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#!/usr/bin/env python3
# /*##########################################################################
#
# Copyright (c) 2015-2022 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# ###########################################################################*/
__authors__ = ["Jérôme Kieffer", "Thomas Vincent"]
__date__ = "29/08/2022"
__license__ = "MIT"
import sys
import os
import platform
import logging
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger("silx.setup")
try: # setuptools >=62.4.0
from setuptools.command.build import build as _build
except ImportError:
from distutils.command.build import build as _build
from setuptools import Command, Extension, find_packages
from setuptools.command.sdist import sdist
from setuptools.command.build_ext import build_ext
try:
import numpy
except ImportError:
raise ImportError(
"To install this package, you must install numpy first\n"
"(See https://pypi.org/project/numpy)")
PROJECT = "silx"
if sys.version_info.major < 3:
logger.error(PROJECT + " no longer supports Python2")
if "LANG" not in os.environ and sys.platform == "darwin":
print("""WARNING: the LANG environment variable is not defined,
an utf-8 LANG is mandatory to use setup.py, you may face unexpected UnicodeError.
export LANG=en_US.utf-8
export LC_ALL=en_US.utf-8
""")
def get_version(debian=False):
"""Returns current version number from _version.py file"""
dirname = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "src", PROJECT)
sys.path.insert(0, dirname)
import _version
sys.path = sys.path[1:]
return _version.debianversion if debian else _version.strictversion
def get_readme():
"""Returns content of README.rst file"""
dirname = os.path.dirname(os.path.abspath(__file__))
filename = os.path.join(dirname, "README.rst")
with open(filename, "r", encoding="utf-8") as fp:
long_description = fp.read()
return long_description
classifiers = ["Development Status :: 5 - Production/Stable",
"Environment :: Console",
"Environment :: MacOS X",
"Environment :: Win32 (MS Windows)",
"Environment :: X11 Applications :: Qt",
"Intended Audience :: Education",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Operating System :: MacOS",
"Operating System :: Microsoft :: Windows",
"Operating System :: POSIX",
"Programming Language :: Cython",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: Implementation :: CPython",
"Topic :: Scientific/Engineering :: Physics",
"Topic :: Software Development :: Libraries :: Python Modules",
]
class BuildMan(Command):
"""Command to build man pages"""
description = "Build man pages of the provided entry points"
user_options = []
def initialize_options(self):
pass
def finalize_options(self):
pass
def entry_points_iterator(self):
"""Iterate other entry points available on the project."""
entry_points = self.distribution.entry_points
console_scripts = entry_points.get('console_scripts', [])
gui_scripts = entry_points.get('gui_scripts', [])
scripts = []
scripts.extend(console_scripts)
scripts.extend(gui_scripts)
for script in scripts:
# Remove ending extra dependencies
script = script.split("[")[0]
elements = script.split("=")
target_name = elements[0].strip()
elements = elements[1].split(":")
module_name = elements[0].strip()
function_name = elements[1].strip()
yield target_name, module_name, function_name
def run_targeted_script(self, target_name, script_name, env, log_output=False):
"""Execute targeted script using --help and --version to help checking
errors. help2man is not very helpful to do it for us.
:return: True is both return code are equal to 0
:rtype: bool
"""
import subprocess
if log_output:
extra_args = {}
else:
try:
# Python 3
from subprocess import DEVNULL
except ImportError:
# Python 2
import os
DEVNULL = open(os.devnull, 'wb')
extra_args = {'stdout': DEVNULL, 'stderr': DEVNULL}
succeeded = True
command_line = [sys.executable, script_name, "--help"]
if log_output:
logger.info("See the following execution of: %s", " ".join(command_line))
p = subprocess.Popen(command_line, env=env, **extra_args)
status = p.wait()
if log_output:
logger.info("Return code: %s", status)
succeeded = succeeded and status == 0
command_line = [sys.executable, script_name, "--version"]
if log_output:
logger.info("See the following execution of: %s", " ".join(command_line))
p = subprocess.Popen(command_line, env=env, **extra_args)
status = p.wait()
if log_output:
logger.info("Return code: %s", status)
succeeded = succeeded and status == 0
return succeeded
@staticmethod
def _write_script(target_name, lst_lines=None):
"""Write a script to a temporary file and return its name
:paran target_name: base of the script name
:param lst_lines: list of lines to be written in the script
:return: the actual filename of the script (for execution or removal)
"""
import tempfile
import stat
script_fid, script_name = tempfile.mkstemp(prefix="%s_" % target_name, text=True)
with os.fdopen(script_fid, 'wt') as script:
for line in lst_lines:
if not line.endswith("\n"):
line += "\n"
script.write(line)
# make it executable
mode = os.stat(script_name).st_mode
os.chmod(script_name, mode + stat.S_IEXEC)
return script_name
def get_synopsis(self, module_name, env, log_output=False):
"""Execute a script to retrieve the synopsis for help2man
:return: synopsis
:rtype: single line string
"""
import subprocess
script_name = None
synopsis = None
script = ["#!%s\n" % sys.executable,
"import logging",
"logging.basicConfig(level=logging.ERROR)",
"import %s as app" % module_name,
"print(app.__doc__)"]
try:
script_name = self._write_script(module_name, script)
command_line = [sys.executable, script_name]
p = subprocess.Popen(command_line, env=env, stdout=subprocess.PIPE)
status = p.wait()
if status != 0:
logger.warning("Error while getting synopsis for module '%s'.", module_name)
synopsis = p.stdout.read().decode("utf-8").strip()
if synopsis == 'None':
synopsis = None
finally:
# clean up the script
if script_name is not None:
os.remove(script_name)
return synopsis
def run(self):
build = self.get_finalized_command('build')
path = sys.path
path.insert(0, os.path.abspath(build.build_lib))
env = dict((str(k), str(v)) for k, v in os.environ.items())
# env["PYTHONPATH"] = os.pathsep.join(path)
if not os.path.isdir("build/man"):
os.makedirs("build/man")
import subprocess
import tempfile
import stat
script_name = None
workdir = tempfile.mkdtemp()
entry_points = self.entry_points_iterator()
for target_name, module_name, function_name in entry_points:
logger.info("Build man for entry-point target '%s'" % target_name)
# help2man expect a single executable file to extract the help
# we create it, execute it, and delete it at the end
try:
# create a launcher using the right python interpreter
script_name = os.path.join(workdir, target_name)
with open(script_name, "wt") as script:
script.write("#!%s\n" % sys.executable)
script.write("import %s as app\n" % module_name)
script.write("app.%s()\n" % function_name)
# make it executable
mode = os.stat(script_name).st_mode
os.chmod(script_name, mode + stat.S_IEXEC)
# execute help2man
man_file = "build/man/%s.1" % target_name
command_line = ["help2man", "-N", script_name, "-o", man_file]
synopsis = self.get_synopsis(module_name, env)
if synopsis:
command_line += ["-n", synopsis]
p = subprocess.Popen(command_line, env=env)
status = p.wait()
if status != 0:
logger.info("Error while generating man file for target '%s'.", target_name)
self.run_targeted_script(target_name, script_name, env, True)
raise RuntimeError("Fail to generate '%s' man documentation" % target_name)
finally:
# clean up the script
if script_name is not None:
os.remove(script_name)
os.rmdir(workdir)
# ############## #
# Compiler flags #
# ############## #
class Build(_build):
"""Command to support more user options for the build."""
user_options = [
('no-openmp', None,
"DEPRECATED: Instead, set the environment variable SILX_WITH_OPENMP to False"),
('openmp', None,
"DEPRECATED: Instead, set the environment variable SILX_WITH_OPENMP to True"),
('force-cython', None,
"DEPRECATED: Instead, set the environment variable SILX_FORCE_CYTHON to True"),
]
user_options.extend(_build.user_options)
boolean_options = ['no-openmp', 'openmp', 'force-cython']
boolean_options.extend(_build.boolean_options)
def initialize_options(self):
_build.initialize_options(self)
self.no_openmp = None
self.openmp = None
self.force_cython = None
def finalize_options(self):
_build.finalize_options(self)
if self.no_openmp is not None:
logger.warning("--no-openmp is deprecated: Instead, set the environment variable SILX_WITH_OPENMP to False")
if self.openmp is not None:
logger.warning("--openmp is deprecated: Instead, set the environment variable SILX_WITH_OPENMP to True")
if self.force_cython is not None:
logger.warning("--force-cython is deprecated: Instead, set the environment variable SILX_FORCE_CYTHON to True")
if not self.force_cython:
self.force_cython = self._parse_env_as_bool("SILX_FORCE_CYTHON") is True
self.finalize_openmp_options()
def _parse_env_as_bool(self, key):
content = os.environ.get(key, "")
value = content.lower()
if value in ["1", "true", "yes", "y"]:
return True
if value in ["0", "false", "no", "n"]:
return False
if value in ["none", ""]:
return None
msg = "Env variable '%s' contains '%s'. But a boolean or an empty \
string was expected. Variable ignored."
logger.warning(msg, key, content)
return None
def finalize_openmp_options(self):
"""Check if extensions must be compiled with OpenMP.
The result is stored into the object.
"""
if self.openmp:
use_openmp = True
elif self.no_openmp:
use_openmp = False
else:
env_with_openmp = self._parse_env_as_bool("SILX_WITH_OPENMP")
if env_with_openmp is not None:
use_openmp = env_with_openmp
else:
# Use it by default
use_openmp = True
if use_openmp and platform.system() == "Darwin":
logger.warning("OpenMP support ignored. Your platform does not support it.")
use_openmp = False
# Remove attributes used by distutils parsing
# use 'use_openmp' instead
del self.no_openmp
del self.openmp
self.use_openmp = use_openmp
class BuildExt(build_ext):
"""Handle extension compilation.
Command-line argument and environment can custom:
- The use of cython to cythonize files, else a default version is used
- Build extension with support of OpenMP (by default it is enabled)
- If building with MSVC, compiler flags are converted from gcc flags.
"""
COMPILE_ARGS_CONVERTER = {'-fopenmp': '/openmp'}
LINK_ARGS_CONVERTER = {'-fopenmp': ''}
description = 'Build extensions'
def finalize_options(self):
build_ext.finalize_options(self)
build_obj = self.distribution.get_command_obj("build")
self.use_openmp = build_obj.use_openmp
self.force_cython = build_obj.force_cython
def patch_extension(self, ext):
"""
Patch an extension according to requested Cython and OpenMP usage.
:param Extension ext: An extension
"""
# Cytonize
from Cython.Build import cythonize
patched_exts = cythonize(
[ext],
compiler_directives={'embedsignature': True,
'language_level': 3},
force=self.force_cython
)
ext.sources = patched_exts[0].sources
# Remove OpenMP flags if OpenMP is disabled
if not self.use_openmp:
ext.extra_compile_args = [
f for f in ext.extra_compile_args if f != '-fopenmp']
ext.extra_link_args = [
f for f in ext.extra_link_args if f != '-fopenmp']
# Convert flags from gcc to MSVC if required
if self.compiler.compiler_type == 'msvc':
extra_compile_args = [self.COMPILE_ARGS_CONVERTER.get(f, f)
for f in ext.extra_compile_args]
# Avoid empty arg
ext.extra_compile_args = [arg for arg in extra_compile_args if arg]
extra_link_args = [self.LINK_ARGS_CONVERTER.get(f, f)
for f in ext.extra_link_args]
# Avoid empty arg
ext.extra_link_args = [arg for arg in extra_link_args if arg]
def build_extensions(self):
for ext in self.extensions:
self.patch_extension(ext)
build_ext.build_extensions(self)
################################################################################
# Debian source tree
################################################################################
class sdist_debian(sdist):
"""
Tailor made sdist for debian
* remove auto-generated doc
* remove cython generated .c files
* remove cython generated .cpp files
* remove .bat files
* include .l man files
"""
description = "Create a source distribution for Debian (tarball, zip file, etc.)"
@staticmethod
def get_debian_name():
name = "%s_%s" % (PROJECT, get_version(debian=True))
return name
def prune_file_list(self):
sdist.prune_file_list(self)
to_remove = ["doc/build", "doc/pdf", "doc/html", "pylint", "epydoc"]
print("Removing files for debian")
for rm in to_remove:
self.filelist.exclude_pattern(pattern="*", anchor=False, prefix=rm)
# this is for Cython files specifically: remove C & html files
search_root = os.path.dirname(os.path.abspath(__file__))
for root, _, files in os.walk(search_root):
for afile in files:
if os.path.splitext(afile)[1].lower() == ".pyx":
base_file = os.path.join(root, afile)[len(search_root) + 1:-4]
self.filelist.exclude_pattern(pattern=base_file + ".c")
self.filelist.exclude_pattern(pattern=base_file + ".cpp")
self.filelist.exclude_pattern(pattern=base_file + ".html")
# do not include third_party/_local files
self.filelist.exclude_pattern(pattern="*", prefix="silx/third_party/_local")
def make_distribution(self):
self.prune_file_list()
sdist.make_distribution(self)
dest = self.archive_files[0]
dirname, basename = os.path.split(dest)
base, ext = os.path.splitext(basename)
while ext in [".zip", ".tar", ".bz2", ".gz", ".Z", ".lz", ".orig"]:
base, ext = os.path.splitext(base)
# if ext:
# dest = "".join((base, ext))
# else:
# dest = base
# sp = dest.split("-")
# base = sp[:-1]
# nr = sp[-1]
debian_arch = os.path.join(dirname, self.get_debian_name() + ".orig.tar.gz")
os.rename(self.archive_files[0], debian_arch)
self.archive_files = [debian_arch]
print("Building debian .orig.tar.gz in %s" % self.archive_files[0])
# ##### #
# setup #
# ##### #
def get_project_configuration():
"""Returns project arguments for setup"""
# Use installed numpy version as minimal required version
# This is useful for wheels to advertise the numpy version they were built with
numpy_requested_version = ">=%s" % numpy.version.version
logger.info("Install requires: numpy %s", numpy_requested_version)
install_requires = [
# for most of the computation
"numpy%s" % numpy_requested_version,
# for the script launcher and pkg_resources
"setuptools",
# for io support
"h5py",
"fabio>=0.9",
]
# extras requirements: target 'full' to install all dependencies at once
full_requires = [
# opencl
'pyopencl',
'Mako',
# gui
'qtconsole',
'matplotlib>=1.2.0',
'PyOpenGL',
'python-dateutil',
'PyQt5',
# extra
'scipy',
'Pillow']
test_requires = [
"pytest",
"pytest-xvfb"
]
extras_require = {
'full': full_requires,
'test': test_requires,
}
# Here for packaging purpose only
# Setting the SILX_FULL_INSTALL_REQUIRES environment variable
# put all dependencies as install_requires
if os.environ.get('SILX_FULL_INSTALL_REQUIRES') is not None:
install_requires += full_requires
# Set the SILX_INSTALL_REQUIRES_STRIP env. var. to a comma-separated
# list of package names to remove them from install_requires
install_requires_strip = os.environ.get('SILX_INSTALL_REQUIRES_STRIP')
if install_requires_strip is not None:
for package_name in install_requires_strip.split(','):
install_requires.remove(package_name)
package_data = {
# Resources files for silx
'silx.resources': [
'gui/logo/*.png',
'gui/logo/*.svg',
'gui/icons/*.png',
'gui/icons/*.svg',
'gui/icons/*.mng',
'gui/icons/*.gif',
'gui/icons/*/*.png',
'opencl/*.cl',
'opencl/image/*.cl',
'opencl/sift/*.cl',
'opencl/codec/*.cl',
'gui/colormaps/*.npy'],
'silx.examples': ['*.png'],
}
entry_points = {
'console_scripts': ['silx = silx.__main__:main'],
# 'gui_scripts': [],
}
cmdclass = dict(
build=Build,
build_ext=BuildExt,
build_man=BuildMan,
debian_src=sdist_debian)
def silx_io_specfile_define_macros():
# Locale and platform management
if sys.platform == "win32":
return [('WIN32', None), ('SPECFILE_POSIX', None)]
elif os.name.lower().startswith('posix'):
# the best choice is to have _GNU_SOURCE defined
# as a compilation flag because that allows the
# use of strtod_l
use_gnu_source = os.environ.get("SPECFILE_USE_GNU_SOURCE", "False")
if use_gnu_source in ("True", "1"): # 1 was the initially supported value
return [('_GNU_SOURCE', 1)]
return [('SPECFILE_POSIX', None)]
else:
return []
ext_modules = [
# silx.image
Extension(
name='silx.image.bilinear',
sources=["src/silx/image/bilinear.pyx"],
language='c',
),
Extension(
name='silx.image.marchingsquares._mergeimpl',
sources=['src/silx/image/marchingsquares/_mergeimpl.pyx'],
include_dirs=[
numpy.get_include(),
os.path.join(os.path.dirname(__file__), "src", "silx", "utils", "include")
],
language='c++',
extra_link_args=['-fopenmp'],
extra_compile_args=['-fopenmp'],
),
Extension(
name='silx.image.shapes',
sources=["src/silx/image/shapes.pyx"],
language='c',
),
# silx.io
Extension(
name='silx.io.specfile',
sources=[
'src/silx/io/specfile/src/sfheader.c',
'src/silx/io/specfile/src/sfinit.c',
'src/silx/io/specfile/src/sflists.c',
'src/silx/io/specfile/src/sfdata.c',
'src/silx/io/specfile/src/sfindex.c',
'src/silx/io/specfile/src/sflabel.c',
'src/silx/io/specfile/src/sfmca.c',
'src/silx/io/specfile/src/sftools.c',
'src/silx/io/specfile/src/locale_management.c',
'src/silx/io/specfile.pyx',
],
define_macros=silx_io_specfile_define_macros(),
include_dirs=['src/silx/io/specfile/include'],
language='c',
),
# silx.math
Extension(
name='silx.math._colormap',
sources=["src/silx/math/_colormap.pyx"],
language='c',
include_dirs=[
'src/silx/math/include',
numpy.get_include(),
],
extra_link_args=['-fopenmp'],
extra_compile_args=['-fopenmp'],
),
Extension(
name='silx.math.chistogramnd',
sources=[
'src/silx/math/histogramnd/src/histogramnd_c.c',
'src/silx/math/chistogramnd.pyx',
],
include_dirs=[
'src/silx/math/histogramnd/include',
numpy.get_include(),
],
language='c',
),
Extension(
name='silx.math.chistogramnd_lut',
sources=['src/silx/math/chistogramnd_lut.pyx'],
include_dirs=[
'src/silx/math/histogramnd/include',
numpy.get_include(),
],
language='c',
),
Extension(
name='silx.math.combo',
sources=['src/silx/math/combo.pyx'],
include_dirs=['src/silx/math/include'],
language='c',
),
Extension(
name='silx.math.interpolate',
sources=["src/silx/math/interpolate.pyx"],
language='c',
include_dirs=[
'src/silx/math/include',
numpy.get_include(),
],
extra_link_args=['-fopenmp'],
extra_compile_args=['-fopenmp'],
),
Extension(
name='silx.math.marchingcubes',
sources=[
'src/silx/math/marchingcubes/mc_lut.cpp',
'src/silx/math/marchingcubes.pyx',
],
include_dirs=[
'src/silx/math/marchingcubes',
numpy.get_include(),
],
language='c++',
),
Extension(
name='silx.math.medianfilter.medianfilter',
sources=['src/silx/math/medianfilter/medianfilter.pyx'],
include_dirs=[
'src/silx/math/medianfilter/include',
numpy.get_include(),
],
language='c++',
extra_link_args=['-fopenmp'],
extra_compile_args=['-fopenmp'],
),
# silx.math.fit
Extension(
name='silx.math.fit.filters',
sources=[
'src/silx/math/fit/filters/src/smoothnd.c',
'src/silx/math/fit/filters/src/snip1d.c',
'src/silx/math/fit/filters/src/snip2d.c',
'src/silx/math/fit/filters/src/snip3d.c',
'src/silx/math/fit/filters/src/strip.c',
'src/silx/math/fit/filters.pyx',
],
include_dirs=['src/silx/math/fit/filters/include'],
language='c',
),
Extension(
name='silx.math.fit.functions',
sources=[
'src/silx/math/fit/functions/src/funs.c',
'src/silx/math/fit/functions.pyx',
],
include_dirs=['src/silx/math/fit/functions/include'],
language='c',
),
Extension(
name='silx.math.fit.peaks',
sources=[
'src/silx/math/fit/peaks/src/peaks.c',
'src/silx/math/fit/peaks.pyx',
],
include_dirs=['src/silx/math/fit/peaks/include'],
language='c',
),
]
# silx.third_party
if os.path.exists(os.path.join(
os.path.dirname(__file__), "src", "silx", "third_party", "_local")
):
ext_modules.append(
Extension(
name='silx.third_party._local.scipy_spatial.qhull',
sources=[
'src/silx/third_party/_local/scipy_spatial/qhull/src/' + fname for fname in (
'geom2_r.c', 'geom_r.c', 'global_r.c', 'io_r.c', 'libqhull_r.c', 'mem_r.c',
'merge_r.c', 'poly2_r.c', 'poly_r.c', 'qset_r.c', 'random_r.c', 'rboxlib_r.c',
'stat_r.c', 'usermem_r.c', 'userprintf_rbox_r.c', 'userprintf_r.c', 'user_r.c'
)] + [
'src/silx/third_party/_local/scipy_spatial/qhull.pyx',
],
include_dirs=[numpy.get_include()],
)
)
return dict(
name=PROJECT,
version=get_version(),
license="MIT",
url="http://www.silx.org/",
author="data analysis unit",
author_email="silx@esrf.fr",
classifiers=classifiers,
description="Software library for X-ray data analysis",
long_description=get_readme(),
install_requires=install_requires,
extras_require=extras_require,
python_requires='>=3.5',
cmdclass=cmdclass,
zip_safe=False,
entry_points=entry_points,
packages=find_packages(where='src', include=['silx*']) + ['silx.examples'],
package_dir={
"": "src",
"silx.examples": "examples",
},
ext_modules=ext_modules,
package_data=package_data,
)
if __name__ == "__main__":
from setuptools import setup
setup(**get_project_configuration())
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