0.4, (keep existing compat) (#393) (@github-actions[bot])
CompatHelper: bump compat for AdvancedHMC to 0.4, (keep existing compat) (#395) (@github-actions[bot])
Dependencies (#396) (@oschulz)
CompatHelper: bump compat for Clustering to 0.15, (keep existing compat) (#398) (@github-actions[bot])
CompatHelper: bump compat for FillArrays to 1, (keep existing compat) (#399) (@github-actions[bot])
CompatHelper: bump compat for HypothesisTests to 0.11, (keep existing compat) (#403) (@github-actions[bot])
Update depencencies plus some fixes (#404) (@oschulz)
Use BATTestCases (#407) (@oschulz)
Use Pkg extensions (#408) (@oschulz)
Use AutoDiffOperators and add BATContext (#411) (@oschulz)
Move HMC backend into a package extension (#412) (@oschulz)
Move Optim-support to a Pkg extension (#413) (@oschulz)
API and doc polish, some more deprecations to prepare for measures (#414) (@oschulz)

Contributors

oschulz, briochemc, and 6 other contributors

Assets 2

01 Sep 03:17

github-actions

v2.0.5

bf22df1

v2.0.5

BAT v2.0.5

Diff since v2.0.4

Closed issues:

Tutorial is missing package installation (#93)
Error of iid sampler with a truncated mixture distribution (#109)
Add support for UltraNest (#236)
HMC warmup not implemented correctly? (#267)
example of DataFrames data (#274)

Merged pull requests:

Introduce unshaped for densities (#270) (@oschulz)
Fix distribution transforms for cases with non-trivial effective NDOF (#271) (@oschulz)
Add differentiation API (#272) (@oschulz)
CompatHelper: add new compat entry for "FiniteDiff" at version "2.8" (#276) (@github-actions[bot])
Support matrix-variate distributions in trafos (#277) (@oschulz)
Partitioned sampling (#278) (@jlrestrepol)
CompatHelper: bump compat for "Distributions" to "0.25" (#279) (@github-actions[bot])
Support ValueShapes v0.9 (#281) (@oschulz)
ahmc fixes (#282) (@sthayashi)
Adds tests for convolutions (#283) (@jlrestrepol)
Add DensityEvalException and improve show and display for BAT types (#284) (@oschulz)
Allow selection of autodiff algorithm and add Zygote support (#285) (@oschulz)
Adding nested sampling with NestedSamplers.jl (#287) (@WillyHK)
Add BAT.error_log (#288) (@oschulz)
Tests multimodal distributions (#289) (@jlrestrepol)
Resolve type instablity of logpdf for multimodal cauchy (#290) (@sthayashi)
Move deps deps to tests/Project.toml (#292) (@oschulz)
Require ChainRulesCore v0.9.44 or higher and use NoTangent (#293) (@oschulz)
Add list of algorithms to docs (#294) (@oschulz)
Overhaul HMC and HMC tuning implementation (#295) (@oschulz)
Space partitioning - Resampling Update (#296) (@VasylHafych)
Remove TruncatedDensity, add RenormalizedDensity, adapt PartitionedSampling (#297) (@oschulz)
ahmc type stability fixes (#298) (@sthayashi)
CompatHelper: bump compat for "StructArrays" to "0.6" (#299) (@github-actions[bot])
Tests for modified partitioned sampling (#300) (@jlrestrepol)
Implemented bridge sampling (#301) (@celaue)
CompatHelper: bump compat for "FillArrays" to "0.12" (#302) (@github-actions[bot])
Error correction and design update of bridge sampler (#303) (@celaue)
Multimodal t distribution (#305) (@jlrestrepol)
AHMC compat fixes for v0.3 (#307) (@sthayashi)
Add executors (#311) (@oschulz)
Improve SampledDensity and add BridgeSampling (#312) (@oschulz)

Contributors

oschulz, sthayashi, and 4 other contributors

Assets 2

19 Mar 21:00

github-actions

v2.0.4

3734788

v2.0.4

BAT v2.0.4

Diff since v2.0.3

Merged pull requests:

CompatHelper: bump compat for "FillArrays" to "0.11" (#246) (@github-actions[bot])
transform tests (#247) (@sthayashi)
Bugfix: Replace nsubspaces with npartitions in PartitionedSampling (#250) (@Cornelius-G)
Fixed minor issues with space partitioning (#251) (@VasylHafych)
Allow keywords when running UltraNest ? (#253) (@Cornelius-G)
Update ValueShapes, Documenter and StructArrays (#255) (@oschulz)
Release cand 2.0.4 (#258) (@oschulz)
Don't use StructArrays.StructArrayStyle explicitly (#259) (@oschulz)
Add LogUniform distribution (#260) (@oschulz)
Fix quantile precision issues for Truncated (#261) (@oschulz)
Test Cuba integration for failures and multithreading (#262) (@sthayashi)
CompatHelper: bump compat for "PDMats" to "0.11" (#264) (@github-actions[bot])
Adds test for RandResampling and OrderedResampling test to test_bat_sample.jl (#265) (@jlrestrepol)
Add smoothing of contour plots using Gaussian filtering (#268) (@Cornelius-G)
Tests for SobolSampler and GridSampler (#269) (@sthayashi)

Assets 2

19 Jan 20:40

github-actions

v2.0.3

eaa6fe8

v2.0.3

BAT v2.0.3

Diff since v2.0.2

Merged pull requests:

Update v2.0 release branch (#243) (@oschulz)
Add ReactiveNestedSampling via UltraNest.jl (#244) (@oschulz)
Add explicit precompile statements for core functionality (#245) (@oschulz)
HDF5 Updates (#248) (@oschulz)

Assets 2

22 Dec 14:59

github-actions

v2.0.2

a3283d8

v2.0.2

BAT v2.0.2

Diff since v2.0.1

Merged pull requests:

GaussianShell sampling fixes (#229) (@sthayashi)
Allow change of number of dimensions in distribution transformations (#233) (@oschulz)
Improve stability of tests (#234) (@oschulz)
Dirichlet transform (#235) (@jknollm)
Include MC samples generated during init in tuner stats (#237) (@oschulz)
Update index.md (#238) (@pitmonticone)
Transform ExplicitInit values if necessary (#239) (@oschulz)
Refactor variate transforms (#240) (@oschulz)
Break infinite recursion on generic dist trafo via uniform (#241) (@oschulz)
Update v2.0 release (#242) (@oschulz)

Assets 2

17 Dec 10:57

github-actions

v2.0.1

7564d60

v2.0.1

BAT v2.0.1

Diff since v2.0.0

Merged pull requests:

Custom ForwardDiff for uniform trafos (#231) (@oschulz)

Assets 2

14 Dec 01:15

github-actions

v2.0.0

f40135f

v2.0.0

BAT v2.0.0

Diff since v1.0.1

Closed issues:

"My first BAT script" example documentation. (#42)
Multi-proposal MCMC (#47)
Update License (#65)
Trim function of AHMI not working as expected (#97)
Type of Sample Weights (#100)
AHMI fails with multiple workers (#110)
BAT Precomiler Error: ZeroVector not defined (#111)
Plotting Warnings (#118)
HMC sampler returns repeated samples (#142)
Mapping between names and indices fails for constant prior parameters (#146)
Can not sample with current master (5369acd) (#160)

Merged pull requests:

Add optimization, output shaped samples, API changes (#84) (@oschulz)
Update CI config and dependency bounds (#85) (@oschulz)
Update CI config and deps bounds (#86) (@oschulz)
Backport: Run all testing on Travis (#87) (@oschulz)
Backport fixes (#89) (@oschulz)
New hierarchical RNG partitioning method and related changes (#90) (@oschulz)
Keep statistics of previous tuning cycles with a configurable weight (#91) (@oschulz)
Update deps version bounds (#92) (@oschulz)
Update deps and CI (#94) (@oschulz)
AHMI Bugfixes (#95) (@VasylHafych)
Install TagBot as a GitHub Action (#96) (@JuliaTagBot)
Add HierarchicalDensity (#99) (@oschulz)
Bias correction and trim function replacement (Addressing issue #97) (#101) (@VasylHafych)
Require Julia v1.3 (#102) (@oschulz)
CompatHelper: bump compat for "ArgCheck" to "2.0" (#103) (@github-actions[bot])
CompatHelper: bump compat for "Tables" to "1.0" (#104) (@github-actions[bot])
CompatHelper: bump compat for "Colors" to "0.12" (#106) (@github-actions[bot])
CompatHelper: bump compat for "Distributions" to "0.23" (#107) (@github-actions[bot])
CompatHelper: bump compat for "StatsBase" to "0.33" (#108) (@github-actions[bot])
Funnel and Multimodal Cauchy distributions for testing bat_integrate (#112) (@sthayashi)
CompatHelper: bump compat for "RecipesBase" to "1.0" (#113) (@github-actions[bot])
Pre-installation of HDF5.jl during CI testing no longer necessary (#114) (@oschulz)
CompatHelper: bump compat for "Clustering" to "0.14" (#115) (@github-actions[bot])
CompatHelper: bump compat for "IntervalSets" to "0.5" (#116) (@github-actions[bot])
Fix AHMI to be able to run on worker processes (#117) (@oschulz)
Ahmi Bugfix (#119) (@VasylHafych)
CompatHelper: bump compat for "Optim" to "0.21" (#120) (@github-actions[bot])
update of plotting recipes, modify plotting examples and add documentation of plotting (#121) (@Cornelius-G)
CompatHelper: bump compat for "PDMats" to "0.10" (#122) (@github-actions[bot])
Fix bug in plotting of 1D samples (#123) (@Cornelius-G)
Add HMC sampler (#124) (@Cornelius-G)
CompatHelper: add new compat entry for "Bijectors" at version "0.7" (#125) (@github-actions[bot])
CompatHelper: add new compat entry for "AdvancedHMC" at version "0.2" (#126) (@github-actions[bot])
Increase support for density gradients (#127) (@oschulz)
Function to estimate modes in marginalizations (#128) (@VasylHafych)
Plotting recipe for showing error bars on a fit function (#129) (@VasylHafych)
Introduce MarginalDist (#130) (@Cornelius-G)
Add first versions of sobol, grid and prior samplers (#131) (@Cornelius-G)
Make bat_marginalize return namedtuple (#133) (@Cornelius-G)
Add bat_autocorr and bat_integrated_autocorr_time (#134) (@oschulz)
Improve autocorrelation length estimation (#135) (@oschulz)
Improve effective sample size estimation (#136) (@oschulz)
Improve integration API (#137) (@oschulz)
CompatHelper: bump compat for "DistributionsAD" to "0.6" (#138) (@github-actions[bot])
[WIP] Partitioned Sampling (#139) (@VasylHafych)
CompatHelper: bump compat for "Bijectors" to "0.8" (#140) (@github-actions[bot])
Add bat_defaults API (#141) (@oschulz)
CompatHelper: add new compat entry for "Sobol" at version "1.4" (#143) (@github-actions[bot])
Make AHMC return weighted unique samples (#144) (@Cornelius-G)
[WIP] Performance Test Suite (#145) (@salvolc)
[WIP] Gaussian shell rejection sampling (#147) (@sthayashi)
Improve density evaluation and support MCMC sampling from truncated densities (#149) (@oschulz)
CompatHelper: bump compat for "Optim" to "0.22" (#150) (@github-actions[bot])
Change/refactor density evaluation (#152) (@oschulz)
Fix mapping between indices and names for plotting when some parameters are fixed (#153) (@Cornelius-G)
CompatHelper: add new compat entry for "CPUTime" at version "1.0" (#154) (@github-actions[bot])
CompatHelper: add new compat entry for "HypothesisTests" at version "0.10" (#155) (@github-actions[bot])
Rename AnyPosterior and other types, generalize sampling (#157) (@oschulz)
Adjusted errors used in test_integration.jl to no longer fail in trav… (#158) (@sthayashi)
[WIP] Run CI on Julia v1.5 instead of v1.4 (#159) (@oschulz)
Change ConstDensity structure (#162) (@oschulz)
Kolmogorov-Smirnov Goodness of Fit Test (#163) (@VasylHafych)
AHMI Float32 Issue (#164) (@VasylHafych)
Plotting now allows to specify bin edges (#165) (@Cornelius-G)
[WIP] Small changes to fix any problems with implemented distributions (#167) (@sthayashi)
Include gaussian shell (#168) (@sthayashi)
[WIP] Introduce SampledDensity (#170) (@Cornelius-G)
CompatHelper: add new compat entry for "ElasticArrays" at version "1.2" (#171) (@github-actions[bot])
CompatHelper: add new compat entry for "NamedArrays" at version "0.9" (#176) (@github-actions[bot])
Add Cuba integration and use SampledDensity in tutorial (#177) (@oschulz)
CompatHelper: bump compat for "FillArrays" to "0.9" (#178) (@github-actions[bot])
Tests for distributions (#179) (@sthayashi)
Multimodal cauchy assertion (#180) (@sthayashi)
Gaussian shell docstring fix (#181) (@sthayashi)
Integration distribution rtols (#182) (@sthayashi)
CompatHelper: bump compat for "KernelDensity" to "0.6" (#183) (@github-actions[bot])
Density sample tests (#184) (@sthayashi)
CompatHelper: bump compat for "DataStructures" to "0.18" (#185) (@github-actions[bot])
tests for abstract densities (#186) (@sthayashi)
Fixes (#190) (@oschulz)
Fix AdvancedHMC warmup with StanHMCAdaptor (#191) (@cescalara)
Update to ValueShapes v0.7 (#192) (@oschulz)
Add new AHMCSampleID to store Hamiltonian transition info (#194) (@cescalara)
Update to EmpiricalDistributions v0.2 (#196) (@oschulz)
Substantial refactoring (#197) (@oschulz)
Rename parsel to vsel (#198) (@oschulz)
CompatHelper: bump compat for "Distributions" to "0.24" (#199) (@github-actions[bot])
Fix Cauchy dimension error, default plotting plots weighted samples (#200) (@salvolc)
Space Partitioning Fix-ups (#201) (@VasylHafych)
Refactor logvalof (#202) (@oschulz)
Prior Plot Bugfix (#203) (@VasylHafych)
Bugfixes, running AHMC benchmarks does not use cauchy anymore (#204) (@salvolc)
tests for algodefaults (#205) (@sthayashi)
Add variate space transformations (#206) (@oschulz)
CompatHelper: bump compat for "FillArrays" to "0.10" (#207) (@github-actions[bot])
Don't automatically convert histograms to dists anymore (#209) (@oschulz)
Replace Travis with GitHub actions, update GitHub actions (#212) (@oschulz)
Move number of samples argument(s) into algorithm structs (#213) (@oschulz)
Change fields of MCMCChainPoolInit and MCMCMultiCycleBurnin (#215) (@oschulz)
Automatic space transformations (#216) (@oschulz)
Hide colorbar by default in 2d plots (#217) (@Cornelius-G)
Rename field MCMCSampling.sampler to mcalg (#218) (@oschulz)
Remove BoundsType and renormalize_variate (#221) (@oschulz)
Minor bugfix when plotting ahmi values (#222) (@salvolc)
Trafo extensions (#224) (@oschulz)
Improve density logval typing mechanism (#225) (@oschulz)
Add example for BAT.jl paper (#226) (@oschulz)
Add EffSampleSizeAlgorithm (#227) (@oschulz)
Rename variate, MH and HMC src files (#228) (@oschulz)