Merge remote-tracking branch 'origin/main' into breaking

Author: penelopeysm

.github/workflows/CompatHelper.yml

@@ -14,4 +14,4 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia -e 'using CompatHelper; CompatHelper.main(; subdirs = ["", "docs", "test"])'
+        run: julia -e 'using CompatHelper; CompatHelper.main(; subdirs = ["", "docs", "test", "benchmarks"])'

.github/workflows/DocTest.yml

@@ -0,0 +1,41 @@
+# We want to only run doctests on a single version of Julia, because
+# things like error messages / output can change between versions and
+# is fragile to test against.
+name: Doctests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  merge_group:
+    types: [checks_requested]
+
+# needed to allow julia-actions/cache to delete old caches that it has created
+permissions:
+  actions: write
+  contents: read
+
+# Cancel existing tests on the same PR if a new commit is added to a pull request
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+
+      - uses: julia-actions/cache@v2
+
+      - uses: julia-actions/julia-buildpkg@v1
+
+      - uses: julia-actions/julia-runtest@v1
+        env:
+          GROUP: Doctests

.github/workflows/Docs.yml

@@ -17,7 +17,7 @@ concurrency:
 
 permissions:
   contents: write
-  pull-requests: read
+  pull-requests: write
 
 jobs:
   docs:

.github/workflows/JuliaPre.yml

@@ -14,6 +14,14 @@ permissions:
 jobs:
   test:
     runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        test_group:
+          - Group1
+          - Group2
+
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
@@ -22,3 +30,5 @@ jobs:
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+        env:
+          GROUP: ${{ matrix.test_group }}

HISTORY.md

@@ -18,6 +18,56 @@ This release overhauls how VarInfo objects track variables such as the log joint
   - `getlogp` now returns a `NamedTuple` with keys `logprior` and `loglikelihood`. If you want the log joint probability, which is what `getlogp` used to return, use `getlogjoint`.
   - Correspondingly `setlogp!!` and `acclogp!!` should now be called with a `NamedTuple` with keys `logprior` and `loglikelihood`. The `acclogp!!` method with a single scalar value has been deprecated and falls back on `accloglikelihood!!`, and the single scalar version of `setlogp!!` has been removed. Corresponding setter/accumulator functions exist for the log prior as well.
 
+## 0.36.11
+
+Make `ThreadSafeVarInfo` hold a total of `Threads.nthreads() * 2` logp values, instead of just `Threads.nthreads()`.
+This fix helps to paper over the cracks in using `threadid()` to index into the `ThreadSafeVarInfo` object.
+
+## 0.36.10
+
+Added compatibility with ForwardDiff 1.0.
+
+## 0.36.9
+
+Fixed a failure when sampling from `ProductNamedTupleDistribution` due to
+missing `tovec` methods for `NamedTuple` and `Tuple`.
+
+## 0.36.8
+
+Made `LogDensityFunction` a subtype of `AbstractMCMC.AbstractModel`.
+
+## 0.36.7
+
+Added compatibility with MCMCChains 7.0.
+
+## 0.36.6
+
+`DynamicPPL.TestUtils.run_ad` now takes an extra `context` keyword argument, which is passed to the `LogDensityFunction` constructor.
+
+## 0.36.5
+
+`varinfo[:]` now returns an empty vector if `varinfo::DynamicPPL.NTVarInfo` is empty, rather than erroring.
+
+In its place, `check_model` now issues a warning if the model is empty.
+
+## 0.36.4
+
+Added compatibility with DifferentiationInterface.jl 0.7, and also with JET.jl 0.10.
+
+The JET compatibility entry should only affect you if you are using DynamicPPL on the Julia 1.12 pre-release.
+
+## 0.36.3
+
+Moved the `bijector(model)`, where `model` is a `DynamicPPL.Model`, function from the Turing main repo.
+
+## 0.36.2
+
+Improved docstrings for AD testing utilities.
+
+## 0.36.1
+
+Fixed a missing method for `tilde_assume`.
+
 ## 0.36.0
 
 **Breaking changes**

Project.toml

@@ -55,17 +55,17 @@ ChainRulesCore = "1"
 Chairmarks = "1.3.1"
 Compat = "4"
 ConstructionBase = "1.5.4"
-DifferentiationInterface = "0.6.41"
+DifferentiationInterface = "0.6.41, 0.7"
 Distributions = "0.25"
 DocStringExtensions = "0.9"
 EnzymeCore = "0.6 - 0.8"
-ForwardDiff = "0.10.12"
+ForwardDiff = "0.10.12, 1"
 InteractiveUtils = "1"
-JET = "0.9"
+JET = "0.9, 0.10"
 KernelAbstractions = "0.9.33"
 LinearAlgebra = "1.6"
 LogDensityProblems = "2"
-MCMCChains = "6"
+MCMCChains = "6, 7"
 MacroTools = "0.5.6"
 Mooncake = "0.4.95"
 OrderedCollections = "1"

benchmarks/Project.toml

@@ -19,7 +19,10 @@ StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 ADTypes = "1.14.0"
 BenchmarkTools = "1.6.0"
 Distributions = "0.25.117"
-ForwardDiff = "0.10.38"
+DynamicPPL = "0.36"
+ForwardDiff = "0.10.38, 1"
 LogDensityProblems = "2.1.2"
+Mooncake = "0.4"
 PrettyTables = "2.4.0"
 ReverseDiff = "1.15.3"
+StableRNGs = "1"

benchmarks/src/DynamicPPLBenchmarks.jl

@@ -23,7 +23,7 @@ Return the dimension of `model`, accounting for linking, if any.
 """
 function model_dimension(model, islinked)
     vi = VarInfo()
-    model(vi)
+    model(StableRNG(23), vi)
     if islinked
         vi = DynamicPPL.link(vi, model)
     end

docs/Project.toml

@@ -14,14 +14,16 @@ MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 
 [compat]
+AbstractPPL = "0.11"
 Accessors = "0.1"
 DataStructures = "0.18"
 Distributions = "0.25"
 Documenter = "1"
 DocumenterMermaid = "0.1, 0.2"
+DynamicPPL = "0.36"
 FillArrays = "0.13, 1"
-ForwardDiff = "0.10"
-JET = "0.9"
+ForwardDiff = "0.10, 1"
+JET = "0.9, 0.10"
 LogDensityProblems = "2"
-MCMCChains = "5, 6"
+MCMCChains = "5, 6, 7"
 StableRNGs = "1"

src/DynamicPPL.jl

@@ -191,6 +191,7 @@ include("logdensityfunction.jl")
 include("model_utils.jl")
 include("extract_priors.jl")
 include("values_as_in_model.jl")
+include("bijector.jl")
 
 include("debug_utils.jl")
 using .DebugUtils