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

* CompatHelper: bump compat for DynamicPPL to 0.29, (keep existing compat) (#2339) Co-authored-by: CompatHelper Julia <[email protected]> * CompatHelper: bump compat for DynamicPPL to 0.29 for package test, (keep existing compat) (#2340) Co-authored-by: CompatHelper Julia <[email protected]> * Replace vectorize(d, r) -> DynamicPPL.tovec(r) vectorize was removed in DynamicPPL 0.29.0 * Require Julia >= 1.9 * Add Julia 1.9 tests back * Fix essential/ad tests * Fix reconstruct calls in MH * Update src/mcmc/mh.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Require Julia 1.10 * Change 1 -> I in MvNormal() setting a real number as σ is deprecated * Simplify tests as we no longer support Julia <1.8 * Simplify `set_namedtuple!` * Remove conditional loading/exporting of Tapir * Tapir -> Mooncake * Update src/essential/Essential.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Remove Requires from Project.toml * Bump minor version instead * Restrict ADTypes to 1.9.0 for AutoMooncake() * Re-enable Mooncake tests in mcmc/abstractmcmc * Update the currently buggy and incorrect tilde overloads in `mh.jl` (#2360) * More autoformatting (#2359) * Bring more files into autoformatting fold * Run JuliaFormatter * Remove trailing whitespace * Update comment in .JuliaFormatter.toml * Fix bad merge * Restrict Mooncake to >= 0.4.9 * Add MH test for LKJCholesky * Remove Tracker * Format imports Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Add AD imports to Optimisation test * Bump Mooncake compat in tests * Bump Libtask version * Get Optimization tests to pass CI * Update API docs * Write a changelog entry * Update docs/src/api.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Tor Erlend Fjelde <[email protected]> Co-authored-by: Markus Hauru <[email protected]>
TuringLang · Oct 23, 2024 · f388e61 · f388e61 · penelopeysm · Oct 23, 2024
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diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
@@ -8,25 +8,35 @@ on:
 
 jobs:
   test:
+    # Use matrix.test.name here to avoid it taking up the entire window width
+    name: test ${{matrix.test.name}} (${{ matrix.os }}, ${{ matrix.version }}, ${{ matrix.arch }}, ${{ matrix.num_threads }})
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ matrix.version == 'nightly' }}
 
     strategy:
       fail-fast: false
       matrix:
-        test-args:
+        test:
           # Run some of the slower test files individually. The last one catches everything
           # not included in the others.
-          - "essential/ad.jl"
-          - "mcmc/gibbs.jl"
-          - "mcmc/hmc.jl"
-          - "mcmc/abstractmcmc.jl"
-          - "mcmc/Inference.jl"
-          - "experimental/gibbs.jl"
-          - "mcmc/ess.jl"
-          - "--skip essential/ad.jl mcmc/gibbs.jl mcmc/hmc.jl mcmc/abstractmcmc.jl mcmc/Inference.jl experimental/gibbs.jl mcmc/ess.jl"
+          - name: "essential/ad"
+            args: "essential/ad.jl"
+          - name: "mcmc/gibbs"
+            args: "mcmc/gibbs.jl"
+          - name: "mcmc/hmc"
+            args: "mcmc/hmc.jl"
+          - name: "mcmc/abstractmcmc"
+            args: "mcmc/abstractmcmc.jl"
+          - name: "mcmc/Inference"
+            args: "mcmc/Inference.jl"
+          - name: "experimental/gibbs"
+            args: "experimental/gibbs.jl"
+          - name: "mcmc/ess"
+            args: "mcmc/ess.jl"
+          - name: "everything else"
+            args: "--skip essential/ad.jl mcmc/gibbs.jl mcmc/hmc.jl mcmc/abstractmcmc.jl mcmc/Inference.jl experimental/gibbs.jl mcmc/ess.jl"
         version:
-          - '1.7'
+          - '1.10'
           - '1'
         os:
           - ubuntu-latest
@@ -39,7 +49,7 @@ jobs:
           - 1
           - 2
         exclude:
-          # With Windows and macOS, only run Julia 1.7, x64, 2 threads. We just want to see
+          # With Windows and macOS, only run x64, 2 threads. We just want to see
           # some combination work on OSes other than Ubuntu.
           - os: windows-latest
             version: '1'
@@ -53,11 +63,11 @@ jobs:
             num_threads: 1
           - os: macOS-latest
             num_threads: 1
-          # It's sufficient to test x86 with one version of Julia and one thread.
-          - version: '1'
-            arch: x86
-          - num_threads: 2
-            arch: x86
+          # It's sufficient to test x86 with only Julia 1.10 and 1 thread.
+          - arch: x86
+            version: '1'
+          - arch: x86
+            num_threads: 2
 
     steps:
       - name: Print matrix variables
@@ -66,7 +76,7 @@ jobs:
           echo "Architecture: ${{ matrix.arch }}"
           echo "Julia version: ${{ matrix.version }}"
           echo "Number of threads: ${{ matrix.num_threads }}"
-          echo "Test arguments: ${{ matrix.test-args }}"
+          echo "Test arguments: ${{ matrix.test.args }}"
       - name: (De)activate coverage analysis
         run: echo "COVERAGE=${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.num_threads == 2 }}" >> "$GITHUB_ENV"
         shell: bash
@@ -81,7 +91,7 @@ jobs:
       # Custom calls of Pkg.test tend to miss features such as e.g. adjustments for CompatHelper PRs
       # Ref https://github.com/julia-actions/julia-runtest/pull/73
       - name: Call Pkg.test
-        run: julia --color=yes --inline=yes --depwarn=yes --check-bounds=yes --threads=${{ matrix.num_threads }} --project=@. -e 'import Pkg; Pkg.test(; coverage=parse(Bool, ENV["COVERAGE"]), test_args=ARGS)' -- ${{ matrix.test-args }}
+        run: julia --color=yes --inline=yes --depwarn=yes --check-bounds=yes --threads=${{ matrix.num_threads }} --project=@. -e 'import Pkg; Pkg.test(; coverage=parse(Bool, ENV["COVERAGE"]), test_args=ARGS)' -- ${{ matrix.test.args }}
       - uses: julia-actions/julia-processcoverage@v1
         if: ${{ env.COVERAGE }}
       - uses: codecov/codecov-action@v4

diff --git a/HISTORY.md b/HISTORY.md
@@ -1,3 +1,14 @@
+# Release 0.35.0
+
+## Breaking changes
+
+Julia 1.10 is now the minimum required version for Turing.
+
+Tapir.jl has been removed and replaced with its successor, Mooncake.jl.
+You can use Mooncake.jl by passing `adbackend=AutoMooncake(; config=nothing)` to the relevant samplers.
+
+Support for Tracker.jl as an AD backend has been removed.
+
 # Release 0.33.0
 
 ## Breaking changes

diff --git a/Project.toml b/Project.toml
@@ -1,6 +1,6 @@
 name = "Turing"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.34.1"
+version = "0.35.0"
 
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
@@ -32,7 +32,6 @@ OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
@@ -49,45 +48,44 @@ TuringDynamicHMCExt = "DynamicHMC"
 TuringOptimExt = "Optim"
 
 [compat]
-ADTypes = "0.2, 1"
+ADTypes = "1.9"
 AbstractMCMC = "5.2"
 Accessors = "0.1"
 AdvancedHMC = "0.3.0, 0.4.0, 0.5.2, 0.6"
 AdvancedMH = "0.8"
 AdvancedPS = "0.6.0"
 AdvancedVI = "0.2"
-BangBang = "0.4"
+BangBang = "0.4.2"
 Bijectors = "0.13.6"
+Compat = "4.15.0"
 DataStructures = "0.18"
 Distributions = "0.23.3, 0.24, 0.25"
 DistributionsAD = "0.6"
 DocStringExtensions = "0.8, 0.9"
 DynamicHMC = "3.4"
-DynamicPPL = "0.28.2"
-Compat = "4.15.0"
+DynamicPPL = "0.29"
 EllipticalSliceSampling = "0.5, 1, 2"
 ForwardDiff = "0.10.3"
-Libtask = "0.7, 0.8"
+Libtask = "0.8.8"
 LinearAlgebra = "1"
 LogDensityProblems = "2"
 LogDensityProblemsAD = "1.7.0"
 MCMCChains = "5, 6"
 NamedArrays = "0.9, 0.10"
+Optim = "1"
 Optimization = "3"
 OptimizationOptimJL = "0.1, 0.2, 0.3"
 OrderedCollections = "1"
 Printf = "1"
 Random = "1"
-Optim = "1"
 Reexport = "0.2, 1"
-Requires = "0.5, 1.0"
-SciMLBase = "1.92.1, 2"
+SciMLBase = "2"
 SpecialFunctions = "0.7.2, 0.8, 0.9, 0.10, 1, 2"
 Statistics = "1.6"
 StatsAPI = "1.6"
 StatsBase = "0.32, 0.33, 0.34"
 StatsFuns = "0.8, 0.9, 1"
-julia = "1.7"
+julia = "1.10"
 
 [extras]
 DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"

diff --git a/docs/src/api.md b/docs/src/api.md
@@ -85,13 +85,12 @@ See the [variational inference tutorial](https://turinglang.org/docs/tutorials/0
 These are used to specify the automatic differentiation backend to use.
 See the [AD guide](https://turinglang.org/docs/tutorials/docs-10-using-turing-autodiff/) for more information.
 
-| Exported symbol   | Documentation                        | Description                               |
-|:----------------- |:------------------------------------ |:----------------------------------------- |
-| `AutoForwardDiff` | [`ADTypes.AutoForwardDiff`](@extref) | ForwardDiff.jl backend                    |
-| `AutoReverseDiff` | [`ADTypes.AutoReverseDiff`](@extref) | ReverseDiff.jl backend                    |
-| `AutoZygote`      | [`ADTypes.AutoZygote`](@extref)      | Zygote.jl backend                         |
-| `AutoTracker`     | [`ADTypes.AutoTracker`](@extref)     | Tracker.jl backend                        |
-| `AutoTapir`       | [`ADTypes.AutoTapir`](@extref)       | Tapir.jl backend, only for ADTypes >= 1.0 |
+| Exported symbol   | Documentation                        | Description            |
+|:----------------- |:------------------------------------ |:---------------------- |
+| `AutoForwardDiff` | [`ADTypes.AutoForwardDiff`](@extref) | ForwardDiff.jl backend |
+| `AutoReverseDiff` | [`ADTypes.AutoReverseDiff`](@extref) | ReverseDiff.jl backend |
+| `AutoZygote`      | [`ADTypes.AutoZygote`](@extref)      | Zygote.jl backend      |
+| `AutoMooncake`    | [`ADTypes.AutoMooncake`](@extref)    | Mooncake.jl backend    |
 
 ### Debugging
 

diff --git a/src/Turing.jl b/src/Turing.jl
@@ -106,7 +106,7 @@ export @model,                 # modelling
     AutoForwardDiff,        # ADTypes
     AutoReverseDiff,
     AutoZygote,
-    AutoTracker,
+    AutoMooncake,
     setprogress!,           # debugging
     Flat,
     FlatPos,
@@ -136,24 +136,4 @@ export @model,                 # modelling
     MAP,
     MLE
 
-# AutoTapir is only supported by ADTypes v1.0 and above.
-@static if VERSION >= v"1.10" && pkgversion(ADTypes) >= v"1"
-    export AutoTapir
-end
-
-if !isdefined(Base, :get_extension)
-    using Requires
-end
-
-function __init__()
-    @static if !isdefined(Base, :get_extension)
-        @require Optim = "429524aa-4258-5aef-a3af-852621145aeb" include(
-            "../ext/TuringOptimExt.jl"
-        )
-        @require DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb" include(
-            "../ext/TuringDynamicHMCExt.jl"
-        )
-    end
-end
-
 end
diff --git a/src/essential/Essential.jl b/src/essential/Essential.jl
@@ -11,7 +11,7 @@ using Bijectors: PDMatDistribution
 using AdvancedVI
 using StatsFuns: logsumexp, softmax
 @reexport using DynamicPPL
-using ADTypes: ADTypes, AutoForwardDiff, AutoTracker, AutoReverseDiff, AutoZygote
+using ADTypes: ADTypes, AutoForwardDiff, AutoReverseDiff, AutoZygote, AutoMooncake
 
 using AdvancedPS: AdvancedPS
 
@@ -20,16 +20,10 @@ include("container.jl")
 export @model,
     @varname,
     AutoForwardDiff,
-    AutoTracker,
     AutoZygote,
     AutoReverseDiff,
+    AutoMooncake,
     @logprob_str,
     @prob_str
 
-# AutoTapir is only supported by ADTypes v1.0 and above.
-@static if VERSION >= v"1.10" && pkgversion(ADTypes) >= v"1"
-    using ADTypes: AutoTapir
-    export AutoTapir
-end
-
 end # module
diff --git a/src/mcmc/Inference.jl b/src/mcmc/Inference.jl
@@ -14,7 +14,6 @@ using DynamicPPL:
     getlogp,
     VarName,
     getsym,
-    vectorize,
     _getvns,
     getdist,
     Model,

diff --git a/src/mcmc/ess.jl b/src/mcmc/ess.jl
@@ -85,7 +85,7 @@ struct ESSPrior{M<:Model,S<:Sampler{<:ESS},V<:AbstractVarInfo,T}
             dist = getdist(varinfo, vn)
             EllipticalSliceSampling.isgaussian(typeof(dist)) ||
                 error("[ESS] only supports Gaussian prior distributions")
-            vectorize(dist, mean(dist))
+            DynamicPPL.tovec(mean(dist))
         end
         return new{M,S,V,typeof(μ)}(model, sampler, varinfo, μ)
     end