pigeons.jl - v0.4.9

Pigeons v0.4.9

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)

- Julia
Published by github-actions[bot] 10 months ago

pigeons.jl - 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])

- Julia
Published by github-actions[bot] about 1 year ago

pigeons.jl - 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)

- Julia
Published by github-actions[bot] over 1 year ago

pigeons.jl - 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)

- Julia
Published by github-actions[bot] over 1 year ago

pigeons.jl - v0.4.5

Pigeons v0.4.5

What's Changed

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

Full Changelog: https://github.com/Julia-Tempering/Pigeons.jl/compare/v0.4.4...v0.4.5

- Julia
Published by nikola-sur over 1 year ago

pigeons.jl - 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)

- Julia
Published by github-actions[bot] over 1 year ago

pigeons.jl - 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)

- Julia
Published by github-actions[bot] over 1 year ago

pigeons.jl - 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)

- Julia
Published by github-actions[bot] over 1 year ago

pigeons.jl - 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)

- Julia
Published by github-actions[bot] about 2 years ago

pigeons.jl - 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)

- Julia
Published by github-actions[bot] about 2 years ago

pigeons.jl - 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)

- Julia
Published by github-actions[bot] about 2 years ago

pigeons.jl - 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)