Added action that builds and uploads wheels

* Builds both linux and MacOS
* Only run on tags

.github/workflows/package.yml

@@ -0,0 +1,103 @@
+name: Packaging
+
+# on: [push]
+on:
+  push:
+    tags:
+      - '*'
+
+jobs:
+  setup:
+    name: Build SWIG wrappers
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - name: Install numpy
+        run: python -m pip install numpy
+
+      - run: bash swig/python-packaging/setup.sh
+      - uses: actions/upload-artifact@v2
+        with:
+          name: my-artifact
+          path: build/swig/python-packaging/
+      - name: List
+        run: pwd && ls build/swig/python-packaging
+
+  build_wheels:
+    needs: setup
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # os: [ubuntu-20.04, windows-2019, macos-11]
+        os: [ubuntu-20.04, macos-11]
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.13.1
+
+      - uses: actions/download-artifact@v2
+        with:
+          name: my-artifact
+
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
+        env:
+          # Use boost 1_72, since this allows c++11. We need c++11, since manylinux2014 only has gcc 4.8
+          # Can't use boost 1.53 (default on linux) because it doesn't have rtree functionality
+          # CIBW_BUILD: cp36-manylinux_x86_64 cp36-win_amd64 cp36-macosx_x86_64
+          # CIBW_BUILD: cp310-macosx_x86_64
+          # PyPy compilation on MACOS doesn't work, possibly since there is no available numpy release for this
+          # Armadillo isn't available for i687 on Centos 7, making compilation more complicated
+          # # Musllinux doesn't use yum as its package manager
+          CIBW_SKIP: pp*-macosx* *i686* *musllinux*
+          CIBW_BEFORE_ALL_LINUX: |
+              yum install -y lapack-devel armadillo-devel
+              curl -L -O https://boostorg.jfrog.io/artifactory/main/release/1.72.0/source/boost_1_72_0.tar.gz
+              tar -xf boost_1_72_0.tar.gz
+              cd boost_1_72_0
+              cp -r boost /usr/include
+          CIBW_BEFORE_ALL_MACOS: |
+              # Other than the latest version, Brew only has boost 1.76. Therefore we must install boost from source
+              # brew reinstall gcc lapack gsl armadillo
+              brew reinstall lapack armadillo
+              curl -L -O https://boostorg.jfrog.io/artifactory/main/release/1.72.0/source/boost_1_72_0.tar.gz
+              tar -xf boost_1_72_0.tar.gz
+              cd boost_1_72_0
+              cp -r boost /usr/local/include
+              # Link in gcc, otherwise the default Apple compiler will be used, which doesn't support openmp by default
+              # ln -s /usr/local/bin/gcc-13 /usr/local/bin/gcc
+              # ln -s /usr/local/bin/g++-13 /usr/local/bin/g++
+          # CIBW_ENVIRONMENT_MACOS: CC='/usr/local/bin/gcc' LDSHARED='/usr/local/bin/gcc' CXX='/usr/local/bin/g++'
+          CIBW_ENVIRONMENT_MACOS: CFLAGS='-Wno-c++11-narrowing'
+          CIBW_BEFORE_ALL_WINDOWS: choco install -y lapack-devel
+          CIBW_TEST_COMMAND: >
+              python {project}/tests/check_installation.py
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: ./wheelhouse/*.whl
+
+
+  pypi-publish:
+    needs: build_wheels
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: wheels
+          path: wheelhouse
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: wheelhouse/
+          name: pypi
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}
+          url: https://pypi.org/p/gridpp
+          skip_existing: true

CMakeLists.txt

@@ -7,60 +7,67 @@ string(REGEX REPLACE "^.+define GRIDPP_VERSION \"([^\n]+)\".+" "\\1" PROJECT_VER
 
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
-# Boost 1.75 and above requires c++14 for the geometry library. For creating the python packages on
-# CentOS5, c++11 is more readily available, so this is preferred.
-find_package(Boost REQUIRED)
-find_package(Armadillo 6.5 REQUIRED)
-if(${Boost_MINOR_VERSION} GREATER 74)
-    set(CMAKE_CXX_STANDARD 14)
+option(BUILD_PACKAGE "Build package" OFF)
+
+if (BUILD_PACKAGE)
+
 else()
-    set(CMAKE_CXX_STANDARD 11)
-endif()
+    # Boost 1.75 and above requires c++14 for the geometry library. For creating the python packages on
+    # CentOS5, c++11 is more readily available, so this is preferred.
+    find_package(Boost REQUIRED)
+    find_package(Armadillo 6.5 REQUIRED)
+    if(${Boost_MINOR_VERSION} GREATER 74)
+        set(CMAKE_CXX_STANDARD 14)
+    else()
+        set(CMAKE_CXX_STANDARD 11)
+    endif()
 
-# Set compiler flags
-enable_language(CXX)
+    # Set compiler flags
+    enable_language(CXX)
 
-set(CMAKE_CXX_STANDARD_REQUIRED ON)
-set(CMAKE_CXX_EXTENSIONS OFF)
-if (NOT CMAKE_BUILD_TYPE)
-   message(STATUS "CMAKE_BUILD_TYPE is not set, switching to RELEASE")
-   set(CMAKE_BUILD_TYPE "RELEASE" CACHE STRING
-      "Choose the type of build, options are: NONE DEBUG RELEASE."
-      FORCE)
-endif()
-string(TOUPPER ${CMAKE_BUILD_TYPE} CMAKE_BUILD_TYPE)
+    set(CMAKE_CXX_STANDARD_REQUIRED ON)
+    set(CMAKE_CXX_EXTENSIONS OFF)
+    if (NOT CMAKE_BUILD_TYPE)
+       message(STATUS "CMAKE_BUILD_TYPE is not set, switching to RELEASE")
+       set(CMAKE_BUILD_TYPE "RELEASE" CACHE STRING
+          "Choose the type of build, options are: NONE DEBUG RELEASE."
+          FORCE)
+    endif()
+    string(TOUPPER ${CMAKE_BUILD_TYPE} CMAKE_BUILD_TYPE)
 
-if(APPLE)
-    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wfatal-errors -Wno-reorder -Wno-unused-variable -Wno-unused-value -Wno-narrowing -Wno-sign-compare -Wno-Wdelete-non-virtual-dtor -Wno-c++11-narrowing")
-else()
-    # SWIG generates a lot of warnings
-    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wfatal-errors -Wno-reorder -Wno-unused-variable -Wno-unused-value -Wno-narrowing -Wno-sign-compare -Wno-delete-non-virtual-dtor -Wl,-init,initialize_omp")
-endif()
+    if(APPLE)
+        set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wfatal-errors -Wno-reorder -Wno-unused-variable -Wno-unused-value -Wno-narrowing -Wno-sign-compare -Wno-Wdelete-non-virtual-dtor -Wno-c++11-narrowing")
+    else()
+        # SWIG generates a lot of warnings
+        set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wfatal-errors -Wno-reorder -Wno-unused-variable -Wno-unused-value -Wno-narrowing -Wno-sign-compare -Wno-delete-non-virtual-dtor -Wl,-init,initialize_omp")
+    endif()
 
-if (CMAKE_BUILD_TYPE MATCHES "DEBUG")
-   set(CMAKE_CXX_FLAGS_DEBUG "-O0 -fPIC -g -pg -rdynamic --coverage")
-   set(CMAKE_LFLAGS_DEBUG " --coverage")
-   add_definitions("-DDEBUG")
-elseif(CMAKE_BUILD_TYPE MATCHES "RELEASE")
-   find_package(OpenMP REQUIRED)
-   if(APPLE)
-        set(CMAKE_CXX_FLAGS_RELEASE "-O3 -fPIC")
+    if (CMAKE_BUILD_TYPE MATCHES "DEBUG")
+       set(CMAKE_CXX_FLAGS_DEBUG "-O0 -fPIC -g -pg -rdynamic --coverage")
+       set(CMAKE_LFLAGS_DEBUG " --coverage")
+       add_definitions("-DDEBUG")
+    elseif(CMAKE_BUILD_TYPE MATCHES "RELEASE")
+       find_package(OpenMP REQUIRED)
+       if(APPLE)
+            set(CMAKE_CXX_FLAGS_RELEASE "-O3 -fPIC")
+        else()
+            set(CMAKE_CXX_FLAGS_RELEASE "-O3 -fPIC ${OpenMP_CXX_FLAGS}")
+        endif()
     else()
-        set(CMAKE_CXX_FLAGS_RELEASE "-O3 -fPIC ${OpenMP_CXX_FLAGS}")
+        message(FATAL_ERROR "Unknown release type")
     endif()
-else()
-    message(FATAL_ERROR "Unknown release type")
-endif()
 
-# Required packages
+    # Required packages
+
+    add_library(gridpp ${SOURCES})
+    target_link_libraries(gridpp "${Boost_LIBRARIES}")
+    target_link_libraries(gridpp "${ARMADILLO_LIBRARIES}")
+    target_include_directories(gridpp PUBLIC "${Boost_INCLUDE_DIR}")
+    target_include_directories(gridpp PUBLIC "${ARMADILLO_INCLUDE_DIRS}")
 
+endif()
 include_directories(./include)
 file(GLOB SOURCES "src/api/*.cpp")
-add_library(gridpp ${SOURCES})
-target_link_libraries(gridpp "${Boost_LIBRARIES}")
-target_link_libraries(gridpp "${ARMADILLO_LIBRARIES}")
-target_include_directories(gridpp PUBLIC "${Boost_INCLUDE_DIR}")
-target_include_directories(gridpp PUBLIC "${ARMADILLO_INCLUDE_DIRS}")
 
 # Documentation
 option(BUILD_DOC "Build documentation" ON)

include/gridpp.h

@@ -13,7 +13,7 @@
 #endif
 #include <exception>
 
-#define GRIDPP_VERSION "0.7.0.dev2"
+#define GRIDPP_VERSION "0.7.0.dev4"
 #define __version__ GRIDPP_VERSION
 
 namespace gridpp {

swig/CMakeLists.txt

@@ -4,11 +4,14 @@ include(${SWIG_USE_FILE})
 
 # Add subdirectories for each language if desired
 option(BUILD_PYTHON "Build Python SWIG module" ON)
-if(BUILD_PYTHON)
-    add_subdirectory(python)
+if(BUILD_PACKAGE)
     add_subdirectory(python-packaging)
-endif()
-option(BUILD_R "Build R SWIG module" ON)
-if(BUILD_R)
-    add_subdirectory(R)
+else()
+    if(BUILD_PYTHON)
+        add_subdirectory(python)
+    endif()
+    option(BUILD_R "Build R SWIG module" ON)
+    if(BUILD_R)
+        add_subdirectory(R)
+    endif()
 endif()

swig/python-packaging/CMakeLists.txt

@@ -5,6 +5,7 @@ include_directories(${PYTHON_INCLUDE_PATH})
 # Files to install with Python
 file(GLOB CPP_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/include/*.h)
 file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/MANIFEST.in DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/pyproject.toml DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 
 # Configure setup.py and copy to output directory
 set(SETUP_PY_IN ${CMAKE_CURRENT_SOURCE_DIR}/setup.in.py)
@@ -22,8 +23,9 @@ add_custom_target(package-python
     COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/README.md ${CMAKE_CURRENT_BINARY_DIR}
     COMMAND ${CMAKE_COMMAND} -E copy ${SOURCES} ${CMAKE_CURRENT_BINARY_DIR}/src/api
     COMMAND ${CMAKE_COMMAND} -E copy ${CPP_INCLUDE_FILES} ${CMAKE_CURRENT_BINARY_DIR}/include
-    COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/include/dependencies ${CMAKE_CURRENT_BINARY_DIR}/include
+    # COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/include/dependencies ${CMAKE_CURRENT_BINARY_DIR}/include
     COMMAND ${SWIG_EXECUTABLE} -python -outdir ${CMAKE_CURRENT_BINARY_DIR} -c++ -I./include -o ${CMAKE_CURRENT_BINARY_DIR}/gridppPYTHON_wrap.cxx ${SWIG_INTERFACE}
-    COMMAND ${PYTHON_EXECUTABLE} ${SETUP_PY_OUT} sdist --dist-dir ${CMAKE_BINARY_DIR}
+    # COMMAND ${PYTHON_EXECUTABLE} ${SETUP_PY_OUT} sdist --dist-dir ${CMAKE_BINARY_DIR}
+    COMMAND python ${SETUP_PY_OUT} sdist --dist-dir ${CMAKE_BINARY_DIR}
     )
 # add_dependencies(package-python _gridpp2)

swig/python-packaging/pyproject.toml

@@ -0,0 +1,10 @@
+[build-system]
+requires = [
+    "setuptools>=42",
+    "wheel",
+    "Cython",
+    "numpy==1.12.1; python_version<'3.5'",
+    "oldest-supported-numpy; python_version>='3.5'",
+]
+
+build-backend = "setuptools.build_meta"

swig/python-packaging/setup.in.py

@@ -7,7 +7,8 @@
 from setuptools import setup, Extension
 import glob
 import itertools
-import numpy
+import numpy as np
+import sys
 
 __version__ = '${PROJECT_VERSION}'
 
@@ -29,14 +30,18 @@ def run(self):
         # self.do_egg_install()
         orig.install.run(self)
 
+args = []
+if sys.platform != "darwin":
+    args = "-fopenmp -fopenmp".split()
 
+# NOTE: We need c++11 because manylinux2014 has gcc 4.8, which preceedes c++14
 module = Extension('_gridpp',
         sources=glob.glob('src/api/*.cpp') + glob.glob('src/api/*.c') + ['gridppPYTHON_wrap.cxx'],
         libraries=["armadillo"],
-        extra_compile_args="${CMAKE_CXX_FLAGS_RELEASE} ${OpenMP_CXX_FLAGS} -std=c++${CMAKE_CXX_STANDARD}".split(),
-        extra_link_args="${CMAKE_CXX_FLAGS_RELEASE} ${OpenMP_CXX_FLAGS} -std=c++${CMAKE_CXX_STANDARD}".split(),
-        library_dirs=["/usr/lib64"],
-        include_dirs=['./include', numpy.get_include()]
+        extra_compile_args="-O3 -fPIC -std=c++11".split() + args,
+        extra_link_args="-O3 -fPIC -std=c++11".split() + args,
+        library_dirs=["/usr/lib64", "/usr/local/lib", "/usr/local/opt/armadillo/lib"],
+        include_dirs=['./include', np.get_include(), '/usr/local/opt/armadillo/include',  "/usr/include", "/usr/local/include"]
 )
 
 setup (
@@ -66,7 +71,7 @@ def run(self):
         #   3 - Alpha
         #   4 - Beta
         #   5 - Production/Stable
-        'Development Status :: 4 - Beta',
+        'Development Status :: 5 - Production/Stable',
 
         # Indicate who your project is intended for
         'Intended Audience :: Science/Research',
@@ -83,6 +88,9 @@ def run(self):
         'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
     ],
 
     # What does your project relate to?

swig/python-packaging/setup.sh

@@ -0,0 +1,4 @@
+mkdir build
+cd build
+cmake .. -DBUILD_PACKAGE=ON
+VERBOSE=1 make package-python

tests/check_installation.py

@@ -0,0 +1,6 @@
+import gridpp
+import numpy as np
+
+gridpp.neighbourhood(np.zeros([10, 10]), 3, gridpp.Mean)
+
+print("Check complete")