Beispiel #1
0
from setuptools import setup, find_packages, Extension
from setup_helper import SetupHelper
from Cython.Distutils import build_ext

name = "jcvi"
classifiers = [
    'Development Status :: 4 - Beta',
    'Intended Audience :: Science/Research',
    'License :: OSI Approved :: BSD License',
    'Programming Language :: Python',
    'Programming Language :: Python :: 2',
    'Topic :: Scientific/Engineering :: Bio-Informatics',
]

# Use the helper
h = SetupHelper(initfile="jcvi/__init__.py", readmefile="README.md")
h.check_version(name, majorv=2, minorv=7)
setup_dir = op.abspath(op.dirname(__file__))
requirements = [
    x.strip() for x in open(op.join(setup_dir, 'requirements.txt'))
]
h.install_requirements(requires=["cython", "numpy"])

# Now these are available

# Start the show
ext_modules = [
    Extension("jcvi.assembly.chic", ["jcvi/assembly/chic.pyx"],
              include_dirs=[np.get_include()],
              extra_compile_args=["-O3"]),
    Extension("jcvi.formats.cblast", ["jcvi/formats/cblast.pyx"],
Beispiel #2
0
import versioneer

NAME = "goatools"
CLASSIFIERS = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Programming Language :: Python",
    "Programming Language :: Python :: 2",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

# Use the helper
HLPR = SetupHelper(initfile="goatools/__init__.py", readmefile="README.md")

SETUP_DIR = op.abspath(op.dirname(__file__))
REQUIREMENTS = [
    x.strip()
    for x in open(op.join(SETUP_DIR, "requirements.txt")).readlines()
]

setup(
    name=NAME,
    version=versioneer.get_version(),
    author=HLPR.author,
    author_email=HLPR.email,
    license=HLPR.license,
    long_description=HLPR.long_description,
    long_description_content_type="text/markdown",
Beispiel #3
0

name = 'treecut'
classifiers = [
    'Development Status :: 4 - Beta',
    'Intended Audience :: Science/Research',
    'License :: OSI Approved :: BSD License',
    'Programming Language :: Python',
    'Programming Language :: Python :: 2',
    'Topic :: Scientific/Engineering :: Bio-Informatics',
    ]
with open('requirements.txt') as f:
    required = f.read().splitlines()

# Use the helper
h = SetupHelper(initfile="treecut/__init__.py", readmefile="README.md")
h.check_version(name, majorv=2, minorv=7)

setup(
    name=name,
    version=h.version,
    author=h.author,
    author_email=h.email,
    license=h.license,
    long_description=h.long_description,
    packages=[name],
    scripts=glob('scripts/*.py') + ["treecut.py"],
    classifiers=classifiers,
    url='http://github.com/tanghaibao/treecut',
    description="Find nodes in hierarchical clustering that are statistically significant",
    install_requires=required + ["ete2"],
Beispiel #4
0
from setuptools import setup, find_packages, Extension
from setup_helper import SetupHelper


name = "jcvi"
classifiers = [
    'Development Status :: 4 - Beta',
    'Intended Audience :: Science/Research',
    'License :: OSI Approved :: BSD License',
    'Programming Language :: Python',
    'Programming Language :: Python :: 2',
    'Topic :: Scientific/Engineering :: Bio-Informatics',
]

# Use the helper
h = SetupHelper(initfile="__init__.py", readmefile="README.md")
h.check_version(name, majorv=2, minorv=7)
h.install_requirements(requires=["cython", "numpy"])

# Now these are available
import numpy as np
from Cython.Distutils import build_ext

# Start the show
ext_modules = [
    Extension("jcvi.assembly.chic", ["assembly/chic.pyx"],
                     include_dirs=[np.get_include()],
                     extra_compile_args=["-O3"]),
    Extension("jcvi.formats.cblast", ["formats/cblast.pyx"],
                     extra_compile_args=["-O3"])
]
Beispiel #5
0
from setuptools import setup
from setup_helper import SetupHelper

name = "travis_example"
classifiers = [
    'Development Status :: 1 - Planning',
    'Intended Audience :: Other Audience',
    'License :: OSI Approved :: BSD License',
    'Programming Language :: Python',
    'Programming Language :: Python :: 2',
    'Programming Language :: Python :: 3',
    'Topic :: Documentation',
]

# Use the helper
h = SetupHelper(initfile="src/travis_example/__init__.py",
                readmefile="README.md")

setup_dir = op.abspath(op.dirname(__file__))
requirements = ['wget'] + [
    x.strip()
    for x in open(op.join(setup_dir, 'requirements.txt')).readlines()
]

setup(
    name=name,
    version=h.version,
    author=h.author,
    author_email=h.email,
    license=h.license,
    long_description=h.long_description,
    packages=[
Beispiel #6
0
classifiers = [
    'Development Status :: 4 - Beta',
    'Intended Audience :: Science/Research',
    'License :: OSI Approved :: BSD License',
    'Programming Language :: Python',
    'Programming Language :: Python :: 2',
    'Topic :: Scientific/Engineering :: Bio-Informatics',
]
with open('requirements.txt') as f:
    required = f.read().splitlines()

# Install Splithunter binary
subprocess.call("cd src && make -j 8 && cd ..", shell=True)

# Use the helper
h = SetupHelper(initfile=op.join(name, "__init__.py"), readmefile="README.md")
h.check_version(name, majorv=2, minorv=7)

setup(
      name=name,
      version=h.version,
      author=h.author,
      author_email=h.email,
      license=h.license,
      long_description=h.long_description,
      packages=[name],
      package_dir={name : name},
      include_package_data=True,
      package_data={name: ["data/*.*"]},
      scripts=["splithunter_run.py", "splithunter_report.py"],
      classifiers=classifiers,
Beispiel #7
0

name = "tredparse"
classifiers = [
    'Development Status :: 4 - Beta',
    'Intended Audience :: Science/Research',
    'License :: OSI Approved :: BSD License',
    'Programming Language :: Python',
    'Programming Language :: Python :: 2',
    'Topic :: Scientific/Engineering :: Bio-Informatics',
]
with open('requirements.txt') as f:
    required = f.read().splitlines()

# Use the helper
h = SetupHelper(initfile="tredparse/__init__.py", readmefile="README.md")
h.check_version(name, majorv=2, minorv=7)

libssw_ext = {"sources": ["src/ssw.c"], "include_dirs": ["src"]}

setup(
      name=name,
      version=h.version,
      author=h.author,
      author_email=h.email,
      license=h.license,
      long_description=h.long_description,
      packages=[name, "ssw"],
      package_dir={'ssw': 'src', 'tredparse': 'tredparse'},
      include_package_data=True,
      package_data={name: ["data/*.*"]},