setup.py 28.1 KB
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#!/usr/bin/python
# coding: utf8
# /*##########################################################################
#
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# Copyright (c) 2015-2018 European Synchrotron Radiation Facility
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#
# 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.
#
# ###########################################################################*/

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__authors__ = ["Jérôme Kieffer", "Thomas Vincent"]
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__date__ = "23/04/2018"
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__license__ = "MIT"

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import sys
import os
import platform
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import shutil
import logging
import glob
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# io import has to be here also to fix a bug on Debian 7 with python2.7
# Without this, the system io module is not loaded from numpy.distutils.
# The silx.io module seems to be loaded instead.
import io
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logging.basicConfig(level=logging.INFO)

logger = logging.getLogger("xsocs.setup")
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from distutils.command.clean import clean as Clean
from distutils.command.build import build as _build
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try:
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    from setuptools import Command
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    from setuptools.command.build_py import build_py as _build_py
    from setuptools.command.build_ext import build_ext
    from setuptools.command.sdist import sdist
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    logger.info("Use setuptools")
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except ImportError:
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    try:
        from numpy.distutils.core import Command
    except ImportError:
        from distutils.core import Command
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    from distutils.command.build_py import build_py as _build_py
    from distutils.command.build_ext import build_ext
    from distutils.command.sdist import sdist
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    logger.info("Use distutils")
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try:
    import sphinx
    import sphinx.util.console
    sphinx.util.console.color_terminal = lambda: False
    from sphinx.setup_command import BuildDoc
except ImportError:
    sphinx = None
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PROJECT = "xsocs"

if "LANG" not in os.environ and sys.platform == "darwin" and sys.version_info[0] > 2:
    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
""")
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def get_version():
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    """Returns current version number from version.py file"""
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    import version
    return version.strictversion


def get_readme():
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    """Returns content of README.rst file"""
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    dirname = os.path.dirname(os.path.abspath(__file__))
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    filename = os.path.join(dirname, "README.rst")
    with io.open(filename, "r", encoding="utf-8") as fp:
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        long_description = fp.read()
    return long_description


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classifiers = ["Development Status :: 4 - Beta",
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               "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 :: POSIX",
               "Programming Language :: Cython",
               "Programming Language :: Python :: 2.7",
               "Programming Language :: Python :: 3.4",
               "Programming Language :: Python :: 3.5",
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               "Programming Language :: Python :: 3.6",
               "Programming Language :: Python :: 3.7",
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               "Programming Language :: Python :: Implementation :: CPython",
               "Topic :: Scientific/Engineering :: Physics",
               "Topic :: Software Development :: Libraries :: Python Modules",
               ]


# ########## #
# version.py #
# ########## #

class build_py(_build_py):
    """
    Enhanced build_py which copies version.py to <PROJECT>._version.py
    """
    def find_package_modules(self, package, package_dir):
        modules = _build_py.find_package_modules(self, package, package_dir)
        if package == PROJECT:
            modules.append((PROJECT, '_version', 'version.py'))
        return modules


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########
# Test #
########

class PyTest(Command):
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    """Command to start tests running the script: run_tests.py"""
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    user_options = []

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    description = "Execute the unittests"

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    def initialize_options(self):
        pass

    def finalize_options(self):
        pass

    def run(self):
        import subprocess
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        errno = subprocess.call([sys.executable, 'run_tests.py'])
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        if errno != 0:
            raise SystemExit(errno)
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# ################### #
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# build_doc command   #
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# ################### #

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if sphinx is None:
    class SphinxExpectedCommand(Command):
        """Command to inform that sphinx is missing"""
        user_options = []

        def initialize_options(self):
            pass

        def finalize_options(self):
            pass

        def run(self):
            raise RuntimeError(
                'Sphinx is required to build or test the documentation.\n'
                'Please install Sphinx (http://www.sphinx-doc.org).')


if sphinx is not None:
    class BuildDocCommand(BuildDoc):
        """Command to build documentation using sphinx.

        Project should have already be built.
        """
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        def run(self):
            # make sure the python path is pointing to the newly built
            # code so that the documentation is built on this and not a
            # previously installed version

            build = self.get_finalized_command('build')
            sys.path.insert(0, os.path.abspath(build.build_lib))
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            # # Copy .ui files to the path:
            # dst = os.path.join(
            #     os.path.abspath(build.build_lib), "silx", "gui")
            # if not os.path.isdir(dst):
            #     os.makedirs(dst)
            # for i in os.listdir("gui"):
            #     if i.endswith(".ui"):
            #         src = os.path.join("gui", i)
            #         idst = os.path.join(dst, i)
            #         if not os.path.exists(idst):
            #             shutil.copy(src, idst)
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            # Build the Users Guide in HTML and TeX format
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            for builder in ['html', 'latex']:
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                self.builder = builder
                self.builder_target_dir = os.path.join(self.build_dir, builder)
                self.mkpath(self.builder_target_dir)
                BuildDoc.run(self)
            sys.path.pop(0)
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else:
    BuildDocCommand = SphinxExpectedCommand
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# ################### #
# test_doc command    #
# ################### #
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if sphinx is not None:
    class TestDocCommand(BuildDoc):
        """Command to test the documentation using sphynx doctest.
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        http://www.sphinx-doc.org/en/1.4.8/ext/doctest.html
        """
        def run(self):
            # make sure the python path is pointing to the newly built
            # code so that the documentation is built on this and not a
            # previously installed version
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            build = self.get_finalized_command('build')
            sys.path.insert(0, os.path.abspath(build.build_lib))
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            # Build the Users Guide in HTML and TeX format
            for builder in ['doctest']:
                self.builder = builder
                self.builder_target_dir = os.path.join(self.build_dir, builder)
                self.mkpath(self.builder_target_dir)
                BuildDoc.run(self)
            sys.path.pop(0)
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else:
    TestDocCommand = SphinxExpectedCommand
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# ############################# #
# numpy.distutils Configuration #
# ############################# #

def configuration(parent_package='', top_path=None):
    """Recursive construction of package info to be used in setup().

    See http://docs.scipy.org/doc/numpy/reference/distutils.html#numpy.distutils.misc_util.Configuration
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    """
    try:
        from numpy.distutils.misc_util import Configuration
    except ImportError:
        raise ImportError(
            "To install this package, you must install numpy first\n"
            "(See https://pypi.python.org/pypi/numpy)")
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    config = Configuration(None, parent_package, top_path)
    config.set_options(
        ignore_setup_xxx_py=True,
        assume_default_configuration=True,
        delegate_options_to_subpackages=True,
        quiet=True)
    config.add_subpackage(PROJECT)
    return config

# ############## #
# Compiler flags #
# ############## #


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class Build(_build):
    """Command to support more user options for the build."""

    user_options = [
        ('no-openmp', None,
         "do not use OpenMP for compiled extension modules"),
        ('openmp', None,
         "use OpenMP for the compiled extension modules"),
        ('no-cython', None,
         "do not compile Cython extension modules (use default compiled c-files)"),
        ('force-cython', None,
         "recompile all Cython extension modules"),
    ]
    user_options.extend(_build.user_options)

    boolean_options = ['no-openmp', 'openmp', 'no-cython', 'force-cython']
    boolean_options.extend(_build.boolean_options)

    def initialize_options(self):
        _build.initialize_options(self)
        self.no_openmp = None
        self.openmp = None
        self.no_cython = None
        self.force_cython = None

    def finalize_options(self):
        _build.finalize_options(self)
        self.finalize_cython_options(min_version='0.21.1')
        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_force_cython = self._parse_env_as_bool("WITH_OPENMP")
            if env_force_cython is not None:
                use_openmp = env_force_cython
            else:
                # Use it by default
                use_openmp = True

        if use_openmp:
            if platform.system() == "Darwin":
                # By default Xcode5 & XCode6 do not support OpenMP, Xcode4 is OK.
                osx = tuple([int(i) for i in platform.mac_ver()[0].split(".")])
                if osx >= (10, 8):
                    logger.warning("OpenMP support ignored. Your platform do 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

    def finalize_cython_options(self, min_version=None):
        """
        Check if cythonization must be used for the extensions.

        The result is stored into the object.
        """

        if self.force_cython:
            use_cython = "force"
        elif self.no_cython:
            use_cython = "no"
        else:
            env_force_cython = self._parse_env_as_bool("FORCE_CYTHON")
            env_with_cython = self._parse_env_as_bool("WITH_CYTHON")
            if env_force_cython is True:
                use_cython = "force"
            elif env_with_cython is True:
                use_cython = "yes"
            elif env_with_cython is False:
                use_cython = "no"
            else:
                # Use it by default
                use_cython = "yes"

        if use_cython in ["force", "yes"]:
            try:
                import Cython.Compiler.Version
                if min_version and Cython.Compiler.Version.version < min_version:
                    msg = "Cython version is too old. At least version is %s \
                        expected. Cythonization is skipped."
                    logger.warning(msg, str(min_version))
                    use_cython = "no"
            except ImportError:
                msg = "Cython is not available. Cythonization is skipped."
                logger.warning(msg)
                use_cython = "no"

        # Remove attribute used by distutils parsing
        # use 'use_cython' and 'force_cython' instead
        del self.no_cython
        self.force_cython = use_cython == "force"
        self.use_cython = use_cython in ["force", "yes"]


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.
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    """

    COMPILE_ARGS_CONVERTER = {'-fopenmp': '/openmp'}

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    LINK_ARGS_CONVERTER = {'-fopenmp': ''}
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    description = 'Build xsocs 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.use_cython = build_obj.use_cython
        self.force_cython = build_obj.force_cython

    def patch_with_default_cythonized_files(self, ext):
        """Replace cython files by .c or .cpp files in extension's sources.

        It replaces the *.pyx and *.py source files of the extensions
        to either *.cpp or *.c source files.
        No compilation is performed.

        :param Extension ext: An extension to patch.
        """
        new_sources = []
        for source in ext.sources:
            base, file_ext = os.path.splitext(source)
            if file_ext in ('.pyx', '.py'):
                if ext.language == 'c++':
                    cythonized = base + '.cpp'
                else:
                    cythonized = base + '.c'
                if not os.path.isfile(cythonized):
                    raise RuntimeError("Source file not found: %s. Cython is needed" % cythonized)
                print("Use default cythonized file for %s" % source)
                new_sources.append(cythonized)
            else:
                new_sources.append(source)
        ext.sources = new_sources

    def patch_extension(self, ext):
        """
        Patch an extension according to requested Cython and OpenMP usage.

        :param Extension ext: An extension
        """
        # Cytonize
        if not self.use_cython:
            self.patch_with_default_cythonized_files(ext)
        else:
            from Cython.Build import cythonize
            patched_exts = cythonize(
                [ext],
                compiler_directives={'embedsignature': True},
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                force=self.force_cython
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            )
            ext.sources = patched_exts[0].sources

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        # Remove OpenMP flags if OpenMP is disabled
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        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']
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        # Convert flags from gcc to MSVC if required
        if self.compiler.compiler_type == 'msvc':
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            ext.extra_compile_args = [self.COMPILE_ARGS_CONVERTER.get(f, f)
                                      for f in ext.extra_compile_args]
            ext.extra_link_args = [self.LINK_ARGS_CONVERTER.get(f, f)
                                   for f in ext.extra_link_args]

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        elif self.compiler.compiler_type == 'unix':
            # Avoids runtime symbol collision for manylinux1 platform
            # See issue #1070
            extern = 'extern "C" ' if ext.language == 'c++' else ''
            return_type = 'void' if sys.version_info[0] <= 2 else 'PyObject*'

            ext.extra_compile_args.append(
                '''-fvisibility=hidden -D'PyMODINIT_FUNC=%s__attribute__((visibility("default"))) %s ' ''' % (extern, return_type))

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    def is_debug_interpreter(self):
        """
        Returns true if the script is executed with a debug interpreter.

        It looks to be a non-standard code. It is not working for Windows and
        Mac. But it have to work at least for Debian interpreters.

        :rtype: bool
        """
        if sys.version_info >= (3, 0):
            # It is normalized on Python 3
            # But it is not available on Windows CPython
            if hasattr(sys, "abiflags"):
                return "d" in sys.abiflags
        else:
            # It's a Python 2 interpreter
            # pydebug is not available on Windows/Mac OS interpreters
            if hasattr(sys, "pydebug"):
                return sys.pydebug

        # We can't know if we uses debug interpreter
        return False

    def patch_compiler(self):
        """
        Patch the compiler to:
        - always compile extensions with debug symboles (-g)
        - only compile asserts in debug mode (-DNDEBUG)

        Plus numpy.distutils/setuptools/distutils inject a lot of duplicated
        flags. This function tries to clean up default debug options.
        """
        build_obj = self.distribution.get_command_obj("build")
        if build_obj.debug:
            debug_mode = build_obj.debug
        else:
            # Force debug_mode also when it uses python-dbg
            # It is needed for Debian packaging
            debug_mode = self.is_debug_interpreter()

        if self.compiler.compiler_type == "unix":
            args = list(self.compiler.compiler_so)
            # clean up debug flags -g is included later in another way
            must_be_cleaned = ["-DNDEBUG", "-g"]
            args = filter(lambda x: x not in must_be_cleaned, args)
            args = list(args)

            # always insert symbols
            args.append("-g")
            # only strip asserts in release mode
            if not debug_mode:
                args.append('-DNDEBUG')
            # patch options
            self.compiler.compiler_so = list(args)
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    def build_extensions(self):
        self.patch_compiler()
        for ext in self.extensions:
            self.patch_extension(ext)
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        build_ext.build_extensions(self)

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################################################################################
# Clean command
################################################################################
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class CleanCommand(Clean):
    description = "Remove build artifacts from the source tree"
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    def expand(self, path_list):
        """Expand a list of path using glob magic.
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        :param list[str] path_list: A list of path which may contains magic
        :rtype: list[str]
        :returns: A list of path without magic
        """
        path_list2 = []
        for path in path_list:
            if glob.has_magic(path):
                iterator = glob.iglob(path)
                path_list2.extend(iterator)
            else:
                path_list2.append(path)
        return path_list2
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    def find(self, path_list):
        """Find a file pattern if directories.

        Could be done using "**/*.c" but it is only supported in Python 3.5.

        :param list[str] path_list: A list of path which may contains magic
        :rtype: list[str]
        :returns: A list of path without magic
        """
        import fnmatch
        path_list2 = []
        for pattern in path_list:
            for root, _, filenames in os.walk('.'):
                for filename in fnmatch.filter(filenames, pattern):
                    path_list2.append(os.path.join(root, filename))
        return path_list2

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    def run(self):
        Clean.run(self)
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        cython_files = self.find(["*.pyx"])
        cythonized_files = [path.replace(".pyx", ".c") for path in cython_files]
        cythonized_files += [path.replace(".pyx", ".cpp") for path in cython_files]

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        # really remove the directories
        # and not only if they are empty
        to_remove = [self.build_base]
        to_remove = self.expand(to_remove)
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        to_remove += cythonized_files
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        if not self.dry_run:
            for path in to_remove:
                try:
                    if os.path.isdir(path):
                        shutil.rmtree(path)
                    else:
                        os.remove(path)
                    logger.info("removing '%s'", path)
                except OSError:
                    pass
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################################################################################
# Source tree
################################################################################

class SourceDistWithCython(sdist):
    """
    Force cythonization of the extensions before generating the source
    distribution.

    To provide the widest compatibility the cythonized files are provided
    without suppport of OpenMP.
    """

    description = "Create a source distribution including cythonozed files (tarball, zip file, etc.)"

    def finalize_options(self):
        sdist.finalize_options(self)
        self.extensions = self.distribution.ext_modules

    def run(self):
        self.cythonize_extensions()
        sdist.run(self)

    def cythonize_extensions(self):
        from Cython.Build import cythonize
        cythonize(
            self.extensions,
            compiler_directives={'embedsignature': True},
            force=True
        )

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################################################################################
# Debian source tree
################################################################################


class sdist_debian(sdist):
    """
    Tailor made sdist for debian
    * remove auto-generated doc
    * remove cython generated .c files
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    * remove cython generated .cpp files
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    * remove .bat files
    * include .l man files
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    """
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    description = "Create a source distribution for Debian (tarball, zip file, etc.)"

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    @staticmethod
    def get_debian_name():
        import version
        name = "%s_%s" % (PROJECT, version.debianversion)
        return name

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    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")

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        # do not include third_party/_local files
        self.filelist.exclude_pattern(pattern="*", prefix="xsocs/third_party/_local")

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    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)
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        # if ext:
        #     dest = "".join((base, ext))
        # else:
        #     dest = base
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        # sp = dest.split("-")
        # base = sp[:-1]
        # nr = sp[-1]
        debian_arch = os.path.join(dirname, self.get_debian_name() + ".orig.tar.gz")
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        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 #
# ##### #

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def get_project_configuration(dry_run):
    """Returns project arguments for setup"""
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    # Use installed numpy version as minimal required version
    # This is useful for wheels to advertise the numpy version they were built with
    if dry_run:
        numpy_requested_version = ""
    else:
        from numpy.version import version as numpy_version
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        numpy_requested_version = ">=%s" % numpy_version
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        logger.info("Install requires: numpy %s", numpy_requested_version)

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    install_requires = [
        # for most of the computation
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        "numpy%s" % numpy_requested_version,
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        "h5py",
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        "fabio",
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        "silx>=0.9.0",
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        "xrayutilities",
        "scipy",
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        # for the script launcher
        "setuptools"]

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    setup_requires = ["setuptools", "numpy", "Cython>=0.21.1"]
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    extras_require = {
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        "gui": ["PyOpenGL", "matplotlib", "PyQt5"]
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    }

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    package_data = {
        'xsocs.resources': [
            # Add here all resources files
            'gui/icons/*.png',
            'gui/icons/*.svg',
            'gui/icons/*.mng',
            'gui/icons/*.gif']
    }

    entry_points = {
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        'console_scripts': ['xsocs = xsocs.__main__:main [gui]'],
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    }

    cmdclass = dict(
        build=Build,
        build_py=build_py,
        test=PyTest,
        build_doc=BuildDocCommand,
        test_doc=TestDocCommand,
        build_ext=BuildExt,
        clean=CleanCommand,
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        sdist=SourceDistWithCython,
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        debian_src=sdist_debian)

    if dry_run:
        # DRY_RUN implies actions which do not require NumPy
        #
        # And they are required to succeed without Numpy for example when
        # pip is used to install xsocs when Numpy is not yet present in
        # the system.
        setup_kwargs = {}
    else:
        config = configuration()
        setup_kwargs = config.todict()

    setup_kwargs.update(name=PROJECT,
                        version=get_version(),
                        url="https://gitlab.esrf.fr/kmap/xsocs",
                        author="data analysis unit",
                        author_email="silx@esrf.fr",
                        classifiers=classifiers,
                        description="Xray Strain Orientation "
                                    "Calculation Software",
                        long_description=get_readme(),
                        install_requires=install_requires,
                        setup_requires=setup_requires,
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                        extras_require=extras_require,
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                        cmdclass=cmdclass,
                        package_data=package_data,
                        zip_safe=False,
                        entry_points=entry_points,
                        )
    return setup_kwargs


def setup_package():
    """Run setup(**kwargs)

    Depending on the command, it either runs the complete setup which depends on numpy,
    or a *dry run* setup with no dependency on numpy.
    """

    # Check if action requires build/install
    dry_run = len(sys.argv) == 1 or (len(sys.argv) >= 2 and (
        '--help' in sys.argv[1:] or
        sys.argv[1] in ('--help-commands', 'egg_info', '--version',
                        'clean', '--name')))

    if dry_run:
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        # DRY_RUN implies actions which do not require dependencies, like NumPy
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        try:
            from setuptools import setup
            logger.info("Use setuptools.setup")
        except ImportError:
            from distutils.core import setup
            logger.info("Use distutils.core.setup")
    else:
        try:
            from setuptools import setup
        except ImportError:
            from numpy.distutils.core import setup
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            logger.info("Use numpy.distutils.setup")
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    setup_kwargs = get_project_configuration(dry_run)
    setup(**setup_kwargs)


if __name__ == "__main__":
    setup_package()