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

[penelopeysm]

This PR bumps DynamicPPL to 0.29.

Julia

This necessitates dropping support for Julia < 1.10

• the last version of SciMLBase to support Julia 1.9 is 2.24.0
  • which in turn requires ADTypes 0.2
• but DynamicPPL 0.28.3 (and by extension 0.29) requires ADTypes 1.0 (Fix depreciation for AutoReverseDiff.  DynamicPPL.jl#638)

Mooncake

Likewise, I've replaced Tapir -> Mooncake as only the latter has true support for DynamicPPL 0.29.

[codecov]

Codecov Report

Attention: Patch coverage is 0% with 22 lines in your changes missing coverage. Please review.

Project coverage is 0.00%. Comparing base (40a0d84) to head (742364e).

Files with missing lines	Patch %	Lines
src/mcmc/mh.jl	0.00%	20 Missing ⚠️
src/mcmc/ess.jl	0.00%	1 Missing ⚠️
src/mcmc/particle_mcmc.jl	0.00%	1 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (40a0d84) and HEAD (742364e). Click for more details.

HEAD has 25 uploads less than BASE

Flag	BASE (40a0d84)	HEAD (742364e)
	56	31

Additional details and impacted files

@@            Coverage Diff             @@
##           master   #2341       +/-   ##
==========================================
- Coverage   86.67%   0.00%   -86.68%     
==========================================
  Files          24      22        -2     
  Lines        1599    1535       -64     
==========================================
- Hits         1386       0     -1386     
- Misses        213    1535     +1322     

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[coveralls]

Pull Request Test Coverage Report for Build 11218401757

Details

• 16 of 22 (72.73%) changed or added relevant lines in 3 files are covered.
• 1 unchanged line in 1 file lost coverage.
• Overall coverage increased (+0.6%) to 87.516%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/mcmc/mh.jl	14	20	70.0%

Files with Coverage Reduction	New Missed Lines	%
src/stdlib/RandomMeasures.jl	1	34.72%

Totals
Change from base Build 11180921169:	0.6%
Covered Lines:	1381
Relevant Lines:	1578

---

💛 - Coveralls

[penelopeysm]

Tests still aren't passing, there are still a few changes that need to be made to bring it up to date with TuringLang/DynamicPPL.jl#575.

I don't mind handling this, but it will take me a long time, so if anybody else feels like expediting it please feel free to jump in:)

[mhauru]

I'll ask around if anyone objects to dropping <1.9.

[penelopeysm]

In the meantime I can work to get the PR ready to merge, we will need it at some point anyway whether it's sooner or later:)

[penelopeysm]

As it turns out, Julia 1.9 won't work either, because SciMLBase.

(see e.g. https://github.com/TuringLang/Turing.jl/actions/runs/11153561181/job/31001300867)

[penelopeysm]

I think everything almost works, except for a Mooncake-or-further-upstream bug which I'll report tomorrow.

Edit: compintell/Mooncake.jl#283

[penelopeysm]

@yebai / @mhauru Since we're making fairly sweeping changes here, is it an opportune time to remove Tracker support as well? #2356

[penelopeysm]

@torfjelde Could I get you to take a look at my changes to src/mcmc please? The tests all pass, but I'm a little anxious 😄

Also, this PR fixes the following bug, but not entirely sure what's the best way to write a test for it. (Other samplers already work correctly with this, it's just MH that fails.) Would it make sense to extend test/test_utils/models.jl and test/test_utils/numerical_tests.jl?

julia> using Turing

julia> @model f() = x ~ LKJCholesky(2, 1)
f (generic function with 2 methods)

julia> sample(f(), MH(), 100)
ERROR: MethodError: no method matching length(::LinearAlgebra.Cholesky{Float64, Matrix{Float64}})
[...]

[torfjelde]

(Other samplers already work correctly with this, it's just MH that fails.) Would it make sense to extend test/test_utils/models.jl and test/test_utils/numerical_tests.jl?

I'd just add it to the MH specific tests for now 👍

[yebai]

@yebai / @mhauru Since we're making fairly sweeping changes here, is it an opportune time to remove Tracker support as well? #2356

It sounds good to me.

[penelopeysm]

This upgrade is also blocked by TuringLang/docs#521 – ideally we want to make sure any relevant docs build with Mooncake. Because we don't want to upgrade to 0.35.0, patch Mooncake to work for the docs, and then release 0.35.1 with a new compat entry for Mooncake just so that the docs work.

However, the Bayesian NN example errors with Mooncake. Will create specific upstrea issues etc when I get the time

[github-actions]

[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

	using ADTypes:
	ADTypes, AutoForwardDiff, AutoReverseDiff, AutoZygote, AutoMooncake
	using ADTypes: ADTypes, AutoForwardDiff, AutoReverseDiff, AutoZygote, AutoMooncake