Add cmake and ctest to build and run C++/python tests

.github/workflows/python-package.yml

@@ -1,4 +1,4 @@
-name: Python package
+name: Python and C++ package
 
 on: 
   pull_request:
@@ -24,23 +24,39 @@ jobs:
         uses: actions/checkout@v2
         with:
             submodules: recursive
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with: 
           python-version: ${{ matrix.python-version }} 
+
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install .
+          python3 -m pip install --upgrade pip
+          pip3 install -r requirements.txt
+
       - name: Install testing packages
         run: |
-          # pip install flake8
-          # pip install pydocstyle
-          pip install pytest
-          pip install pytest-cov pytest-xdist codecov
-      - name: Test with pytest
+          pip3 install pytest
+          pip3 install pytest-cov pytest-xdist codecov
+
+
+      # Below are the added steps for CMake
+
+      - name: Setup CMake
+        uses: jwlawson/[email protected]
+        with:
+          cmake-version: 3.21.1
+
+      - name: Configure and run CMake
+        shell: bash
         run: |
-          pytest --cov=pyoscode tests
+          mkdir test_build
+          cd test_build
+          PYTHON_PATH=$(which python)
+          cmake .. -DCMAKE_BUILD_TYPE=Debug -DPYTHON_EXECUTABLE=${PYTHON_PATH}
+          cmake --build . --target test 
+
       - name: Upload coverage to codecov
         uses: codecov/codecov-action@v2
+

.gitignore

@@ -4,10 +4,13 @@
 !/JOSS-paper/*
 /examples/*
 !/examples/*.cpp
+/examples/*.txt
+examples/output.txt
 .eggs/*
 .vscode/*
 bin/*
 build/*
+test_build/*
 dist/*
 env/*
 lib/*

CMakeLists.txt

@@ -0,0 +1,140 @@
+cmake_minimum_required(VERSION 3.20.2)
+project(
+    oscode
+    VERSION 1.3.0
+    LANGUAGES C CXX)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED YES)
+if(MSVC)
+    add_compile_options(/std:c++17)
+endif()
+set(CMAKE_CXX_EXTENSIONS NO)
+if (CMAKE_BUILD_TYPE MATCHES Release)
+  set(CMAKE_VERBOSE_MAKEFILE NO)
+else()
+  set(CMAKE_VERBOSE_MAKEFILE YES)
+endif()
+
+# Build Types
+set(CMAKE_BUILD_TYPE ${CMAKE_BUILD_TYPE}
+    CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel tsan asan lsan msan ubsan"
+    FORCE)
+
+# ThreadSanitizer
+set(CMAKE_C_FLAGS_TSAN
+    "-fsanitize=thread -g -O1 -march=native -mtune=native"
+    CACHE STRING "Flags used by the C compiler during ThreadSanitizer builds."
+    FORCE)
+set(CMAKE_CXX_FLAGS_TSAN
+    "-fsanitize=thread -g -O1 -march=native -mtune=native"
+    CACHE STRING "Flags used by the C++ compiler during ThreadSanitizer builds."
+    FORCE)
+
+# AddressSanitize
+set(CMAKE_C_FLAGS_ASAN
+    "-fsanitize=address -fno-optimize-sibling-calls -fsanitize-address-use-after-scope -fno-omit-frame-pointer -g -Og -march=native -mtune=native"
+    CACHE STRING "Flags used by the C compiler during AddressSanitizer builds."
+    FORCE)
+set(CMAKE_CXX_FLAGS_ASAN
+    "-fsanitize=address -fno-optimize-sibling-calls -fsanitize-address-use-after-scope -fno-omit-frame-pointer -g -Og -Wall -march=native -mtune=native"
+    CACHE STRING "Flags used by the C++ compiler during AddressSanitizer builds."
+    FORCE)
+
+# LeakSanitizer
+set(CMAKE_C_FLAGS_LSAN
+    "-fsanitize=leak -fno-omit-frame-pointer -g -O1"
+    CACHE STRING "Flags used by the C compiler during LeakSanitizer builds."
+    FORCE)
+set(CMAKE_CXX_FLAGS_LSAN
+    "-fsanitize=leak -fno-omit-frame-pointer -g -O1"
+    CACHE STRING "Flags used by the C++ compiler during LeakSanitizer builds."
+    FORCE)
+
+
+
+set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
+include(FetchContent)
+# Externally provided libraries
+FetchContent_Declare(googletest
+        GIT_REPOSITORY https://github.com/google/googletest.git
+        GIT_TAG main)
+
+FetchContent_MakeAvailable(googletest)
+
+FetchContent_Declare(
+  Eigen
+  GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
+  GIT_TAG 3.4.0)
+set(EIGEN_BUILD_DOC OFF)
+# note: To disable eigen tests,
+# you should put this code in a add_subdirectory to avoid to change
+# BUILD_TESTING for your own project too since variables are directory
+# scoped
+set(BUILD_TESTING OFF)
+set(EIGEN_BUILD_PKGCONFIG OFF)
+FetchContent_MakeAvailable(Eigen)
+
+set(Boost_USE_STATIC_LIBS ON)
+set(Boost_USE_STATIC_RUNTIME ON)
+set(BOOST_ENABLE_CMAKE ON)
+FetchContent_Declare(
+  boost
+  URL https://boostorg.jfrog.io/artifactory/main/release/1.82.0/source/boost_1_82_0.tar.gz
+)
+
+FetchContent_GetProperties(boost)
+if(NOT boost_POPULATED)
+  FetchContent_Populate(boost)
+  set(boost_INCLUDE_DIR ${boost_SOURCE_DIR})
+endif()
+
+
+if (NOT CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
+  add_compile_options(
+    -DNO_FPRINTF_OUTPUT 
+    -Wall
+    -O3)
+endif()
+
+set(oscode_INCLUDE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/include")
+
+set(PYTHON_EXECUTABLE "" CACHE FILEPATH "Python interpreter to use")
+
+option(OSCODE_HEADER_ONLY "Whether the headers are only included or if the python package should be built. Default builds the python package" OFF)
+
+if (NOT OSCODE_HEADER_ONLY)
+  if(NOT PYTHON_EXECUTABLE)
+    message(FATAL_ERROR "PYTHON_EXECUTABLE must be provided")
+  endif()
+  # Set the location of the eigen headers
+  #set(ENV{SOURCE_DIR} ${eigen_SOURCE_DIR})
+  if (CMAKE_BUILD_TYPE MATCHES Release)    
+    add_custom_target(pyoscode ALL
+      COMMAND ${CMAKE_COMMAND} -E env "OSCODE_EIGEN_INCLUDE_DIR=${eigen_SOURCE_DIR}" ${PYTHON_EXECUTABLE} setup.py build 
+      COMMAND ${CMAKE_COMMAND} -E env "OSCODE_EIGEN_INCLUDE_DIR=${eigen_SOURCE_DIR}" pip3 install -e .
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+      COMMENT "Building Python package using setup.py"
+    )
+  else()
+    add_custom_target(pyoscode ALL
+      COMMAND ${CMAKE_COMMAND} -E env "OSCODE_EIGEN_INCLUDE_DIR=${eigen_SOURCE_DIR}" ${PYTHON_EXECUTABLE} setup.py build_ext -i  
+      COMMAND ${CMAKE_COMMAND} -E env "OSCODE_EIGEN_INCLUDE_DIR=${eigen_SOURCE_DIR}" pip3 install -e .
+      COMMAND ${CMAKE_COMMAND} -E env "OSCODE_EIGEN_INCLUDE_DIR=${eigen_SOURCE_DIR}" ${PYTHON_EXECUTABLE} setup.py build_ext -if 
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+      COMMENT "Building Python package using setup.py"
+    )
+  endif()
+endif()
+unset(OSCODE_HEADER_ONLY CACHE)
+# Allows upstream users to call fetch_content etc.
+add_library(oscode INTERFACE)
+
+target_include_directories(oscode PUBLIC INTERFACE
+  ${oscode_INCLUDE_DIR}
+)
+
+target_link_libraries(oscode INTERFACE Eigen3::Eigen)
+
+include_directories(tests)
+add_subdirectory(tests)

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2020, Fruzsina Julia Agocs
+Copyright (c) 2023, Fruzsina Julia Agocs
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.rst

@@ -99,32 +99,27 @@ Python
 
    pip install pyoscode
 
-or via the setup.py
+Installing from source can be done via cmake with the following
 
 .. code:: bash
-
-   git clone --recursive https://github.com/fruzsinaagocs/oscode
-   cd oscode
-   python setup.py install --user
-
-or
-
-.. code:: bash
-
-   git clone --recursive https://github.com/fruzsinaagocs/oscode
+   git clone https://github.com/fruzsinaagocs/oscode
    cd oscode
-   pip install .
+   # For mac this will be $(which python3)
+   PYTHON_PATH=$(which python)
+   cmake -S . -B "build" -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=${PYTHON_PATH}
+   cd build
+   make oscode
 
 You can then import ``pyoscode`` from anywhere. Omit the ``--user`` option if
 you wish to install globally or in a virtual environment. If you have any
 difficulties, check out the `FAQs - Installation
 <https://github.com/fruzsinaagocs/oscode#installation-1>`__ section below. 
 
-You can check that things are working by running `tests/` (also ran by Travis continuous integration):
+You can check that things are working by running the tests in `tests/` (also ran by github actions):
 
 .. code:: bash
 
-   pytest tests/
+   make tests
 
 C++
 ~~~
@@ -133,7 +128,7 @@ C++
 
 .. code:: bash
 
-   git clone --recursive https://github.com/fruzsinaagocs/oscode
+   git clone https://github.com/fruzsinaagocs/oscode
 
 and then include the relevant header files in your C++ code:
 
@@ -176,16 +171,18 @@ C++
 :Introduction to oscode: `examples/burst.cpp`
 :To plot results from `burst.cpp`: `examples/plot_burst.py`
 
-To compile and run:
+To compile and run the burst example you can use the following:
 
 .. code:: bash
 
     cd examples/
-    g++ -I../include/ -g -Wall -std=c++11 -c -o burst.o burst.cpp
-    g++ -I../include/ -g -Wall -std=c++11 -o burst burst.o
-    ./burst
+    cmake -S . -B "build" -DCMAKE_BUILD_TYPE=Release -DOSCODE_HEADER_ONLY=YES
+    cd build && make burst_ex && ./burst_ex
 
 
+The `OSCODE_HEADER_ONLY` flag tells cmake to not create the python package target.
+You can use the `CMakeLists.txt` file in the examples folder as a reference point for including `oscode` into your own package.
+
 Documentation
 -------------
 
@@ -220,30 +217,41 @@ Further help
 
 You can get help by submitting an issue or posting a message on `Gitter <https://gitter.im/oscode-help/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge>`__.
 
-FAQs
-----
 
-Installation
-~~~~~~~~~~~~
+Development
+-------------
 
-1. Eigen import errors:
-    .. code:: bash
+Run the following to setup an environment for development:
 
-       pyoscode/_pyoscode.hpp:6:10: fatal error: Eigen/Dense: No such file or directory
-        #include <Eigen/Dense>
-                  ^~~~~~~~~~~~~
+    .. code:: bash
+        python -m venv env
+        source ./env/bin/activate
+        pip install numpy scipy pytest
+        PYTHON_PATH=$(which python)
+        cmake -S . -B "build" -DCMAKE_BUILD_TYPE=Debug -DPYTHON_EXECUTABLE=${PYTHON_PATH}
+        cd build
+        make oscode
+        make -j4 test
 
-    Try explicitly including the location of your Eigen library via the
-    ``CPLUS_INCLUDE_PATH`` environment variable, for example:
+Tests for the C++ and python can be run via cmake with 
 
     .. code:: bash
+        # This can take a while the first time because of boost
+        cmake -S . -B "build" -DCMAKE_BUILD_TYPE=Debug -DPYTHON_EXECUTABLE=${PYTHON_PATH}
+        # If your already inside of the build folder then run
+        # cmake .. -DCMAKE_BUILD_TYPE=Debug -DPYTHON_EXECUTABLE=${PYTHON_PATH}
+        cd ./build
+        make -j4 test
 
-       CPLUS_INCLUDE_PATH=/usr/include/eigen3 python setup.py install --user
-       # or 
-       CPLUS_INCLUDE_PATH=/usr/include/eigen3 pip install pyoscode
+Valid `CMAKE_BUILD_TYPE`s are `Release` `Debug`, `LSAN`, `MSAN`, `ASAN`, and `TSAN`
+
+
+Once in the build folder you can run the following to rebuild the cmake if you need to.
+
+    .. code:: bash
+        cmake .. -DCMAKE_BUILD_TYPE=Debug
+        make -j4 test
 
-    where  ``/usr/include/eigen3`` should be replaced with your system-specific
-    eigen location.
 
 Thanks
 ------
@@ -258,6 +266,8 @@ devs of `exhale <https://pypi.org/project/exhale/>`__ for making the beautiful C
 
 Changelog
 ---------
+- 1.3.0:
+    - Add support for cmake build and tests
 - 1.2.0:
     - Update the version of Eigen to 3.4.0
 - 1.1.2:

examples/CMakeLists.txt

@@ -0,0 +1,25 @@
+cmake_minimum_required(VERSION 3.20.2)
+project(
+    oscode_examples
+    VERSION 1.3.0
+    LANGUAGES C CXX)
+
+
+set(CMAKE_VERBOSE_MAKEFILE YES)
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED YES)
+set(CMAKE_CXX_EXTENSIONS NO)
+
+include(FetchContent)
+set(OSCODE_HEADER_ONLY ON)
+FetchContent_Declare(
+  oscode
+  GIT_REPOSITORY https://github.com/SteveBronder/oscode
+  GIT_TAG        feature/cmake
+)
+
+FetchContent_MakeAvailable(oscode)
+
+add_executable(burst_ex burst.cpp)
+
+target_link_libraries(burst_ex PRIVATE oscode)