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DynamicPPL -> 0.29; Julia -> 1.10; Tapir -> Mooncake #2341

Merged
merged 35 commits into from
Oct 23, 2024
Merged

DynamicPPL -> 0.29; Julia -> 1.10; Tapir -> Mooncake #2341

merged 35 commits into from
Oct 23, 2024

Commits on Oct 2, 2024

  1. CompatHelper: bump compat for DynamicPPL to 0.29, (keep existing comp… 

    …at) (#2339)

Co-authored-by: CompatHelper Julia <compathelper_noreply@julialang.org>
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    2 people authored and penelopeysm committed Oct 2, 2024
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  2. CompatHelper: bump compat for DynamicPPL to 0.29 for package test, (k… 

    …eep existing compat) (#2340)

Co-authored-by: CompatHelper Julia <compathelper_noreply@julialang.org>
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    2 people authored and penelopeysm committed Oct 2, 2024
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  3. Replace vectorize(d, r) -> DynamicPPL.tovec(r) 

    vectorize was removed in DynamicPPL 0.29.0
    @penelopeysm
    penelopeysm committed Oct 2, 2024
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  4. Require Julia >= 1.9

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    penelopeysm committed Oct 2, 2024
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  5. Add Julia 1.9 tests back

    @penelopeysm
    penelopeysm committed Oct 2, 2024
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  6. Fix essential/ad tests

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    penelopeysm committed Oct 2, 2024
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Commits on Oct 3, 2024

  1. Fix reconstruct calls in MH

    @penelopeysm
    penelopeysm committed Oct 3, 2024
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  2. Update src/mcmc/mh.jl 

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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    penelopeysm and github-actions[bot] authored Oct 3, 2024
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  3. Require Julia 1.10

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    penelopeysm committed Oct 3, 2024
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  4. Change 1 -> I in MvNormal() 

    setting a real number as σ is deprecated
    @penelopeysm
    penelopeysm committed Oct 3, 2024
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  5. Simplify tests as we no longer support Julia <1.8

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    penelopeysm committed Oct 3, 2024
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  6. Simplify set_namedtuple!

    @penelopeysm
    penelopeysm committed Oct 3, 2024
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  7. Remove conditional loading/exporting of Tapir

    @penelopeysm
    penelopeysm committed Oct 3, 2024
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  8. Tapir -> Mooncake

    @penelopeysm
    penelopeysm committed Oct 3, 2024
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  9. Update src/essential/Essential.jl 

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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    penelopeysm and github-actions[bot] authored Oct 3, 2024
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  10. Remove Requires from Project.toml

    @penelopeysm
    penelopeysm committed Oct 3, 2024
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  11. Bump minor version instead

    @penelopeysm
    penelopeysm committed Oct 3, 2024
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  12. Restrict ADTypes to 1.9.0 for AutoMooncake()

    @penelopeysm
    penelopeysm committed Oct 3, 2024
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  13. Re-enable Mooncake tests in mcmc/abstractmcmc

    @penelopeysm
    penelopeysm committed Oct 3, 2024
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Commits on Oct 7, 2024

  1. Update the currently buggy and incorrect tilde overloads in mh.jl (#… 

    …2360)
    @torfjelde
    torfjelde authored Oct 7, 2024
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  2. More autoformatting (#2359) 

    * Bring more files into autoformatting fold

* Run JuliaFormatter

* Remove trailing whitespace

* Update comment in .JuliaFormatter.toml
    @mhauru @penelopeysm
    mhauru authored and penelopeysm committed Oct 7, 2024
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  3. Fix bad merge

    @penelopeysm
    penelopeysm committed Oct 7, 2024
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  4. Restrict Mooncake to >= 0.4.9

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    penelopeysm committed Oct 7, 2024
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  5. Add MH test for LKJCholesky

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    penelopeysm committed Oct 7, 2024
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  6. Merge branch 'master' into ch

    @penelopeysm
    penelopeysm committed Oct 7, 2024
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Commits on Oct 10, 2024

  1. Remove Tracker

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    penelopeysm committed Oct 10, 2024
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Commits on Oct 11, 2024

  1. Format imports 

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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    penelopeysm and github-actions[bot] authored Oct 11, 2024
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  2. Add AD imports to Optimisation test

    @penelopeysm
    penelopeysm committed Oct 11, 2024
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Commits on Oct 21, 2024

  1. Merge branch 'master' into ch

    @penelopeysm
    penelopeysm authored Oct 21, 2024
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Commits on Oct 22, 2024

  1. Bump Mooncake compat in tests

    @penelopeysm
    penelopeysm committed Oct 22, 2024
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  2. Bump Libtask version

    @penelopeysm
    penelopeysm committed Oct 22, 2024
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  3. Get Optimization tests to pass CI

    @penelopeysm
    penelopeysm committed Oct 22, 2024
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  4. Update API docs

    @penelopeysm
    penelopeysm committed Oct 22, 2024
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  5. Write a changelog entry

    @penelopeysm
    penelopeysm committed Oct 22, 2024
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  6. Update docs/src/api.md 

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    @penelopeysm @github-actions
    penelopeysm and github-actions[bot] authored Oct 22, 2024
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