"""eastr setup.py"""

import os

import platform

import subprocess

from setuptools import find_packages, setup, Extension

from setuptools.command.build_ext import build_ext

class CMakeExtension(Extension):

def __init__(self, name, sourcedir=''):

Extension.__init__(self, name, sources=[])

self.sourcedir = os.path.abspath(sourcedir)

class CMakeBuild(build_ext):

"""CMake build extension."""

def run(self):

extensions = ', '.join(e.name for e in self.extensions)

deps = ['cmake', 'make']

for dep in deps:

try:

subprocess.check_output([dep, '--version'])

except OSError as e:

raise RuntimeError(

f'{dep} must be installed to build the following extensions: {extensions}') from e

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)))

extdir = os.path.join(extdir, ext.name)

cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir]

cmake_args += ['-DEXECUTABLE_OUTPUT_PATH=' + extdir]

cfg = 'Debug' if self.debug else 'Release'

build_args = ['--config', cfg]

if platform.system() == 'Windows':

cmake_args += ['-DCMAKE_GENERATOR_PLATFORM=x64']

cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]

build_args += ['--', '/m']

else:

cmake_args += ['-DCMAKE_BUILD_TYPE=Release .' + cfg]

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)

desc = 'Tool for emending alignments of spuriously spliced transcript reads'

with open('./README.md', 'r', encoding='utf-8') as fh:

long_description = fh.read()

with open('./LICENSE', 'r', encoding='utf-8') as fh:

license_str = fh.read()

setup(

name='eastr',

version='1.1.2',

author='Ida Shinder',

author_email='[email protected]',

description=desc,

long_description=long_description,

long_description_content_type='text/markdown',

url='https://github.com/ishinder/EASTR',

cmdclass=dict(build_ext=CMakeBuild),

ext_modules=[CMakeExtension('eastr', 'utils')],

install_requires=[

'biopython>=1.81,<2.0',

'mappy>=2.26,<3.0',

'numpy>=1.26.1',

'pandas>=2.1.2,<2.3',

'pysam>=0.22.0,<0.23',

],

packages=find_packages(

where='src',

include=['eastr'],

),

package_dir={'': 'src'},

entry_points={

'console_scripts': [

'eastr = eastr.run_eastr:main',

]

},

python_requires='>=3.10',

license='MIT',

license_files=('LICENSE',),

)