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)

v0.2.7

Pigeons v0.2.7

Diff since v0.2.6

Merged pull requests:

• Rng bug fix (#151) (@alexandrebouchard)

Closed issues:

• Pigeons next_exec_folder sometimes initializes seed with negative numbers (#150)

v0.2.6

Pigeons v0.2.6

Diff since v0.2.5

Merged pull requests:

• Initialize AAPS step size using auto_step_size (#144) (@miguelbiron)
• aaps: bail on divergences and remove adapt (#146) (@miguelbiron)
• Fix #145 (#147) (@alexandrebouchard)
• Export increment_n_rounds! (#148) (@alexandrebouchard)
• Add leapfrog eval count to MALA (#149) (@nikola-sur)

Closed issues:

• MPI runs fail with Intel v2023.0.0 (#141)
• Checkpoints do not restart past round 10 (#145)

v0.2.5

Pigeons v0.2.5

Diff since v0.2.4

Merged pull requests:

• AAPS implementation (#137) (@miguelbiron)
• Mala (#138) (@nikola-sur)
• Add extended traces (#143) (@alexandrebouchard)

v0.2.4

Pigeons v0.2.4

Diff since v0.2.3

Merged pull requests:

• more automala tests (#136) (@miguelbiron)

v0.2.3

Pigeons v0.2.3

Diff since v0.2.2

Merged pull requests:

• Minor fixes (#124) (@alexandrebouchard)
• basic diagnostic tests for slice_shrink! (#125) (@miguelbiron)
• delete results folder before deploying docs (#126) (@miguelbiron)
• Draft instructions for parallelization, dependencies/env (#129) (@alexandrebouchard)
• fix dirichlet prior, add galaxy ex back to tests (#131) (@miguelbiron)
• Stan banana example (#132) (@miguelbiron)
• Fix needed due to change in interface in AdvancedHMC (#133) (@alexandrebouchard)
• scale parameter for funnel (#134) (@miguelbiron)
• fix leapfrog (#135) (@miguelbiron)

Closed issues:

• Errors from unclean environments (especially on ChildProcess/MPI) (#128)

v0.2.2

Pigeons v0.2.2

Diff since v0.2.1

Closed issues:

• Can it be used to simulate the Ising model or alike? (#103)
• variable_names does not handle arrays (#108)
• Add paper to docs (#113)
• Misleading info message (#114)

Merged pull requests:

• Improving CompatHelper integration (#109) (@miguelbiron)
• Flattened names for variable_names in Turing (#110) (@alexandrebouchard)
• Increment versions in the pluto file (#112) (@alexandrebouchard)
• Programmatic reports (#115) (@alexandrebouchard)
• Add paper cite info (#116) (@nikola-sur)
• Update URL in readme to pigeons.run (#117) (@trevorcampbell)
• Fix doc on MPI setup (#118) (@alexandrebouchard)
• CompatHelper: add new compat entry for DataFrames at version 1, (keep existing compat) (#120) (@github-actions[bot])
• less restrictive dep for statsbase (#122) (@miguelbiron)
• bump version (#123) (@miguelbiron)

v0.2.1

What's Changed

• fix documentation under the hood by @miguelbiron in #97
• Fixing typos, adding links (WIP) by @alexandrebouchard in #100
• add a DistributionLogPotential by @miguelbiron in #102
• MPI presets; doc improvements by @alexandrebouchard in #104
• Batch update all compat entries by @miguelbiron in #107

Full Changelog: v0.2.0...v0.2.1

v0.2.0

What's Changed

• change java_seed by @miguelbiron in #35
• Example of how to specify a custom log potential by @alexandrebouchard in #39
• Single leg vpt fix by @nikola-sur in #40
• Simplify interpolator, update and test examples/ by @alexandrebouchard in #42
• Fix auto-sorting of source files+add test to ensure doesn't happen again by @alexandrebouchard in #43
• Add n_passes option to SliceSampler by @nikola-sur in #45
• Store samples by @alexandrebouchard in #46
• Slurm by @alexandrebouchard in #47
• Comrade example running on MPI by @alexandrebouchard in #49
• Test that the variational ref is being used by @alexandrebouchard in #48
• Fix allocation leak, various other allocs improvements, regression test by @alexandrebouchard in #52
• Basic hmc by @alexandrebouchard in #54
• Improve ergonomics on sample processing by @alexandrebouchard in #55
• Turing RNG fix by @nikola-sur in #53
• Add custom reference example by @nikola-sur in #58
• Traces array abstraction by @ptiede in #59
• Variational PT (two references) by @nikola-sur in #41
• Improved slicer by @trevorcampbell in #64
• Better hmc by @alexandrebouchard in #56
• Fix doc by @alexandrebouchard in #69
• Improving test infrastructure by @alexandrebouchard in #70
• Improved Turing integration by @alexandrebouchard in #78
• Fix AutoMALA+Comrade by @alexandrebouchard in #79
• Stan log_potentials by @nikola-sur in #73
• Ising example by @alexandrebouchard in #81
• Fix #76 by @alexandrebouchard in #82
• Catch BoundsError for Turing by @nikola-sur in #85
• Add sample_matrix, refactor n_chains name, some doc by @alexandrebouchard in #86
• Api refactors by @alexandrebouchard in #87
• Trying an overdispersed normal as default ref for Stan models... by @alexandrebouchard in #88
• increase test coverage by @miguelbiron in #89
• Migrate complex examples into tests by @alexandrebouchard in #91
• Enable multithreading in various tests by @alexandrebouchard in #90
• new attempt at Turing galaxy by @miguelbiron in #95
• A full pass on the documentation by @alexandrebouchard in #93
• bump version by @miguelbiron in #96

New Contributors

• @miguelbiron made their first contribution in #35
• @trevorcampbell made their first contribution in #64

Full Changelog: v0.1.1...v0.2.0

v0.1.1

Pigeons v0.1.1

Diff since v0.1.0

Closed issues:

• Non-concrete field in TuringLogPotential (#20)
• Remove allocations in reference chain for Turing models (#27)

Merged pull requests:

• Int slice sampler (#21) (@nikola-sur)
• Standard stream targets (#22) (@alexandrebouchard)
• Test other platforms in CI (#23) (@alexandrebouchard)
• Add doc and export for stepping stone pair (#24) (@alexandrebouchard)
• Improve output of code snippets, make single thread by default (#25) (@alexandrebouchard)
• Ess proto 2 - WIP (#26) (@alexandrebouchard)
• Segfault fix (#30) (@alexandrebouchard)