setup.py

#!/usr/bin/env python
# coding: utf-8

from __future__ import print_function, division, with_statement, absolute_import

"""
Setup script for python distutils package and fabio
"""
import os
import sys
import os.path as op
import glob
import shutil
import numpy as np
try:
    # setuptools allows the creation of wheels
    from setuptools import setup, Extension, Command
    from setuptools.command.sdist import sdist
except ImportError:
    from distutils.core import setup
    from distutils.core import Extension, Command
    from distutils.command.sdist import sdist
from distutils.filelist import FileList

################################################################################
# Remove MANIFEST file ... it needs to be re-generated on the fly
################################################################################
if op.isfile("MANIFEST"):
    os.unlink("MANIFEST")


################################################################################
# Check for Cython and use it if it is available
################################################################################
USE_CYTHON = True
try:
    import Cython.Compiler.Version
    from Cython.Distutils import build_ext
except ImportError:
    USE_CYTHON = False
else:
    if tuple(int(i) for i in Cython.Compiler.Version.version.split(".")[:2]) < (0, 17):
        USE_CYTHON = False
    else:
        USE_CYTHON = True

if USE_CYTHON:
    ext = ".pyx"
else:
    from distutils.command.build_ext import build_ext
    ext = ".c"


cf_backend = Extension('cf_io',
                       include_dirs=[np.get_include()],
                       sources=['src/cf_io' + ext, 'src/columnfile.c'])
byteOffset_backend = Extension("byte_offset",
                               include_dirs=[np.get_include()],
                               sources=['src/byte_offset' + ext])

mar345_backend = Extension('mar345_IO',
                           include_dirs=[np.get_include()],
                           sources=['src/mar345_IO' + ext,
                                    'src/ccp4_pack.c',
                                      ])
_cif_backend = Extension('_cif',
                         include_dirs=[np.get_include()],
                         sources=['src/_cif' + ext])


extensions = [cf_backend, byteOffset_backend, mar345_backend, _cif_backend]


def get_version():
    sys.path.insert(0, op.join(op.dirname(op.abspath(__file__)), "fabio-src"))
    import _version
    sys.path.pop(0)
    return _version.version

#######################
# build_doc commandes #
#######################
cmdclass = {}

try:
    import sphinx
    import sphinx.util.console
    sphinx.util.console.color_terminal = lambda: False
    from sphinx.setup_command import BuildDoc
except ImportError:
    sphinx = None
else:
    # i.e. if sphinx:
    class build_doc(BuildDoc):

        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')
            print(op.abspath(build.build_lib))
            sys.path.insert(0, op.abspath(build.build_lib))
            # Build the Users Guide in HTML and TeX format
            for builder in ('html', 'latex'):
                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)
    cmdclass['build_doc'] = build_doc


class PyTest(Command):
    user_options = []

    def initialize_options(self):
        pass

    def finalize_options(self):
        pass

    def run(self):
        import subprocess
        os.chdir(op.join(op.dirname(op.abspath(__file__)), "test"))
        errno = subprocess.call([sys.executable, 'test_all.py'])
        if errno != 0:
            raise SystemExit(errno)
        else:
            os.chdir("..")

cmdclass['test'] = PyTest

# We subclass the build_ext class in order to handle compiler flags
# for openmp and opencl etc in a cross platform way
translator = {
        # Compiler
          # name, compileflag, linkflag
        'msvc':{
            'openmp': ('/openmp', ' '),
            'debug' : ('/Zi', ' '),
            'OpenCL': 'OpenCL',
            },
        'mingw32':{
            'openmp': ('-fopenmp', '-fopenmp'),
            'debug' : ('-g', '-g'),
            'stdc++': 'stdc++',
            'OpenCL': 'OpenCL'
            },
        'default':{
            'openmp': ('-fopenmp', '-fopenmp'),
            'debug' : ('-g', '-g'),
            'stdc++': 'stdc++',
            'OpenCL': 'OpenCL'
            }
        }


class build_ext_FabIO(build_ext):
    def build_extensions(self):
        if self.compiler.compiler_type in translator:
            trans = translator[self.compiler.compiler_type]
        else:
            trans = translator['default']

        for e in self.extensions:
            e.extra_compile_args = [trans[a][0] if a in trans else a
                                    for a in e.extra_compile_args]
            e.extra_link_args = [trans[a][1] if a in trans else a
                                 for a in e.extra_link_args]
            e.libraries = [trans[arg] for arg in e.libraries if arg in trans]
        build_ext.build_extensions(self)
cmdclass['build_ext'] = build_ext_FabIO


################################################################################
# Debian source tree
################################################################################
def download_images():
    """
    Download all test images and
    """
    test_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "test")
    sys.path.insert(0, test_dir)
    from utilstest import UtilsTest
    for afile in UtilsTest.ALL_DOWNLOADED_FILES.copy():
        if afile.endswith(".bz2"):
            UtilsTest.ALL_DOWNLOADED_FILES.add(afile[:-4] + ".gz")
            UtilsTest.ALL_DOWNLOADED_FILES.add(afile[:-4])
        elif afile.endswith(".gz"):
            UtilsTest.ALL_DOWNLOADED_FILES.add(afile[:-3] + ".bz2")
            UtilsTest.ALL_DOWNLOADED_FILES.add(afile[:-3])
        else:
            UtilsTest.ALL_DOWNLOADED_FILES.add(afile + ".gz")
            UtilsTest.ALL_DOWNLOADED_FILES.add(afile + ".bz2")
    UtilsTest.download_images()
    return list(UtilsTest.ALL_DOWNLOADED_FILES)


class sdist_debian(sdist):
    """
    Tailor made sdist for debian
    * remove auto-generated doc
    * remove cython generated .c files
    * add image files from test/testimages/*
    """
    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
        self.filelist.exclude_pattern(pattern="*.html", anchor=True, prefix="src")
        for pyxf in glob.glob("src/*.pyx"):
            cf = op.splitext(pyxf)[0] + ".c"
            if op.isfile(cf):
                self.filelist.exclude_pattern(pattern=cf)

    def make_distribution(self):
        self.prune_file_list()
        sdist.make_distribution(self)
        dest = self.archive_files[0]
        dirname, basename = op.split(dest)
        base, ext = op.splitext(basename)
        while ext in [".zip", ".tar", ".bz2", ".gz", ".Z", ".lz", ".orig"]:
            base, ext = op.splitext(base)
        if ext:
            dest = "".join((base, ext))
        else:
            dest = base
        sp = dest.split("-")
        base = sp[:-1]
        nr = sp[-1]
        debian_arch = op.join(dirname, "-".join(base) + "_" + nr + ".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])

cmdclass['debian_src'] = sdist_debian


class sdist_testimages(sdist):
    """
    Tailor made sdist for debian containing only testimages
    * remove everything
    * add image files from testimages/*
    """
    to_remove = ["PKG-INFO", "setup.cfg"]

    def run(self):
        self.filelist = FileList()
        self.add_defaults()
        self.make_distribution()

    def add_defaults(self):
        print("in sdist_testimages.add_defaults")
        self.filelist.extend([op.join("testimages", i)\
                              for i in download_images()])
        print(self.filelist.files)

    def make_release_tree(self, base_dir, files):
        print("in sdist_testimages.make_release_tree")
        sdist.make_release_tree(self, base_dir, files)
        for afile in self.to_remove:
            dest = os.path.join(base_dir, afile)
            if os.path.exists(dest):
                os.unlink(dest)


    def make_distribution(self):
        print("in sdist_testimages.make_distribution")
        sdist.make_distribution(self)
        dest = self.archive_files[0]
        dirname, basename = op.split(dest)
        base, ext = op.splitext(basename)
        while ext in [".zip", ".tar", ".bz2", ".gz", ".Z", ".lz", ".orig"]:
            base, ext = op.splitext(base)
        if ext:
            dest = "".join((base, ext))
        else:
            dest = base
        sp = dest.split("-")
        base = sp[:-1]
        nr = sp[-1]
        debian_arch = op.join(dirname, "-".join(base) + "_" + nr + ".orig-testimages.tar.gz")
        os.rename(self.archive_files[0], debian_arch)
        self.archive_files = [debian_arch]
        print("Building debian orig-testimages.tar.gz in %s" % self.archive_files[0])

cmdclass['debian_testimages'] = sdist_testimages


if sys.platform == "win32":
    root = op.dirname(op.abspath(__file__))
    tocopy_files = []
    script_files = []
    for i in os.listdir(op.join(root, "scripts")):
        if op.isfile(op.join(root, "scripts", i)):
            if i.endswith(".py"):
                script_files.append(op.join("scripts", i))
            else:
                tocopy_files.append(op.join("scripts", i))
    for i in tocopy_files:
        filein = op.join(root, i)
        if (filein + ".py") not in script_files:
            shutil.copyfile(filein, filein + ".py")
            script_files.append(filein + ".py")
else:
    script_files = glob.glob("scripts/*")


# adaptation for Debian packaging (without third_party)
packages = ["fabio", "fabio.test"]
package_dir = {"fabio": "fabio-src",
             "fabio.test": "test" }
if os.path.isdir("third_party"):
    package_dir["fabio.third_party"] = "third_party"
    packages.append("fabio.third_party")


if __name__ == "__main__":
    setup(name='fabio',
          version=get_version(),
          author="Henning Sorensen, Erik Knudsen, Jon Wright, Regis Perdreau, Jérôme Kieffer, Gael Goret, Brian Pauw",
          author_email="fable-talk@lists.sourceforge.net",
          description='Image IO for fable',
          url="http://fable.wiki.sourceforge.net/fabio",
          download_url="http://sourceforge.net/projects/fable/files/fabio/",
          ext_package="fabio",
          ext_modules=extensions,
          packages=["fabio", "fabio.third_party", "fabio.test"],
          package_dir={"fabio": "fabio-src",
                       "fabio.third_party": "third_party",
                       "fabio.test": "test"
                       },
          test_suite="test",
          cmdclass=cmdclass,
          scripts=script_files,
          classifiers=[
              'Development Status :: 5 - Production/Stable',
              'Environment :: Console',
              'Intended Audience :: End Users/Desktop',
              'Intended Audience :: Developers',
              'Intended Audience :: Science/Research',
              "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
              'Operating System :: MacOS :: MacOS X',
              'Operating System :: Microsoft :: Windows',
              'Operating System :: POSIX',
              'Programming Language :: Python',
              'Programming Language :: Cython',
              'Programming Language :: C',
              'Topic :: Scientific/Engineering :: Chemistry',
              'Topic :: Scientific/Engineering :: Bio-Informatics',
              'Topic :: Scientific/Engineering :: Physics',
              'Topic :: Scientific/Engineering :: Visualization',
              'Topic :: Software Development :: Libraries :: Python Modules',
              ],)