#!/usr/bin/env python """Setup script for scikit-bio installation. ---------------------------------------------------------------------------- Copyright (c) 2013--, scikit-bio development team. Distributed under the terms of the Modified BSD License. The full license is in the file LICENSE.txt, distributed with this software. ---------------------------------------------------------------------------- """ import os import platform import re import ast import sys import sysconfig import subprocess from setuptools import find_packages, setup from setuptools.extension import Extension import numpy as np from Cython.Build import cythonize if sys.version_info.major != 3: sys.exit( "scikit-bio can only be used with Python 3. You are currently " "running Python %d." % sys.version_info.major ) def check_bin(ccbin, source, allow_dash): """Check if a given compiler matches the specified name.""" # remove any parameters (e.g. gcc -I /a/b/c -> gcc) source0 = source.split()[0] # remove any path bsource = os.path.basename(source0) # now let's go search for ccbin if allow_dash: found = False # allow for the ccbin to be between - (e.g. gcc-1.2) for el in bsource.split("-"): if el == ccbin: found = True break else: found = bsource == ccbin return found # Note: We are looking for Apple/MacOS clang, which does not support omp # Will treat "real clang" (e.g. llvm based) same as gcc clang = False # icc uses slightly different omp cmdline arguments icc = False # Are we using the default gcc as the compiler? gcc = True try: if os.environ["CC"] == "gcc": gcc = True elif os.environ["CC"] != "": gcc = False except KeyError: pass if not gcc: try: if check_bin("clang", os.environ["CC"], False): # note, the conda provideed clang is not detected here # and this is on purpose, as MacOS clang is very different # than conda-provised one (which is llvm based) # so do not look for substrings # (e.g. do not match x86_64-apple-darwin13.4.0-clang) clang = True elif check_bin("icc", os.environ["CC"], True): icc = True except KeyError: pass else: try: if check_bin("clang", sysconfig.get_config_vars()["CC"], False): # as above clang = True gcc = False elif check_bin("icc", sysconfig.get_config_vars()["CC"], True): icc = True gcc = False except KeyError: pass if gcc: # check if the default gcc is just a wrapper around clang try: if ( subprocess.check_output(["gcc", "--version"], universal_newlines=True).find( "clang" ) != -1 ): clang = True except (subprocess.CalledProcessError, FileNotFoundError): pass # version parsing from __init__ pulled from Flask's setup.py # https://github.com/mitsuhiko/flask/blob/master/setup.py _version_re = re.compile(r"__version__\s+=\s+(.*)") with open("skbio/__init__.py", "rb") as f: hit = _version_re.search(f.read().decode("utf-8")).group(1) version = str(ast.literal_eval(hit)) classes = """ Development Status :: 4 - Beta License :: OSI Approved :: BSD License Topic :: Software Development :: Libraries Topic :: Scientific/Engineering Topic :: Scientific/Engineering :: Bio-Informatics Programming Language :: Python :: 3 Programming Language :: Python :: 3 :: Only Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 Programming Language :: Python :: 3.13 Operating System :: Unix Operating System :: POSIX Operating System :: MacOS :: MacOS X Operating System :: Microsoft :: Windows """ classifiers = [s.strip() for s in classes.split("\n") if s] description = ( "Data structures, algorithms and educational " "resources for bioinformatics." ) with open("README.rst") as f: long_description = f.read() # Compile SSW module ssw_extra_compile_args = ["-I."] if platform.system() != "Windows": if icc: ssw_extra_compile_args.extend(["-qopenmp-simd", "-DSIMDE_ENABLE_OPENMP"]) elif not clang: ssw_extra_compile_args.extend(["-fopenmp-simd", "-DSIMDE_ENABLE_OPENMP"]) elif platform.system() == "Windows": ssw_extra_compile_args.extend(["-openmp:experimental"]) stats_extra_compile_args = [] + ssw_extra_compile_args stats_extra_link_args = [] if platform.system() != "Windows": if icc: stats_extra_compile_args.extend(["-qopenmp"]) stats_extra_link_args.extend(["-qopenmp"]) elif not clang: stats_extra_compile_args.extend(["-fopenmp"]) stats_extra_link_args.extend(["-fopenmp"]) # Cython modules (*.pyx). They will be compiled into C code (*.c) during build. ext = ".pyx" extensions = [ Extension("skbio.metadata._intersection", ["skbio/metadata/_intersection" + ext]), Extension( "skbio.alignment._ssw_wrapper", ["skbio/alignment/_ssw_wrapper" + ext], include_dirs=[np.get_include()], libraries=['ssw'] ), Extension( "skbio.diversity._phylogenetic", ["skbio/diversity/_phylogenetic" + ext], include_dirs=[np.get_include()], ), Extension( "skbio.stats.ordination._cutils", ["skbio/stats/ordination/_cutils" + ext], extra_compile_args=stats_extra_compile_args, extra_link_args=stats_extra_link_args, ), Extension( "skbio.stats.distance._cutils", ["skbio/stats/distance/_cutils" + ext], extra_compile_args=stats_extra_compile_args, extra_link_args=stats_extra_link_args, ), ] extensions = cythonize(extensions, force=True) setup( name="scikit-bio", version=version, license="BSD-3-Clause", description=description, long_description=long_description, author="scikit-bio development team", author_email="qiyunzhu@gmail.com", maintainer="scikit-bio development team", maintainer_email="qiyunzhu@gmail.com", url="https://scikit.bio", packages=find_packages(), ext_modules=extensions, include_dirs=[np.get_include()], tests_require=["pytest", "coverage"], install_requires=[ "requests >= 2.20.0", "decorator >= 3.4.2", "natsort >= 4.0.3", "numpy >= 1.17.0", "pandas >= 1.5.0", "scipy >= 1.9.0", "h5py >= 3.6.0", "biom-format >= 2.1.16", "statsmodels >= 0.14.0", ], classifiers=classifiers, package_data={ "skbio.diversity.alpha.tests": ["data/qiime-191-tt/*"], "skbio.diversity.beta.tests": ["data/qiime-191-tt/*"], "skbio.io.tests": ["data/*"], "skbio.io.format.tests": ["data/*"], "skbio.stats.tests": ["data/*"], "skbio.stats.distance.tests": ["data/*"], "skbio.stats.ordination.tests": ["data/*"], "skbio.metadata.tests": ["data/invalid/*", "data/valid/*"], "skbio.embedding.tests": ["data/*"], }, )