Added setup.py for installing directly from pip

.gitignore

@@ -1,2 +1,8 @@
 build/
+dist/
+_build/
+_generate/
+*.so
+*.py[cod]
+*.egg-info
 *.pyd

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "pybind11"]
+	path = pybind11
+	url = https://github.com/pybind/pybind11.git

CMakeLists.txt

@@ -15,26 +15,13 @@ endif()
 
 find_package(OpenMP)
 
-
-find_package(Boost REQUIRED)
-include_directories(${Boost_INCLUDE_DIRS})
-
-
-find_package(pybind11 REQUIRED)
-include_directories(${pybind11_INCLUDE_DIRS})
-
-
 if (OPENMP_FOUND)
     set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
     set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
 endif()
 
 
-# set(WINDOWS_EXPORT_ALL_SYMBOLS 1)
-# set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS 1)
-
-
-include_directories(src)
+add_subdirectory(pybind11)
 
 pybind11_add_module(marching_cubes
     src/python_wrapper.cpp
@@ -44,23 +31,3 @@ pybind11_add_module(marching_cubes
     src/laplacian_smoothing.cpp)
 
 
-
-#################################
-# INSTALL THE PYTHON MODULE
-#################################
-
-if(NOT DEFINED PYTHON_MODULE_INSTALL_DIR OR PYTHON_MODULE_INSTALL_DIR MATCHES "^$")
-  execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
-                    "from distutils.sysconfig import *; print(get_python_lib(1))"
-                    OUTPUT_VARIABLE PYTHON_SITE_PACKAGES OUTPUT_STRIP_TRAILING_WHITESPACE)
-  FILE(TO_CMAKE_PATH ${PYTHON_SITE_PACKAGES} PYTHON_MODULE_INSTALL_DIR)
-endif()
-
-SET(PYTHON_MODULE_INSTALL_DIR ${PYTHON_MODULE_INSTALL_DIR}
-    CACHE PATH "where to install the marching cubres Python package" FORCE)
-
-# this is the install path relative to CMAKE_INSTALL_PREFIX,
-# use this in INSTALL() commands to get packaging right
-FILE(RELATIVE_PATH PYTHON_MODULE_INSTALL_DIR ${CMAKE_INSTALL_PREFIX} ${PYTHON_MODULE_INSTALL_DIR})
-
-install(TARGETS marching_cubes DESTINATION ${PYTHON_MODULE_INSTALL_DIR})

MANIFEST.in

@@ -0,0 +1,4 @@
+include README.md LICENSE
+global-include CMakeLists.txt *.cmake
+recursive-include src *
+recursive-include pybind11/include *.h

conda-recipe/bld.bat

@@ -1,17 +1,2 @@
-mkdir build
-cd build
-
-set CONFIGURATION=Release
-
-cmake .. -G "%CMAKE_GENERATOR%" ^
-    -DCMAKE_PREFIX_PATH="%LIBRARY_PREFIX%" ^
-    -DCMAKE_INSTALL_PREFIX="%LIBRARY_PREFIX%" ^
-    -DPYTHON_EXECUTABLE="%PYTHON%"
-
-if errorlevel 1 exit 1
-
-cmake --build . --target ALL_BUILD --config %CONFIGURATION%
-if errorlevel 1 exit 1
-
-cmake --build . --target INSTALL --config %CONFIGURATION%
+"%PYTHON%" setup.py install
 if errorlevel 1 exit 1

conda-recipe/build.sh

@@ -1,43 +1,3 @@
-export CXXFLAGS=""
-export CFLAGS=""
-export LDFLAGS=""
-
-PY_VER=$(python -c "import sys; print('{}.{}'.format(*sys.version_info[:2]))")
-PY_ABIFLAGS=$(python -c "import sys; print('' if sys.version_info.major == 2 else sys.abiflags)")
-PY_ABI=${PY_VER}${PY_ABIFLAGS}
-
-# Depending on our platform, shared libraries end with either .so or .dylib
-if [[ $(uname) == 'Darwin' ]]; then
-    DYLIB_EXT=dylib
-    CC=clang
-    CXX=clang++
-    CXXFLAGS="${CFLAGS} -std=c++11 -stdlib=libc++"
-else
-    DYLIB_EXT=so
-    CC=gcc
-    CXX=g++
-    CXXFLAGS="${CFLAGS} -std=c++11"
-    # enable compilation without CXX abi to stay compatible with gcc < 5 built packages
-    if [[ ${DO_NOT_BUILD_WITH_CXX11_ABI} == '1' ]]; then
-        CXXFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0 ${CXXFLAGS}"
-    fi
-fi
-
-mkdir build
-cd build
-cmake ..\
-    -DCMAKE_C_COMPILER=${CC} \
-    -DCMAKE_CXX_COMPILER=${CXX} \
-    -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
-    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-    -DCMAKE_PREFIX_PATH=${PREFIX} \
-    -DPYTHON_EXECUTABLE=${PYTHON} \
-    -DPYTHON_LIBRARY=${PREFIX}/lib/libpython${PY_ABI}.${DYLIB_EXT} \
-    -DPYTHON_INCLUDE_DIR=${PREFIX}/include/python${PY_ABI} \
-##
-
-make -j${CPU_COUNT}
-
-make install
-
-#cp ${SRC_DIR}/build/marching_cubes*.so ${PREFIX}/lib/python${PY_VER}/site-packages/
+#!/bin/bash
+unset MACOSX_DEPLOYMENT_TARGET
+${PYTHON} setup.py install;

conda-recipe/meta.yaml

@@ -1,43 +1,33 @@
 package:
-    name: marching_cubes
-
-  {% if GIT_DESCRIBE_NUMBER|int == 0 %}
-    version: {{GIT_DESCRIBE_TAG}}
-  {% else %}
-    # If we're using a non-tagged revision, append '.postN' to the version
-    version: {{GIT_DESCRIBE_TAG}}.post{{GIT_DESCRIBE_NUMBER}}
-  {% endif %}
-
-source:
-  path: ../
+  name: cmake_example
+  version: {{ environ.get('GIT_DESCRIBE_TAG', 'dev') }}
 
 build:
-  number: 0
-  string: py{{CONDA_PY}}_{{PKG_BUILDNUM}}_h{{PKG_HASH}}_g{{GIT_FULL_HASH[:7]}}
+  number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
+  {% if environ.get('GIT_DESCRIBE_NUMBER', '0') == '0' %}string: py{{ environ.get('PY_VER').replace('.', '') }}_0
+  {% else %}string: py{{ environ.get('PY_VER').replace('.', '') }}_{{ environ.get('GIT_BUILD_STR', 'GIT_STUB') }}{% endif %}
   script_env:
-    # Control building with CXX11 abi
-    - DO_NOT_BUILD_WITH_CXX11_ABI  # [linux]
+    - CC
+    - CXX
+
+source:
+  git_url: ../
 
 requirements:
   build:
-    - cmake
-    - python >=2.7
-    - python {{ python }}
-    - boost {{ boost }}
+    - python
+    - setuptools
     - pybind11
+    - cmake
+
   run:
     - python
-    - boost
-    # in order to suppor older linux distros after gcc5 switch:
-    - libstdcxx-ng >={{ libstdcxxng }}  # [linux]
-    - numpy
+    - vs2015_runtime  # [win]
 
 test:
   imports:
-    - marching_cubes
+    - cmake_example
 
 about:
-  home: http://ilastik.org
-  license: BSD (3-clause)
-  liscense_file: LICENSE
-  summary: A fast marching cubes implementation in C++ with python bindings.
+  summary: An example project built with pybind11.
+  license_file: LICENSE

setup.py

@@ -0,0 +1,67 @@
+import os
+import re
+import sys
+import platform
+import subprocess
+
+from setuptools import setup, Extension
+from setuptools.command.build_ext import build_ext
+from distutils.version import LooseVersion
+
+
+class CMakeExtension(Extension):
+    def __init__(self, name, sourcedir=''):
+        Extension.__init__(self, name, sources=[])
+        self.sourcedir = os.path.abspath(sourcedir)
+
+
+class CMakeBuild(build_ext):
+    def run(self):
+        try:
+            out = subprocess.check_output(['cmake', '--version'])
+        except OSError:
+            raise RuntimeError("CMake must be installed to build the following extensions: " +
+                               ", ".join(e.name for e in self.extensions))
+
+        if platform.system() == "Windows":
+            cmake_version = LooseVersion(re.search(r'version\s*([\d.]+)', out.decode()).group(1))
+            if cmake_version < '3.1.0':
+                raise RuntimeError("CMake >= 3.1.0 is required on Windows")
+
+        for ext in self.extensions:
+            self.build_extension(ext)
+
+    def build_extension(self, ext):
+        extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.name)))
+        cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
+                      '-DPYTHON_EXECUTABLE=' + sys.executable]
+
+        cfg = 'Debug' if self.debug else 'Release'
+        build_args = ['--config', cfg]
+
+        if platform.system() == "Windows":
+            cmake_args += ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}'.format(cfg.upper(), extdir)]
+            if sys.maxsize > 2**32:
+                cmake_args += ['-A', 'x64']
+            build_args += ['--', '/m']
+        else:
+            cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]
+            build_args += ['--', '-j2']
+
+        env = os.environ.copy()
+        env['CXXFLAGS'] = '{} -DVERSION_INFO=\\"{}\\"'.format(env.get('CXXFLAGS', ''),
+                                                              self.distribution.get_version())
+        if not os.path.exists(self.build_temp):
+            os.makedirs(self.build_temp)
+        subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
+        subprocess.check_call(['cmake', '--build', '.'] + build_args, cwd=self.build_temp)
+
+setup(
+    name='marching_cubes',
+    version='0.0.1',
+    description='Standalone marching cubes implementation and Python bindings',
+    long_description='',
+    ext_modules=[CMakeExtension('marching_cubes')],
+    cmdclass=dict(build_ext=CMakeBuild),
+    zip_safe=False,
+)

src/laplacian_smoothing.cpp

@@ -1,14 +1,14 @@
 #include "laplacian_smoothing.h"
 #include <vector>
-// #include <set>
+#include <set>
 // #include <unordered_set>
 #include <iostream>
 
 
-#include <boost/container/flat_set.hpp>
+// #include <boost/container/flat_set.hpp>
 
-typedef std::vector<boost::container::flat_set<size_t>> Adjacency;
-//typedef std::vector<std::set<size_t> > Adjacency;
+// typedef std::vector<boost::container::flat_set<size_t>> Adjacency;
+typedef std::vector<std::set<size_t> > Adjacency;
 //typedef std::vector<std::unordered_set<size_t> > Adjacency;
 /**
  * maps each vertex to all its neighbours