Python 使用numpy和测试套件进行打包介绍_Python_Numpy_Fortran_Distutils_F2py

Python 使用numpy和测试套件进行打包介绍

python numpy fortran

Python 使用numpy和测试套件进行打包介绍,python,numpy,fortran,distutils,f2py,Python,Numpy,Fortran,Distutils,F2py,免责声明：我对使用distutils的python打包非常陌生。到目前为止，我只是将所有内容都隐藏到模块中，并手动打包并在此基础上开发。我以前从未编写过setup.py文件我有一个Fortran模块，我想在使用numpy的python代码中使用它。我认为最好的方法是f2py，因为它包含在numpy中。为了自动化构建过程，我想使用distutils和相应的numpy增强功能，其中包括用于f2py包装器的方便功能我不明白我应该如何组织我的文件，以及如何包含我的测试套件我想要的是能够使用/set

免责声明：我对使用distutils的python打包非常陌生。到目前为止，我只是将所有内容都隐藏到模块中，并手动打包并在此基础上开发。我以前从未编写过

setup.py

文件

我有一个Fortran模块，我想在使用numpy的python代码中使用它。我认为最好的方法是f2py，因为它包含在numpy中。为了自动化构建过程，我想使用distutils和相应的numpy增强功能，其中包括用于f2py包装器的方便功能

我不明白我应该如何组织我的文件，以及如何包含我的测试套件

我想要的是能够使用

/setup.py

进行构建、安装、测试和开发

我的目录结构如下所示：

volterra
├── setup.py
└── volterra
    ├── __init__.py
    ├── integral.f90
    ├── test
    │   ├── __init__.py
    │   └── test_volterra.py
    └── volterra.f90

而

setup.py

文件包含以下内容：

def configuration(parent_package='', top_path=None):
    from numpy.distutils.misc_util import Configuration
    config = Configuration('volterra', parent_package, top_path)
    config.add_extension('_volterra',
                         sources=['volterra/integral.f90', 'volterra/volterra.f90'])
    return config


if __name__ == '__main__':
    from numpy.distutils.core import setup
    setup(**configuration(top_path='').todict())

运行

/setup.py build

后，我得到一个

build/lib.linux-x86_64-2.7/
└── volterra
    └── _volterra.so

它既不包括

\uuuu init\uuuu.py

文件，也不包括测试

问题

是否真的需要将路径添加到扩展名的每个源文件中？（例如，
```
volterra/integral.f90
```
）我不能给出一个参数，表示在
```
volterra/
```
中查找内容吗？
```
top\u路径
```
和
```
package\u目录
```
参数没有起作用
当前，
```
\uuuuu init\uuuuuu.py
```
文件未包含在生成中。为什么呢
如何在此设置中运行测试
在这样的环境中进行开发的最佳工作流是什么？我不想为我所做的每一次更改安装我的软件包。当您需要编译一些扩展模块时，如何在源目录中进行开发

```
find_packages
```
，它消除了包含大量文件或在生成清单时乱来的繁琐工作
```
package_data
```
允许您轻松指定要包含的非.py文件
```
安装要求
```
/
```
测试要求
```

是否真的需要将路径添加到每个源文件分机？（即volterra/integral.f90）我不能给出一个参数吗也就是说，在volterra/中寻找东西？顶部路径和包目录参数没有起作用
当前，init.py文件不可用包括在构建中。为什么呢

find_packages（）

如何在这种情况下运行测试设置

volterra/volterra

volterra/tests

在这样的环境中进行开发的最佳工作流是什么环境我不想为每个人安装我的软件包我会改变的。您如何在源目录中进行开发您需要编译一些扩展模块吗

try:
    from setuptools import setup, find_packages
except ImportError:
    from distribute_setup import use_setuptools
    use_setuptools()
    from setuptools import setup, find_packages


setup(
    # ... other stuff
    py_modules=['distribute_setup'],
    packages=find_packages(),
    package_data={'': ['*.png']},  # for me to include anything with png
    install_requires=['numpy', 'treenode', 'investigators'],
    tests_require=['mock', 'numpy', 'treenode', 'investigators'],
)

# pkg - A fancy software package
# Copyright (C) 2013  author (email)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see http://www.gnu.org/licenses/gpl.html.
"""pkg: a software suite for 

Hey look at me I'm a long description
But how long am I?

"""

from __future__ import division, print_function

#ideas for setup/f2py came from:
#    -numpy setup.py: https://github.com/numpy/numpy/blob/master/setup.py 2013-11-07
#    -winpython setup.py: http://code.google.com/p/winpython/source/browse/setup.py 2013-11-07
#    -needing to use 
#        import setuptools; from numpy.distutils.core import setup, Extension: 
#        http://comments.gmane.org/gmane.comp.python.f2py.user/707 2013-11-07
#    -wrapping FORTRAN code with f2py: http://www2-pcmdi.llnl.gov/cdat/tutorials/f2py-wrapping-fortran-code 2013-11-07
#    -numpy disutils: http://docs.scipy.org/doc/numpy/reference/distutils.html 2013-11-07
#    -manifest files in disutils: 
#        'distutils doesn't properly update MANIFEST. when the contents of directories change.'
#        https://github.com/numpy/numpy/blob/master/setup.py         
#    -if things are not woring try deleting build, sdist, egg directories  and try again: 
#        https://stackoverflow.com/a/9982133/2530083 2013-11-07
#    -getting fortran extensions to be installed in their appropriate sub package
#        i.e. "my_ext = Extension(name = 'my_pack._fortran', sources = ['my_pack/code.f90'])" 
#        Note that sources is a list even if one file: 
#        http://numpy-discussion.10968.n7.nabble.com/f2py-and-setup-py-how-can-I-specify-where-the-so-file-goes-tp34490p34497.html 2013-11-07
#    -install fortran source files into their appropriate sub-package 
#        i.e. "package_data={'': ['*.f95','*.f90']}# Note it's a dict and list":
#        https://stackoverflow.com/a/19373744/2530083 2013-11-07
#    -Chapter 9 Fortran Programming with NumPy Arrays: 
#        Langtangen, Hans Petter. 2013. Python Scripting for Computational Science. 3rd edition. Springer.
#    -Hitchhikers guide to packaging :
#        http://guide.python-distribute.org/
#    -Python Packaging: Hate, hate, hate everywhere : 
#        http://lucumr.pocoo.org/2012/6/22/hate-hate-hate-everywhere/
#    -How To Package Your Python Code: 
#        http://www.scotttorborg.com/python-packaging/
#    -install testing requirements: 
#        https://stackoverflow.com/a/7747140/2530083 2013-11-07

import setuptools
from numpy.distutils.core import setup, Extension
import os
import os.path as osp

def readme(filename='README.rst'):
    with open('README.rst') as f:
        text=f.read()
    f.close()
    return text

def get_package_data(name, extlist):
    """Return data files for package *name* with extensions in *extlist*"""
    #modified slightly from taken from http://code.google.com/p/winpython/source/browse/setup.py 2013-11-7
    flist = []
    # Workaround to replace os.path.relpath (not available until Python 2.6):
    offset = len(name)+len(os.pathsep)
    for dirpath, _dirnames, filenames in os.walk(name):
        for fname in filenames:            
            if not fname.startswith('.') and osp.splitext(fname)[1] in extlist:
#                flist.append(osp.join(dirpath, fname[offset:]))
                flist.append(osp.join(dirpath, fname))
    return flist

DOCLINES = __doc__.split("\n")
CLASSIFIERS = """\
Development Status :: 1 - Planning
License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
Programming Language :: Python :: 2.7
Topic :: Scientific/Engineering
"""

NAME = 'pkg'
MAINTAINER = "me"
MAINTAINER_EMAIL = "me@me.com"
DESCRIPTION = DOCLINES[0]
LONG_DESCRIPTION = "\n".join(DOCLINES[2:])#readme('readme.rst')
URL = "http://meeeee.mmemem"
DOWNLOAD_URL = "https://github.com/rtrwalker/geotecha.git"
LICENSE = 'GNU General Public License v3 or later (GPLv3+)'
CLASSIFIERS = [_f for _f in CLASSIFIERS.split('\n') if _f]
KEYWORDS=''
AUTHOR = "me"
AUTHOR_EMAIL = "me.com"
PLATFORMS = ["Windows"]#, "Linux", "Solaris", "Mac OS-X", "Unix"]
MAJOR = 0
MINOR = 1
MICRO = 0
ISRELEASED = False
VERSION = '%d.%d.%d' % (MAJOR, MINOR, MICRO)

INSTALL_REQUIRES=[]
ZIP_SAFE=False
TEST_SUITE='nose.collector'
TESTS_REQUIRE=['nose']

DATA_FILES = [(NAME, ['LICENSE.txt','README.rst'])]
PACKAGES=setuptools.find_packages()
PACKAGES.remove('tools')

PACKAGE_DATA={'': ['*.f95','*f90']}               
ext_files = get_package_data(NAME,['.f90', '.f95','.F90', '.F95'])
ext_module_names = ['.'.join(osp.splitext(v)[0].split(osp.sep)) for v in ext_files]
EXT_MODULES = [Extension(name=x,sources=[y]) for x, y in zip(ext_module_names, ext_files)]      


setup(
    name=NAME,
    version=VERSION,
    maintainer=MAINTAINER,
    maintainer_email=MAINTAINER_EMAIL,
    description=DESCRIPTION,
    long_description=LONG_DESCRIPTION,
    url=URL,
    download_url=DOWNLOAD_URL,
    license=LICENSE,
    classifiers=CLASSIFIERS,
    author=AUTHOR,
    author_email=AUTHOR_EMAIL,
    platforms=PLATFORMS,
    packages=PACKAGES,
    data_files=DATA_FILES,
    install_requires=INSTALL_REQUIRES,
    zip_safe=ZIP_SAFE,
    test_suite=TEST_SUITE,
    tests_require=TESTS_REQUIRE,
    package_data=PACKAGE_DATA,    
    ext_modules=EXT_MODULES,
    )

python setup.py install
python setup.py clean --all

C:\Python27\Lib\site packages\pkg-0.1.0-py2.7-win32.egg\pkg

C:\Python27\Lib\site packages\pkg

nosetests package_name -v

python setup.py develope

numpy setup.py:2013-11-07
winpython setup.py:2013-11-07
需要使用导入设置工具；从numpy.distutils.core导入设置，扩展名： 2013-11-07
用f2py包装FORTRAN代码：2013-11-07
纽比分裂：2013-11-07
不完整的清单文件： 'distutils无法正确更新清单。当目录的内容更改时。”
如果情况不正常，请尝试删除生成目录、sdist目录和egg目录，然后重试： 2013-11-07
在相应的子包中安装fortran扩展 i、 e.“my_ext=扩展名（name='my_pack.\u fortran'，sources=['my_pack/code.f90']）” 请注意，即使一个文件： 2013-11-07
将fortran源文件安装到相应的子包中 i、 e.“数据包={'：['.f95'，'.f90']}#注意这是一个dict和list”： 2013-11-07
第9章使用NumPy阵列进行Fortran编程：朗坦根，汉斯·佩特。2013用于计算科学的Python脚本。第三版。斯普林格
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