Merge commit '5c14b88cac9bcb057741e8c6b517f61cbf4305b9' as 'stanc3'

stanc3/.git-blame-ignore-revs

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+# usage: git config blame.ignoreRevsFile .git-blame-ignore-revs
+# generated with: git log --grep "[fF]ormat.*ocamlformat" --format="format:%H # %s"
+
+2030298f84a95a78953866bf46bc6564f9faee1b # Migrate to Core and format with ocamlformat 0.26.1
+845f34e165e16c95596fd48da67bb987bbbe2446 # Format with ocamlformat 0.19.0
+9c75bd01015157bae5a133417acf1f7e8af71887 # reformatting using ocamlformat 0.9
+b98f92d6a970967bd51158c1b555bf338d4da3b7 # Reformat master with ocamlformat.

stanc3/.gitattributes

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+# Set the default behavior, in case people don't have core.autocrlf set.
+# This makes sure all text files are automatically converted to lf line endings.
+* text eol=lf
+*.png binary
+
+# this sets where github can look for language stats
+*.ml linguist-language=OCaml
+test/integration/** linguist-vendored

stanc3/.github/FUNDING.yml

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+github: stan-dev
+custom: https://mc-stan.org/support/

stanc3/.github/ISSUE_TEMPLATE/bug-report.md

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+---
+name: Bug report
+about: File a bug/issue
+title: '[BUG] <title>'
+labels: ''
+assignees: ''
+---
+<!-- Thank you for submitting a bug report! -->
+
+### Current Behavior:
+<!-- A concise description of what you're experiencing. -->
+
+### Expected Behavior:
+<!-- A concise description of what you expected to happen. -->
+
+### Model Code
+<!-- If a specific model is causing this issue, it really helps if you can share it -->
+<details><summary>Model which exhibits the issue</summary>
+
+```stan
+// Please put your code here
+
+```
+</details>
+
+### Environment:
+<!--
+Example:
+- OS: Ubuntu 20.04
+- stanc: 2.28.0
+- cmdstan/rstan/other Stanversions
+-->
+
+### Anything else:
+<!--
+Links? References? Anything that will give us more context about the issue that you are encountering!
+-->

stanc3/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: Question about using Stan, modeling, etc
+    url: https://discourse.mc-stan.org/
+    about: |
+      Ask questions and discuss with other community members here.
+      If your question involves a specific model, including it will
+      improve the quality of help the community can provide.

stanc3/.github/ISSUE_TEMPLATE/feature-request.md

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+---
+name: Feature request
+about: Suggest a new feature for the language or compiler
+title: ''
+labels: 'feature'
+assignees: ''
+---
+
+<!-- Please do a quick search of existing issues to make sure that this has not been suggested before.
+    Thank you for helping us improve Stan!
+ -->
+
+**Is your feature request related to a problem? Please describe.**
+<!-- A description of what the problem is. e.g., "I'm always frustrated when [...]" -->
+
+**Describe the solution you'd like**
+<!-- A description of what you're proposing, e.g., "The auto-formatter should allow users to set a line length" -->
+
+**Describe alternatives you've considered**
+<!-- A description of any alternative solutions to this problem or features you've considered. -->
+
+**Additional context**
+<!-- Add any other context about the feature request here. -->

stanc3/.github/ISSUE_TEMPLATE/todo.md

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+---
+name: TODO Item
+about: (For existing developers) Open a generic issue related to the build process or something that needs to be worked on.
+title: ''
+labels: ''
+assignees: ''
+---
+

stanc3/.github/codecov.yml

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+codecov:
+  require_ci_to_pass: false
+  ci:
+    - jenkins.flatironinstitute.org
+
+coverage:
+  status:
+    project:
+      default:
+        informational: true
+        threshold: 100%
+        target: 0%
+    patch:
+      default:
+        informational: true
+        threshold: 100%
+        target: 0%
+
+comment:
+  layout: "diff, files"
+  behavior: once
+  require_changes: true

stanc3/.github/pull_request_template.md

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+#### Submission Checklist
+
+- [ ] Run unit tests
+- Documentation
+    - [ ] If a user-facing facing change was made, the documentation PR is here: <LINK>
+    - [ ] OR, no user-facing changes were made
+
+## Release notes
+
+Replace this text with a short note on what will change if this pull request is merged. This will be included in the release notes.
+
+## Copyright and Licensing
+
+By submitting this pull request, the copyright holder is agreeing to 
+license the submitted work under the BSD 3-clause license (https://opensource.org/licenses/BSD-3-Clause)

stanc3/.github/workflows/binaries.yml

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+name: Build binaries
+
+on:
+  workflow_dispatch: {}
+
+env:
+  OCAML_VERSION: 4.14.1
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            sdk: ""
+            profile: static
+            name: ubuntu
+          - os: macos-13
+            sdk: "10.11"
+            profile: release
+            name: macos-x86_64
+          - os: macos-latest
+            sdk: "11.0"
+            profile: release
+            name: macos-arm64
+
+    runs-on: ${{ matrix.os }}
+    name: Build ${{ matrix.name }} stanc
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Download older SDK
+        if: matrix.sdk != ''
+        run: |
+          wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX${{matrix.sdk}}.sdk.tar.xz
+          tar -xvf MacOSX${{matrix.sdk}}.sdk.tar.xz
+          sudo mv MacOSX${{matrix.sdk}}.sdk /Library/Developer/CommandLineTools/SDKs
+
+          echo "MACOSX_DEPLOYMENT_TARGET=${{matrix.sdk}}" >> $GITHUB_ENV
+          echo "SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX${{matrix.sdk}}.sdk/" >> $GITHUB_ENV
+
+      - name: Use OCaml ${{ env.OCAML_VERSION }}
+        uses: ocaml/setup-ocaml@v3
+        with:
+          ocaml-compiler: ${{ env.OCAML_VERSION }}
+          dune-cache: ${{ matrix.name != 'macos-x86_64' }}
+
+      - if: matrix.name == 'macos-x86_64'
+        run: opam pin -y dune 3.6.0 --no-action
+
+      - run: bash -x scripts/install_build_deps.sh
+
+      - name: Build ${{ matrix.name }}
+        run: opam exec -- dune subst; opam exec -- dune build --profile ${{ matrix.profile }}
+
+      - run: mv _build/default/src/stanc/stanc.exe ${{ matrix.name }}-stanc
+
+      - name: Upload ${{ matrix.name }} stanc
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.name }}-stanc
+          path: ${{ matrix.name }}-stanc
+
+  build-universal:
+    needs: build
+    runs-on: macos-latest
+    name: Build MacOS universal stanc
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+
+      - name: Run lipo
+        run: |
+          ls
+          lipo -create -output macos-stanc macos-*-stanc
+          lipo -archs macos-stanc
+
+      - name: Upload macos-stanc
+        uses: actions/upload-artifact@v4
+        with:
+          name: macos-stanc
+          path: macos-stanc
+
+  xbuild-windows:
+    runs-on: ubuntu-latest
+    name: Build Windows stanc (cross-compiler)
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install cross-compiler
+        run: sudo apt-get update; sudo apt-get install -y gcc-mingw-w64-x86-64
+
+      - name: Use OCaml ${{ env.OCAML_VERSION }}
+        uses: ocaml/setup-ocaml@v3
+        with:
+          cache-prefix: v1-windows
+          dune-cache: true
+          ocaml-compiler: ocaml-windows64.${{ env.OCAML_VERSION }}
+          opam-repositories: |
+            windows: http://github.com/ocaml-cross/opam-cross-windows.git
+            default: https://github.com/ocaml/opam-repository.git
+
+      - run: bash -x scripts/install_build_deps_windows.sh
+
+      - name: Build
+        run: |
+          opam exec -- dune subst
+          opam exec -- dune build -x windows
+
+      - run: mv _build/default.windows/src/stanc/stanc.exe windows-stanc
+
+      - name: Upload Windows stanc
+        uses: actions/upload-artifact@v4
+        with:
+          name: windows-stanc
+          path: windows-stanc
+
+  build-js:
+    runs-on: ubuntu-latest
+    name: Build stanc.js
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Use OCaml ${{ env.OCAML_VERSION }}
+        uses: ocaml/setup-ocaml@v3
+        with:
+          ocaml-compiler: ${{ env.OCAML_VERSION }}
+          dune-cache: true
+          cache-prefix: v1-js
+
+      - run: bash -x scripts/install_build_deps.sh
+      - run: bash -x scripts/install_js_deps.sh
+
+      - run: opam exec -- dune build --profile release src/stancjs
+
+      - run: mv _build/default/src/stancjs/stancjs.bc.js stanc.js
+
+      - name: Upload stanc.js
+        uses: actions/upload-artifact@v4
+        with:
+          name: stanc.js
+          path: stanc.js
+
+  test-builds:
+    needs: [build, build-universal, xbuild-windows]
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            name: ubuntu
+          - os: macos-latest
+            name: macos
+          - os: macos-13
+            name: macos
+          - os: windows-latest
+            name: windows
+
+    runs-on: ${{ matrix.os }}
+
+    name: Test built stanc on ${{ matrix.os }}
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: ${{ matrix.name }}-stanc
+
+      - name: Update permissions
+        if: matrix.name != 'windows'
+        run: chmod +x ${{ matrix.name }}-stanc
+
+      - name: Run tests
+        run: |
+          mv ${{ matrix.name }}-stanc stanc.exe
+          ./stanc.exe --help

stanc3/.gitignore

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+# rust
+/rust/target
+/bindgen_test/target
+**/*.rs.bk
+Cargo.lock
+math_iface/gen/*
+*.a
+
+# ocaml
+_opam
+_build
+_coverage/
+*.coverage
+*.merlin
+stanc.install
+
+# js
+node_modules/*
+
+# python
+*.pyc
+
+# tests
+test/*.log
+
+# Visual Studio settings
+.vscode/**
+
+# temporary editor files
+*~
+\#*#
+.#*
+.*.swp
+
+# Mac OS X hidden files
+*.DS_Store
+
+# .hpp files in test folder
+test/**/*.hpp
+
+# .omir files in test folder
+test/**/*.omir

stanc3/.ocamlformat

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+version=0.26.1
+# loosely re-creates the now-removed "compact" profile
+break-separators=before
+break-before-in=auto
+break-collection-expressions=wrap
+dock-collection-brackets=false
+doc-comments=before-except-val
+indicate-nested-or-patterns=space
+field-space=tight
+space-around-lists=false
+space-around-records=false
+space-around-variants=false
+sequence-blank-line=compact