v3.3.2

BAT v3.3.2

Diff since v3.3.1

Merged pull requests:

• Space transformations refactor (#449) (@Micki-D)
• Trafo sampling changes (#454) (@oschulz)
• CompatHelper: bump compat for Colors to 0.13, (keep existing compat) (#456) (@github-actions[bot])
• Add MGVI and rename several things in API (#457) (@oschulz)
• Store multivariate proposal in MHProposalState (#458) (@oschulz)
• Make sampling, integration and mode-estimation also return an EvaluatedMeasure (#459) (@oschulz)

v3.3.1

BAT v3.3.1

Diff since v3.3.0

Closed issues:

• Error with truncated distribution as prior (#450)

v3.3.0

BAT v3.3.0

Diff since v3.2.1

v3.2.1

BAT v3.2.1

Diff since v3.2.0

Merged pull requests:

• Fix handing of const parameters in bat_report (#447) (@oschulz)

v3.2.0

BAT v3.2.0

Diff since v3.1.2

Merged pull requests:

• Bump actions/checkout from 3 to 4 (#424) (@dependabot[bot])
• Bump codecov/codecov-action from 3 to 4 (#434) (@dependabot[bot])
• Switch more fully to measures terminology (#435) (@oschulz)
• Added 90% credible interval (#437) (@Shoram444)
• Update dependencies (#438) (@oschulz)
• Optim options update (#442) (@Micki-D)
• CompatHelper: bump compat for ADTypes in [weakdeps] to 1, (keep existing compat) (#444) (@github-actions[bot])

v3.1.2

BAT v3.1.2

Diff since v3.1.1

Merged pull requests:

• CompatHelper: bump compat for AffineMaps to 0.3, (keep existing compat) (#430) (@github-actions[bot])
• Improve _dist_params_numtype (#433) (@oschulz)

v3.1.1

BAT v3.1.1

Diff since v3.1.0

v3.1.0

BAT v3.1.0

Diff since v3.0.0

Merged pull requests:

• Fix HierarchicalDistributions w/ dof smaller than length (#415) (@waldie11)
• Fix HierarchicalDistributions w/ dof smaller than length (#417) (@waldie11)
• Dropped call to deprecated bat_sample(::RNG,..) / non-context (#418) (@waldie11)
• Support bat_transform from Distribution (#419) (@oschulz)
• Update AdvancedHMC to v0.5 (#421) (@oschulz)
• CompatHelper: bump compat for NamedArrays to 0.10, (keep existing compat) (#422) (@github-actions[bot])
• Update deps (#425) (@oschulz)
• Fix numerical instability in tutorial likelihood (#427) (@oschulz)
• CompatHelper: add new compat entry for Statistics at version 1, (keep existing compat) (#428) (@github-actions[bot])
• Add mean for HierarchicalDistribution (#429) (@oschulz)

Closed issues:

• HamiltonianMC() is failed on the tutorial model (#426)

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)

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)