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setup.py
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setup.py
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#!/usr/bin/env python3
# /*##########################################################################
#
# Copyright (c) 2015-2024 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__ = "07/11/2022"
__license__ = "MIT"
import sys
import os
import platform
import logging
from typing import Optional
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger("silx.setup")
from setuptools import Extension
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
"""
)
# ############## #
# Compiler flags #
# ############## #
def parse_env_as_bool(key: str, default: Optional[bool] = None) -> Optional[bool]:
"""Parse `key` env. var. and convert its value to a boolean or None.
If it cannot parse it or if None, `default` is returned.
"""
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 default
msg = "Env variable '%s' contains '%s'. But a boolean or an empty \
string was expected. Variable ignored."
logger.warning(msg, key, content)
return default
def get_use_openmp_from_env_var() -> bool:
"""Returns whether or not to build with OpenMP"""
use_openmp = parse_env_as_bool("SILX_WITH_OPENMP", default=True)
if use_openmp and platform.system() == "Darwin":
logger.warning("OpenMP support ignored. Your platform does not support it.")
return False
return use_openmp
USE_OPENMP = get_use_openmp_from_env_var()
FORCE_CYTHON = parse_env_as_bool("SILX_FORCE_CYTHON", default=False)
class BuildExt(build_ext):
"""Handle extension compilation.
Environment variables can custom the build of extensions, see the install documentation.
If building with MSVC, compiler flags are converted from gcc flags.
"""
COMPILE_ARGS_CONVERTER = {"-fopenmp": "/openmp"}
LINK_ARGS_CONVERTER = {"-fopenmp": ""}
description = "Build extensions"
def patch_extension(self, ext: Extension):
"""Patch an extension according to requested Cython and OpenMP usage."""
from Cython.Build import cythonize
patched_exts = cythonize(
[ext],
compiler_directives={"embedsignature": True, "language_level": 3},
force=FORCE_CYTHON,
)
ext.sources = patched_exts[0].sources
# Remove OpenMP flags if OpenMP is disabled
if not 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)
# ##### #
# setup #
# ##### #
def get_project_configuration():
"""Returns project arguments for setup"""
install_requires = [
# for most of the computation
"numpy",
# for version parsing
"packaging",
# for io support
"h5py",
"fabio>=0.9",
]
if sys.version_info < (3, 9):
install_requires.append("importlib_resources")
# extras requirements: target 'full' to install all dependencies at once
full_requires = [
# opencl
"pyopencl",
"Mako",
# gui
"qtconsole",
"matplotlib>=3.1.0",
"PyOpenGL",
"python-dateutil",
"PyQt5",
# extra
"hdf5plugin",
"scipy",
"Pillow",
]
test_requires = [
"pytest>=6.0",
"pytest-xvfb",
"pytest-mock",
"bitshuffle",
"scipy>=1.10",
"pooch",
]
doc_requires = {
"nbsphinx",
"pandoc",
"pillow",
"pydata_sphinx_theme",
"sphinx",
"sphinx-autodoc-typehints",
"sphinx-design",
}
extras_require = {
"full": full_requires,
"doc": doc_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)
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=[
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"],
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"],
language="c",
),
Extension(
name="silx.math.chistogramnd_lut",
sources=["src/silx/math/chistogramnd_lut.pyx"],
include_dirs=["src/silx/math/histogramnd/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"],
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"],
language="c++",
),
Extension(
name="silx.math.medianfilter.medianfilter",
sources=["src/silx/math/medianfilter/medianfilter.pyx"],
include_dirs=["src/silx/math/medianfilter/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",
),
]
return dict(
install_requires=install_requires,
extras_require=extras_require,
cmdclass=dict(build_ext=BuildExt),
ext_modules=ext_modules,
)
if __name__ == "__main__":
from setuptools import setup
setup(**get_project_configuration())