WIP: CPP and PY integration

.devcontainer/Dockerfile

@@ -0,0 +1,22 @@
+# FROM mcr.microsoft.com/devcontainers/cpp:1-ubuntu-24.04
+FROM mcr.microsoft.com/devcontainers/cpp:dev-ubuntu-24.04
+
+ARG REINSTALL_CMAKE_VERSION_FROM_SOURCE="none"
+
+# Optionally install the cmake for vcpkg
+COPY ./reinstall-cmake.sh /tmp/
+
+RUN if [ "${REINSTALL_CMAKE_VERSION_FROM_SOURCE}" != "none" ]; then \
+        chmod +x /tmp/reinstall-cmake.sh && /tmp/reinstall-cmake.sh ${REINSTALL_CMAKE_VERSION_FROM_SOURCE}; \
+    fi \
+    && rm -f /tmp/reinstall-cmake.sh
+
+# [Optional] Uncomment this section to install additional vcpkg ports.
+# RUN su vscode -c "${VCPKG_ROOT}/vcpkg install clangd"
+
+# [Optional] Uncomment this section to install additional packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+RUN apt update && export DEBIAN_FRONTEND=noninteractive && apt -y install clangd-19 clang-tidy-19 python3-pip
+RUN update-alternatives --install /usr/bin/clangd clangd /usr/bin/clangd-19 100
+RUN update-alternatives --install /usr/bin/clang-tidy clang-tidy /usr/bin/clang-tidy-19 100

.devcontainer/devcontainer.json

@@ -0,0 +1,21 @@
+// 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++",
+	"build": {
+		"dockerfile": "Dockerfile"
+	},
+	"containerEnv": {
+		"CLIPPY_BACKEND_PATH": "${containerWorkspaceFolder}/build/test"
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"llvm-vs-code-extensions.vscode-clangd",
+				"ms-python.python"
+				// add other extensions as needed
+			]
+		}
+	},
+	//"postCreateCommand": "pip install --break-system-packages -r  ${containerWorkspaceFolder}/test/requirements.txt"
+}

.devcontainer/reinstall-cmake.sh

@@ -0,0 +1,59 @@
+#!/usr/bin/env bash
+#-------------------------------------------------------------------------------------------------------------
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information.
+#-------------------------------------------------------------------------------------------------------------
+#
+set -e
+
+CMAKE_VERSION=${1:-"none"}
+
+if [ "${CMAKE_VERSION}" = "none" ]; then
+    echo "No CMake version specified, skipping CMake reinstallation"
+    exit 0
+fi
+
+# Cleanup temporary directory and associated files when exiting the script.
+cleanup() {
+    EXIT_CODE=$?
+    set +e
+    if [[ -n "${TMP_DIR}" ]]; then
+        echo "Executing cleanup of tmp files"
+        rm -Rf "${TMP_DIR}"
+    fi
+    exit $EXIT_CODE
+}
+trap cleanup EXIT
+
+
+echo "Installing CMake..."
+apt-get -y purge --auto-remove cmake
+mkdir -p /opt/cmake
+
+architecture=$(dpkg --print-architecture)
+case "${architecture}" in
+    arm64)
+        ARCH=aarch64 ;;
+    amd64)
+        ARCH=x86_64 ;;
+    *)
+        echo "Unsupported architecture ${architecture}."
+        exit 1
+        ;;
+esac
+
+CMAKE_BINARY_NAME="cmake-${CMAKE_VERSION}-linux-${ARCH}.sh"
+CMAKE_CHECKSUM_NAME="cmake-${CMAKE_VERSION}-SHA-256.txt"
+TMP_DIR=$(mktemp -d -t cmake-XXXXXXXXXX)
+
+echo "${TMP_DIR}"
+cd "${TMP_DIR}"
+
+curl -sSL "https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/${CMAKE_BINARY_NAME}" -O
+curl -sSL "https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/${CMAKE_CHECKSUM_NAME}" -O
+
+sha256sum -c --ignore-missing "${CMAKE_CHECKSUM_NAME}"
+sh "${TMP_DIR}/${CMAKE_BINARY_NAME}" --prefix=/opt/cmake --skip-license
+
+ln -s /opt/cmake/bin/cmake /usr/local/bin/cmake
+ln -s /opt/cmake/bin/ctest /usr/local/bin/ctest

.github/workflows/pr.yml

@@ -17,16 +17,18 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-          if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
+          if [ -f py/requirements.txt ]; then pip install -r py/requirements.txt; fi
+          if [ -f py/requirements-dev.txt ]; then pip install -r py/requirements-dev.txt; fi
 
-      - name: Lint with flake8
+      - name: Lint with ruff
         run: |
-          flake8 src/clippy --count --show-source --statistics --max-line-length=120
+          cd py
+          ruff check src/clippy --output-format=concise --statistics --line-length=120
 
 
       - name: MyPy
         run: |
+          cd py
           mypy src/clippy --ignore-missing-imports
 
       - name: Install Boost
@@ -40,33 +42,35 @@ jobs:
           # OPTIONAL: Specify a platform version
           # platform_version: 18.04
           # OPTIONAL: Specify a custom install location
-          boost_install_dir: /home/runner/work/boost
+          # boost_install_dir: /home/runner/work/boost
           # OPTIONAL: Specify a toolset
           toolset: gcc
           # OPTIONAL: Specify an architecture
           # arch: x86
 
+      # - name: Setup ccache
+      #   uses: hendrikmuhs/[email protected]
+      #   with:
+      #     key: ${{ github.job }}-${{ runner.os }}
+      #     max-size: 500M  # limit cache size
       - name: Build backend
         id: build-backend
         env:
           BOOST_ROOT: ${{ steps.install-boost.outputs.BOOST_ROOT }}
         run: |
           echo BOOST_ROOT is $BOOST_ROOT /end/
-          sudo apt install doxygen
-          TMPDIR=$(mktemp -d)
-          git clone https://github.com/LLNL/clippy-cpp --branch ${{ github.head_ref }} $TMPDIR || git clone https://github.com/LLNL/clippy-cpp --branch master $TMPDIR
-          mkdir -p $TMPDIR/build
-          cd $TMPDIR/build && cmake -DMODERN_CMAKE_BUILD_TESTING=ON  -DBUILD_TESTING=ON -DBOOST_ROOT=$BOOST_ROOT .. && make 
-          ls -l $TMPDIR/build/test
-          BACKEND=$TMPDIR/build/test
-          echo "BACKEND=$BACKEND" >> $GITHUB_ENV
+          sudo apt install -y doxygen
+          CPPDIR=cpp
+          mkdir -p $CPPDIR/build
+          cd $CPPDIR/build && cmake -DMODERN_CMAKE_BUILD_TESTING=ON -DBUILD_TESTING=ON -DBOOST_ROOT=$BOOST_ROOT .. && make 
+          ls -l examples
+          BACKEND=$CPPDIR/build/examples
+          # echo "BACKEND=$BACKEND" >> $GITHUB_ENV
 
       - name: Pytest
-        env:
-          CLIPPY_BACKEND_PATH: ${{ env.BACKEND }}
         run: |
-          echo "backend = $BACKEND"
-          pytest .
+          cd test
+          ./run_tests.sh
       # - name: Pytest
       #   run: |
       #     coverage run --source clippy/ -m pytest && coverage report -m --fail-under 99

.gitignore

@@ -1,9 +1,11 @@
 __pycache__
 **/build
 venv
-*.core
-build
 setup.cfg
 .vscode
 *.egg-info
 .coverage
+**/attic
+build
+*/.cache
+.cache/

README.md

@@ -23,51 +23,50 @@ environment – at the REPL, for example, or within a notebook – without the n
 complex HPC behavior and arcane job submission commands.
 
 ## Installation of Python Code
+There are three ways to use the Python code:
+1. Install from PyPI:
 ```console
-$ pip install .
+$ pip install llnl-clippy
 ```
 
-## Building C++ Examples on LC
+2. Install from the cloned repository:
+```console
+$ cd py/src && pip install .
+```
+
+3. Via `PYTHONPATH` (see below)
+
+## Building C++ Examples
 
 ```console
-$ . /usr/workspace/llamag/spack/share/spack/setup-env.sh
-$ git clone https://github.com/LLNL/clippy-cpp.git
-$ spack load gcc
-$ spack load boost
-$ cd clippy-cpp
-$ mkdir build
-$ cd build
-$ cmake ../
+$ cd cpp && mkdir build && cd build
+$ cmake ..
 $ make
-$ cd ../.. #back to root project directory 
 ```
 
-## Running Current C++ Examples
+## Running Current C++ Examples (after building)
+### From the repository root (using `PYTHONPATH`):
 ```python
-$ CLIPPY_BACKEND_PATH=/path/to/binaries ipython3
+$ PYTHONPATH=py/src:$PYTHONPATH CLIPPY_BACKEND_PATH=$(pwd)/cpp/build/examples ipython
 
-In [1]: from clippy import *
+In [1]: from clippy import ExampleBag
 
- ╭────────────────────────────────────╮
- │ It looks like you want to use HPC. │ 
- │ Would you like help with that?     │
- ╰────────────────────────────────────╯
-  ╲
-   ╲
-    ╭──╮  
-    ⊙ ⊙│╭
-    ││ ││
-    │╰─╯│
-    ╰───╯
+In [2]: b = ExampleBag()
+
+In [3]: b.insert(5).insert(6).insert(7)    # can chain methods
+Out[3]: <clippy.backends.fs.ExampleBag at 0x107d50830>
+
+In [4]: b.insert(5).insert(8)
+Out[4]: <clippy.backends.fs.ExampleBag at 0x107d50830>
 
-In [2]: c = ClippyBag()  # creates a bag datastructure.
+In [5]: b.size()
+Out[5]: 5
 
-In [3]: c.insert("foo").insert("bar")  # mutating methods can be chained
-
-Out[3]: foo bar
+In [6]: b.remove_if(b.value > 6)  # removes 2 elements
+Out[6]: <clippy.backends.fs.ExampleBag at 0x107d50830>
 
-In [4]: c.size()  # nonmutating methods return the appropriate output.
-Out[4]: 2
+In [7]: b.size()
+Out[7]: 3
 
 ```
 ## Authors

cpp/CMakeLists.txt

@@ -0,0 +1,96 @@
+# Copyright 2020 Lawrence Livermore National Security, LLC and other CLIPPy
+# Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: MIT
+
+
+cmake_minimum_required(VERSION 3.26)
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+set(ALLOW_DUPLICATE_CUSTOM_TARGETS TRUE)
+
+# Avoid warning about DOWNLOAD_EXTRACT_TIMESTAMP in CMake 3.24:
+if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.24.0")
+cmake_policy(SET CMP0135 NEW)
+endif()
+
+project(CLIPPy
+    VERSION 0.5
+    DESCRIPTION "Command Line Interface Plus Python"
+    LANGUAGES CXX)
+
+include(FetchContent) 
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+# Only do these if this is the main project, and not if it is included through add_subdirectory
+if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
+
+    set(CMAKE_CXX_STANDARD 20)
+    set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+    # Let's ensure -std=c++xx instead of -std=g++xx
+    set(CMAKE_CXX_EXTENSIONS OFF)
+
+    # Let's nicely support folders in IDE's
+    set_property(GLOBAL PROPERTY USE_FOLDERS ON)
+
+    # Testing only available if this is the main app
+    # Note this needs to be done in the main CMakeLists
+    # since it calls enable_testing, which must be in the
+    # main CMakeLists.
+    # include(CTest)
+
+    # Docs only available if this is the main app
+    find_package(Doxygen)
+    if(Doxygen_FOUND)
+	#add_subdirectory(docs)
+    else()
+	message(STATUS "Doxygen not found, not building docs")
+    endif()
+endif()
+
+
+#
+# Boost
+# Download and build Boost::json
+set(BOOST_URL
+    "https://github.com/boostorg/boost/releases/download/boost-1.87.0/boost-1.87.0-cmake.tar.gz"
+    CACHE STRING "URL to fetch Boost tarball")
+
+
+set(BOOST_INCLUDE_LIBRARIES json lexical_cast range)
+set(BUILD_SHARED_LIBS ON)
+FetchContent_Declare(
+    Boost
+    URL ${BOOST_URL})
+FetchContent_MakeAvailable(Boost)
+
+
+#
+# JSONLogic
+set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_BINARY_DIR}/boost-install) # needed for jsonlogic
+
+FetchContent_Declare(jsonlogic
+    GIT_REPOSITORY https://github.com/LLNL/jsonlogic.git
+    GIT_TAG v0.2.0
+    SOURCE_SUBDIR cpp
+)
+# set(jsonlogic_INCLUDE_DIR ${jsonlogic_SOURCE_DIR}/cpp/include/jsonlogic)
+FetchContent_MakeAvailable(jsonlogic)
+message(STATUS "jsonlogic source dir: ${jsonlogic_SOURCE_DIR}")
+
+
+
+### Require out-of-source builds
+file(TO_CMAKE_PATH "${PROJECT_BINARY_DIR}/CMakeLists.txt" LOC_PATH)
+if(EXISTS "${LOC_PATH}")
+    message(FATAL_ERROR "You cannot build in a source directory (or any directory with a CMakeLists.txt file). Please make a build subdirectory. Feel free to remove CMakeCache.txt and CMakeFiles.")
+endif()
+
+include_directories("${PROJECT_SOURCE_DIR}/include")
+
+option(TEST_WITH_SLURM "Run tests with Slurm" OFF)
+
+# Testing & examples are only available if this is the main app
+if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
+    add_subdirectory(examples)
+endif()

cpp/CMakePresets.json

@@ -0,0 +1,11 @@
+{
+  "version": 3,
+  "configurePresets": [
+    {
+      "name": "cfg",
+      "generator": "Ninja",
+      "sourceDir": "src",
+      "binaryDir": "build"
+    }
+  ]
+}