import ast import os import platform import re import sys from distutils.core import Command from glob import glob try: from setuptools import setup, find_packages except ImportError: print >> sys.stderr, "ERROR: setuptools not installed. Please report this bug as instructed on https://bugs.debian.org/cgi-bin/pkgreport.cgi?package=python-bx" sys.exit() from setuptools import Extension # noqa: E402 version_file = os.path.join('lib', 'bx', '__init__.py') reg = re.compile(r'__version__\s*=\s*(.+)') with open(version_file) as f: for line in f: m = reg.match(line) if m: version = ast.literal_eval(m.group(1)) break else: raise Exception("Version not found in " + version_file) with open('README.md') as f: long_description = f.read() def main(): metadata = dict( name="bx-python", version=version, python_requires='>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*', setup_requires=['numpy', 'cython'], install_requires=[ 'numpy', 'six>=1.13.0'], py_modules=['psyco_full'], package_dir={'': 'lib'}, package_data={'': ['*.ps']}, scripts=glob("scripts/*.py"), test_suite='nose.collector', tests_require=['nose', 'python-lzo'], author="James Taylor, Bob Harris, David King, Brent Pedersen, Kanwei Li, and others", author_email="james@jamestaylor.org", description="Tools for manipulating biological data, particularly multiple sequence alignments", long_description=long_description, long_description_content_type='text/markdown', url="https://github.com/bxlab/bx-python", project_urls={ "Bug Tracker": "https://github.com/bxlab/bx-python/issues", "Source Code": "https://github.com/bxlab/bx-python", }, license="MIT", classifiers=[ "Development Status :: 5 - Production/Stable", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: POSIX", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries :: Python Modules"], zip_safe=False, dependency_links=[], cmdclass=command_classes) numpy = None try: import numpy # Suppress numpy tests numpy.test = None except Exception: pass if len(sys.argv) >= 2 and \ ('--help' in sys.argv[1:] or sys.argv[1] in ('--help-commands', 'egg_info', '--version', 'clean')): # For these actions, NumPy is not required. # # They are required to succeed without Numpy for example when # pip is used to install when Numpy is not yet present in # the system. pass else: if numpy is None: raise Exception("numpy must be installed to build") metadata['packages'] = find_packages('lib') metadata['ext_modules'] = get_extension_modules(numpy_include=numpy.get_include()) setup(**metadata) # ---- Commands ------------------------------------------------------------- # Use build_ext from Cython if found command_classes = {} try: import Cython.Distutils command_classes['build_ext'] = Cython.Distutils.build_ext except Exception: pass # Run 2to3 builder if we're on Python 3.x, from # http://wiki.python.org/moin/PortingPythonToPy3k try: from distutils.command.build_py import build_py_2to3 as build_py except ImportError: # 2.x from distutils.command.build_py import build_py command_classes['build_py'] = build_py # Use epydoc if found try: import pkg_resources pkg_resources.require("epydoc") import epydoc.cli import os import os.path # Create command class to build API documentation class BuildAPIDocs(Command): user_options = [] def initialize_options(self): pass def finalize_options(self): pass def run(self): # Save working directory and args old_argv = sys.argv old_cwd = os.getcwd() # Build command line for Epydoc sys.argv = """epydoc.py bx --verbose --html --simple-term --exclude=._ --exclude=_tests --docformat=reStructuredText --output=../doc/docbuild/html/apidoc""".split() # Make output directory if not os.path.exists("./doc/docbuild/html/apidoc"): os.mkdir("./doc/docbuild/html/apidoc") # Move to lib directory (so bx package is in current directory) os.chdir("./lib") # Invoke epydoc epydoc.cli.cli() # Restore args and working directory sys.argv = old_argv os.chdir(old_cwd) # Add to extra_commands command_classes['build_apidocs'] = BuildAPIDocs except Exception: pass # ---- Extension Modules ---------------------------------------------------- # # suppress C++ #warning, e.g., to silence NumPy deprecation warnings: # from functools import partial # _Extension = Extension # Extension = partial(_Extension, extra_compile_args=["-Wno-cpp"]) def get_extension_modules(numpy_include=None): extensions = [] # Bitsets extensions.append(Extension("bx.bitset", ["lib/bx/bitset.pyx", "src/binBits.c", "src/kent/bits.c", "src/kent/common.c"], include_dirs=["src/kent", "src"])) # Interval intersection extensions.append(Extension("bx.intervals.intersection", ["lib/bx/intervals/intersection.pyx"])) # Alignment object speedups extensions.append(Extension("bx.align._core", ["lib/bx/align/_core.pyx"])) # NIB reading speedups extensions.append(Extension("bx.seq._nib", ["lib/bx/seq/_nib.pyx"])) # 2bit reading speedups extensions.append(Extension("bx.seq._twobit", ["lib/bx/seq/_twobit.pyx"])) # Translation if character / integer strings extensions.append(Extension("bx._seqmapping", ["lib/bx/_seqmapping.pyx"])) # BGZF extensions.append(Extension("bx.misc.bgzf", ["lib/bx/misc/bgzf.pyx", "src/samtools/bgzf.c"], include_dirs=["src/samtools"], libraries=['z'])) # The following extensions won't (currently) compile on windows if platform.system() not in ('Microsoft', 'Windows'): # Interval clustering extensions.append(Extension("bx.intervals.cluster", ["lib/bx/intervals/cluster.pyx", "src/cluster.c"], include_dirs=["src"])) # Position weight matrices extensions.append(Extension("bx.pwm._position_weight_matrix", ["lib/bx/pwm/_position_weight_matrix.pyx", "src/pwm_utils.c"], include_dirs=["src"])) extensions.append(Extension("bx.motif._pwm", ["lib/bx/motif/_pwm.pyx"], include_dirs=[numpy_include])) # Sparse arrays with summaries organized as trees on disk extensions.append(Extension("bx.arrays.array_tree", ["lib/bx/arrays/array_tree.pyx"], include_dirs=[numpy_include])) # Reading UCSC "big binary index" files extensions.append(Extension("bx.bbi.bpt_file", ["lib/bx/bbi/bpt_file.pyx"])) extensions.append(Extension("bx.bbi.cirtree_file", ["lib/bx/bbi/cirtree_file.pyx"])) extensions.append(Extension("bx.bbi.bbi_file", ["lib/bx/bbi/bbi_file.pyx"], include_dirs=[numpy_include])) extensions.append(Extension("bx.bbi.bigwig_file", ["lib/bx/bbi/bigwig_file.pyx"], include_dirs=[numpy_include])) extensions.append(Extension("bx.bbi.bigbed_file", ["lib/bx/bbi/bigbed_file.pyx"], include_dirs=[numpy_include])) # EPO and Chain arithmetics and IO speedups extensions.append(Extension("bx.align._epo", ["lib/bx/align/_epo.pyx"], include_dirs=[numpy_include])) # Reading UCSC bed and wiggle formats extensions.append(Extension("bx.arrays.bed", ["lib/bx/arrays/bed.pyx"])) extensions.append(Extension("bx.arrays.wiggle", ["lib/bx/arrays/wiggle.pyx"])) # CpG masking extensions.append(Extension("bx.align.sitemask._cpg", ["lib/bx/align/sitemask/_cpg.pyx", "lib/bx/align/sitemask/find_cpg.c"])) # Counting n-grams in integer strings extensions.append(Extension("bx.intseq.ngramcount", ["lib/bx/intseq/ngramcount.pyx"], include_dirs=["src"])) # Seekable access to bzip2 files extensions.append(Extension("bx.misc._seekbzip2", ["lib/bx/misc/_seekbzip2.pyx", "src/bunzip/micro-bunzip.c"], include_dirs=["src/bunzip"])) return extensions if __name__ == "__main__": main()