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# -*- coding: utf-8 -*-
# PyNX - Python tools for Nano-structures Crystallography
# (c) 2008-2015 : Univ. Joseph Fourier (Grenoble 1), CEA/INAC/SP2M
# (c) 2016-present : ESRF-European Synchrotron Radiation Facility
# authors:
# Vincent Favre-Nicolin, favre@esrf.fr
# Ondrej Mandula
import platform
import os
import sys
from setuptools import setup, find_packages, Extension
from setuptools.command.install_lib import install_lib as su_install_lib
from setuptools.command.sdist import sdist as su_sdist
from pynx.version import __version__, get_git_version, get_git_date
from setuptools.command.bdist_egg import bdist_egg
cmdclass = {}
setup_requires = ['setuptools', 'wheel']
if 'x86_64' in platform.machine():
try:
from Cython.Distutils import build_ext
import numpy
cython_modules = [
Extension("pynx.scattering.cpu", sources=["pynx/scattering/cpu.pyx", "pynx/scattering/c_cpu.c"],
include_dirs=[numpy.get_include()],
extra_compile_args=['-O3', '-ffast-math', '-msse', '-msse2', '-mssse3', '-msse4.1',
'-march=native', '-mfpmath=sse', '-fstrict-aliasing', '-pipe',
'-fomit-frame-pointer', '-funroll-loops', '-ftree-vectorize',
'-DSSE_MATHFUN_WITH_CODE'])]
cmdclass['build_ext'] = build_ext
setup_requires.append('cython')
except:
cython_modules = []
else:
cython_modules = []
class pynx_sdist(su_sdist):
def make_release_tree(self, base_dir, files):
super(pynx_sdist, self).make_release_tree(base_dir, files)
try:
# Replace git_version_placeholder by real git version
version_file = os.path.join(base_dir, "pynx/version.py")
vers = open(version_file).read()
os.remove(version_file)
with open(version_file, "w") as fh:
print(get_git_version())
print(get_git_date())
vers = vers.replace("git_version_placeholder", get_git_version())
vers = vers.replace("git_date_placeholder", get_git_date())
fh.write(vers)
except:
print("sdist: replacing git_version_placeholder failed")
class pynx_install_lib(su_install_lib):
def run(self):
super(pynx_install_lib, self).run()
try:
# print(self.install_dir, self.build_dir)
# Replace git_version_placeholder by real git version
version_file = os.path.join(self.install_dir, "pynx/version.py")
vers = open(version_file).read()
os.remove(version_file)
with open(version_file, "w") as fh:
print(get_git_version())
print(get_git_date())
vers = vers.replace("git_version_placeholder", get_git_version())
vers = vers.replace("git_date_placeholder", get_git_date())
fh.write(vers)
except:
print("install_lib: replacing git_version_placeholder failed")
cmdclass['sdist'] = pynx_sdist
cmdclass['install_lib'] = pynx_install_lib
# Converts scripts to console_scripts
scripts = ['pynx/cdi/scripts/pynx_id10cdi.py',
'pynx/cdi/scripts/pynx_id01cdi.py',
'pynx/cdi/scripts/pynx_cdi_analysis.py',
'pynx/cdi/scripts/pynx_cdi_regrid.py',
'pynx/ptycho/scripts/pynx_cristalpty.py',
'pynx/ptycho/scripts/pynx_cxipty.py',
'pynx/ptycho/scripts/pynx_hermespty.py',
'pynx/ptycho/scripts/pynx_id01pty.py',
'pynx/ptycho/scripts/pynx_id13pty.py',
'pynx/ptycho/scripts/pynx_id16apty.py',
'pynx/ptycho/scripts/pynx_id16a_nfpty.py',
'pynx/ptycho/scripts/pynx_nanomaxpty.py',
'pynx/ptycho/scripts/pynx_nanoscopiumpty.py',
'pynx/ptycho/scripts/pynx_ptypy.py',
'pynx/ptycho/scripts/pynx_ptycho_analysis.py',
'pynx/ptycho/scripts/pynx_simulationpty.py',
'pynx/ptycho/scripts/pynx_tps25apty.py',
'pynx/scripts/pynx_info.py',
'pynx/scripts/pynx_test.py',
'pynx/utils/scripts/pynx_resolution_FSC.py'
]
console_scripts = ['pynx-cdi-id10 = pynx.cdi.scripts.pynx_id10cdi:main',
'pynx-cdi-id01 = pynx.cdi.scripts.pynx_id01cdi:main',
'pynx-cdi-analysis = pynx.cdi.scripts.pynx_cdi_analysis:main',
'pynx-cdi-regrid = pynx.cdi.scripts.pynx_cdi_regrid:main',
'pynx-cdi-simulation = pynx.cdi.scripts.pynx_cdi_simulation:main',
# 'pynx-holotomo-id16a = pynx.holotomo.runner.__init__:main',
'pynx-holotomo-id16b = pynx.holotomo.runner.__init__:main',
'pynx-ptycho-cristal = pynx.ptycho.scripts.pynx_cristalpty:main',
'pynx-ptycho-cxi = pynx.ptycho.scripts.pynx_cxipty:main',
'pynx-ptycho-hermes = pynx.ptycho.scripts.pynx_hermespty:main',
'pynx-ptycho-id01 = pynx.ptycho.scripts.pynx_id01pty:main',
'pynx-ptycho-id13 = pynx.ptycho.scripts.pynx_id13pty:main',
'pynx-ptycho-id16a = pynx.ptycho.scripts.pynx_id16apty:main',
'pynx-ptycho-id16a-nf = pynx.ptycho.scripts.pynx_id16a_nfpty:main',
'pynx-ptycho-nanomax = pynx.ptycho.scripts.pynx_nanomaxpty:main',
'pynx-ptycho-nanoscopium = pynx.ptycho.scripts.pynx_nanoscopiumpty:main',
'pynx-nfp2nxtomo = pynx.ptycho.scripts.pynx_nfp2nxtomo:main',
'pynx-ptycho-p06 = pynx.ptycho.scripts.pynx_p06pty:main',
'pynx-ptycho-ptypy = pynx.ptycho.scripts.pynx_ptypy:main',
'pynx-ptycho-analysis = pynx.ptycho.scripts.pynx_ptycho_analysis:main',
'pynx-ptycho-simulation = pynx.ptycho.scripts.pynx_simulationpty:main',
'pynx-ptycho-tps25a = pynx.ptycho.scripts.pynx_tps25apty:main',
'pynx-info = pynx.scripts.pynx_info:main',
'pynx-test = pynx.scripts.pynx_test:main',
'pynx-resolution-fsc = pynx.utils.scripts.pynx_resolution_FSC:main',
]
# Add deprecated version of scripts
for s in scripts:
s1 = os.path.split(s)[1]
s0 = os.path.splitext(s)[0]
console_scripts.append("%s = %s:main" % (s1.replace('_', '-'), s0.replace('/', '.')))
class bdist_egg_disabled(bdist_egg):
""" Disabled bdist_egg, to prevent use of 'python setup.py install' """
def run(self):
sys.exit("Aborting building of eggs. Please use `pip install .` to install from source.")
cmdclass['bdist_egg'] = bdist_egg if 'bdist_egg' in sys.argv else bdist_egg_disabled
setup(
name="PyNX",
version=__version__,
packages=find_packages(),
entry_points={'console_scripts': console_scripts,
# 'gui_scripts': [],
},
cmdclass=cmdclass,
ext_modules=cython_modules,
python_requires='>=3.9',
setup_requires=setup_requires,
install_requires=['numpy>=1.23', 'scipy>=1.10', 'matplotlib', 'scikit-image>=0.17',
'fabio', 'silx', 'packaging', 'psutil', 'scikit-learn',
'mako', 'numexpr', 'pyopencl>=2022', 'pyvkfft>=2024', 'nxtomo>=1.3',
'pooch', 'tomoscan>=2.1', 'pytools'],
extras_require={'cuda': ['pycuda>=2023'], 'gid': ["cctbx"], 'mpi': ['mpi4py'],
'doc': ['sphinx', 'nbsphinx', 'nbsphinx-link', 'sphinx-argparse', 'pydata-sphinx-theme'],
'holotomo': ['nabu~=2024.2', 'tifffile'],
'gui': ["ipywidgets", "jupyter", "jupyterlab", "ipympl", "pyopengl", "ipyvolume",
"ipyfilechooser", "voila"]},
include_package_data=True,
data_files=[],
# metadata for upload to PyPI
author="vincefn",
author_email="favre@esrf.fr",
description="PyNX - GPU-accelerated python toolkit for coherent X-ray imaging and nano-crystallography",
license="CeCILL-B",
keywords="PyNX GPU OpenCL CUDA crystallography diffraction scattering coherent X-rays Imaging ptychography CDI",
# Should also run under windows, as long as PyOpenCL and/or PyCUDA are properly installed
platforms=["MacOS", "POSIX", "Linux"],
url="https://gitlab.esrf.fr/favre/PyNX",
long_description=
"PyNX provides Python tools for coherent X-ray imaging and nano-crystallography: \
* compute the X-ray scattering for nano-structures, using GPU (CUDA or OpenCL)"
" acceleration, including in grazing incidence conditions.\
* X-rays scattering atomic scattering factors\
* 2D X-ray wavefront propagation\
* tools for ptychography reconstruction\
* Coherent Diffraction Imaging (2D and 3D) reconstruction algorithms\
* Holo-tomography reconstructions (beta)",
classifiers=[
'Development Status :: 5 - Production/Stable',
'Environment :: Console',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'Intended Audience :: Education',
'License :: License :: CEA CNRS Inria Logiciel Libre License B (CeCILL-B)',
'Operating System :: MacOS :: MacOS X',
'Operating System :: POSIX :: Linux',
'Programming Language :: Python',
'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', # Dependencies need upgrade
'Topic :: Scientific/Engineering :: Physics',
'Environment :: GPU :: NVIDIA CUDA'
],
)
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