Get MarginalLogDensities extension working with Turing v0.40

.JuliaFormatter.toml

@@ -1,11 +1,4 @@
 style="blue"
 format_markdown = true
 import_to_using = false
-# TODO
-# We ignore these files because when formatting was first put in place they were being worked on.
-# These ignores should be removed once the relevant PRs are merged/closed.
-ignore = [
-    # https://github.com/TuringLang/Turing.jl/pull/2328/files
-    "src/experimental/gibbs.jl",
-    "test/experimental/gibbs.jl",
-]
+ignore = ["README.md"]

.github/workflows/Docs.yml

@@ -3,11 +3,12 @@ name: Documentation
 on:
   push:
     branches:
-      - master
+      - main
     tags: '*'
   pull_request:
-    branches:
-      - master
+  merge_group:
+    types: [checks_requested]
+  workflow_dispatch:
 
 concurrency:
   # Skip intermediate builds: always.
@@ -17,21 +18,12 @@ concurrency:
 
 permissions:
   contents: write
-  pull-requests: read
-  statuses: write
+  pull-requests: write
 
 jobs:
   docs:
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: '1'
-      - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia --project=docs/ docs/make.jl
+      - name: Build and deploy Documenter.jl docs
+        uses: TuringLang/actions/DocsDocumenter@main

.github/workflows/DocsNav.yml

@@ -1,49 +1,39 @@
-name: Add Navbar
+name: Rebuild docs with newest navbar
 
 on:
-  page_build:  # Triggers the workflow on push events to gh-pages branch
-  workflow_dispatch:  # Allows manual triggering
+  # 3:25 AM UTC every Sunday -- choose an uncommon time to avoid
+  # periods of heavy GitHub Actions usage
   schedule:
-    - cron: '0 0 * * 0'  # Runs every week on Sunday at midnight (UTC)
+    - cron: '25 3 * * 0'
+  # Whenever needed
+  workflow_dispatch:
+
+permissions:
+  contents: write
 
 jobs:
-  add-navbar:
+  update-navbar:
     runs-on: ubuntu-latest
-    permissions:
-      contents: write
+
     steps:
-      - name: Checkout gh-pages
+      - name: Checkout gh-pages branch
         uses: actions/checkout@v4
         with:
           ref: gh-pages
-          fetch-depth: 0
 
-      - name: Download insert_navbar.sh
-        run: |
-          curl -O https://github.com/raw/TuringLang/turinglang.github.io/main/assets/scripts/insert_navbar.sh
-          chmod +x insert_navbar.sh
+      - name: Insert navbar
+        uses: TuringLang/actions/DocsNav@main
+        with:
+          doc-path: '.'
 
-      - name: Update Navbar
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Commit and push changes
         run: |
-          git config user.name github-actions[bot]
-          git config user.email github-actions[bot]@users.noreply.github.com
-
-          # Define the URL of the navbar to be used
-          NAVBAR_URL="https://github.com/raw/TuringLang/turinglang.github.io/main/assets/scripts/TuringNavbar.html"
-
-          # Update all HTML files in the current directory (gh-pages root)
-          ./insert_navbar.sh . $NAVBAR_URL
-
-          # Remove the insert_navbar.sh file
-          rm insert_navbar.sh
-
-          # Check if there are any changes
           if [[ -n $(git status -s) ]]; then
-            git add .
-            git commit -m "Added navbar and removed insert_navbar.sh"
-            git push "https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" gh-pages
+            git config user.name github-actions[bot]
+            git config user.email github-actions[bot]@users.noreply.github.com
+            git add -A
+            git commit -m "Update navbar (automated)"
+            git push
           else
             echo "No changes to commit"
           fi

.github/workflows/Format.yml

@@ -3,10 +3,8 @@ name: Format
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
-    branches:
-      - master
   merge_group:
     types: [checks_requested]
 
@@ -20,26 +18,6 @@ jobs:
   format:
     runs-on: ubuntu-latest
 
-    permissions:
-      contents: read
-      checks: write
-      issues: write
-      pull-requests: write
-
     steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: 1
       - name: Format code
-        run: |
-          using Pkg
-          Pkg.add(; name="JuliaFormatter", uuid="98e50ef6-434e-11e9-1051-2b60c6c9e899")
-          using JuliaFormatter
-          format("."; verbose=true)
-        shell: julia --color=yes {0}
-      - uses: reviewdog/action-suggester@v1
-        if: github.event_name == 'pull_request'
-        with:
-          tool_name: JuliaFormatter
-          fail_on_error: true
+        uses: TuringLang/actions/Format@main

.github/workflows/PRAssign.yml

@@ -0,0 +1,15 @@
+name: Automatically assign PR authors
+
+on:
+  pull_request:
+    types:
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  assign-author:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: TuringLang/actions/PRAssign@main

.github/workflows/Tests.yml

@@ -3,13 +3,20 @@ name: Tests
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
+  merge_group:
+    types: [checks_requested]
+
+# 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:
     # Use matrix.test.name here to avoid it taking up the entire window width
-    name: test ${{matrix.test.name}} (${{ matrix.runner.os }}, ${{ matrix.runner.version }}, ${{ matrix.runner.arch }}, ${{ matrix.runner.num_threads }})
+    name: test ${{matrix.test.name}} (${{ matrix.runner.version }}, ${{ matrix.runner.os }}, ${{ matrix.runner.num_threads }})
     runs-on: ${{ matrix.runner.os }}
     continue-on-error: ${{ matrix.runner.version == 'pre' }}
 
@@ -19,69 +26,48 @@ jobs:
         test:
           # Run some of the slower test files individually. The last one catches everything
           # not included in the others.
-          - 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: "ad"
+            args: "ad.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"
+            args: "--skip mcmc/gibbs.jl mcmc/Inference.jl ad.jl"
         runner:
           # Default
           - version: '1'
             os: ubuntu-latest
-            arch: x64
-            num_threads: 1
-          # x86
-          - version: '1'
-            os: ubuntu-latest
-            arch: x86
             num_threads: 1
           # Multithreaded
           - version: '1'
             os: ubuntu-latest
-            arch: x64
             num_threads: 2
           # Windows
           - version: '1'
             os: windows-latest
-            arch: x64
             num_threads: 1
           # macOS
           - version: '1'
             os: macos-latest
-            arch: aarch64
             num_threads: 1
           # Minimum supported Julia version
           - version: 'min'
             os: ubuntu-latest
-            arch: x64
             num_threads: 1
           # Minimum supported Julia version, multithreaded
           - version: 'min'
             os: ubuntu-latest
-            arch: x64
             num_threads: 2
           # Pre-release Julia version
           - version: 'pre'
             os: ubuntu-latest
-            arch: x64
             num_threads: 1
 
     steps:
       - name: Print matrix variables
         run: |
           echo "OS: ${{ matrix.runner.os }}"
-          echo "Architecture: ${{ matrix.runner.arch }}"
           echo "Julia version: ${{ matrix.runner.version }}"
           echo "Number of threads: ${{ matrix.runner.num_threads }}"
           echo "Test arguments: ${{ matrix.test.args }}"
@@ -92,7 +78,6 @@ jobs:
       - uses: julia-actions/setup-julia@v2
         with:
           version: '${{ matrix.runner.version }}'
-          arch: ${{ matrix.runner.arch }}
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       # TODO: Use julia-actions/julia-runtest when test_args are supported

CITATION.bib

@@ -1,13 +1,27 @@
-@inproceedings{ge2018t,
-  author    = {Hong Ge and
-               Kai Xu and
-               Zoubin Ghahramani},
-  title     = {Turing: a language for flexible probabilistic inference},
-  booktitle = {International Conference on Artificial Intelligence and Statistics,
-               {AISTATS} 2018, 9-11 April 2018, Playa Blanca, Lanzarote, Canary Islands,
-               Spain},
-  pages     = {1682--1690},
-  year      = {2018},
-  url       = {http://proceedings.mlr.press/v84/ge18b.html},
-  biburl    = {https://dblp.org/rec/bib/conf/aistats/GeXG18},
+@article{10.1145/3711897,
+author = {Fjelde, Tor Erlend and Xu, Kai and Widmann, David and Tarek, Mohamed and Pfiffer, Cameron and Trapp, Martin and Axen, Seth D. and Sun, Xianda and Hauru, Markus and Yong, Penelope and Tebbutt, Will and Ghahramani, Zoubin and Ge, Hong},
+title = {Turing.jl: a general-purpose probabilistic programming language},
+year = {2025},
+publisher = {Association for Computing Machinery},
+address = {New York, NY, USA},
+url = {https://doi.org/10.1145/3711897},
+doi = {10.1145/3711897},
+note = {Just Accepted},
+journal = {ACM Trans. Probab. Mach. Learn.},
+month = feb,
+}
+
+@InProceedings{pmlr-v84-ge18b,
+  title = 	 {Turing: A Language for Flexible Probabilistic Inference},
+  author = 	 {Ge, Hong and Xu, Kai and Ghahramani, Zoubin},
+  booktitle = 	 {Proceedings of the Twenty-First International Conference on Artificial Intelligence and Statistics},
+  pages = 	 {1682--1690},
+  year = 	 {2018},
+  editor = 	 {Storkey, Amos and Perez-Cruz, Fernando},
+  volume = 	 {84},
+  series = 	 {Proceedings of Machine Learning Research},
+  month = 	 {09--11 Apr},
+  publisher =    {PMLR},
+  pdf = 	 {http://proceedings.mlr.press/v84/ge18b/ge18b.pdf},
+  url = 	 {https://proceedings.mlr.press/v84/ge18b.html},
 }