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setup.py
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setup.py
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# -*- coding: utf-8 -*-
import os
import sys
import subprocess
from setuptools import setup, Extension,find_packages
from setuptools.command.build_ext import build_ext
# Convert distutils Windows platform specifiers to CMake -A arguments
PLAT_TO_CMAKE = {
"win32": "Win32",
"win-amd64": "x64",
"win-arm32": "ARM",
"win-arm64": "ARM64",
}
# A CMakeExtension needs a sourcedir instead of a file list.
class CMakeExtension(Extension):
def __init__(self, name, sourcedir=""):
Extension.__init__(self, name, sources=[])
self.sourcedir = os.path.abspath(sourcedir)
class CMakeBuild(build_ext):
def run(self):
# This is optional - will print a nicer error if CMake is missing.
# Since we force CMake via PEP 518 in the pyproject.toml, this should
# never happen and this whole method can be removed in your code if you
# want.
try:
subprocess.check_output(["cmake", "--version"])
except OSError:
msg = "CMake missing - probably upgrade to a newer version of Pip?"
raise RuntimeError(msg)
# To support Python 2, we have to avoid super(), since distutils is all
# old-style classes.
build_ext.run(self)
def build_extension(self, ext):
extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.name)))
# required for auto-detection of auxiliary "native" libs
if not extdir.endswith(os.path.sep):
extdir += os.path.sep
extdir +="pahelix/toolkit/"
cfg = "Debug" if self.debug else "Release"
# CMake lets you override the generator - we need to check this.
# Can be set with Conda-Build, for example.
cmake_generator = os.environ.get("CMAKE_GENERATOR", "")
# Set Python_EXECUTABLE instead if you use PYBIND11_FINDPYTHON
# EXAMPLE_VERSION_INFO shows you how to pass a value into the C++ code
# from Python.
cmake_args = [
"-DCMAKE_LIBRARY_OUTPUT_DIRECTORY={}".format(extdir),
"-DPYTHON_EXECUTABLE={}".format(sys.executable),
"-DEXAMPLE_VERSION_INFO={}".format(self.distribution.get_version()),
"-DCMAKE_BUILD_TYPE={}".format(cfg), # not used on MSVC, but no harm
]
build_args = []
if self.compiler.compiler_type != "msvc":
# Using Ninja-build since it a) is available as a wheel and b)
# multithreads automatically. MSVC would require all variables be
# exported for Ninja to pick it up, which is a little tricky to do.
# Users can override the generator with CMAKE_GENERATOR in CMake
# 3.15+.
if not cmake_generator:
cmake_args += ["-GNinja"]
else:
# Single config generators are handled "normally"
single_config = any(x in cmake_generator for x in {"NMake", "Ninja"})
# CMake allows an arch-in-generator style for backward compatibility
contains_arch = any(x in cmake_generator for x in {"ARM", "Win64"})
# Specify the arch if using MSVC generator, but only if it doesn't
# contain a backward-compatibility arch spec already in the
# generator name.
if not single_config and not contains_arch:
cmake_args += ["-A", PLAT_TO_CMAKE[self.plat_name]]
# Multi-config generators have a different way to specify configs
if not single_config:
cmake_args += [
"-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}".format(cfg.upper(), extdir)
]
build_args += ["--config", cfg]
# Set CMAKE_BUILD_PARALLEL_LEVEL to control the parallel build level
# across all generators.
if "CMAKE_BUILD_PARALLEL_LEVEL" not in os.environ:
# self.parallel is a Python 3 only way to set parallel jobs by hand
# using -j in the build_ext call, not supported by pip or PyPA-build.
if hasattr(self, "parallel") and self.parallel:
# CMake 3.12+ only.
build_args += ["-j{}".format(self.parallel)]
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
)
subprocess.check_call(
["cmake", "--build", "."] + build_args, cwd=self.build_temp
)
requires = [
'numpy',
'pandas',
'networkx',
"sklearn",
]
setup(
name="paddlehelix",
version="1.0.0b",
author="baidu-nlp-bio",
author_email="nlp-bio@baidu.com",
description="Adding version check",
long_description="",
packages = find_packages(),
ext_modules=[CMakeExtension("linear_rna")],
cmdclass={"build_ext": CMakeBuild},
install_requires = requires,
zip_safe=False,
)