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

Author: mhauru

.github/workflows/Tests.yml

@@ -66,47 +66,33 @@ jobs:
 
     steps:
       - name: Print matrix variables
+
         run: |
           echo "OS: ${{ matrix.runner.os }}"
           echo "Julia version: ${{ matrix.runner.version }}"
           echo "Number of threads: ${{ matrix.runner.num_threads }}"
           echo "Test arguments: ${{ matrix.test.args }}"
-      - name: (De)activate coverage analysis
-        run: echo "COVERAGE=${{ matrix.runner.version == '1' && matrix.runner.os == 'ubuntu-latest' && matrix.runner.num_threads == 2 }}" >> "$GITHUB_ENV"
-        shell: bash
+
       - uses: actions/checkout@v4
+
       - uses: julia-actions/setup-julia@v2
         with:
           version: '${{ matrix.runner.version }}'
+
       - uses: julia-actions/cache@v2
+
       - uses: julia-actions/julia-buildpkg@v1
-      # TODO: Use julia-actions/julia-runtest when test_args are supported
-      # 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.runner.num_threads }} --project=@. -e 'import Pkg; Pkg.test(; coverage=parse(Bool, ENV["COVERAGE"]), test_args=ARGS)' -- ${{ matrix.test.args }}
+
+      - uses: julia-actions/julia-runtest@v1
+        with:
+          test_args: ${{ matrix.test.args }}
+        env:
+          JULIA_NUM_THREADS: ${{ matrix.runner.num_threads }}
+
       - uses: julia-actions/julia-processcoverage@v1
-        if: ${{ env.COVERAGE }}
-      - uses: codecov/codecov-action@v4
-        if: ${{ env.COVERAGE }}
+
+      - uses: codecov/codecov-action@v5
         with:
-          fail_ci_if_error: true
+          files: lcov.info
           token: ${{ secrets.CODECOV_TOKEN }}
-          file: lcov.info
-      - uses: coverallsapp/github-action@v2
-        if: ${{ env.COVERAGE }}
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          path-to-lcov: lcov.info
-          flag-name: run-${{ join(matrix.*, '-') }}
-          parallel: true
-
-  finish:
-    needs: test
-    if: ${{ always() }}
-    runs-on: ubuntu-latest
-    steps:
-    - name: Coveralls Finished
-      uses: coverallsapp/github-action@v2
-      with:
-        parallel-finished: true
+          fail_ci_if_error: true

HISTORY.md

@@ -7,6 +7,10 @@ Note that if the initial sample is included, the corresponding sampler statistic
 Due to a technical limitation of MCMCChains.jl, this causes all indexing into MCMCChains to return `Union{Float64, Missing}` or similar.
 If you want the old behaviour, you can discard the first sample (e.g. using `discard_initial=1`).
 
+# 0.40.4
+
+Fixes a bug where `initial_state` was not respected for NUTS if `resume_from` was not also specified.
+
 # 0.40.3
 
 This patch makes the `resume_from` keyword argument work correctly when sampling multiple chains.

README.md

@@ -5,7 +5,7 @@
 <a href="https://turinglang.org/"><img src="https://img.shields.io/badge/docs-tutorials-blue.svg" alt="Tutorials" /></a>
 <a href="https://turinglang.org/Turing.jl/stable"><img src="https://img.shields.io/badge/docs-API-blue.svg" alt="API docs" /></a>
 <a href="https://github.com/TuringLang/Turing.jl/actions/workflows/Tests.yml"><img src="https://github.com/TuringLang/Turing.jl/actions/workflows/Tests.yml/badge.svg" alt="Tests" /></a>
-<a href="https://coveralls.io/github/TuringLang/Turing.jl?branch=main"><img src="https://coveralls.io/repos/github/TuringLang/Turing.jl/badge.svg?branch=main" alt="Coverage" /></a>
+<a href="https://codecov.io/gh/TuringLang/Turing.jl"><img src="https://codecov.io/gh/TuringLang/Turing.jl/branch/main/graph/badge.svg" alt="Code Coverage" /></a>
 <a href="https://github.com/SciML/ColPrac"><img src="https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet" alt="ColPrac: Contributor's Guide on Collaborative Practices for Community Packages" /></a>
 </p>
 

src/mcmc/hmc.jl

@@ -120,6 +120,7 @@ function AbstractMCMC.sample(
             sampler,
             N;
             chain_type=chain_type,
+            initial_state=initial_state,
             progress=progress,
             nadapts=_nadapts,
             discard_initial=_discard_initial,

test/mcmc/hmc.jl

@@ -219,6 +219,27 @@ using Turing
         @test_throws ErrorException sample(demo_impossible(), NUTS(), 5)
     end
 
+    @testset "NUTS initial parameters" begin
+        @model function f()
+            x ~ Normal()
+            return 10 ~ Normal(x)
+        end
+        chn1 = sample(StableRNG(468), f(), NUTS(), 100; save_state=true)
+        # chn1 should end up around x = 5.
+        chn2 = sample(
+            StableRNG(468),
+            f(),
+            NUTS(),
+            10;
+            nadapts=0,
+            discard_adapt=false,
+            initial_state=chn1.info.samplerstate,
+        )
+        # if chn2 uses initial_state, its first sample should be somewhere around 5. if
+        # initial_state isn't used, it will be sampled from [-2, 2] so this test should fail
+        @test isapprox(chn2[:x][1], 5.0; atol=2.0)
+    end
+
     @testset "(partially) issue: #2095" begin
         @model function vector_of_dirichlet((::Type{TV})=Vector{Float64}) where {TV}
             xs = Vector{TV}(undef, 2)