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#!/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/*"],
},
)
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