RFC 0004 / RFC 0005: Refactor all remaining sampling logic from R / Python to C++ and standardize serialization

.clang-format

@@ -0,0 +1,5 @@
+BasedOnStyle: Google
+IndentWidth: 2
+AccessModifierOffset: -1
+ColumnLimit: 0
+SortIncludes: false

.clang-tidy

@@ -0,0 +1,32 @@
+---
+# Conservative clang-tidy config for stochtree.
+# Focuses on real bugs and performance issues; style is handled by clang-format.
+# To run manually: clang-tidy <file> -- (or via clangd in the editor)
+
+Checks: >
+  clang-analyzer-*,
+  bugprone-branch-clone,
+  bugprone-copy-constructor-init,
+  bugprone-dangling-handle,
+  bugprone-incorrect-roundings,
+  bugprone-infinite-loop,
+  bugprone-redundant-branch-condition,
+  bugprone-suspicious-include,
+  bugprone-use-after-move,
+  modernize-redundant-void-arg,
+  modernize-use-emplace,
+  modernize-use-nullptr,
+  modernize-use-override,
+  performance-for-range-copy,
+  performance-move-const-arg,
+  performance-unnecessary-copy-initialization,
+  -clang-analyzer-optin.performance.Padding
+
+# Leave empty to warn only, not fail the build.
+WarningsAsErrors: ""
+
+# Only surface warnings for project headers, not dependencies.
+HeaderFilterRegex: "include/stochtree/.*"
+
+# Respect .clang-format for any fixes clang-tidy applies.
+FormatStyle: file

.clangd

@@ -0,0 +1,14 @@
+---
+# Fallback compile flags for files not captured by compile_commands.json
+# (e.g. R wrapper files when BUILD_PYTHON=OFF, or before cmake has been run).
+# Files compiled by cmake use compile_commands.json and ignore these flags.
+CompileFlags:
+  Add:
+    - "-std=c++17"
+    - "-Iinclude"
+    - "-Ideps/boost_math/include"
+    - "-Ideps/eigen"
+    - "-Ideps/fast_double_parser/include"
+    - "-Ideps/fmt/include"
+    - "-Ideps/pybind11/include"
+  Compiler: clang++

.devcontainer/Dockerfile

@@ -5,7 +5,7 @@ RUN apt-get update -y && \
         valgrind && \
     rm -rf /var/lib/apt/lists/*
 
-ARG REINSTALL_CMAKE_VERSION_FROM_SOURCE="3.22.2"
+ARG REINSTALL_CMAKE_VERSION_FROM_SOURCE="3.29.3"
 
 # Optionally install the cmake for vcpkg
 COPY ./reinstall-cmake.sh /tmp/

.devcontainer/devcontainer.json

@@ -1,23 +1,34 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
 // README at: https://github.com/devcontainers/templates/tree/main/src/cpp
 {
-	"name": "C++",
+	"name": "stochtree C++ Dev",
 	"build": {
 		"dockerfile": "Dockerfile"
-	}
+	},
 
-	// Features to add to the dev container. More info: https://containers.dev/features.
-	// "features": {},
+	"features": {
+		"ghcr.io/devcontainers/features/git:1": {},
+		"ghcr.io/devcontainers/features/github-cli:1": {}
+	},
 
-	// Use 'forwardPorts' to make a list of ports inside the container available locally.
-	// "forwardPorts": [],
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"ms-vscode.cmake-tools",
+				"llvm-vs-code-extensions.vscode-clangd",
+				"vadimcn.vscode-lldb"
+			],
+			"settings": {
+				"clangd.path": "/usr/bin/clangd",
+				"clangd.arguments": ["--compile-commands-dir=${workspaceFolder}/build"],
+				"cmake.configureOnOpen": true,
+				"cmake.defaultConfigurePreset": "dev-quick",
+				"cmake.defaultBuildPreset": "dev-quick"
+			}
+		}
+	},
 
-	// Use 'postCreateCommand' to run commands after the container is created.
-	// "postCreateCommand": "gcc -v",
-
-	// Configure tool-specific properties.
-	// "customizations": {},
-
-	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
-	// "remoteUser": "root"
+	// Configure dev build (no test download) on container creation.
+	// Switch to the "dev" preset and re-run cmake when you need GoogleTest.
+	"postCreateCommand": "cmake --preset dev-quick && cmake --build --preset dev-quick"
 }

.github/workflows/cross-language-parity.yml

@@ -0,0 +1,77 @@
+name: Cross-Language Parity Tests
+
+# Runs on every push/PR to main. Ubuntu only — this is a correctness check,
+# not a platform-portability check. Python generates prediction fixtures;
+# R reproduces the same model with the same seed and compares.
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  parity:
+    name: cross-language-parity
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
+
+      # -----------------------------------------------------------------------
+      # Python
+      # -----------------------------------------------------------------------
+      - name: Setup Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+
+      - name: Install Python package
+        run: |
+          pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install .
+
+      # -----------------------------------------------------------------------
+      # R
+      # -----------------------------------------------------------------------
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::testthat, any::decor, any::rcmdcheck, any::jsonlite, any::devtools
+          needs: check
+
+      - name: Build and install R package
+        run: |
+          Rscript cran-bootstrap.R 0 0 1
+          R CMD INSTALL stochtree_cran
+
+      # -----------------------------------------------------------------------
+      # Parity tests
+      # -----------------------------------------------------------------------
+      - name: Generate Python predictions
+        run: |
+          python test/cross_language/generate_predictions.py \
+            --output-dir /tmp/parity_fixtures
+
+      - name: Verify R predictions match Python
+        run: |
+          Rscript test/cross_language/verify_predictions.R /tmp/parity_fixtures
+
+      # Upload fixtures on failure so they can be inspected
+      - name: Upload fixtures on failure
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: parity-fixtures
+          path: /tmp/parity_fixtures

.gitignore

@@ -3,10 +3,15 @@
 *.csv
 *.DS_Store
 lib/
-build*/
-.vscode/
+build/
+build-release*/
+.vscode/positron/
 xcode/
 *.json
+!.vscode/extensions.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!CMakePresets.json
 !test/R/testthat/fixtures/*.json
 !test/python/fixtures/*.json
 .vs/
@@ -15,7 +20,7 @@ cpp_docs/doxyoutput/xml
 cpp_docs/doxyoutput/latex
 stochtree_cran
 *.trace
-*.clangd
+.cache/clangd/
 *.claude
 *release_notes.md
 

.vscode/extensions.json

@@ -0,0 +1,8 @@
+{
+  "recommendations": [
+    "ms-vscode.cmake-tools",
+    "vadimcn.vscode-lldb",
+    "llvm-vs-code-extensions.vscode-clangd",
+    "Posit.air-vscode"
+  ]
+}

.vscode/launch.json

@@ -0,0 +1,107 @@
+{
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "bart_debug (macOS)",
+      "type": "lldb",
+      "request": "launch",
+      "program": "${workspaceFolder}/build/bart_debug",
+      "args": ["--scenario", "1", "--n", "500", "--n_test", "100", "--p", "5", "--num_trees", "200", "--num_gfr", "10", "--num_mcmc", "100", "--seed", "-1"],
+      "cwd": "${workspaceFolder}",
+      "preLaunchTask": "CMake: Build (dev-quick)"
+    },
+    {
+      "name": "bcf_debug (macOS)",
+      "type": "lldb",
+      "request": "launch",
+      "program": "${workspaceFolder}/build/bcf_debug",
+      "args": ["--scenario", "0", "--n", "500", "--n_test", "100", "--p", "5", "--num_trees_mu", "200", "--num_trees_tau", "50", "--num_gfr", "10", "--num_mcmc", "100", "--seed", "-1"],
+      "cwd": "${workspaceFolder}",
+      "preLaunchTask": "CMake: Build (dev-quick)"
+    },
+    {
+      "name": "teststochtree (macOS)",
+      "type": "lldb",
+      "request": "launch",
+      "program": "${workspaceFolder}/build/teststochtree",
+      "args": [],
+      "cwd": "${workspaceFolder}",
+      "preLaunchTask": "CMake: Build (dev)"
+    },
+    {
+      "name": "bart_debug (Linux/Container)",
+      "type": "cppdbg",
+      "request": "launch",
+      "program": "${workspaceFolder}/build/bart_debug",
+      "args": ["--scenario", "1", "--n", "500", "--n_test", "100", "--p", "5", "--num_trees", "200", "--num_gfr", "10", "--num_mcmc", "100", "--seed", "-1"],
+      "cwd": "${workspaceFolder}",
+      "MIMode": "gdb",
+      "preLaunchTask": "CMake: Build (dev-quick)"
+    },
+    {
+      "name": "bcf_debug (Linux/Container)",
+      "type": "cppdbg",
+      "request": "launch",
+      "program": "${workspaceFolder}/build/bcf_debug",
+      "args": ["--scenario", "1", "--n", "200", "--n_test", "100", "--p", "5", "--num_trees_mu", "200", "--num_trees_tau", "50", "--num_gfr", "10", "--num_mcmc", "100", "--seed", "-1"],
+      "cwd": "${workspaceFolder}",
+      "MIMode": "gdb",
+      "preLaunchTask": "CMake: Build (dev-quick)"
+    },
+    {
+      "name": "teststochtree (Linux/Container)",
+      "type": "cppdbg",
+      "request": "launch",
+      "program": "${workspaceFolder}/build/teststochtree",
+      "args": [],
+      "cwd": "${workspaceFolder}",
+      "MIMode": "gdb",
+      "preLaunchTask": "CMake: Build (dev)"
+    },
+    {
+      "name": "bart_debug (macOS, Release)",
+      "type": "lldb",
+      "request": "launch",
+      "program": "${workspaceFolder}/build-release-drivers/bart_debug",
+      "args": ["--scenario", "1", "--n", "500", "--n_test", "100", "--p", "5", "--num_trees", "200", "--num_gfr", "10", "--num_mcmc", "100", "--seed", "-1"],
+      "cwd": "${workspaceFolder}",
+      "preLaunchTask": "CMake: Build (release-drivers)"
+    },
+    {
+      "name": "bart_debug (Linux/Container, Release)",
+      "type": "cppdbg",
+      "request": "launch",
+      "program": "${workspaceFolder}/build-release-drivers/bart_debug",
+      "args": ["--scenario", "1", "--n", "500", "--n_test", "100", "--p", "5", "--num_trees", "200", "--num_gfr", "10", "--num_mcmc", "100", "--seed", "-1"],
+      "cwd": "${workspaceFolder}",
+      "MIMode": "gdb",
+      "preLaunchTask": "CMake: Build (release-drivers)"
+    },
+    {
+      "name": "bcf_debug (macOS, Release)",
+      "type": "lldb",
+      "request": "launch",
+      "program": "${workspaceFolder}/build-release-drivers/bcf_debug",
+      "args": ["--scenario", "1", "--n", "200", "--n_test", "100", "--p", "5", "--num_trees_mu", "200", "--num_trees_tau", "50", "--num_gfr", "10", "--num_mcmc", "100", "--seed", "-1"],
+      "cwd": "${workspaceFolder}",
+      "preLaunchTask": "CMake: Build (release-drivers)"
+    },
+    {
+      "name": "bcf_debug (Linux/Container, Release)",
+      "type": "cppdbg",
+      "request": "launch",
+      "program": "${workspaceFolder}/build-release-drivers/bcf_debug",
+      "args": ["--scenario", "1", "--n", "200", "--n_test", "100", "--p", "5", "--num_trees_mu", "200", "--num_trees_tau", "50", "--num_gfr", "10", "--num_mcmc", "100", "--seed", "-1"],
+      "cwd": "${workspaceFolder}",
+      "MIMode": "gdb",
+      "preLaunchTask": "CMake: Build (release-drivers)"
+    },
+    {
+      "name": "Python Debugger: Current File",
+      "type": "debugpy",
+      "request": "launch",
+      "program": "${file}",
+      "console": "integratedTerminal"
+    }
+  ]
+}