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from __future__ import print_function
import os
import os.path
import re
import sys
from copy import copy
from distutils.command.build_ext import build_ext
from distutils.util import strtobool
from setuptools import setup, Extension
from shutil import copy2, rmtree
from subprocess import Popen
def iteritems(d):
if sys.version_info >= (3, 0):
return d.items()
return d.iteritems()
def ParseVersion():
thisDir = os.path.dirname(os.path.realpath(__file__))
cmakeLists = os.path.join(thisDir, "CMakeLists.txt")
regexp = re.compile(r'project\([^ ]+ VERSION (\d+\.\d+\.\d+) [^\)]+\)')
with open(cmakeLists) as handle:
for line in handle:
m = regexp.search(line)
if m:
return m.group(1)
raise RuntimeError("unable to find version string!")
def which(program, env=os.environ):
def isExe(fpath):
return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
fpath, fname = os.path.split(program)
if fpath:
if isExe(program):
return program
else:
for path in env.get("PATH", "").split(os.pathsep):
path = path.strip("\"")
exe = os.path.join(path, program)
if isExe(exe):
return exe
return None
class CMake(object):
def __init__(self, env=os.environ, verbose=False):
cmake = env.get("CMAKE_COMMAND", "cmake") or which("cmake", env)
if cmake is None:
raise RuntimeError("cannot find `cmake` command, "
"please populate CMAKE_COMMAND environment variable")
self.build = ["make"]
self.env = env
self.configure = [cmake]
self.definitions = dict()
self.generator = None
rpath = self.env.get("CMAKE_SKIP_RPATH", "")
try:
rpath = bool(strtobool(rpath))
except ValueError:
rpath = False
if rpath:
self.add_definition("CMAKE_SKIP_RPATH", "TRUE")
verbose = self.env.get("VERBOSE", "{0}".format(verbose))
try:
verbose = bool(strtobool(verbose))
except ValueError:
verbose = False
self.verbose = verbose
def add_definition(self, key, value):
self.definitions[key] = value
def add_definition_from_env(self, key, default=None):
value = self.env.get(key, default)
if value:
self.add_definition(key, value)
def set_build_type(self, buildType):
if buildType not in set(["Release", "Debug", "RelWithDebInfo"]):
raise ValueError("CMAKE_BUILD_TYPE must be in (Release, Debug, RelWithDebInfo)")
self.add_definition("CMAKE_BUILD_TYPE", buildType)
def set_generator(self, gen):
if gen not in set(["Default", "Ninja"]):
raise ValueError("valid generators must be in (Default, Ninja)")
if gen == "Default":
gen = None
self.build = ["make"]
if self.verbose:
self.build.append("VERBOSE=1")
elif gen == "Ninja":
self.ninja = self.env.get("NINJA_COMMAND", None) or which("ninja", self.env)
if not self.ninja:
raise RuntimeError("cannot find `ninja` command, "
"please populate NINJA_COMMAND environment variable")
self.build = [self.ninja]
if self.verbose:
self.build.append("-v")
self.generator = gen
def __call__(self, sourceDir, binaryDir, targets=[]):
configure = copy(self.configure)
if self.generator:
configure.append("-G{0}".format(self.generator))
for k, v in iteritems(self.definitions):
configure.append("-D{0}={1}".format(k, v))
configure.append(sourceDir)
print("Configuring with command `{0}`".format(" ".join(configure)), file=sys.stderr)
retcode = Popen(configure, cwd=binaryDir, env=self.env).wait()
if retcode != 0:
raise RuntimeError("failed to configure the project")
build = self.build + targets
print("Building with command `{0}`".format(" ".join(build)), file=sys.stderr)
retcode = Popen(build, cwd=binaryDir).wait()
if retcode != 0:
raise RuntimeError("failed to build the project")
class MyBuildExt(build_ext):
def build_extension(self, ext):
destDir = os.path.dirname(self.get_ext_fullpath(ext.name))
thisDir = os.path.dirname(os.path.realpath(__file__))
os.environ['CCACHE_BASEDIR'] = thisDir
try:
os.makedirs(self.build_temp)
os.makedirs(destDir)
except OSError:
pass
env = os.environ.copy()
cmake = CMake(env, verbose=("--verbose" in sys.argv or "-v" in sys.argv))
cmake.add_definition_from_env("Boost_INCLUDE_DIRS")
cmake.add_definition_from_env("PYTHON_INCLUDE_DIRS")
cmake.add_definition_from_env("pbcopper_INCLUDE_DIRS")
cmake.add_definition_from_env("pbcopper_LIBRARIES")
cmake.add_definition_from_env("GIT_EXECUTABLE")
cmake.add_definition_from_env("SWIG_COMMAND")
cmake.add_definition_from_env("UNY_use_ccache")
cmake.add_definition_from_env("CMAKE_BUILD_TYPE", "RelWithDebInfo")
cmake.add_definition_from_env("PYTHON_EXECUTABLE", sys.executable)
cmake.add_definition("PYTHON_SWIG", "1")
cmake.add_definition("UNY_build_tests", "0")
cmake.add_definition("UNY_build_bin", "0")
availableGenerator = "Ninja" if which("ninja", env) else "Default"
desiredGenerator = cmake.env.get("CMAKE_GENERATOR", availableGenerator)
cmake.set_generator(desiredGenerator)
targets = ["_ConsensusCore2"]
try:
cmake(thisDir, self.build_temp, targets)
except RuntimeError:
# if this happens we're probably under pip and need to regenerate
rmtree(self.build_temp)
os.makedirs(self.build_temp)
cmake(thisDir, self.build_temp, targets)
for fname in ["_ConsensusCore2.so", "ConsensusCore2.py"]:
copy2(os.path.join(self.build_temp, "swig", "lib", fname), destDir)
setup(
name="ConsensusCore2",
version=ParseVersion(),
author="PacificBiosciences",
author_email="devnet@pacb.com",
url="http://www.github.com/PacificBiosciences/ConsensusCore2",
description="A library for generating consensus sequences for PacBio data",
license="BSD",
ext_modules=[Extension("_ConsensusCore2", [])],
package_dir={"": "swig"},
py_modules=["ConsensusCore2"],
install_requires=["numpy >= 1.6.0"],
setup_requires=["numpy >= 1.6.0"],
cmdclass={"build_ext": MyBuildExt}
)
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