Squashed 'deps/data/bridgestan/' changes from a8cfe61..c7a425a

c7a425a Allow JSON data as a string (#60) 50fe2ec Update README examples section e380e82 Reword docstrings fb513e3 Reorganize and update documentation (#57) 96805fd Compile methods: split stanc args from make args, add default include path (#58) f62bf46 Fix broken link 676db6b Bump actions/setup-python from 2 to 4 (#55) 34f10dd Remove CmdStan Dependency (#51) 821883f Prefix any C-exposed symbols with `bs_` (#54) 81129b0 Add the option for autodiff Hessian calculations (#52) git-subtree-dir: deps/data/bridgestan git-subtree-split: c7a425aac54120bafa643b722ed24b2a32111782
StanJulia · Dec 7, 2022 · 543bfc5 · 543bfc5
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -8,3 +8,9 @@ updates:
     schedule:
       # Check for updates to GitHub Actions every month
       interval: "monthly"
+
+  # checks if stan-dev/stan@master has changed
+  - package-ecosystem: "gitsubmodule"
+    directory: "/"
+    schedule:
+      interval: "daily"
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
@@ -6,9 +6,6 @@ on:
       - 'main'
   workflow_dispatch: {}
 
-env:
-  CMDSTAN_VERSION: "2.31.0"
-
 jobs:
   build-docs:
     name: Publish documentation to gh-pages
@@ -23,16 +20,18 @@ jobs:
     steps:
       - name: Check out github
         uses: actions/checkout@v3
+        with:
+          submodules: recursive
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies (python)
         run: |
           python -m pip install --upgrade pip wheel
-          python -m pip install --upgrade "sphinx>5" nbsphinx ipython ipykernel ipywidgets pydata-sphinx-theme breathe myst-parser
+          python -m pip install --upgrade "sphinx>5" nbsphinx ipython ipykernel ipywidgets sphinx-copybutton pydata-sphinx-theme breathe myst-parser
 
       - name: Install os dependencies
         run: |
@@ -42,18 +41,12 @@ jobs:
       - name: Set up Julia
         uses: julia-actions/setup-julia@v1
 
-      - name: CmdStan installation cacheing
-        id: cmdstan-cache
+      - name: Stan submodule cacheing
         uses: actions/cache@v3
+        id: stan-cache
         with:
-          path: ~/.cmdstan
-          key: ${{ runner.os }}-cmdstan-${{ env.CMDSTAN_VERSION }}
-
-      - name: Install CmdStan
-        if: steps.cmdstan-cache.outputs.cache-hit != 'true'
-        run: |
-          python -m pip install cmdstanpy
-          python -m cmdstanpy.install_cmdstan --version "${{ env.CMDSTAN_VERSION }}" --cores 2
+          path: ./stan/
+          key: ${{ runner.os }}-stan-${{ hashFiles('stan/src/stan/version.hpp') }}-v${{ env.CACHE_VERSION }}
 
       - name: Install package
         run: |

diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -8,8 +8,7 @@ on:
   workflow_dispatch: {}
 
 env:
-  CMDSTAN_VERSION: "2.31.0"
-  CACHE_VERSION: 0
+  CACHE_VERSION: 1
 
 jobs:
   build_test_models:
@@ -22,28 +21,19 @@ jobs:
     steps:
       - name: Check out github
         uses: actions/checkout@v3
+        with:
+          submodules: recursive
 
-      - name: CmdStan installation cacheing
+      - name: Stan build caching
         uses: actions/cache@v3
-        id: cmdstan-cache
+        id: stan-cache
         with:
-          path: ~/.cmdstan
-          key: ${{ runner.os }}-cmdstan-${{ env.CMDSTAN_VERSION }}
-
-      - name: Install CmdStan (Unix)
-        if: matrix.os != 'windows-latest'
-        run: |
-          pipx run --spec cmdstanpy install_cmdstan --version "${{ env.CMDSTAN_VERSION }}" --cores 2 --verbose
-
-      - name: Install CmdStan (Windows)
-        if: matrix.os == 'windows-latest'
-        run: |
-          pipx run --spec cmdstanpy install_cmdstan --version "${{ env.CMDSTAN_VERSION }}" --cores 2 --verbose --compiler
+          path: ./stan/
+          key: ${{ runner.os }}-stan-${{ hashFiles('stan/src/stan/version.hpp') }}-v${{ env.CACHE_VERSION }}
 
       - name: Build C example (Unix)
         if: matrix.os != 'windows-latest'
         run: |
-          export CMDSTAN=~/.cmdstan/cmdstan-${{ env.CMDSTAN_VERSION }}/
           cd c-example/
           make example
           make example_static
@@ -60,20 +50,17 @@ jobs:
         id: test-models
         with:
           path: ./test_models/
-          key: ${{ hashFiles('**/*.stan', 'src/*') }}-${{ matrix.os }}-cmdstan-${{ env.CMDSTAN_VERSION }}-v${{ env.CACHE_VERSION }}
+          key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp') }}-${{ matrix.os }}-v${{ env.CACHE_VERSION }}
 
       - name: Build test models (Unix)
         if: matrix.os != 'windows-latest' && steps.test-models.outputs.cache-hit != 'true'
         run: |
-          export CMDSTAN=~/.cmdstan/cmdstan-${{ env.CMDSTAN_VERSION }}/
           make STAN_THREADS=true O=0 test_models -j2
         shell: bash
 
       - name: Build test models (Windows)
         if: matrix.os == 'windows-latest' && steps.test-models.outputs.cache-hit != 'true'
         run: |
-          $raw_cmdstan = "$($HOME)/.cmdstan/cmdstan-${{ env.CMDSTAN_VERSION }}/"
-          $env:CMDSTAN = $raw_cmdstan.replace('\', '/')
           mingw32-make.exe STAN_THREADS=true O=0 test_models -j2
         shell: pwsh
 
@@ -88,23 +75,27 @@ jobs:
     steps:
       - name: Check out github
         uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Restore CmdStan
+      - name: Restore Stan
         uses: actions/cache@v3
+        id: stan-cache
         with:
-          path: ~/.cmdstan
-          key: ${{ runner.os }}-cmdstan-${{ env.CMDSTAN_VERSION }}
+          path: ./stan/
+          key: ${{ runner.os }}-stan-${{ hashFiles('stan/src/stan/version.hpp') }}-v${{ env.CACHE_VERSION }}
 
       - name: Restore built models
         uses: actions/cache@v3
         id: test-models
         with:
           path: ./test_models/
-          key: ${{ hashFiles('**/*.stan', 'src/*') }}-${{ matrix.os }}-cmdstan-${{ env.CMDSTAN_VERSION }}-v${{ env.CACHE_VERSION }}
+          key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp') }}-${{ matrix.os }}-v${{ env.CACHE_VERSION }}
 
       - name: Install package
         run: |
@@ -117,6 +108,7 @@ jobs:
           export BRIDGESTAN=$(pwd)
           cd python/
           pytest -v
+          pytest -v --run-type=ad_hessian
 
   test_julia_client:
     needs: [build_test_models]
@@ -128,21 +120,25 @@ jobs:
     steps:
       - name: Check out github
         uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
       - name: Set up Julia
         uses: julia-actions/setup-julia@v1
 
-      - name: Restore CmdStan
+      - name: Restore Stan
         uses: actions/cache@v3
+        id: stan-cache
         with:
-          path: ~/.cmdstan
-          key: ${{ runner.os }}-cmdstan-${{ env.CMDSTAN_VERSION }}
+          path: ./stan/
+          key: ${{ runner.os }}-stan-${{ hashFiles('stan/src/stan/version.hpp') }}-v${{ env.CACHE_VERSION }}
 
       - name: Restore built models
         uses: actions/cache@v3
         id: test-models
         with:
           path: ./test_models/
-          key: ${{ hashFiles('**/*.stan', 'src/*') }}-${{ matrix.os }}-cmdstan-${{ env.CMDSTAN_VERSION }}-v${{ env.CACHE_VERSION }}
+          key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp') }}-${{ matrix.os }}-v${{ env.CACHE_VERSION }}
 
       - name: Run tests
         run: |
@@ -159,6 +155,8 @@ jobs:
     steps:
       - name: Check out github
         uses: actions/checkout@v3
+        with:
+          submodules: recursive
 
       - name: Install R
         uses: r-lib/actions/setup-r@v2.3.1
@@ -171,18 +169,18 @@ jobs:
             any::testthat
             any::devtools
 
-      - name: Restore CmdStan
+      - name: Restore Stan
         uses: actions/cache@v3
         with:
-          path: ~/.cmdstan
-          key: ${{ runner.os }}-cmdstan-${{ env.CMDSTAN_VERSION }}
+          path: ./stan/
+          key: ${{ runner.os }}-stan-${{ hashFiles('stan/src/stan/version.hpp') }}-v${{ env.CACHE_VERSION }}
 
       - name: Restore built models
         uses: actions/cache@v3
         id: test-models
         with:
           path: ./test_models/
-          key: ${{ hashFiles('**/*.stan', 'src/*') }}-${{ matrix.os }}-cmdstan-${{ env.CMDSTAN_VERSION }}-v${{ env.CACHE_VERSION }}
+          key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp') }}-${{ matrix.os }}-v${{ env.CACHE_VERSION }}
 
       - name: Run tests
         run: |
@@ -198,24 +196,26 @@ jobs:
     steps:
       - name: Check out github
         uses: actions/checkout@v3
+        with:
+          submodules: recursive
 
-      - name: Restore CmdStan
+      - name: Restore Stan
         uses: actions/cache@v3
+        id: stan-cache
         with:
-          path: ~/.cmdstan
-          key: ${{ runner.os }}-cmdstan-${{ env.CMDSTAN_VERSION }}
+          path: ./stan/
+          key: ${{ runner.os }}-stan-${{ hashFiles('stan/src/stan/version.hpp') }}-v${{ env.CACHE_VERSION }}
 
       - name: Setup TBB
         run: |
-          cd ~/.cmdstan/cmdstan-${{ env.CMDSTAN_VERSION }}
           Add-Content $env:GITHUB_PATH "$(pwd)/stan/lib/stan_math/lib/tbb"
 
       - name: Restore built models
         uses: actions/cache@v3
         id: test-models
         with:
           path: ./test_models/
-          key: ${{ hashFiles('**/*.stan', 'src/*') }}-windows-latest-cmdstan-${{ env.CMDSTAN_VERSION }}-v${{ env.CACHE_VERSION }}
+          key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp') }}-windows-latest-v${{ env.CACHE_VERSION }}
 
       - name: Install R
         uses: r-lib/actions/setup-r@v2.3.1

diff --git a/.gitignore b/.gitignore
@@ -33,3 +33,5 @@ bridgestan.Rcheck/
 build/
 
 .DS_Store
+
+bin/*
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,4 @@
+[submodule "stan"]
+	path = stan
+	url = https://github.com/stan-dev/stan
+	branch = master
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -2,7 +2,7 @@
 
 We welcome contributions to the project in any form, including bug reports, bug fixes, new features, improved documentation, or improved test coverage.
 
-Our next goal is a stable 1.0 release, which is mostly a matter of more thorough testing and documentation.
+Developer-specific documentation is available at https://roualdes.github.io/bridgestan/internals.html
 
 ## Licensing
 
@@ -29,26 +29,9 @@ We follow standard open source and GitHub practices:
 * We propose updates through [GitHub Pull Requests](https://github.com/roualdes/bridgestan/pulls) so that we can do code review.  We do not push directly to the main branch.
 
 
-## Documentation
-
-We use [Sphinx](https://www.sphinx-doc.org/en/master/) to generate documentation, with the goal of publishing on [Read the Docs](https://readthedocs.org) for the first release.  The docs are currently hosted on the [GitHub pages](https://roualdes.github.io/bridgestan/) for this repository.
-
-We use the following developer-specific tools for documentation.
-
-* [Sphinx 5.0 or above](https://www.sphinx-doc.org/en/master/)
-* [nbsphinx](https://nbsphinx.readthedocs.io/en/0.8.9/)
-* [pydata-sphinx-theme](https://pydata-sphinx-theme.readthedocs.io/en/stable/)
-* [MySt-Parser](https://myst-parser.readthedocs.io/en/latest/)
-
-If you wish to build the C++ portions of the documentation, you should also have:
-
-* [Doxygen](https://doxygen.nl/)
-* [Breathe](https://breathe.readthedocs.io/en/stable/index.html)
-
-
 ## Builds
 
-We use [Gnu make](https://www.gnu.org/software/make/) for builds.  If you have installed [CmdStan](https://mc-stan.org/users/interfaces/cmdstan) as required for the source to work, then you will already have Gnu make and a sufficient C++ compiler.
+We use [Gnu make](https://www.gnu.org/software/make/) for builds.  If you have previously used [CmdStan](https://mc-stan.org/users/interfaces/cmdstan), then you will already have Gnu make and a sufficient C++ compiler.
 
 
 ## Language specific practices
@@ -71,13 +54,8 @@ We use [Gnu make](https://www.gnu.org/software/make/) for builds.  If you have i
 ### Python development
 
 * Python development relies on the external dependencies:
-    * [pytest](https://docs.pytest.org/en/7.1.x/)
     * [NumPy](https://numpy.org/)
 
-* We integrate a C wrapper of Stan's model class using the [ctypes](https://docs.python.org/3/library/ctypes.html) foreign function interface.
-
-* We use the [numpy.testing](https://numpy.org/doc/stable/reference/routines.testing.html) unit testing framework and run the tests by calling [pytest](https://docs.pytest.org/en/7.1.x/) from the top-level Python directory `bridgestan/python`.
-
 * We autoformat code with [black](https://black.readthedocs.io/en/stable/).
 
 * We recommend but do not require checking the code style and semantics with [PyLint](https://www.pylint.org) using [BridgeStan .pylintrc](https://github.com/roualdes/bridgestan/blob/main/.pylintrc).
@@ -86,17 +64,14 @@ We use [Gnu make](https://www.gnu.org/software/make/) for builds.  If you have i
 
 * R dependencies beyond those included in this repo:
     * [R6 package](https://cran.r-project.org/web/packages/R6/index.html) for reference classes
-    * [testthat](https://testthat.r-lib.org) for unit testing
-
-* We use the most basic [.C interface](https://www.biostat.jhsph.edu/~rpeng/docs/interface.pdf) for calling C from R.
 
 ### Julia development
 
 * Julia dependencies beyond those included in this repo:
     * [Test](https://docs.julialang.org/en/v1/stdlib/Test/)
     * [LinearAlgebra](https://docs.julialang.org/en/v1/stdlib/LinearAlgebra/)
 
-* We use Julia's C foreign function interface, which is documented for [base C](https://docs.julialang.org/en/v1/base/c/) and the [C standard library](https://docs.julialang.org/en/v1/stdlib/Libdl/).
+* Julia code is formatted using [JuliaFormatter](https://github.com/domluna/JuliaFormatter.jl).
 
 
 ## Proposing a new interface language