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Replace old Gibbs sampler with the experimental one. #2328

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Replace old Gibbs sampler with the experimental one. #2328

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Commits on Sep 23, 2024

  1. Replace old Gibbs sampler with the experimental one.

    @mhauru
    mhauru committed Sep 23, 2024
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  2. Remove dead references to experimental

    @mhauru
    mhauru committed Sep 23, 2024
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  3. Remove mention of experimental from JuliaFormatter conf

    @mhauru
    mhauru committed Sep 23, 2024
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Commits on Sep 24, 2024

  1. Add tests for deprecated constructor

    @mhauru
    mhauru committed Sep 24, 2024
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  2. Fix deprecated Gibbs constructors. Add HISTORY entry.

    @mhauru
    mhauru committed Sep 24, 2024
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  3. Bump version to 0.35.0

    @mhauru
    mhauru committed Sep 24, 2024
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  4. Add Gibbs constructor test for repeat samplers

    @mhauru
    mhauru committed Sep 24, 2024
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  5. Fix typo in test/mcmc/ess.jl

    @mhauru
    mhauru committed Sep 24, 2024
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  6. Use provided rng to initialise VarInfo in Gibbs

    @mhauru
    mhauru committed Sep 24, 2024
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Commits on Oct 8, 2024

  1. Fix a typo in GibbsContext

    @mhauru
    mhauru committed Oct 8, 2024
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Commits on Oct 11, 2024

  1. Merge remote-tracking branch 'origin/master' into mhauru/change-gibbs… 

    …-sampler
    @mhauru
    mhauru committed Oct 11, 2024
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Commits on Oct 16, 2024

  1. Fix the Gibbs sampler

    @mhauru
    mhauru committed Oct 16, 2024
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Commits on Oct 17, 2024

  1. Fix the Gibbs sampler more

    @mhauru
    mhauru committed Oct 17, 2024
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Commits on Oct 18, 2024

  1. Remove mentions of old Gibbs sampler from MH docs 

    Co-authored-by: Penelope Yong <[email protected]>
    @mhauru @penelopeysm
    mhauru and penelopeysm committed Oct 18, 2024
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Commits on Oct 21, 2024

  1. Merge remote-tracking branch 'origin/master' into mhauru/change-gibbs… 

    …-sampler
    @mhauru
    mhauru committed Oct 21, 2024
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  2. Bump DPPL to 0.28.6

    @mhauru
    mhauru committed Oct 21, 2024
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Commits on Oct 24, 2024

  1. Merge remote-tracking branch 'origin/master' into mhauru/change-gibbs… 

    …-sampler
    @mhauru
    mhauru committed Oct 24, 2024
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  2. Merge remote-tracking branch 'origin/master' into mhauru/change-gibbs… 

    …-sampler
    @mhauru
    mhauru committed Oct 24, 2024
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Commits on Oct 28, 2024

  1. Redesign GibbsContext, work in progress

    @mhauru
    mhauru committed Oct 28, 2024
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  2. Fixing new Gibbs, adding a broken test

    @mhauru
    mhauru committed Oct 28, 2024
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  3. Merge remote-tracking branch 'origin/master' into mhauru/change-gibbs… 

    …-sampler
    @mhauru
    mhauru committed Oct 28, 2024
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  4. Document and clean up GibbsContext

    @mhauru
    mhauru committed Oct 28, 2024
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  5. Code style and docs improvements to Gibbs

    @mhauru
    mhauru committed Oct 28, 2024
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Commits on Oct 29, 2024

  1. Change how AdvancedHMC Gibbs state treats momenta

    @mhauru
    mhauru committed Oct 29, 2024
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  2. Remove unnecessary invlinking

    @mhauru
    mhauru committed Oct 29, 2024
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  3. Change how AdvancedHMC Gibbs state treats momenta, again

    @mhauru
    mhauru committed Oct 29, 2024
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  4. Merge remote-tracking branch 'origin/master' into mhauru/change-gibbs… 

    …-sampler
    @mhauru
    mhauru committed Oct 29, 2024
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Commits on Oct 30, 2024

  1. Merge remote-tracking branch 'origin/master' into mhauru/change-gibbs… 

    …-sampler
    @mhauru
    mhauru committed Oct 30, 2024
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Commits on Nov 1, 2024

  1. Use setparams!! rather than reset_state!!

    @mhauru
    mhauru committed Nov 1, 2024
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Commits on Nov 4, 2024

  1. Don't overload setparams\!\! with VarInfo

    @mhauru
    mhauru committed Nov 4, 2024
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Commits on Nov 5, 2024

  1. A fix for ESS in Gibbs

    @mhauru
    mhauru committed Nov 5, 2024
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  2. Remove recompute_logprob!!

    @mhauru
    mhauru committed Nov 5, 2024
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Commits on Nov 7, 2024

  1. Fix setparams_varinfo!! for MH

    @mhauru
    mhauru committed Nov 7, 2024
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  2. Stop hard coding the leafcontext for MH setparams_varinfo!!

    @mhauru
    mhauru committed Nov 7, 2024
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  3. Fix setparams_varinfo!! for ESS

    @mhauru
    mhauru committed Nov 7, 2024
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  4. Fix the context used by setparams_varinfo!! ESS

    @mhauru
    mhauru committed Nov 7, 2024
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  5. Add GibbsContext type stability tests

    @mhauru
    mhauru committed Nov 7, 2024
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Commits on Nov 12, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Tor Erlend Fjelde <[email protected]>
    @mhauru @torfjelde
    mhauru and torfjelde authored Nov 12, 2024
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  2. Merge remote-tracking branch 'origin/master' into mhauru/change-gibbs… 

    …-sampler
    @mhauru
    mhauru committed Nov 12, 2024
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  3. Add clarifying comment

    @mhauru
    mhauru committed Nov 12, 2024
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  4. Add setparams_varinfo!! type bounds

    @mhauru
    mhauru committed Nov 12, 2024
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  5. Fix an import

    @mhauru
    mhauru committed Nov 12, 2024
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  6. Style improvement

    @mhauru
    mhauru committed Nov 12, 2024
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  7. Improve GibbsContext type stability test

    @mhauru
    mhauru committed Nov 12, 2024
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  8. Add comment to constructor tests

    @mhauru
    mhauru committed Nov 12, 2024
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  9. Fix a Gibbs test

    @mhauru
    mhauru committed Nov 12, 2024
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  10. Document the methods of varinfo better

    @mhauru
    mhauru committed Nov 12, 2024
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Commits on Nov 13, 2024

  1. Check whether a sampler is a valid Gibbs component

    @mhauru
    mhauru committed Nov 13, 2024
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  2. Move varinfo methods where they belong

    @mhauru
    mhauru committed Nov 13, 2024
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  3. Fix calling of child context in GibbsContext

    @mhauru
    mhauru committed Nov 13, 2024
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Commits on Nov 15, 2024

  1. Fix Selectors and type stability of Gibbs

    @mhauru
    mhauru committed Nov 15, 2024
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  2. Fix broken short circuit in MH

    @mhauru
    mhauru committed Nov 15, 2024
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Commits on Nov 18, 2024

  1. Stop unnecessary use of Val in GibbsContext

    @mhauru
    mhauru committed Nov 18, 2024
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  2. Enforce GibbsContext being next to a leaf

    @mhauru
    mhauru committed Nov 18, 2024
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Commits on Nov 19, 2024

  1. Fix setparams_varinfo!! for ESS

    @mhauru
    mhauru committed Nov 19, 2024
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  2. Fix a small Gibbs bug

    @mhauru
    mhauru committed Nov 19, 2024
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  3. Fix Gibbs sampler test

    @mhauru
    mhauru committed Nov 19, 2024
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Commits on Nov 20, 2024

  1. Add back tests that were accidentally commented out

    @mhauru
    mhauru committed Nov 20, 2024
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  2. Relax a test tolerance

    @mhauru
    mhauru committed Nov 20, 2024
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Commits on Nov 26, 2024

  1. Add a Gibbs test for dynamic model with ESS

    @mhauru
    mhauru committed Nov 26, 2024
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  2. Use ESS in Gibbs DEMO_MODELS tests

    @mhauru
    mhauru committed Nov 26, 2024
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Commits on Nov 27, 2024

  1. Add Gibbs component call order test

    @mhauru
    mhauru committed Nov 27, 2024
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Commits on Nov 28, 2024

  1. Fix Gibbs linking bug, add tests

    @mhauru
    mhauru committed Nov 28, 2024
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  2. Make Gibbs constructor more flexible

    @mhauru
    mhauru committed Nov 28, 2024
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  3. Introduce RepeatSampler

    @mhauru
    mhauru committed Nov 28, 2024
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  4. Switch gold standard sample Gibbs test back to HMC 

    I tried using ESS instead, because I thought it would test behavior a
bit more broadly, given similarities between HMC and NUTS. It worked
locally, but the KS test fails in one or two cases on CI.
    @mhauru
    mhauru committed Nov 28, 2024
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  5. Clean up RepeatSamplerTests preamble

    @mhauru
    mhauru committed Nov 28, 2024
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  6. Fix RepeatSampler in Gibbs bug

    @mhauru
    mhauru committed Nov 28, 2024
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  7. Rename a function in Gibbs

    @mhauru
    mhauru committed Nov 28, 2024
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  8. Test HMCDA in Gibbs tests

    @mhauru
    mhauru committed Nov 28, 2024
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Commits on Nov 29, 2024

  1. Simplify is_target_varname

    @mhauru
    mhauru committed Nov 29, 2024
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  2. Add suggestions from code review 

    Co-authored-by: Tor Erlend Fjelde <[email protected]>
    @mhauru @torfjelde
    mhauru and torfjelde committed Nov 29, 2024
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  3. Add a couple of issue references

    @mhauru
    mhauru committed Nov 29, 2024
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  4. Merge remote-tracking branch 'origin/master' into mhauru/change-gibbs… 

    …-sampler
    @mhauru
    mhauru committed Nov 29, 2024
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  5. Restructure Gibbs inference tests and reduce iteration counts

    @mhauru
    mhauru committed Nov 29, 2024
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  6. Reduce another iter count in Gibbs tests

    @mhauru
    mhauru committed Nov 29, 2024
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Commits on Dec 2, 2024

  1. Merge remote-tracking branch 'origin/master' into mhauru/change-gibbs… 

    …-sampler
    @mhauru
    mhauru committed Dec 2, 2024
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  2. Add an info print to Gibbs tests

    @mhauru
    mhauru committed Dec 2, 2024
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Commits on Dec 3, 2024

  1. Use StableRNG, relax test tolerance

    @mhauru
    mhauru committed Dec 3, 2024
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