Use CMake and vcpkg

krypty · Apr 27, 2018 · 34579b5 · 34579b5
1 parent c816676
commit 34579b5
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Showing 13 changed files with 204 additions and 79 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -0,0  1,30 @@
 cmake_minimum_required(VERSION 3.1)
 project(pyFUGE)
 set(SOURCE_DIR pyfuge/py_fiseval)
 
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
 find_package(Eigen3 3.3 REQUIRED NO_MODULE)
 find_package(Catch2 REQUIRED NO_MODULE)
 find_package(OpenMP)
 if(OPENMP_FOUND)
         set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
         set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
 endif()
 include_directories(
     # ${SOURCE_DIR}
     ${CMAKE_SOURCE_DIR}/pyfuge/py_fiseval/FISEval/include
     ${EIGEN3_INCLUDE_DIR}
     )
 # get_cmake_property(_variableNames VARIABLES)
 # list (SORT _variableNames)
 # foreach (_variableName ${_variableNames})
 #     message(STATUS "${_variableName}=${${_variableName}}")
 # endforeach()
 add_subdirectory(${SOURCE_DIR}/FISEval)
 add_subdirectory(${SOURCE_DIR}/pybind11)
 pybind11_add_module(pyfuge_c SHARED "${SOURCE_DIR}/fiseval_bindings.cpp" ${SOURCE_DIR}/FISEval)
 target_link_libraries(pyfuge_c PRIVATE pyfuge)
 
 message(STATUS "${SOURCES}")
diff --git a/README.md b/README.md
@@ -31,3  31,9 @@ from pyfuge.evo.examples import evo_cancer
 evo_cancer.run_with_simple_evo()
 ```
 
 # NEW !
 ```bash
 export VCPKG_ROOT=/home/gary/CI4CB/PyFUGE/pyfuge/py_fiseval/FISEval/vcpkg
 #activate your virtualenv
 python setup.py install
 ```
diff --git a/pyfuge/evo/examples/evo_cancer.py b/pyfuge/evo/examples/evo_cancer.py
@@ -169,6  169,8 @@ def run_with_simple_evo():
         acc = _compute_accuracy(ds_test.y, y_pred_test)
         print("acc test ", acc)
 
 def run():
     run_with_simple_evo()
 
 if __name__ == '__main__':
     t0 = time()

diff --git a/pyfuge/py_fiseval/FISEval/CMakeLists.txt b/pyfuge/py_fiseval/FISEval/CMakeLists.txt
@@ -0,0  1,63 @@
 cmake_minimum_required(VERSION 3.1)
 project(FISEval)
 
 # set( CMAKE_VERBOSE_MAKEFILE on )
 
 # Enable C 14 features
 set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
 # Set build type
 # set(CMAKE_BUILD_TYPE Release)
 
 
 find_package(Eigen3 3.3 REQUIRED NO_MODULE)
 find_package(Catch2 REQUIRED NO_MODULE)
 find_package(OpenMP)
 
 if(OPENMP_FOUND)
         set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
         set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
 endif()
 
 # Compiler specific flags
 if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
         set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -ftree-vectorize -mtune=native -march=native -mavx")
 elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
 elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
 elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
 endif()
 
 include_directories(include)
 
 set(LINK_LIBRARIES
         Catch2::Catch
         Eigen3::Eigen
         )
 
 set(SOURCES
         src/fis.cpp
         )
 
 set(SOURCES_TEST
         tests/fis_lininterp_test.cpp
         tests/tests.cpp
         )
 set(SOURCES_TEST ${SOURCES_TEST} ${SOURCES})
 
 
 # Make executable
 add_library(pyfuge ${SOURCES})
 target_link_libraries(pyfuge ${LINK_LIBRARIES})
 
 
 # compile tests only if debug
 # TODO: use cmake built-in test mecanisms
 if (CMAKE_BUILD_TYPE STREQUAL "Debug")
         # remove the main from SOURCE to only use the main from tests.cpp
         list(REMOVE_ITEM SOURCES_TEST src/main.cpp)
         add_executable(run_tests ${SOURCES_TEST})
         target_link_libraries(run_tests ${LINK_LIBRARIES})
 endif()
diff --git a/pyfuge/py_fiseval/FISEval/Makefile b/pyfuge/py_fiseval/FISEval/Makefile
diff --git a/pyfuge/py_fiseval/FISEval/cpp/build/.gitkeep b/pyfuge/py_fiseval/FISEval/cpp/build/.gitkeep
diff --git a/...fiseval/FISEval/cpp/hpp/custom_eigen_td.h → ...fiseval/FISEval/include/custom_eigen_td.h b/...fiseval/FISEval/cpp/hpp/custom_eigen_td.h → ...fiseval/FISEval/include/custom_eigen_td.h
@@ -1,6  1,7 @@
 #ifndef CUSTOM_EG_TD
 #define CUSTOM_EG_TD
 
 
 #include <Eigen/Core>
 
 typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor> MatXd;

diff --git a/pyfuge/py_fiseval/FISEval/cpp/hpp/fis.h → pyfuge/py_fiseval/FISEval/include/fis.h b/pyfuge/py_fiseval/FISEval/cpp/hpp/fis.h → pyfuge/py_fiseval/FISEval/include/fis.h
@@ -1,7  1,7 @@
 #ifndef FIS_H
 #define FIS_H
 
-#include "../hpp/custom_eigen_td.h"
 #include "custom_eigen_td.h"
 #include <Eigen/Core>
 #include <iostream>
 #include <vector>

diff --git a/pyfuge/py_fiseval/FISEval/cpp/src/fis.cpp → pyfuge/py_fiseval/FISEval/src/fis.cpp b/pyfuge/py_fiseval/FISEval/cpp/src/fis.cpp → pyfuge/py_fiseval/FISEval/src/fis.cpp
@@ -1,4  1,4 @@
-#include "../hpp/fis.h"
 #include "fis.h"
 #include "omp.h"
 #include <algorithm>
 #include <cmath>

diff --git a/.../FISEval/cpp/tests/fis_lininterp_test.cpp → ...eval/FISEval/tests/fis_lininterp_test.cpp b/.../FISEval/cpp/tests/fis_lininterp_test.cpp → ...eval/FISEval/tests/fis_lininterp_test.cpp
@@ -1,8  1,8 @@
-#include "../vendor/catch/catch.hpp"
 #include "catch.hpp"
 
-#include "../hpp/fis.h"
 #include "fis.h"
 
-#include "../hpp/custom_eigen_td.h"
 #include "custom_eigen_td.h"
 #include <Eigen/Core>
 
 using namespace std;

diff --git a/...ge/py_fiseval/FISEval/cpp/tests/tests.cpp → pyfuge/py_fiseval/FISEval/tests/tests.cpp b/...ge/py_fiseval/FISEval/cpp/tests/tests.cpp → pyfuge/py_fiseval/FISEval/tests/tests.cpp
@@ -4,7  4,7 @@
 // Let Catch provide main():
 #define CATCH_CONFIG_MAIN
 
-#include "../vendor/catch/catch.hpp"
 #include "catch.hpp"
 
 // That's it
 

diff --git a/pyfuge/py_fiseval/fiseval_bindings.cpp b/pyfuge/py_fiseval/fiseval_bindings.cpp
@@ -1,4  1,4 @@
-#include "FISEval/cpp/hpp/fis.h"
 #include "fis.h"
 #include <pybind11/numpy.h>
 #include <pybind11/pybind11.h>
 

diff --git a/setup.py b/setup.py
@@ -1,40  1,102 @@
-import glob
 import os
 import platform
 import re
 import subprocess
 import sys
 import sysconfig
 from distutils.version import LooseVersion
 from shutil import copyfile, copymode
 
-from setuptools import setup, find_packages, Extension
 from setuptools import Extension, find_packages, setup
 from setuptools.command.build_ext import build_ext
 
 HERE = os.path.dirname(os.path.abspath(__file__))
 
-extra_compile_args = ["-fopenmp"]
-extra_link_args = ["-fopenmp"]
-
-if sys.platform == "win32":
-    extra_compile_args = ["-D_hypot=hypot", "-openmp"]
-    extra_link_args = ["-static"]
-
-pyfuge_module = Extension(
-    'pyfuge_c',
-    include_dirs=[
-        os.path.join(HERE,
-                     'pyfuge/py_fiseval/FISEval/cpp/vendor/catch'),
-        os.path.join(HERE,
-                     'pyfuge/py_fiseval/FISEval/cpp/vendor/eigen'),
-        os.path.join(HERE,
-                     'pyfuge/py_fiseval/pybind11/include'),
-    ],
-    sources=(
-        # sources for fiseval itself
-        glob.glob(os.path.join(HERE, 'pyfuge/py_fiseval/FISEval/cpp/src/*.cpp'))
-
-        # sources for the python bindings
-          glob.glob(os.path.join(HERE, 'pyfuge/py_fiseval/*.cpp'))
-    ),
-    depends=glob.glob(
-        os.path.join(HERE, 'pyfuge/py_fiseval/FISEval/cpp/src/*.hpp')),
-    extra_compile_args=extra_compile_args,
-    extra_link_args=extra_link_args,
-)
 
 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_TOOLCHAIN_FILE={}/scripts/buildsystems/vcpkg.cmake'.format(
                 os.environ["VCPKG_ROOT"]),
             '-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)
         # Copy *_test file to tests directory
         # test_bin = os.path.join(self.build_temp, 'python_cpp_example_test')
         # self.copy_test_file(test_bin)
         print()  # Add an empty line for cleaner output
 
     def copy_test_file(self, src_file):
         '''
         Copy ``src_file`` to ``dest_file`` ensuring parent directory exists.
         By default, message like `creating directory /path/to/package` and
         `copying directory /src/path/to/package -> path/to/package` are displayed on standard output. Adapted from scikit-build.
         '''
         # Create directory if needed
         dest_dir = os.path.join(os.path.dirname(
             os.path.abspath(__file__)), 'tests', 'bin')
         if dest_dir != "" and not os.path.exists(dest_dir):
             print("creating directory {}".format(dest_dir))
             os.makedirs(dest_dir)
 
         # Copy file
         dest_file = os.path.join(dest_dir, os.path.basename(src_file))
         print("copying {} -> {}".format(src_file, dest_file))
         copyfile(src_file, dest_file)
         copymode(src_file, dest_file)
 
 
 pyfuge_module = CMakeExtension("pyfuge")
 
 setup(
     name='pyfuge',
@@ -44,6  106,7 @@
     url='http://iict-space.heig-vd.ch/cpn/',
     long_description=open(os.path.join(HERE, "README.md")).read(),
     ext_modules=[pyfuge_module],
     cmdclass=dict(build_ext=CMakeBuild),
     packages=find_packages(exclude=[
         "*playground*", "*.tests", "*.tests.*", "tests.*", "tests"
     ]),
@@ -58,4  121,5 @@
     ],
     setup_requires=['pytest-runner'],
     tests_require=["pytest==3.3.2"],
     zip_safe=False,
 )