v0.4.7

Pigeons v0.4.7

Diff since v0.4.6

Merged pull requests:

• Add contribution guidelines (#289) (@miguelbiron)
• Fix detection of target chain for VariationalDEO (#292) (@miguelbiron)

Closed issues:

• Sampling issue when adding variational chains (#290)

v0.4.6

Pigeons v0.4.6

Diff since v0.4.5

Merged pull requests:

• First version of about us page (#277) (@nikola-sur)
• Force insert HTML in About Us (#278) (@nikola-sur)
• Use images from githubusercontent (#279) (@nikola-sur)
• Fix checkpoint+ad second try (#281) (@alexandrebouchard)
• CompatHelper: bump compat for DynamicPPL in [weakdeps] to 0.30, (keep existing compat) (#285) (@github-actions[bot])
• Fix CI to a specific minor version of Julia (#286) (@miguelbiron)
• Minimize usage of get_extension inside our extensions (#288) (@miguelbiron)

Closed issues:

• Not sampling high density areas (#282)
• PigeonsForwardDiffExt fails to precompile on 1.11.1 (#287)

v0.4.5

Pigeons v0.4.5

What's Changed

• Buffered enzyme, second attempt by @miguelbiron in #261
• Clarify n_chains_variational docstring by @miguelbiron in #262
• Fix #263 by @alexandrebouchard in #265
• Switch macos-latest to macos-13 due to segfault by @miguelbiron in #267
• Robustify slicer by @alexandrebouchard in #268
• Initialization fixed by @alexandrebouchard in #269
• Add missing sampler stat accounting by @alexandrebouchard in #270
• Invariance test: switch to 2 indep samples instead of paired design by @miguelbiron in #271
• Document gradient, invariance test, ... by @alexandrebouchard in #272

Full Changelog: v0.4.4...v0.4.5

v0.4.4

Pigeons v0.4.4

Diff since v0.4.3

Merged pull requests:

• Make variational refs elide AD buffering (#260) (@miguelbiron)

Closed issues:

• Method ambiguity introduced on latest release (#259)

v0.4.3

Pigeons v0.4.3

Diff since v0.4.2

Merged pull requests:

• fix for using homebew MPI in macos-latest (#231) (@miguelbiron)
• Bump compats (#243) (@miguelbiron)
• Invariance tests with arbitrary continuous DynamicPPL models (#246) (@miguelbiron)
• CompatHelper: add new compat entry for HypothesisTests in [weakdeps] at version 0.11, (keep existing compat) (#248) (@github-actions[bot])
• drop a couple of dependencies we are not using (#250) (@miguelbiron)
• reduce allocations in ADgradient and TuringLogPotential code (#251) (@miguelbiron)
• Fix dispatch of ADgradient calls (#255) (@miguelbiron)
• make Augmentations immutable (#256) (@miguelbiron)
• Full caching of BufferedAD objects (#257) (@miguelbiron)

Closed issues:

• Add KS test for samplers (#240)
• Buffered versions of ADgradient (#249)
• Gradient-samplers + DynamicPPL: flatten vi in place instead of using getall (#253)

v0.4.2

Pigeons v0.4.2

Diff since v0.4.1

Merged pull requests:

• Update developers.md (#205) (@miguelbiron)
• Note what PT stands for (#208) (@alecloudenback)
• Add DynamicPPL.@addlogprob! to docs (#211) (@itsdfish)
• Draft doc for Turing initialization (#213) (@alexandrebouchard)
• Workaround for blang compilation issue (#217) (@alexandrebouchard)
• Fix DistributionLogPotential interface + add test using mRNA transfection model (#221) (@miguelbiron)
• Update autoMALA citation (#222) (@miguelbiron)
• import DynamicPPL to use toy_turing_unid_target (#224) (@bencwallace)
• warning for DistributionLogPotential+Stan and fix test (#226) (@miguelbiron)
• remove arch argument in CI (#228) (@miguelbiron)
• use macos-12 on brew MPI tests (#230) (@miguelbiron)
• Reversibility rate recorder (#233) (@miguelbiron)
• Add reversibility_rate to report (#234) (@miguelbiron)
• CompatHelper: bump compat for DynamicPPL in [weakdeps] to 0.27, (keep existing compat) (#237) (@github-actions[bot])
• Update index.md (#238) (@alexandrebouchard)
• Update compat entries + bump patch version (#239) (@miguelbiron)

Closed issues:

• Example of custom implementation (#80)
• Sporadic CI blang test crash (#152)
• Rename Pigeons' MPI to avoid clash with module MPI (#185)
• Export conflict with load function (#200)
• Is Pigeons performing correctly on this example? (#201)
• Errors when using any explorer besides SliceSampler() on a turing model (#204)
• Add Documentation for using @addlogprob! correctly (#206)
• Better support for distributed initialization (#210)
• defining how to sample the initial parameter values (#212)
• CI fails due to Blang compilation issue (#215)
• Informal interface for target should use initialization instead of initialize (#223)
• CI: use aarch64 julia when running on M1 runners (#227)

v0.4.1

Pigeons v0.4.1

Diff since v0.4.0

Merged pull requests:

• Stop exporting load (#203) (@alexandrebouchard)

Closed issues:

• Consider renaming the MPI Submission struct (#189)

v0.4.0

Pigeons v0.4.0

Diff since v0.3.0

Merged pull requests:

• Google Summer of Code page (#197) (@nikola-sur)
• Add contributor guidance details for GSoC (#198) (@nikola-sur)
• Add autoMALA references in docs (#199) (@miguelbiron)

Closed issues:

• Discrete and mixed priors (#195)
• DynamicPPL->Turing compat issues (#196)

v0.3.0

Pigeons v0.3.0

Diff since v0.2.8

Merged pull requests:

• Start move to extensions (#127) (@ptiede)
• Add test for resume MPI with another MPI (#157) (@alexandrebouchard)
• Add generated and tranformed qts to stan output; associated test (#159) (@alexandrebouchard)
• CompatHelper: add new compat entry for Statistics at version 1, (keep existing compat) (#166) (@github-actions[bot])
• change default Mix preconditioner (#168) (@miguelbiron)
• Add arXiv badge to README.md (#169) (@nikola-sur)
• bulk update/relax compat entries (#171) (@miguelbiron)
• Fix == piracy (#175) (@miguelbiron)
• use new mpiexec syntax (#176) (@miguelbiron)
• Saving log_density; add MCMCChains ext; improve control over what gets saved to traces (#178) (@alexandrebouchard)
• SliceSampler: simplify code + more detailed errors (#183) (@miguelbiron)
• CompatHelper: bump compat for Interpolations to 0.15 // Manual: DynamicPPL to 0.24 (#184) (@github-actions[bot])
• Citation (#190) (@nikola-sur)
• update MixDiagonalPreconditioner docstring (#192) (@miguelbiron)
• bump julia versions in CI.yml (#193) (@miguelbiron)

Closed issues:

• mpiexec deprecation warning (#130)
• Misleading Error prompt when loading from checkpoints. (#154)
• Exec Folder IO bug when loading MPI runs from checkpoint (#156)
• Fix type piracy of == (#163)
• Update default preconditioner in autoMALA (#167)
• Recorder for target log_potential (#172)
• Multithreading performance (#191)

v0.2.8

Pigeons v0.2.8

Diff since v0.2.7

Merged pull requests:

• Add scale parameter to banana distribution (#153) (@nikola-sur)
• Fix checkpoint failure prompt (#155) (@dchang10)
• Mix: a mixture of explorers (#158) (@miguelbiron)