Merge remote-tracking branch 'origin/master' into dw/enzyme

.JuliaFormatter.toml

@@ -0,0 +1,21 @@
+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/2231/files
+    "src/experimental/gibbs.jl",
+    "src/mcmc/abstractmcmc.jl",
+    "test/experimental/gibbs.jl",
+    "test/test_utils/numerical_tests.jl",
+    # https://github.com/TuringLang/Turing.jl/pull/2218/files 
+    "src/mcmc/Inference.jl",
+    "test/mcmc/Inference.jl",
+    # https://github.com/TuringLang/Turing.jl/pull/1887 # Enzyme PR
+    "test/mcmc/Inference.jl",
+    "test/mcmc/hmc.jl",
+    "test/mcmc/sghmc.jl",
+    "test/runtests.jl",
+]

.github/workflows/Format.yml

@@ -0,0 +1,38 @@
+name: Format
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+  merge_group:
+    types: [checks_requested]
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  format:
+    runs-on: ubuntu-latest
+    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

.github/workflows/Tests.yml

@@ -0,0 +1,87 @@
+name: Tests
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.version == 'nightly' }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        test-args:
+          # 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"
+        version:
+          #- '1.7'  TODO(mhauru): Temporarily disabled for Enzyme
+          - '1'
+        os:
+          - ubuntu-latest
+          #- windows-latest  TODO(mhauru): Temporarily disabled for Enzyme
+          #- macOS-latest  TODO(mhauru): Temporarily disabled for Enzyme
+        arch:
+          - x64
+          #- x86  TODO(mhauru): Temporarily disabled for Enzyme
+        num_threads:
+          - 1
+          - 2
+        exclude:
+          # With Windows and macOS, only run Julia 1.7, x64, 2 threads. We just want to see
+          # some combination work on OSes other than Ubuntu.
+          - os: windows-latest
+            version: '1'
+          - os: macOS-latest
+            version: '1'
+          - os: windows-latest
+            arch: x86
+          - os: macOS-latest
+            arch: x86
+          - os: windows-latest
+            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
+
+    steps:
+      - name: Print matrix variables
+        run: |
+          echo "OS: ${{ matrix.os }}"
+          echo "Architecture: ${{ matrix.arch }}"
+          echo "Julia version: ${{ matrix.version }}"
+          echo "Number of threads: ${{ matrix.num_threads }}"
+          echo "Test arguments: ${{ matrix.test-args }}"
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '${{ matrix.version }}'
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v4
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@latest
+      - name: Call Pkg.test
+        run: julia --color=yes --depwarn=yes --check-bounds=yes --threads=${{ matrix.num_threads }} --project=@. -e 'import Pkg; Pkg.test(; test_args=ARGS)' -- ${{ matrix.test-args }}