Fix MANIFEST.in and etc. (#89)

* Fix MANIFEST.in
Fixed the setup.py file because it conflicts with the version of dimod and its dependent packages.

* fix typo

* Fix Version

* ADD dependencies

* fix numpy version

* fix for poetry

* Update CMakeLists.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update setup.py

* Update requirements_doctest.txt

* Update setup.py

* Update pyproject.toml

* Update setup.py

* Update requirements_rtd.txt

* Update requirements.txt

* Update setup.py

* Update requirements.txt

* Update requirements_rtd.txt

* Update setup.py

* Update requirements.txt

* Update requirements_rtd.txt

* Update requirements_doctest.txt

* Update CMakeLists.txt

* Update requirements.txt

* Update requirements.txt

* Update setup.py

並列実行

* Update setup.py

* Update setup.py

* Update CMakeLists.txt

* Update CMakeLists.txt

* Update CMakeLists.txt

* Update CMakeLists.txt

* Update setup.py

* Update setup.py

* Update setup.py

* Update setup.py

* Update setup.py

* add CMAKE_INTERPROCEDURAL_OPTIMIZATION

* Update CMakeLists.txt

* remove extra_requires

* relax numpy version

* update pyenv initialization

Co-authored-by: Kotaro Tanahashi <colon0722@gmail.com>

.circleci/config.yml

@@ -312,7 +312,10 @@ jobs:
       - run: &create-virtualenv-using-pyenv
           name: create virtualenv
           command: |
-            eval "$(pyenv init -)"
+            export PYENV_ROOT="$HOME/.pyenv"
+            export PATH="$PYENV_ROOT/bin:$PATH"
+            
+            eval "$(pyenv init --path)"
             pyenv local $PYTHON
             which python
             python -m pip install virtualenv

CMakeLists.txt

@@ -1,9 +1,18 @@
 cmake_minimum_required(VERSION 3.11)
 
 project(cpp_pyqubo)
+
+set(CMAKE_INTERPROCEDURAL_OPTIMIZATION True)
+
+set(CXX_STANDARD_REQUIRED TRUE)
+set(CMAKE_VERBOSE_MAKEFILE TRUE)
+
 set(CMAKE_CXX_STANDARD 14)
 #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-declarations")
-set(CMAKE_CXX_FLAGS "-std=c++11 -O4")
+set(CMAKE_C_FLAGS "-Ofast -pipe" )
+set(CMAKE_CXX_FLAGS "-Ofast -pipe")
+set(CMAKE_C_FLAGS_RELEASE "-Ofast -pipe")
+set(CMAKE_CXX_FLAGS_RELEASE "-Ofast -pipe")
 
 include(external/pybind11.cmake)
 include_directories(cpp_dimod)

MANIFEST.in

@@ -1 +1,14 @@
-include README.rst
+include README.rst
+include *.cmake
+include FetchContent/*.cmake.in
+include CMakeLists.txt
+include pyproject.toml
+include requirements.txt
+include setup.py
+
+recursive-include pyqubo *
+recursive-include tests *
+recursive-include src *
+recursive-include external *
+recursive-include include *
+recursive-include cpp_dimod *

cpp_dimod/.CMakeLists.txt

@@ -3,3 +3,4 @@ add_library(cpp_dimod STATIC)
 target_include_directories(cpp_dimod
   PUBLIC ${PROJECT_SOURCE_DIR}
 )
+

external/cimod.cmake

@@ -12,4 +12,5 @@ if(NOT cimod_POPULATED)
     message(STATUS "Fetch cimod")
     FetchContent_Populate(cimod)
     include_directories(${cimod_SOURCE_DIR}/src)
-endif()
+endif()
+

external/googletest.cmake

@@ -12,4 +12,4 @@ if(NOT googletest_POPULATED)
     message(STATUS "Fetch googletest for C++ testing")
     FetchContent_Populate(googletest)
     add_subdirectory(${googletest_SOURCE_DIR} ${googletest_SOURCE_DIR}/googlemock)
-endif()
+endif()

pyproject.toml

@@ -0,0 +1,10 @@
+[build-system]
+requires = [
+    "cmake>=3.18.4",
+    'setuptools>=56.0.0',
+    'scikit-build>=0.11.1',
+    'wheel>=0.36.2',
+    'numpy>=1.17.3, <=1.20.0',
+    'Cython>=0.29.21'
+]
+build-backend = "setuptools.build_meta"

requirements.txt

@@ -1,9 +1,16 @@
-dimod==0.9.13
-numpy==1.18.2
-coverage==4.5.1
-codecov==2.1.9
+numpy==1.19.4; python_version >= '3.6'
+numpy==1.18.5; python_version == '3.5'
+Cython==0.29.21
+dimod==0.9.14
 dwave-neal==0.5.7
-Deprecated==1.2.10
-nbsphinx==0.3.5
+Deprecated>=1.2.10
+six>=1.15.0
+cmake>=3.18.4
+setuptools>=56.0.0; python_version >= '3.8'
 scikit-build>=0.11.1
-cmake>=3.18.2
+wheel>=0.36.2
+coverage>=4.5.1
+codecov>=2.1.9
+nbsphinx>=0.8.3; python_version >= '3.8'
+nbsphinx==0.3.5; python_version < '3.8'
+docutils<0.17,>=0.12; python_version < '3.8'

requirements_doctest.txt

@@ -1,2 +1,3 @@
-sphinx
-sphinx_rtd_theme
+Sphinx>=3.5.4
+sphinx-rtd-theme>=0.5.2
+docutils<0.17,>=0.12; python_version < '3.8'

requirements_rtd.txt

@@ -1,9 +1,12 @@
-dimod==0.9.2
-numpy==1.18.2
-coverage==4.5.1
-codecov==2.1.9
-dwave-neal==0.5.4
-Deprecated==1.2.10
-nbsphinx==0.3.5
-scikit-build>=0.11.1
-cmake>=3.18.2
+coverage>=4.5.1
+codecov>=2.1.9
+dwave-neal>=0.5.4
+nbsphinx>=0.3.5
+Deprecated>=1.2.10
+six>=1.15.0
+numpy==1.19.4; python_version >= '3.6'
+numpy==1.18.5; python_version == '3.5'
+dimod==0.9.14
+nbsphinx>=0.8.3; python_version >= '3.8'
+nbsphinx==0.3.5; python_version < '3.8'
+docutils<0.17,>=0.12; python_version < '3.8'

setup.cfg

@@ -0,0 +1,2 @@
+[metadata]
+description-file = README.rst

setup.py

@@ -1,21 +1,29 @@
 import os
-import re
-import sys
 import platform
+import re
 import subprocess
+import sys
 import sysconfig
-
-from setuptools import Extension
-from setuptools.command.build_ext import build_ext
 from distutils.version import LooseVersion
-from setuptools import Command
+from importlib.util import find_spec
+from multiprocessing import cpu_count
 
+from setuptools import Command, Extension
+from setuptools.command.build_ext import build_ext
 
-if os.getenv('READTHEDOCS') or platform.system() == "Linux":
+if platform.system() == "Windows":
+    from setuptools import setup
+elif find_spec('skbuild'):
+    from skbuild import setup
+elif os.getenv('NOT_USE_SKBUILD'):
+    from setuptools import setup
+elif os.getenv('READTHEDOCS'):
     from skbuild import setup
 else:
     from setuptools import setup
 
+CPU_COUNT = "-j" + str(cpu_count() + 1)
+
 
 class PackageInfo(object):
     def __init__(self, info_file):
@@ -26,8 +34,10 @@ def __init__(self, info_file):
     def __getattribute__(self, name):
         return super(PackageInfo, self).__getattribute__(name)
 
+
 package_info = PackageInfo(os.path.join('pyqubo', 'package_info.py'))
 
+
 class CMakeExtension(Extension):
     def __init__(self, name, sourcedir=''):
         Extension.__init__(self, name, sources=[])
@@ -60,12 +70,12 @@ def build_extension(self, ext):
 
         if platform.system() == "Windows":
             cmake_args += ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}'.format(cfg.upper(), extdir)]
-            if sys.maxsize > 2**32:
+            if sys.maxsize > 2 ** 32:
                 cmake_args += ['-A', 'x64']
             build_args += ['--', '/m']
         else:
             cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]
-            build_args += ['--', '-j2']
+            build_args += ['--', str(CPU_COUNT)]
 
         env = os.environ.copy()
         env['CXXFLAGS'] = '{} -DVERSION_INFO=\\"{}\\"'.format(env.get('CXXFLAGS', ''),
@@ -98,44 +108,63 @@ def run(self):
         subprocess.call(['./tests/pyqubo_test'],
                         cwd=os.path.join('build', self.cpplibdir), shell=True)
 
+
 packages = ['pyqubo', 'pyqubo.integer', 'pyqubo.utils']
 
 install_requires = [
-    'numpy<1.20,>=1.17.3',
-    'dimod>=0.9.13',
-    'dwave-neal>=0.5.7',
-    'Deprecated>=1.2.10',
-    'six>=1.11.0'
-    ]
-
+        'numpy>=1.17.3',
+        'dimod>=0.9.14, <=0.10.0',
+        'dwave-neal>=0.5.7',
+        'Deprecated>=1.2.12',
+        'six>=1.15.0'
+        ]
+
+setup_requires = [
+        'numpy>=1.17.3, <=1.20.0',
+        'scikit-build>=0.11.1',
+        'wheel>=0.36.2',
+        'Cython>=0.29.21'
+        "cmake>=3.18.4",
+        'setuptools',
+        'nbsphinx'
+        ]
+
+
+tests_require = [
+        'coverage>=4.5.1',
+        'codecov>=2.1.9'
+        ]
 
 python_requires = '>=3.5, <3.10'
 
 setup(
-    name=package_info.__package_name__,
-    version=package_info.__version__,
-    description=package_info.__description__,
-    long_description=open('README.rst').read(),
-    author=package_info.__contact_names__,
-    author_email=package_info.__contact_emails__,
-    maintainer=package_info.__contact_names__,
-    maintainer_email=package_info.__contact_emails__,
-    url=package_info.__repository_url__,
-    download_url=package_info.__download_url__,
-    license=package_info.__license__,
-    ext_modules=[CMakeExtension('pyqubo')],
-    cmdclass=dict(build_ext=CMakeBuild, cpp_test=CppTest),
-    zip_safe=False,
-    packages=packages,
-    keywords=package_info.__keywords__,
-    install_requires=install_requires,
-    python_requires=python_requires,
-    classifiers=[
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
-        'License :: OSI Approved :: Apache Software License',
-    ]
-)
+        name=package_info.__package_name__,
+        version=package_info.__version__,
+        description=package_info.__description__,
+        long_description=open('README.rst').read(),
+        author=package_info.__contact_names__,
+        author_email=package_info.__contact_emails__,
+        maintainer=package_info.__contact_names__,
+        maintainer_email=package_info.__contact_emails__,
+        url=package_info.__repository_url__,
+        download_url=package_info.__download_url__,
+        license=package_info.__license__,
+        ext_modules=[CMakeExtension('pyqubo')],
+        cmdclass=dict(build_ext=CMakeBuild, cpp_test=CppTest),
+        zip_safe=False,
+        packages=packages,
+        keywords=package_info.__keywords__,
+        install_requires=install_requires,
+        setup_requires=setup_requires,
+        python_requires=python_requires,
+        tests_require=tests_require,
+        include_package_data=True,
+        classifiers=[
+                'Programming Language :: Python :: 3.5',
+                'Programming Language :: Python :: 3.6',
+                'Programming Language :: Python :: 3.7',
+                'Programming Language :: Python :: 3.8',
+                'Programming Language :: Python :: 3.9',
+                'License :: OSI Approved :: Apache Software License',
+                ]
+        )