setup.py 20.8 KB
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#!/usr/bin/env python3
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# Copyright 2011-2018 Kwant authors.
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#
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# This file is part of Kwant.  It is subject to the license terms in the file
# LICENSE.rst found in the top-level directory of this distribution and at
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# https://kwant-project.org/license.  A list of Kwant authors can be found in
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# the file AUTHORS.rst at the top-level directory of this distribution and at
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# https://kwant-project.org/authors.
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from __future__ import print_function

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import sys
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import re
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import os
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import glob
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import importlib
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import subprocess
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import configparser
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import collections
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from setuptools import setup, find_packages, Extension, Command
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from distutils.errors import DistutilsError, CCompilerError
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from distutils.command.build import build as build_orig
from setuptools.command.sdist import sdist as sdist_orig
from setuptools.command.build_ext import build_ext as build_ext_orig
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from setuptools.command.test import test as test_orig
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from distutils.ccompiler import new_compiler
from distutils.sysconfig import customize_compiler
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STATIC_VERSION_PATH = ('kwant', '_kwant_version.py')
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distr_root = os.path.dirname(os.path.abspath(__file__))


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def configure_extensions(exts, aliases=(), build_summary=None):
    """Modify extension configuration according to the configuration file

    `exts` must be a dict of (name, kwargs) tuples that can be used like this:
    `Extension(name, **kwargs).  This function modifies the kwargs according to
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    the configuration file.

    This function modifies `sys.argv`.
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    """
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    global config_file, config_file_present

    #### Determine the name of the configuration file.
    config_file_option = '--configfile'
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    config_file_option_present = False
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    # Handle command line option
    for i, opt in enumerate(sys.argv):
        if not opt.startswith(config_file_option):
            continue
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        config_file_option_present = True
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        l, _, config_file = opt.partition('=')
        if l != config_file_option or not config_file:
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            print('Error: Expecting {}=PATH'.format(config_file_option),
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                  file=sys.stderr)
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            sys.exit(1)
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        sys.argv.pop(i)
        break
    else:
        config_file = 'build.conf'
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    #### Read build configuration file.
    configs = configparser.ConfigParser()
    try:
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        with open(config_file) as f:
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            configs.read_file(f)
    except IOError:
        config_file_present = False
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        if config_file_option_present:
            print("Error: '{}' option was provided, but '{}' does not exist"
                  .format(config_file_option, config_file))
            sys.exit(1)
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    else:
        config_file_present = True

    #### Handle section aliases.
    for short, long in aliases:
        if short in configs:
            if long in configs:
                print('Error: both {} and {} sections present in {}.'.format(
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                    short, long, config_file))
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                sys.exit(1)
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            configs[long] = configs[short]
            del configs[short]

    #### Apply config from file.  Use [DEFAULT] section for missing sections.
    defaultconfig = configs.defaults()
    for name, kwargs in exts.items():
        config = configs[name] if name in configs else defaultconfig
        for key, value in config.items():

            # Most, but not all, keys are lists of strings
            if key == 'language':
                pass
            elif key == 'optional':
                value = bool(int(value))
            else:
                value = value.split()

            if key == 'define_macros':
                value = [tuple(entry.split('=', maxsplit=1))
                         for entry in value]
                value = [(entry[0], None) if len(entry) == 1 else entry
                         for entry in value]

            if key in kwargs:
                msg = 'Caution: user config in file {} shadows {}.{}.'
                if build_summary is not None:
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                    build_summary.append(msg.format(config_file, name, key))
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            kwargs[key] = value

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        kwargs.setdefault('depends', []).append(config_file)
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        if config is not defaultconfig:
            del configs[name]

    unknown_sections = configs.sections()
    if unknown_sections:
        print('Error: Unknown sections in file {}: {}'.format(
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            config_file, ', '.join(unknown_sections)))
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        sys.exit(1)
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    return exts


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def check_python_version(min_version):
    installed_version = sys.version_info[:3]
    if installed_version < min_version:
        print('Error: Python {} required, but {} is installed'.format(
              '.'.join(map(str, min_version)),
              '.'.join(map(str, installed_version)))
        )
        sys.exit(1)


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def check_versions():
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    global version, version_is_from_git

    # Let Kwant itself determine its own version.  We cannot simply import
    # kwant, as it is not built yet.
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    spec = importlib.util.spec_from_file_location('version', 'kwant/version.py')
    version_module = importlib.util.module_from_spec(spec)
    spec.loader.exec_module(version_module)
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    version_module.ensure_python()
    version = version_module.version
    version_is_from_git = version_module.version_is_from_git
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def init_cython():
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    """Set the global variable `cythonize` (and other related globals).

    The variable `cythonize` can be in three states:

    * If Cython should be run and is ready, it contains the `cythonize()`
      function.

    * If Cython is not to be run, it contains `False`.

    * If Cython should, but cannot be run it contains `None`.  A help message
      on how to solve the problem is stored in `cython_help`.

    This function modifies `sys.argv`.
    """
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    global cythonize, cython_help
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    cython_option = '--cython'
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    required_cython_version = (0, 24)
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    try:
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        sys.argv.remove(cython_option)
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        cythonize = True
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    except ValueError:
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        cythonize = version_is_from_git
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    if cythonize:
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        try:
            import Cython
            from Cython.Build import cythonize
        except ImportError:
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            cythonize = None
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        else:
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            #### Get Cython version.
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            match = re.match('([0-9.]*)(.*)', Cython.__version__)
            cython_version = [int(n) for n in match.group(1).split('.')]
            # Decrease version if the version string contains a suffix.
            if match.group(2):
                while cython_version[-1] == 0:
                    cython_version.pop()
                cython_version[-1] -= 1
            cython_version = tuple(cython_version)
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            if cython_version < required_cython_version:
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                cythonize = None

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        if cythonize is None:
            msg = ("Install Cython >= {0} or use"
                    " a source distribution (tarball) of Kwant.")
            ver = '.'.join(str(e) for e in required_cython_version)
            cython_help = msg.format(ver)
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    else:
        msg = "Run setup.py with the {} option to enable Cython."
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        cython_help = msg.format(cython_option)
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def banner(title=''):
    starred = title.center(79, '*')
    return '\n' + starred if title else starred
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class build_ext(build_ext_orig):
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    def run(self):
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        if not config_file_present:
            # Create an empty config file if none is present so that the
            # extensions will not be rebuilt each time.  Only depending on the
            # config file if it is present would make it impossible to detect a
            # necessary rebuild due to a deleted config file.
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            with open(config_file, 'w') as f:
                f.write('# Build configuration created by setup.py '
                        '- feel free to modify.\n')
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        try:
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            super().run()
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        except (DistutilsError, CCompilerError):
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            error_msg = self.__error_msg.format(
                header=banner(' Error '), sep=banner())
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            print(error_msg.format(file=config_file, summary=build_summary),
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                  file=sys.stderr)
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            raise
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        print(banner(' Build summary '), *build_summary, sep='\n')
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        print(banner())
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    __error_msg = """{header}
The compilation of Kwant has failed.  Please examine the error message
above and consult the installation instructions in README.rst.
You might have to customize {{file}}.

Build configuration was:

{{summary}}
{sep}
"""

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class build(build_orig):
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    def run(self):
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        super().run()
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        write_version(os.path.join(self.build_lib, *STATIC_VERSION_PATH))

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def git_lsfiles():
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    if not version_is_from_git:
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        return

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    try:
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        p = subprocess.Popen(['git', 'ls-files'], cwd=distr_root,
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                             stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    except OSError:
        return

    if p.wait() != 0:
        return
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    return p.communicate()[0].decode().split('\n')[:-1]
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# Make the command "sdist" depend on "build".  This verifies that the
# distribution in the current state actually builds.  It also makes sure that
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# the Cython-made C files will be up-to-date and included in the source.
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class sdist(sdist_orig):
    sub_commands = [('build', None)] + sdist_orig.sub_commands
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    def run(self):
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        """Create MANIFEST.in from git if possible, otherwise check that
        MANIFEST.in is present.
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        Right now (2015) generating MANIFEST.in seems to be the only way to
        include files in the source distribution that setuptools does not think
        should be there.  Setting include_package_data to True makes setuptools
        include *.pyx and other source files in the binary distribution.
        """
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        manifest_in_file = 'MANIFEST.in'
        manifest = os.path.join(distr_root, manifest_in_file)
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        names = git_lsfiles()
        if names is None:
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            if not (os.path.isfile(manifest) and os.access(manifest, os.R_OK)):
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                print("Error:", manifest_in_file,
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                      "file is missing and Git is not available"
                      " to regenerate it.", file=sys.stderr)
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                sys.exit(1)
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        else:
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            with open(manifest, 'w') as f:
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                for name in names:
                    a, sep, b = name.rpartition('/')
                    if b == '.gitignore':
                        continue
                    stem, dot, extension = b.rpartition('.')
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                    f.write('include {}'.format(name))
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                    if extension == 'pyx':
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                        f.write(''.join([' ', a, sep, stem, dot, 'c']))
                    f.write('\n')
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        super().run()
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        if names is None:
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            msg = ("Git was not available to generate the list of files to be "
                   "included in the\nsource distribution. The old {} was used.")
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            msg = msg.format(manifest_in_file)
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            print(banner(' Caution '), msg, banner(), sep='\n', file=sys.stderr)
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    def make_release_tree(self, base_dir, files):
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        super().make_release_tree(base_dir, files)
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        write_version(os.path.join(base_dir, *STATIC_VERSION_PATH))
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# The following class is based on a recipe in
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# https://doc.pytest.org/en/latest/goodpractices.html#manual-integration.
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class test(test_orig):
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    user_options = [('pytest-args=', 'a', "Arguments to pass to pytest")]

    def initialize_options(self):
        super().initialize_options()
        self.pytest_args = ''

    def run_tests(self):
        import shlex
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        try:
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            import pytest
        except:
            print('The Python package "pytest" is required to run tests.',
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                  file=sys.stderr)
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            sys.exit(1)
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        errno = pytest.main(shlex.split(self.pytest_args))
        sys.exit(errno)
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def write_version(fname):
    # This could be a hard link, so try to delete it first.  Is there any way
    # to do this atomically together with opening?
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    try:
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        os.remove(fname)
    except OSError:
        pass
    with open(fname, 'w') as f:
        f.write("# This file has been created by setup.py.\n")
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        f.write("version = '{}'\n".format(version))
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def long_description():
    text = []
    try:
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        with open('README.rst', encoding='utf8') as f:
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            for line in f:
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                if line.startswith('See also in this directory:'):
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                    break
                text.append(line.rstrip())
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            while text[-1] == "":
                text.pop()
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    except:
        return ''
    return '\n'.join(text)


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def search_libs(libs):
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    # This gives us a compiler with the same flags as will be used to
    # compile the extensions.
    cc = new_compiler("c")
    customize_compiler(cc)
    cmd = cc.linker_so
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    cmd.extend(['-l' + lib for lib in libs])
    cmd.extend(['-o/dev/null', '-xc', '-'])
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    try:
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        p = subprocess.Popen(cmd, stdin=subprocess.PIPE, stderr=subprocess.PIPE)
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    except OSError:
        pass
    else:
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        p.communicate(input=b'int main() {}\n')
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        if p.wait() == 0:
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            return libs


def search_mumps():
    """Return the configuration for MUMPS if it is available in a known way.

    This is known to work with the MUMPS provided by the Debian package
    libmumps-scotch-dev and the MUMPS binaries in the conda-forge channel."""
    lib_sets = [
        # Debian
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        ['zmumps_scotch', 'mumps_common_scotch', 'mpiseq_scotch',
         'pord', 'gfortran'],
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        # Conda (via conda-forge).
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        ['zmumps_seq', 'mumps_common_seq'],
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    ]
    for libs in lib_sets:
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        found_libs = search_libs(libs)
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        if found_libs:
            return found_libs
    return []


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def configure_special_extensions(exts, build_summary):
    #### Special config for MUMPS.
    mumps = exts['kwant.linalg._mumps']
    if 'libraries' in mumps:
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        build_summary.append('User-configured MUMPS')
    else:
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        mumps_libs = search_mumps()
        if mumps_libs:
            mumps['libraries'] = mumps_libs
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            build_summary.append('Auto-configured MUMPS')
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        else:
            mumps = None
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            del exts['kwant.linalg._mumps']
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            build_summary.append('No MUMPS support')
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    return exts
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def maybe_cythonize(exts):
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    """Prepare a list of `Extension` instances, ready for `setup()`.
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    The argument `exts` must be a mapping of names to kwargs to be passed
    on to `Extension`.
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    If Cython is to be run, create the extensions and calls `cythonize()` on
    them.  If Cython is not to be run, replace .pyx file with .c or .cpp,
    check timestamps, and create the extensions.
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    """
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    if cythonize:
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        return cythonize([Extension(name, **kwargs)
                          for name, kwargs in exts.items()],
                         language_level=3,
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                         compiler_directives={'linetrace': True})
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    # Cython is not going to be run: replace pyx extension by that of
    # the shipped translated file.

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    result = []
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    problematic_files = []
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    for name, kwargs in exts.items():
        language = kwargs.get('language')
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        if language is None:
            ext = '.c'
        elif language == 'c':
            ext = '.c'
        elif language == 'c++':
            ext = '.cpp'
        else:
            print('Unknown language: {}'.format(language), file=sys.stderr)
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            sys.exit(1)
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        pyx_files = []
        cythonized_files = []
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        sources = []
        for f in kwargs['sources']:
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            if f.endswith('.pyx'):
                pyx_files.append(f)
                f = f.rstrip('.pyx') + ext
                cythonized_files.append(f)
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            sources.append(f)
        kwargs['sources'] = sources
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        # Complain if cythonized files are older than Cython source files.
        try:
            cythonized_oldest = min(os.stat(f).st_mtime
                                    for f in cythonized_files)
        except OSError:
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            msg = "Cython-generated file {} is missing."
            print(banner(" Error "), msg.format(f), "",
                  cython_help, banner(), sep="\n", file=sys.stderr)
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            sys.exit(1)
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        for f in pyx_files + kwargs.get('depends', []):
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            if f == config_file:
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                # The config file is only a dependency for the compilation
                # of the cythonized file, not for the cythonization.
                continue
            if os.stat(f).st_mtime > cythonized_oldest:
                problematic_files.append(f)
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        result.append(Extension(name, **kwargs))
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    if problematic_files:
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        msg = ("Some Cython source files are newer than files that have "
               "been derived from them:\n{}")
        msg = msg.format(", ".join(problematic_files))

        # Cython should be run but won't.  Signal an error if this is because
        # Cython *cannot* be run, warn otherwise.
        error = cythonize is None
        if cythonize is False:
            dontworry = ('(Do not worry about this if you are building Kwant '
                         'from unmodified sources,\n'
                         'e.g. with "pip install".)\n\n')
            msg = dontworry + msg

        print(banner(" Error " if error else " Caution "), msg, "",
              cython_help, banner(), sep="\n", file=sys.stderr)
        if error:
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            sys.exit(1)
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    return result

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def maybe_add_numpy_include(exts):
    # Add NumPy header path to include_dirs of all the extensions.
    try:
        import numpy
    except ImportError:
        print(banner(' Caution '), 'NumPy header directory cannot be determined'
              ' ("import numpy" failed).', banner(), sep='\n', file=sys.stderr)
    else:
        numpy_include = numpy.get_include()
        for ext in exts.values():
            ext.setdefault('include_dirs', []).append(numpy_include)
    return exts


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def add_sys_includes_and_libs(exts):
    # If the shell has not been set up correctly then the include and library paths
    # are not necessarily set correctly, which will cause problems when compiling
    # the Mumps extension (cannot find include files or libs)
    for ext in exts.values():
        ext.setdefault('include_dirs', []).append(os.path.join(sys.prefix, 'include'))
        ext.setdefault('library_dirs', []).append(os.path.join(sys.prefix, 'lib'))
    return exts


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def main():
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    check_python_version((3, 6))
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    check_versions()

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    exts = collections.OrderedDict([
        ('kwant._system',
         dict(sources=['kwant/_system.pyx'],
              include_dirs=['kwant/graph'])),
        ('kwant.operator',
         dict(sources=['kwant/operator.pyx'],
              include_dirs=['kwant/graph'])),
        ('kwant.graph.core',
         dict(sources=['kwant/graph/core.pyx'],
              depends=['kwant/graph/core.pxd', 'kwant/graph/defs.h',
                       'kwant/graph/defs.pxd'])),
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        ('kwant.graph.dijkstra',
         dict(sources=['kwant/graph/dijkstra.pyx'])),
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        ('kwant.linalg.lapack',
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         dict(sources=['kwant/linalg/lapack.pyx'])),
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        ('kwant.linalg._mumps',
         dict(sources=['kwant/linalg/_mumps.pyx'],
              depends=['kwant/linalg/cmumps.pxd']))])

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    aliases = [('mumps', 'kwant.linalg._mumps')]
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    init_cython()

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    global build_summary
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    build_summary = []
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    exts = configure_extensions(exts, aliases, build_summary)
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    exts = configure_special_extensions(exts, build_summary)
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    exts = maybe_add_numpy_include(exts)
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    exts = add_sys_includes_and_libs(exts)
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    exts = maybe_cythonize(exts)

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    classifiers = """\
        Development Status :: 5 - Production/Stable
        Intended Audience :: Science/Research
        Intended Audience :: Developers
        Programming Language :: Python :: 3 :: Only
        Topic :: Software Development
        Topic :: Scientific/Engineering
        Operating System :: POSIX
        Operating System :: Unix
        Operating System :: MacOS :: MacOS X
        Operating System :: Microsoft :: Windows"""

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    packages = find_packages('.')
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    setup(name='kwant',
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          version=version,
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          author='C. W. Groth (CEA), M. Wimmer, '
                 'A. R. Akhmerov, X. Waintal (CEA), and others',
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          author_email='authors@kwant-project.org',
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          description=("Package for numerical quantum transport calculations "
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                       "(Python 3 version)"),
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          long_description=long_description(),
          platforms=["Unix", "Linux", "Mac OS-X", "Windows"],
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          url="https://kwant-project.org/",
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          license="BSD",
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          packages=packages,
          package_data={p: ['*.pxd', '*.h'] for p in packages},
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          cmdclass={'build': build,
                    'sdist': sdist,
                    'build_ext': build_ext,
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                    'test': test},
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          ext_modules=exts,
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          python_requires='>=3.7',
          # The oldest versions between: Debian stable, Ubuntu LTS
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          install_requires=['numpy >= 1.16.2', 'scipy >= 1.1.0, != 1.6.1',
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                            'tinyarray >= 1.2'],
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          extras_require={
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              'plotting': ['matplotlib >= 3.0.2',
                           'plotly >= 3.6.1'],
              'continuum': 'sympy >= 1.3.0',
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              # qsymm is only packaged on PyPI
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              'qsymm': 'qsymm >= 1.3.0',
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          },
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          classifiers=[c.strip() for c in classifiers.split('\n')])
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if __name__ == '__main__':
    main()