v0.4.9

Pigeons v0.4.9

Diff since v0.4.8

Merged pull requests:

• Fix slurm MPI submission bug (#214) (@dominic-chang)
• CompatHelper: bump compat for DynamicPPL in [weakdeps] to 0.29, (keep existing compat) (#276) (@github-actions[bot])
• Support for Julia 1.11 (#284) (@miguelbiron)
• JuliaBUGS support (#303) (@miguelbiron)
• CompatHelper: bump compat for DynamicPPL in [weakdeps] to 0.32, (keep existing compat) (#304) (@github-actions[bot])
• Bump AbstractPPL and Bijectors compat (#306) (@github-actions[bot])
• CompatHelper: bump compat for DynamicPPL in [weakdeps] to 0.33, (keep existing compat) (#309) (@github-actions[bot])
• CompatHelper: bump compat for DynamicPPL in [weakdeps] to 0.34, (keep existing compat) (#310) (@github-actions[bot])
• Fix #311 (#312) (@alexandrebouchard)
• GSOC 2025 Updates (#313) (@nikola-sur)
• Update GSoC project description (#316) (@nikola-sur)
• CompatHelper: bump compat for JuliaBUGS in [weakdeps] to 0.9, (keep existing compat) (#319) (@github-actions[bot])
• CompatHelper: bump compat for AbstractPPL in [weakdeps] to 0.11, (keep existing compat) (#322) (@github-actions[bot])
• Move to ADTypes + support for DynamicPPL >= 0.35 (#328) (@miguelbiron)
• Remove GSOC from pages (#335) (@nikola-sur)

Closed issues:

• Automate adding weak dependencies to MPI/ChildProcess dependency (#186)
• sampling problem not indicated by all diagnostics i found in the manual (#202)
• Error/warning behaviour for NaN logprobs (#296)
• File IO race condition when restarting pigeons with MPI (#311)
• Add time to default printout table (#314)
• Relax type of rng in Replica to AbstractRNG (#317)
• Is there a way to manually set the annealing schedule? (#323)
• MCMCChains Chain error: type NamedTuple has no field traces (#326)

v0.4.8

Pigeons v0.4.8

Diff since v0.4.7

Merged pull requests:

• CompatHelper: bump compat for Enzyme in [weakdeps] to 0.13, (keep existing compat) (#275) (@github-actions[bot])
• re-enable broken codecov (#293) (@miguelbiron)
• Bump julia-actions/setup-julia from 1 to 2 (#294) (@dependabot[bot])
• Update doc: CRT positions, funding, etc (#297) (@alexandrebouchard)
• Revert because of CORB (#298) (@alexandrebouchard)
• Bump codecov/codecov-action from 4 to 5 (#300) (@dependabot[bot])
• CompatHelper: bump compat for DynamicPPL in [weakdeps] to 0.31, (keep existing compat) (#302) (@github-actions[bot])

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)