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penelopeysmgithub-actions[bot]CompatHelper Juliatorfjeldemhauru
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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]>
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‎.github/workflows/Tests.yml‎

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@@ -8,25 +8,35 @@ on:
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jobs:
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test:
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# Use matrix.test.name here to avoid it taking up the entire window width
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name: test ${{matrix.test.name}} (${{ matrix.os }}, ${{ matrix.version }}, ${{ matrix.arch }}, ${{ matrix.num_threads }})
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runs-on: ${{ matrix.os }}
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continue-on-error: ${{ matrix.version == 'nightly' }}
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strategy:
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fail-fast: false
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matrix:
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test-args:
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test:
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# Run some of the slower test files individually. The last one catches everything
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# not included in the others.
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- "essential/ad.jl"
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- "mcmc/gibbs.jl"
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- "mcmc/hmc.jl"
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- "mcmc/abstractmcmc.jl"
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- "mcmc/Inference.jl"
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- "experimental/gibbs.jl"
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- "mcmc/ess.jl"
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- "--skip essential/ad.jl mcmc/gibbs.jl mcmc/hmc.jl mcmc/abstractmcmc.jl mcmc/Inference.jl experimental/gibbs.jl mcmc/ess.jl"
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- name: "essential/ad"
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args: "essential/ad.jl"
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- name: "mcmc/gibbs"
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args: "mcmc/gibbs.jl"
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- name: "mcmc/hmc"
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args: "mcmc/hmc.jl"
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- name: "mcmc/abstractmcmc"
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args: "mcmc/abstractmcmc.jl"
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- name: "mcmc/Inference"
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args: "mcmc/Inference.jl"
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- name: "experimental/gibbs"
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args: "experimental/gibbs.jl"
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- name: "mcmc/ess"
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args: "mcmc/ess.jl"
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- name: "everything else"
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args: "--skip essential/ad.jl mcmc/gibbs.jl mcmc/hmc.jl mcmc/abstractmcmc.jl mcmc/Inference.jl experimental/gibbs.jl mcmc/ess.jl"
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version:
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- '1.7'
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- '1.10'
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- '1'
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os:
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- ubuntu-latest
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- 1
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- 2
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exclude:
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# With Windows and macOS, only run Julia 1.7, x64, 2 threads. We just want to see
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# With Windows and macOS, only run x64, 2 threads. We just want to see
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# some combination work on OSes other than Ubuntu.
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- os: windows-latest
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version: '1'
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num_threads: 1
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- os: macOS-latest
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num_threads: 1
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# It's sufficient to test x86 with one version of Julia and one thread.
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- version: '1'
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arch: x86
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- num_threads: 2
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arch: x86
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# It's sufficient to test x86 with only Julia 1.10 and 1 thread.
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- arch: x86
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version: '1'
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- arch: x86
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num_threads: 2
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steps:
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- name: Print matrix variables
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echo "Architecture: ${{ matrix.arch }}"
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echo "Julia version: ${{ matrix.version }}"
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echo "Number of threads: ${{ matrix.num_threads }}"
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echo "Test arguments: ${{ matrix.test-args }}"
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echo "Test arguments: ${{ matrix.test.args }}"
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- name: (De)activate coverage analysis
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run: echo "COVERAGE=${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.num_threads == 2 }}" >> "$GITHUB_ENV"
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shell: bash
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# Custom calls of Pkg.test tend to miss features such as e.g. adjustments for CompatHelper PRs
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# Ref https://github.com/julia-actions/julia-runtest/pull/73
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- name: Call Pkg.test
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run: julia --color=yes --inline=yes --depwarn=yes --check-bounds=yes --threads=${{ matrix.num_threads }} --project=@. -e 'import Pkg; Pkg.test(; coverage=parse(Bool, ENV["COVERAGE"]), test_args=ARGS)' -- ${{ matrix.test-args }}
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run: julia --color=yes --inline=yes --depwarn=yes --check-bounds=yes --threads=${{ matrix.num_threads }} --project=@. -e 'import Pkg; Pkg.test(; coverage=parse(Bool, ENV["COVERAGE"]), test_args=ARGS)' -- ${{ matrix.test.args }}
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- uses: julia-actions/julia-processcoverage@v1
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if: ${{ env.COVERAGE }}
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- uses: codecov/codecov-action@v4

‎HISTORY.md‎

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

‎Project.toml‎

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

‎docs/src/api.md‎

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

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AutoForwardDiff, # ADTypes
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AutoReverseDiff,
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AutoZygote,
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AutoTracker,
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AutoMooncake,
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setprogress!, # debugging
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Flat,
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FlatPos,
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MAP,
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MLE
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# AutoTapir is only supported by ADTypes v1.0 and above.
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@static if VERSION >= v"1.10" && pkgversion(ADTypes) >= v"1"
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export AutoTapir
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end
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if !isdefined(Base, :get_extension)
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using Requires
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end
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function __init__()
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@static if !isdefined(Base, :get_extension)
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@require Optim = "429524aa-4258-5aef-a3af-852621145aeb" include(
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"../ext/TuringOptimExt.jl"
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)
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@require DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb" include(
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"../ext/TuringDynamicHMCExt.jl"
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)
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end
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end
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end

‎src/essential/Essential.jl‎

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using AdvancedVI
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using StatsFuns: logsumexp, softmax
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@reexport using DynamicPPL
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using ADTypes: ADTypes, AutoForwardDiff, AutoTracker, AutoReverseDiff, AutoZygote
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using ADTypes: ADTypes, AutoForwardDiff, AutoReverseDiff, AutoZygote, AutoMooncake
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using AdvancedPS: AdvancedPS
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export @model,
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@varname,
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AutoForwardDiff,
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AutoTracker,
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AutoZygote,
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AutoReverseDiff,
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AutoMooncake,
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@logprob_str,
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@prob_str
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# AutoTapir is only supported by ADTypes v1.0 and above.
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@static if VERSION >= v"1.10" && pkgversion(ADTypes) >= v"1"
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using ADTypes: AutoTapir
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export AutoTapir
33-
end
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end # module

‎src/mcmc/Inference.jl‎

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getlogp,
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VarName,
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getsym,
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vectorize,
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_getvns,
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getdist,
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Model,

‎src/mcmc/ess.jl‎

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dist = getdist(varinfo, vn)
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EllipticalSliceSampling.isgaussian(typeof(dist)) ||
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error("[ESS] only supports Gaussian prior distributions")
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vectorize(dist, mean(dist))
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DynamicPPL.tovec(mean(dist))
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end
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return new{M,S,V,typeof(μ)}(model, sampler, varinfo, μ)
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end

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