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Lib/site-packages/Babel-2.14.0.dist-info/INSTALLER

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+pip

Lib/site-packages/Babel-2.14.0.dist-info/LICENSE

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+Copyright (c) 2013-2023 by the Babel Team, see AUTHORS for more information.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+ 1. Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in
+    the documentation and/or other materials provided with the
+    distribution.
+ 3. Neither the name of the copyright holder nor the names of its
+    contributors may be used to endorse or promote products derived
+    from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Lib/site-packages/Babel-2.14.0.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: Babel
+Version: 2.14.0
+Summary: Internationalization utilities
+Home-page: https://babel.pocoo.org/
+Author: Armin Ronacher
+Author-email: armin.ronacher@active-4.com
+Maintainer: Aarni Koskela
+Maintainer-email: akx@iki.fi
+License: BSD-3-Clause
+Project-URL: Source, https://github.com/python-babel/babel
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Web Environment
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.7
+License-File: LICENSE
+Requires-Dist: pytz >=2015.7 ; python_version < "3.9"
+Provides-Extra: dev
+Requires-Dist: pytest >=6.0 ; extra == 'dev'
+Requires-Dist: pytest-cov ; extra == 'dev'
+Requires-Dist: freezegun ~=1.0 ; extra == 'dev'
+
+A collection of tools for internationalizing Python applications.

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Lib/site-packages/Babel-2.14.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: bdist_wheel (0.42.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

Lib/site-packages/Babel-2.14.0.dist-info/entry_points.txt

@@ -0,0 +1,20 @@
+[babel.checkers]
+num_plurals = babel.messages.checkers:num_plurals
+python_format = babel.messages.checkers:python_format
+
+[babel.extractors]
+ignore = babel.messages.extract:extract_nothing
+javascript = babel.messages.extract:extract_javascript
+python = babel.messages.extract:extract_python
+
+[console_scripts]
+pybabel = babel.messages.frontend:main
+
+[distutils.commands]
+compile_catalog = babel.messages.setuptools_frontend:compile_catalog
+extract_messages = babel.messages.setuptools_frontend:extract_messages
+init_catalog = babel.messages.setuptools_frontend:init_catalog
+update_catalog = babel.messages.setuptools_frontend:update_catalog
+
+[distutils.setup_keywords]
+message_extractors = babel.messages.setuptools_frontend:check_message_extractors

Lib/site-packages/Babel-2.14.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+babel

Lib/site-packages/Cython-3.0.10.dist-info/COPYING.txt

@@ -0,0 +1,19 @@
+The original Pyrex code as of 2006-04 is licensed under the following
+license: "Copyright stuff: Pyrex is free of restrictions. You may use,
+redistribute, modify and distribute modified versions."
+
+------------------
+
+Cython, which derives from Pyrex, is licensed under the Apache 2.0
+Software License.  More precisely, all modifications and new code
+made to go from Pyrex to Cython are so licensed.
+
+See LICENSE.txt for more details.
+
+------------------
+
+The output of a Cython compilation is NOT considered a derivative
+work of Cython.  Specifically, though the compilation process may
+embed snippets of varying lengths into the final output, these
+snippets, as embedded in the output, do not encumber the resulting
+output with any license restrictions.

Lib/site-packages/Cython-3.0.10.dist-info/INSTALLER

@@ -0,0 +1 @@
+pip

Lib/site-packages/Cython-3.0.10.dist-info/LICENSE.txt

@@ -0,0 +1,176 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        https://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
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+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
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+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
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+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
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+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
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+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS

Lib/site-packages/Cython-3.0.10.dist-info/METADATA

@@ -0,0 +1,63 @@
+Metadata-Version: 2.1
+Name: Cython
+Version: 3.0.10
+Summary: The Cython compiler for writing C extensions in the Python language.
+Home-page: https://cython.org/
+Author: Robert Bradshaw, Stefan Behnel, Dag Seljebotn, Greg Ewing, et al.
+Author-email: cython-devel@python.org
+License: Apache-2.0
+Project-URL: Documentation, https://cython.readthedocs.io/
+Project-URL: Donate, https://cython.readthedocs.io/en/latest/src/donating.html
+Project-URL: Source Code, https://github.com/cython/cython
+Project-URL: Bug Tracker, https://github.com/cython/cython/issues
+Project-URL: User Group, https://groups.google.com/g/cython-users
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 2
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.4
+Classifier: Programming Language :: Python :: 3.5
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Classifier: Programming Language :: C
+Classifier: Programming Language :: Cython
+Classifier: Topic :: Software Development :: Code Generators
+Classifier: Topic :: Software Development :: Compilers
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*
+License-File: LICENSE.txt
+License-File: COPYING.txt
+
+The Cython language makes writing C extensions for the Python language as
+easy as Python itself.  Cython is a source code translator based on Pyrex_,
+but supports more cutting edge functionality and optimizations.
+
+The Cython language is a superset of the Python language (almost all Python
+code is also valid Cython code), but Cython additionally supports optional
+static typing to natively call C functions, operate with C++ classes and
+declare fast C types on variables and class attributes.  This allows the
+compiler to generate very efficient C code from Cython code.
+
+This makes Cython the ideal language for writing glue code for external
+C/C++ libraries, and for fast C modules that speed up the execution of
+Python code.
+
+Note that for one-time builds, e.g. for CI/testing, on platforms that are not
+covered by one of the wheel packages provided on PyPI *and* the pure Python wheel
+that we provide is not used, it is substantially faster than a full source build
+to install an uncompiled (slower) version of Cython with::
+
+    pip install Cython --install-option="--no-cython-compile"
+
+.. _Pyrex: https://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/

Lib/site-packages/Cython-3.0.10.dist-info/RECORD

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Lib/site-packages/Cython-3.0.10.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: bdist_wheel (0.42.0)
+Root-Is-Purelib: false
+Tag: cp38-cp38-win_amd64
+

Lib/site-packages/Cython-3.0.10.dist-info/entry_points.txt

@@ -0,0 +1,4 @@
+[console_scripts]
+cygdb = Cython.Debugger.Cygdb:main
+cython = Cython.Compiler.Main:setuptools_main
+cythonize = Cython.Build.Cythonize:main

Lib/site-packages/Cython-3.0.10.dist-info/top_level.txt

@@ -0,0 +1,3 @@
+Cython
+cython
+pyximport

Lib/site-packages/Cython/Build/BuildExecutable.py

@@ -0,0 +1,170 @@
+"""
+Compile a Python script into an executable that embeds CPython.
+Requires CPython to be built as a shared library ('libpythonX.Y').
+
+Basic usage:
+
+    python -m Cython.Build.BuildExecutable [ARGS] somefile.py
+"""
+
+from __future__ import absolute_import
+
+DEBUG = True
+
+import sys
+import os
+if sys.version_info < (3, 9):
+    from distutils import sysconfig as _sysconfig
+
+    class sysconfig(object):
+
+        @staticmethod
+        def get_path(name):
+            assert name == 'include'
+            return _sysconfig.get_python_inc()
+
+        get_config_var = staticmethod(_sysconfig.get_config_var)
+else:
+    # sysconfig can be trusted from cpython >= 3.8.7
+    import sysconfig
+
+
+def get_config_var(name, default=''):
+    return sysconfig.get_config_var(name) or default
+
+INCDIR = sysconfig.get_path('include')
+LIBDIR1 = get_config_var('LIBDIR')
+LIBDIR2 = get_config_var('LIBPL')
+PYLIB = get_config_var('LIBRARY')
+PYLIB_DYN = get_config_var('LDLIBRARY')
+if PYLIB_DYN == PYLIB:
+    # no shared library
+    PYLIB_DYN = ''
+else:
+    PYLIB_DYN = os.path.splitext(PYLIB_DYN[3:])[0]  # 'lib(XYZ).so' -> XYZ
+
+CC = get_config_var('CC', os.environ.get('CC', ''))
+CFLAGS = get_config_var('CFLAGS') + ' ' + os.environ.get('CFLAGS', '')
+LINKCC = get_config_var('LINKCC', os.environ.get('LINKCC', CC))
+LINKFORSHARED = get_config_var('LINKFORSHARED')
+LIBS = get_config_var('LIBS')
+SYSLIBS = get_config_var('SYSLIBS')
+EXE_EXT = sysconfig.get_config_var('EXE')
+
+
+def _debug(msg, *args):
+    if DEBUG:
+        if args:
+            msg = msg % args
+        sys.stderr.write(msg + '\n')
+
+
+def dump_config():
+    _debug('INCDIR: %s', INCDIR)
+    _debug('LIBDIR1: %s', LIBDIR1)
+    _debug('LIBDIR2: %s', LIBDIR2)
+    _debug('PYLIB: %s', PYLIB)
+    _debug('PYLIB_DYN: %s', PYLIB_DYN)
+    _debug('CC: %s', CC)
+    _debug('CFLAGS: %s', CFLAGS)
+    _debug('LINKCC: %s', LINKCC)
+    _debug('LINKFORSHARED: %s', LINKFORSHARED)
+    _debug('LIBS: %s', LIBS)
+    _debug('SYSLIBS: %s', SYSLIBS)
+    _debug('EXE_EXT: %s', EXE_EXT)
+
+
+def _parse_args(args):
+    cy_args = []
+    last_arg = None
+    for i, arg in enumerate(args):
+        if arg.startswith('-'):
+            cy_args.append(arg)
+        elif last_arg in ('-X', '--directive'):
+            cy_args.append(arg)
+        else:
+            input_file = arg
+            args = args[i+1:]
+            break
+        last_arg = arg
+    else:
+        raise ValueError('no input file provided')
+
+    return input_file, cy_args, args
+
+
+def runcmd(cmd, shell=True):
+    if shell:
+        cmd = ' '.join(cmd)
+        _debug(cmd)
+    else:
+        _debug(' '.join(cmd))
+
+    import subprocess
+    returncode = subprocess.call(cmd, shell=shell)
+
+    if returncode:
+        sys.exit(returncode)
+
+
+def clink(basename):
+    runcmd([LINKCC, '-o', basename + EXE_EXT, basename+'.o', '-L'+LIBDIR1, '-L'+LIBDIR2]
+           + [PYLIB_DYN and ('-l'+PYLIB_DYN) or os.path.join(LIBDIR1, PYLIB)]
+           + LIBS.split() + SYSLIBS.split() + LINKFORSHARED.split())
+
+
+def ccompile(basename):
+    runcmd([CC, '-c', '-o', basename+'.o', basename+'.c', '-I' + INCDIR] + CFLAGS.split())
+
+
+def cycompile(input_file, options=()):
+    from ..Compiler import Version, CmdLine, Main
+    options, sources = CmdLine.parse_command_line(list(options or ()) + ['--embed', input_file])
+    _debug('Using Cython %s to compile %s', Version.version, input_file)
+    result = Main.compile(sources, options)
+    if result.num_errors > 0:
+        sys.exit(1)
+
+
+def exec_file(program_name, args=()):
+    runcmd([os.path.abspath(program_name)] + list(args), shell=False)
+
+
+def build(input_file, compiler_args=(), force=False):
+    """
+    Build an executable program from a Cython module.
+
+    Returns the name of the executable file.
+    """
+    basename = os.path.splitext(input_file)[0]
+    exe_file = basename + EXE_EXT
+    if not force and os.path.abspath(exe_file) == os.path.abspath(input_file):
+        raise ValueError("Input and output file names are the same, refusing to overwrite")
+    if (not force and os.path.exists(exe_file) and os.path.exists(input_file)
+            and os.path.getmtime(input_file) <= os.path.getmtime(exe_file)):
+        _debug("File is up to date, not regenerating %s", exe_file)
+        return exe_file
+    cycompile(input_file, compiler_args)
+    ccompile(basename)
+    clink(basename)
+    return exe_file
+
+
+def build_and_run(args):
+    """
+    Build an executable program from a Cython module and run it.
+
+    Arguments after the module name will be passed verbatimly to the program.
+    """
+    program_name, args = _build(args)
+    exec_file(program_name, args)
+
+
+def _build(args):
+    input_file, cy_args, args = _parse_args(args)
+    program_name = build(input_file, cy_args)
+    return program_name, args
+
+
+if __name__ == '__main__':
+    _build(sys.argv[1:])

Lib/site-packages/Cython/Build/Cythonize.py

@@ -0,0 +1,255 @@
+from __future__ import absolute_import, print_function
+
+import os
+import shutil
+import tempfile
+
+from .Dependencies import cythonize, extended_iglob
+from ..Utils import is_package_dir
+from ..Compiler import Options
+
+try:
+    import multiprocessing
+    parallel_compiles = int(multiprocessing.cpu_count() * 1.5)
+except ImportError:
+    multiprocessing = None
+    parallel_compiles = 0
+
+
+class _FakePool(object):
+    def map_async(self, func, args):
+        try:
+            from itertools import imap
+        except ImportError:
+            imap=map
+        for _ in imap(func, args):
+            pass
+
+    def close(self):
+        pass
+
+    def terminate(self):
+        pass
+
+    def join(self):
+        pass
+
+
+def find_package_base(path):
+    base_dir, package_path = os.path.split(path)
+    while is_package_dir(base_dir):
+        base_dir, parent = os.path.split(base_dir)
+        package_path = '%s/%s' % (parent, package_path)
+    return base_dir, package_path
+
+def cython_compile(path_pattern, options):
+    all_paths = map(os.path.abspath, extended_iglob(path_pattern))
+    _cython_compile_files(all_paths, options)
+
+def _cython_compile_files(all_paths, options):
+    pool = None
+    try:
+        for path in all_paths:
+            if options.build_inplace:
+                base_dir = path
+                while not os.path.isdir(base_dir) or is_package_dir(base_dir):
+                    base_dir = os.path.dirname(base_dir)
+            else:
+                base_dir = None
+
+            if os.path.isdir(path):
+                # recursively compiling a package
+                paths = [os.path.join(path, '**', '*.{py,pyx}')]
+            else:
+                # assume it's a file(-like thing)
+                paths = [path]
+
+            ext_modules = cythonize(
+                paths,
+                nthreads=options.parallel,
+                exclude_failures=options.keep_going,
+                exclude=options.excludes,
+                compiler_directives=options.directives,
+                compile_time_env=options.compile_time_env,
+                force=options.force,
+                quiet=options.quiet,
+                depfile=options.depfile,
+                language=options.language,
+                **options.options)
+
+            if ext_modules and options.build:
+                if len(ext_modules) > 1 and options.parallel > 1:
+                    if pool is None:
+                        try:
+                            pool = multiprocessing.Pool(options.parallel)
+                        except OSError:
+                            pool = _FakePool()
+                    pool.map_async(run_distutils, [
+                        (base_dir, [ext]) for ext in ext_modules])
+                else:
+                    run_distutils((base_dir, ext_modules))
+    except:
+        if pool is not None:
+            pool.terminate()
+        raise
+    else:
+        if pool is not None:
+            pool.close()
+            pool.join()
+
+
+def run_distutils(args):
+    try:
+        from distutils.core import setup
+    except ImportError:
+        try:
+            from setuptools import setup
+        except ImportError:
+            raise ImportError("'distutils' is not available. Please install 'setuptools' for binary builds.")
+
+    base_dir, ext_modules = args
+    script_args = ['build_ext', '-i']
+    cwd = os.getcwd()
+    temp_dir = None
+    try:
+        if base_dir:
+            os.chdir(base_dir)
+            temp_dir = tempfile.mkdtemp(dir=base_dir)
+            script_args.extend(['--build-temp', temp_dir])
+        setup(
+            script_name='setup.py',
+            script_args=script_args,
+            ext_modules=ext_modules,
+        )
+    finally:
+        if base_dir:
+            os.chdir(cwd)
+            if temp_dir and os.path.isdir(temp_dir):
+                shutil.rmtree(temp_dir)
+
+
+def create_args_parser():
+    from argparse import ArgumentParser, RawDescriptionHelpFormatter
+    from ..Compiler.CmdLine import ParseDirectivesAction, ParseOptionsAction, ParseCompileTimeEnvAction
+
+    parser = ArgumentParser(
+        formatter_class=RawDescriptionHelpFormatter,
+        epilog="""\
+Environment variables:
+  CYTHON_FORCE_REGEN: if set to 1, forces cythonize to regenerate the output files regardless
+        of modification times and changes.
+  Environment variables accepted by setuptools are supported to configure the C compiler and build:
+  https://setuptools.pypa.io/en/latest/userguide/ext_modules.html#compiler-and-linker-options"""
+    )
+
+    parser.add_argument('-X', '--directive', metavar='NAME=VALUE,...',
+                      dest='directives', default={}, type=str,
+                      action=ParseDirectivesAction,
+                      help='set a compiler directive')
+    parser.add_argument('-E', '--compile-time-env', metavar='NAME=VALUE,...',
+                      dest='compile_time_env', default={}, type=str,
+                      action=ParseCompileTimeEnvAction,
+                      help='set a compile time environment variable')
+    parser.add_argument('-s', '--option', metavar='NAME=VALUE',
+                      dest='options', default={}, type=str,
+                      action=ParseOptionsAction,
+                      help='set a cythonize option')
+    parser.add_argument('-2', dest='language_level', action='store_const', const=2, default=None,
+                      help='use Python 2 syntax mode by default')
+    parser.add_argument('-3', dest='language_level', action='store_const', const=3,
+                      help='use Python 3 syntax mode by default')
+    parser.add_argument('--3str', dest='language_level', action='store_const', const='3str',
+                      help='use Python 3 syntax mode by default')
+    parser.add_argument('-+', '--cplus', dest='language', action='store_const', const='c++', default=None,
+                        help='Compile as C++ rather than C')
+    parser.add_argument('-a', '--annotate', action='store_const', const='default', dest='annotate',
+                      help='Produce a colorized HTML version of the source.')
+    parser.add_argument('--annotate-fullc', action='store_const', const='fullc', dest='annotate',
+                      help='Produce a colorized HTML version of the source '
+                           'which includes entire generated C/C++-code.')
+    parser.add_argument('-x', '--exclude', metavar='PATTERN', dest='excludes',
+                      action='append', default=[],
+                      help='exclude certain file patterns from the compilation')
+
+    parser.add_argument('-b', '--build', dest='build', action='store_true', default=None,
+                      help='build extension modules using distutils/setuptools')
+    parser.add_argument('-i', '--inplace', dest='build_inplace', action='store_true', default=None,
+                      help='build extension modules in place using distutils/setuptools (implies -b)')
+    parser.add_argument('-j', '--parallel', dest='parallel', metavar='N',
+                      type=int, default=parallel_compiles,
+                      help=('run builds in N parallel jobs (default: %d)' %
+                            parallel_compiles or 1))
+    parser.add_argument('-f', '--force', dest='force', action='store_true', default=None,
+                      help='force recompilation')
+    parser.add_argument('-q', '--quiet', dest='quiet', action='store_true', default=None,
+                      help='be less verbose during compilation')
+
+    parser.add_argument('--lenient', dest='lenient', action='store_true', default=None,
+                      help='increase Python compatibility by ignoring some compile time errors')
+    parser.add_argument('-k', '--keep-going', dest='keep_going', action='store_true', default=None,
+                      help='compile as much as possible, ignore compilation failures')
+    parser.add_argument('--no-docstrings', dest='no_docstrings', action='store_true', default=None,
+                      help='strip docstrings')
+    parser.add_argument('-M', '--depfile', action='store_true', help='produce depfiles for the sources')
+    parser.add_argument('sources', nargs='*')
+    return parser
+
+
+def parse_args_raw(parser, args):
+    options, unknown = parser.parse_known_args(args)
+    sources = options.sources
+    # if positional arguments were interspersed
+    # some of them are in unknown
+    for option in unknown:
+        if option.startswith('-'):
+            parser.error("unknown option "+option)
+        else:
+            sources.append(option)
+    del options.sources
+    return (options, sources)
+
+
+def parse_args(args):
+    parser = create_args_parser()
+    options, args = parse_args_raw(parser, args)
+
+    if not args:
+        parser.error("no source files provided")
+    if options.build_inplace:
+        options.build = True
+    if multiprocessing is None:
+        options.parallel = 0
+    if options.language_level:
+        assert options.language_level in (2, 3, '3str')
+        options.options['language_level'] = options.language_level
+
+    if options.lenient:
+        # increase Python compatibility by ignoring compile time errors
+        Options.error_on_unknown_names = False
+        Options.error_on_uninitialized = False
+
+    if options.annotate:
+        Options.annotate = options.annotate
+
+    if options.no_docstrings:
+        Options.docstrings = False
+
+    return options, args
+
+
+def main(args=None):
+    options, paths = parse_args(args)
+
+    all_paths = []
+    for path in paths:
+        expanded_path = [os.path.abspath(p) for p in extended_iglob(path)]
+        if not expanded_path:
+            import sys
+            print("{}: No such file or directory: '{}'".format(sys.argv[0], path), file=sys.stderr)
+            sys.exit(1)
+        all_paths.extend(expanded_path)
+    _cython_compile_files(all_paths, options)
+
+
+if __name__ == '__main__':
+    main()

Lib/site-packages/Cython/Build/Dependencies.py

@@ -0,0 +1,1380 @@
+from __future__ import absolute_import, print_function
+
+import cython
+from .. import __version__
+
+import collections
+import contextlib
+import hashlib
+import os
+import shutil
+import subprocess
+import re, sys, time
+from glob import iglob
+from io import open as io_open
+from os.path import relpath as _relpath
+import zipfile
+
+try:
+    from collections.abc import Iterable
+except ImportError:
+    from collections import Iterable
+
+try:
+    import gzip
+    gzip_open = gzip.open
+    gzip_ext = '.gz'
+except ImportError:
+    gzip_open = open
+    gzip_ext = ''
+
+try:
+    import zlib
+    zipfile_compression_mode = zipfile.ZIP_DEFLATED
+except ImportError:
+    zipfile_compression_mode = zipfile.ZIP_STORED
+
+try:
+    import pythran
+except:
+    pythran = None
+
+from .. import Utils
+from ..Utils import (cached_function, cached_method, path_exists,
+    safe_makedirs, copy_file_to_dir_if_newer, is_package_dir, write_depfile)
+from ..Compiler import Errors
+from ..Compiler.Main import Context
+from ..Compiler.Options import (CompilationOptions, default_options,
+    get_directive_defaults)
+
+join_path = cached_function(os.path.join)
+copy_once_if_newer = cached_function(copy_file_to_dir_if_newer)
+safe_makedirs_once = cached_function(safe_makedirs)
+
+if sys.version_info[0] < 3:
+    # stupid Py2 distutils enforces str type in list of sources
+    _fs_encoding = sys.getfilesystemencoding()
+    if _fs_encoding is None:
+        _fs_encoding = sys.getdefaultencoding()
+    def encode_filename_in_py2(filename):
+        if not isinstance(filename, bytes):
+            return filename.encode(_fs_encoding)
+        return filename
+else:
+    def encode_filename_in_py2(filename):
+        return filename
+    basestring = str
+
+
+def _make_relative(file_paths, base=None):
+    if not base:
+        base = os.getcwd()
+    if base[-1] != os.path.sep:
+        base += os.path.sep
+    return [_relpath(path, base) if path.startswith(base) else path
+            for path in file_paths]
+
+
+def extended_iglob(pattern):
+    if '{' in pattern:
+        m = re.match('(.*){([^}]+)}(.*)', pattern)
+        if m:
+            before, switch, after = m.groups()
+            for case in switch.split(','):
+                for path in extended_iglob(before + case + after):
+                    yield path
+            return
+
+    # We always accept '/' and also '\' on Windows,
+    # because '/' is generally common for relative paths.
+    if '**/' in pattern or os.sep == '\\' and '**\\' in pattern:
+        seen = set()
+        first, rest = re.split(r'\*\*[%s]' % ('/\\\\' if os.sep == '\\' else '/'), pattern, 1)
+        if first:
+            first = iglob(first + os.sep)
+        else:
+            first = ['']
+        for root in first:
+            for path in extended_iglob(join_path(root, rest)):
+                if path not in seen:
+                    seen.add(path)
+                    yield path
+            for path in extended_iglob(join_path(root, '*', '**', rest)):
+                if path not in seen:
+                    seen.add(path)
+                    yield path
+    else:
+        for path in iglob(pattern):
+            yield path
+
+
+def nonempty(it, error_msg="expected non-empty iterator"):
+    empty = True
+    for value in it:
+        empty = False
+        yield value
+    if empty:
+        raise ValueError(error_msg)
+
+
+@cached_function
+def file_hash(filename):
+    path = os.path.normpath(filename)
+    prefix = ('%d:%s' % (len(path), path)).encode("UTF-8")
+    m = hashlib.sha1(prefix)
+    with open(path, 'rb') as f:
+        data = f.read(65000)
+        while data:
+            m.update(data)
+            data = f.read(65000)
+    return m.hexdigest()
+
+
+def update_pythran_extension(ext):
+    if pythran is None:
+        raise RuntimeError("You first need to install Pythran to use the np_pythran directive.")
+    try:
+        pythran_ext = pythran.config.make_extension(python=True)
+    except TypeError:  # older pythran version only
+        pythran_ext = pythran.config.make_extension()
+
+    ext.include_dirs.extend(pythran_ext['include_dirs'])
+    ext.extra_compile_args.extend(pythran_ext['extra_compile_args'])
+    ext.extra_link_args.extend(pythran_ext['extra_link_args'])
+    ext.define_macros.extend(pythran_ext['define_macros'])
+    ext.undef_macros.extend(pythran_ext['undef_macros'])
+    ext.library_dirs.extend(pythran_ext['library_dirs'])
+    ext.libraries.extend(pythran_ext['libraries'])
+    ext.language = 'c++'
+
+    # These options are not compatible with the way normal Cython extensions work
+    for bad_option in ["-fwhole-program", "-fvisibility=hidden"]:
+        try:
+            ext.extra_compile_args.remove(bad_option)
+        except ValueError:
+            pass
+
+
+def parse_list(s):
+    """
+    >>> parse_list("")
+    []
+    >>> parse_list("a")
+    ['a']
+    >>> parse_list("a b c")
+    ['a', 'b', 'c']
+    >>> parse_list("[a, b, c]")
+    ['a', 'b', 'c']
+    >>> parse_list('a " " b')
+    ['a', ' ', 'b']
+    >>> parse_list('[a, ",a", "a,", ",", ]')
+    ['a', ',a', 'a,', ',']
+    """
+    if len(s) >= 2 and s[0] == '[' and s[-1] == ']':
+        s = s[1:-1]
+        delimiter = ','
+    else:
+        delimiter = ' '
+    s, literals = strip_string_literals(s)
+    def unquote(literal):
+        literal = literal.strip()
+        if literal[0] in "'\"":
+            return literals[literal[1:-1]]
+        else:
+            return literal
+    return [unquote(item) for item in s.split(delimiter) if item.strip()]
+
+
+transitive_str = object()
+transitive_list = object()
+bool_or = object()
+
+distutils_settings = {
+    'name':                 str,
+    'sources':              list,
+    'define_macros':        list,
+    'undef_macros':         list,
+    'libraries':            transitive_list,
+    'library_dirs':         transitive_list,
+    'runtime_library_dirs': transitive_list,
+    'include_dirs':         transitive_list,
+    'extra_objects':        list,
+    'extra_compile_args':   transitive_list,
+    'extra_link_args':      transitive_list,
+    'export_symbols':       list,
+    'depends':              transitive_list,
+    'language':             transitive_str,
+    'np_pythran':           bool_or
+}
+
+
+def _legacy_strtobool(val):
+    # Used to be "distutils.util.strtobool", adapted for deprecation warnings.
+    if val == "True":
+        return True
+    elif val == "False":
+        return False
+
+    import warnings
+    warnings.warn("The 'np_python' option requires 'True' or 'False'", category=DeprecationWarning)
+    val = val.lower()
+    if val in ('y', 'yes', 't', 'true', 'on', '1'):
+        return True
+    elif val in ('n', 'no', 'f', 'false', 'off', '0'):
+        return False
+    else:
+        raise ValueError("invalid truth value %r" % (val,))
+
+
+@cython.locals(start=cython.Py_ssize_t, end=cython.Py_ssize_t)
+def line_iter(source):
+    if isinstance(source, basestring):
+        start = 0
+        while True:
+            end = source.find('\n', start)
+            if end == -1:
+                yield source[start:]
+                return
+            yield source[start:end]
+            start = end+1
+    else:
+        for line in source:
+            yield line
+
+
+class DistutilsInfo(object):
+
+    def __init__(self, source=None, exn=None):
+        self.values = {}
+        if source is not None:
+            for line in line_iter(source):
+                line = line.lstrip()
+                if not line:
+                    continue
+                if line[0] != '#':
+                    break
+                line = line[1:].lstrip()
+                kind = next((k for k in ("distutils:","cython:") if line.startswith(k)), None)
+                if kind is not None:
+                    key, _, value = [s.strip() for s in line[len(kind):].partition('=')]
+                    type = distutils_settings.get(key, None)
+                    if line.startswith("cython:") and type is None: continue
+                    if type in (list, transitive_list):
+                        value = parse_list(value)
+                        if key == 'define_macros':
+                            value = [tuple(macro.split('=', 1))
+                                     if '=' in macro else (macro, None)
+                                     for macro in value]
+                    if type is bool_or:
+                        value = _legacy_strtobool(value)
+                    self.values[key] = value
+        elif exn is not None:
+            for key in distutils_settings:
+                if key in ('name', 'sources','np_pythran'):
+                    continue
+                value = getattr(exn, key, None)
+                if value:
+                    self.values[key] = value
+
+    def merge(self, other):
+        if other is None:
+            return self
+        for key, value in other.values.items():
+            type = distutils_settings[key]
+            if type is transitive_str and key not in self.values:
+                self.values[key] = value
+            elif type is transitive_list:
+                if key in self.values:
+                    # Change a *copy* of the list (Trac #845)
+                    all = self.values[key][:]
+                    for v in value:
+                        if v not in all:
+                            all.append(v)
+                    value = all
+                self.values[key] = value
+            elif type is bool_or:
+                self.values[key] = self.values.get(key, False) | value
+        return self
+
+    def subs(self, aliases):
+        if aliases is None:
+            return self
+        resolved = DistutilsInfo()
+        for key, value in self.values.items():
+            type = distutils_settings[key]
+            if type in [list, transitive_list]:
+                new_value_list = []
+                for v in value:
+                    if v in aliases:
+                        v = aliases[v]
+                    if isinstance(v, list):
+                        new_value_list += v
+                    else:
+                        new_value_list.append(v)
+                value = new_value_list
+            else:
+                if value in aliases:
+                    value = aliases[value]
+            resolved.values[key] = value
+        return resolved
+
+    def apply(self, extension):
+        for key, value in self.values.items():
+            type = distutils_settings[key]
+            if type in [list, transitive_list]:
+                value = getattr(extension, key) + list(value)
+            setattr(extension, key, value)
+
+
+@cython.locals(start=cython.Py_ssize_t, q=cython.Py_ssize_t,
+               single_q=cython.Py_ssize_t, double_q=cython.Py_ssize_t,
+               hash_mark=cython.Py_ssize_t, end=cython.Py_ssize_t,
+               k=cython.Py_ssize_t, counter=cython.Py_ssize_t, quote_len=cython.Py_ssize_t)
+def strip_string_literals(code, prefix='__Pyx_L'):
+    """
+    Normalizes every string literal to be of the form '__Pyx_Lxxx',
+    returning the normalized code and a mapping of labels to
+    string literals.
+    """
+    new_code = []
+    literals = {}
+    counter = 0
+    start = q = 0
+    in_quote = False
+    hash_mark = single_q = double_q = -1
+    code_len = len(code)
+    quote_type = None
+    quote_len = -1
+
+    while True:
+        if hash_mark < q:
+            hash_mark = code.find('#', q)
+        if single_q < q:
+            single_q = code.find("'", q)
+        if double_q < q:
+            double_q = code.find('"', q)
+        q = min(single_q, double_q)
+        if q == -1:
+            q = max(single_q, double_q)
+
+        # We're done.
+        if q == -1 and hash_mark == -1:
+            new_code.append(code[start:])
+            break
+
+        # Try to close the quote.
+        elif in_quote:
+            if code[q-1] == u'\\':
+                k = 2
+                while q >= k and code[q-k] == u'\\':
+                    k += 1
+                if k % 2 == 0:
+                    q += 1
+                    continue
+            if code[q] == quote_type and (
+                    quote_len == 1 or (code_len > q + 2 and quote_type == code[q+1] == code[q+2])):
+                counter += 1
+                label = "%s%s_" % (prefix, counter)
+                literals[label] = code[start+quote_len:q]
+                full_quote = code[q:q+quote_len]
+                new_code.append(full_quote)
+                new_code.append(label)
+                new_code.append(full_quote)
+                q += quote_len
+                in_quote = False
+                start = q
+            else:
+                q += 1
+
+        # Process comment.
+        elif -1 != hash_mark and (hash_mark < q or q == -1):
+            new_code.append(code[start:hash_mark+1])
+            end = code.find('\n', hash_mark)
+            counter += 1
+            label = "%s%s_" % (prefix, counter)
+            if end == -1:
+                end_or_none = None
+            else:
+                end_or_none = end
+            literals[label] = code[hash_mark+1:end_or_none]
+            new_code.append(label)
+            if end == -1:
+                break
+            start = q = end
+
+        # Open the quote.
+        else:
+            if code_len >= q+3 and (code[q] == code[q+1] == code[q+2]):
+                quote_len = 3
+            else:
+                quote_len = 1
+            in_quote = True
+            quote_type = code[q]
+            new_code.append(code[start:q])
+            start = q
+            q += quote_len
+
+    return "".join(new_code), literals
+
+
+# We need to allow spaces to allow for conditional compilation like
+# IF ...:
+#     cimport ...
+dependency_regex = re.compile(r"(?:^\s*from +([0-9a-zA-Z_.]+) +cimport)|"
+                              r"(?:^\s*cimport +([0-9a-zA-Z_.]+(?: *, *[0-9a-zA-Z_.]+)*))|"
+                              r"(?:^\s*cdef +extern +from +['\"]([^'\"]+)['\"])|"
+                              r"(?:^\s*include +['\"]([^'\"]+)['\"])", re.M)
+dependency_after_from_regex = re.compile(
+    r"(?:^\s+\(([0-9a-zA-Z_., ]*)\)[#\n])|"
+    r"(?:^\s+([0-9a-zA-Z_., ]*)[#\n])",
+    re.M)
+
+
+def normalize_existing(base_path, rel_paths):
+    return normalize_existing0(os.path.dirname(base_path), tuple(set(rel_paths)))
+
+
+@cached_function
+def normalize_existing0(base_dir, rel_paths):
+    """
+    Given some base directory ``base_dir`` and a list of path names
+    ``rel_paths``, normalize each relative path name ``rel`` by
+    replacing it by ``os.path.join(base, rel)`` if that file exists.
+
+    Return a couple ``(normalized, needed_base)`` where ``normalized``
+    if the list of normalized file names and ``needed_base`` is
+    ``base_dir`` if we actually needed ``base_dir``. If no paths were
+    changed (for example, if all paths were already absolute), then
+    ``needed_base`` is ``None``.
+    """
+    normalized = []
+    needed_base = None
+    for rel in rel_paths:
+        if os.path.isabs(rel):
+            normalized.append(rel)
+            continue
+        path = join_path(base_dir, rel)
+        if path_exists(path):
+            normalized.append(os.path.normpath(path))
+            needed_base = base_dir
+        else:
+            normalized.append(rel)
+    return (normalized, needed_base)
+
+
+def resolve_depends(depends, include_dirs):
+    include_dirs = tuple(include_dirs)
+    resolved = []
+    for depend in depends:
+        path = resolve_depend(depend, include_dirs)
+        if path is not None:
+            resolved.append(path)
+    return resolved
+
+
+@cached_function
+def resolve_depend(depend, include_dirs):
+    if depend[0] == '<' and depend[-1] == '>':
+        return None
+    for dir in include_dirs:
+        path = join_path(dir, depend)
+        if path_exists(path):
+            return os.path.normpath(path)
+    return None
+
+
+@cached_function
+def package(filename):
+    dir = os.path.dirname(os.path.abspath(str(filename)))
+    if dir != filename and is_package_dir(dir):
+        return package(dir) + (os.path.basename(dir),)
+    else:
+        return ()
+
+
+@cached_function
+def fully_qualified_name(filename):
+    module = os.path.splitext(os.path.basename(filename))[0]
+    return '.'.join(package(filename) + (module,))
+
+
+@cached_function
+def parse_dependencies(source_filename):
+    # Actual parsing is way too slow, so we use regular expressions.
+    # The only catch is that we must strip comments and string
+    # literals ahead of time.
+    with Utils.open_source_file(source_filename, error_handling='ignore') as fh:
+        source = fh.read()
+    distutils_info = DistutilsInfo(source)
+    source, literals = strip_string_literals(source)
+    source = source.replace('\\\n', ' ').replace('\t', ' ')
+
+    # TODO: pure mode
+    cimports = []
+    includes = []
+    externs  = []
+    for m in dependency_regex.finditer(source):
+        cimport_from, cimport_list, extern, include = m.groups()
+        if cimport_from:
+            cimports.append(cimport_from)
+            m_after_from = dependency_after_from_regex.search(source, pos=m.end())
+            if m_after_from:
+                multiline, one_line = m_after_from.groups()
+                subimports = multiline or one_line
+                cimports.extend("{0}.{1}".format(cimport_from, s.strip())
+                                for s in subimports.split(','))
+
+        elif cimport_list:
+            cimports.extend(x.strip() for x in cimport_list.split(","))
+        elif extern:
+            externs.append(literals[extern])
+        else:
+            includes.append(literals[include])
+    return cimports, includes, externs, distutils_info
+
+
+class DependencyTree(object):
+
+    def __init__(self, context, quiet=False):
+        self.context = context
+        self.quiet = quiet
+        self._transitive_cache = {}
+
+    def parse_dependencies(self, source_filename):
+        if path_exists(source_filename):
+            source_filename = os.path.normpath(source_filename)
+        return parse_dependencies(source_filename)
+
+    @cached_method
+    def included_files(self, filename):
+        # This is messy because included files are textually included, resolving
+        # cimports (but not includes) relative to the including file.
+        all = set()
+        for include in self.parse_dependencies(filename)[1]:
+            include_path = join_path(os.path.dirname(filename), include)
+            if not path_exists(include_path):
+                include_path = self.context.find_include_file(include, source_file_path=filename)
+            if include_path:
+                if '.' + os.path.sep in include_path:
+                    include_path = os.path.normpath(include_path)
+                all.add(include_path)
+                all.update(self.included_files(include_path))
+            elif not self.quiet:
+                print(u"Unable to locate '%s' referenced from '%s'" % (filename, include))
+        return all
+
+    @cached_method
+    def cimports_externs_incdirs(self, filename):
+        # This is really ugly. Nested cimports are resolved with respect to the
+        # includer, but includes are resolved with respect to the includee.
+        cimports, includes, externs = self.parse_dependencies(filename)[:3]
+        cimports = set(cimports)
+        externs = set(externs)
+        incdirs = set()
+        for include in self.included_files(filename):
+            included_cimports, included_externs, included_incdirs = self.cimports_externs_incdirs(include)
+            cimports.update(included_cimports)
+            externs.update(included_externs)
+            incdirs.update(included_incdirs)
+        externs, incdir = normalize_existing(filename, externs)
+        if incdir:
+            incdirs.add(incdir)
+        return tuple(cimports), externs, incdirs
+
+    def cimports(self, filename):
+        return self.cimports_externs_incdirs(filename)[0]
+
+    def package(self, filename):
+        return package(filename)
+
+    def fully_qualified_name(self, filename):
+        return fully_qualified_name(filename)
+
+    @cached_method
+    def find_pxd(self, module, filename=None):
+        is_relative = module[0] == '.'
+        if is_relative and not filename:
+            raise NotImplementedError("New relative imports.")
+        if filename is not None:
+            module_path = module.split('.')
+            if is_relative:
+                module_path.pop(0)  # just explicitly relative
+            package_path = list(self.package(filename))
+            while module_path and not module_path[0]:
+                try:
+                    package_path.pop()
+                except IndexError:
+                    return None   # FIXME: error?
+                module_path.pop(0)
+            relative = '.'.join(package_path + module_path)
+            pxd = self.context.find_pxd_file(relative, source_file_path=filename)
+            if pxd:
+                return pxd
+        if is_relative:
+            return None   # FIXME: error?
+        return self.context.find_pxd_file(module, source_file_path=filename)
+
+    @cached_method
+    def cimported_files(self, filename):
+        filename_root, filename_ext = os.path.splitext(filename)
+        if filename_ext in ('.pyx', '.py') and path_exists(filename_root + '.pxd'):
+            pxd_list = [filename_root + '.pxd']
+        else:
+            pxd_list = []
+        # Cimports generates all possible combinations package.module
+        # when imported as from package cimport module.
+        for module in self.cimports(filename):
+            if module[:7] == 'cython.' or module == 'cython':
+                continue
+            pxd_file = self.find_pxd(module, filename)
+            if pxd_file is not None:
+                pxd_list.append(pxd_file)
+        return tuple(pxd_list)
+
+    @cached_method
+    def immediate_dependencies(self, filename):
+        all_deps = {filename}
+        all_deps.update(self.cimported_files(filename))
+        all_deps.update(self.included_files(filename))
+        return all_deps
+
+    def all_dependencies(self, filename):
+        return self.transitive_merge(filename, self.immediate_dependencies, set.union)
+
+    @cached_method
+    def timestamp(self, filename):
+        return os.path.getmtime(filename)
+
+    def extract_timestamp(self, filename):
+        return self.timestamp(filename), filename
+
+    def newest_dependency(self, filename):
+        return max([self.extract_timestamp(f) for f in self.all_dependencies(filename)])
+
+    def transitive_fingerprint(self, filename, module, compilation_options):
+        r"""
+        Return a fingerprint of a cython file that is about to be cythonized.
+
+        Fingerprints are looked up in future compilations. If the fingerprint
+        is found, the cythonization can be skipped. The fingerprint must
+        incorporate everything that has an influence on the generated code.
+        """
+        try:
+            m = hashlib.sha1(__version__.encode('UTF-8'))
+            m.update(file_hash(filename).encode('UTF-8'))
+            for x in sorted(self.all_dependencies(filename)):
+                if os.path.splitext(x)[1] not in ('.c', '.cpp', '.h'):
+                    m.update(file_hash(x).encode('UTF-8'))
+            # Include the module attributes that change the compilation result
+            # in the fingerprint. We do not iterate over module.__dict__ and
+            # include almost everything here as users might extend Extension
+            # with arbitrary (random) attributes that would lead to cache
+            # misses.
+            m.update(str((
+                module.language,
+                getattr(module, 'py_limited_api', False),
+                getattr(module, 'np_pythran', False)
+            )).encode('UTF-8'))
+
+            m.update(compilation_options.get_fingerprint().encode('UTF-8'))
+            return m.hexdigest()
+        except IOError:
+            return None
+
+    def distutils_info0(self, filename):
+        info = self.parse_dependencies(filename)[3]
+        kwds = info.values
+        cimports, externs, incdirs = self.cimports_externs_incdirs(filename)
+        basedir = os.getcwd()
+        # Add dependencies on "cdef extern from ..." files
+        if externs:
+            externs = _make_relative(externs, basedir)
+            if 'depends' in kwds:
+                kwds['depends'] = list(set(kwds['depends']).union(externs))
+            else:
+                kwds['depends'] = list(externs)
+        # Add include_dirs to ensure that the C compiler will find the
+        # "cdef extern from ..." files
+        if incdirs:
+            include_dirs = list(kwds.get('include_dirs', []))
+            for inc in _make_relative(incdirs, basedir):
+                if inc not in include_dirs:
+                    include_dirs.append(inc)
+            kwds['include_dirs'] = include_dirs
+        return info
+
+    def distutils_info(self, filename, aliases=None, base=None):
+        return (self.transitive_merge(filename, self.distutils_info0, DistutilsInfo.merge)
+            .subs(aliases)
+            .merge(base))
+
+    def transitive_merge(self, node, extract, merge):
+        try:
+            seen = self._transitive_cache[extract, merge]
+        except KeyError:
+            seen = self._transitive_cache[extract, merge] = {}
+        return self.transitive_merge_helper(
+            node, extract, merge, seen, {}, self.cimported_files)[0]
+
+    def transitive_merge_helper(self, node, extract, merge, seen, stack, outgoing):
+        if node in seen:
+            return seen[node], None
+        deps = extract(node)
+        if node in stack:
+            return deps, node
+        try:
+            stack[node] = len(stack)
+            loop = None
+            for next in outgoing(node):
+                sub_deps, sub_loop = self.transitive_merge_helper(next, extract, merge, seen, stack, outgoing)
+                if sub_loop is not None:
+                    if loop is not None and stack[loop] < stack[sub_loop]:
+                        pass
+                    else:
+                        loop = sub_loop
+                deps = merge(deps, sub_deps)
+            if loop == node:
+                loop = None
+            if loop is None:
+                seen[node] = deps
+            return deps, loop
+        finally:
+            del stack[node]
+
+
+_dep_tree = None
+
+def create_dependency_tree(ctx=None, quiet=False):
+    global _dep_tree
+    if _dep_tree is None:
+        if ctx is None:
+            ctx = Context(["."], get_directive_defaults(),
+                          options=CompilationOptions(default_options))
+        _dep_tree = DependencyTree(ctx, quiet=quiet)
+    return _dep_tree
+
+
+# If this changes, change also docs/src/reference/compilation.rst
+# which mentions this function
+def default_create_extension(template, kwds):
+    if 'depends' in kwds:
+        include_dirs = kwds.get('include_dirs', []) + ["."]
+        depends = resolve_depends(kwds['depends'], include_dirs)
+        kwds['depends'] = sorted(set(depends + template.depends))
+
+    t = template.__class__
+    ext = t(**kwds)
+    metadata = dict(distutils=kwds, module_name=kwds['name'])
+    return (ext, metadata)
+
+
+# This may be useful for advanced users?
+def create_extension_list(patterns, exclude=None, ctx=None, aliases=None, quiet=False, language=None,
+                          exclude_failures=False):
+    if language is not None:
+        print('Warning: passing language={0!r} to cythonize() is deprecated. '
+              'Instead, put "# distutils: language={0}" in your .pyx or .pxd file(s)'.format(language))
+    if exclude is None:
+        exclude = []
+    if patterns is None:
+        return [], {}
+    elif isinstance(patterns, basestring) or not isinstance(patterns, Iterable):
+        patterns = [patterns]
+
+    from distutils.extension import Extension
+    if 'setuptools' in sys.modules:
+        # Support setuptools Extension instances as well.
+        extension_classes = (
+            Extension,  # should normally be the same as 'setuptools.extension._Extension'
+            sys.modules['setuptools.extension']._Extension,
+            sys.modules['setuptools'].Extension,
+        )
+    else:
+        extension_classes = (Extension,)
+
+    explicit_modules = {m.name for m in patterns if isinstance(m, extension_classes)}
+    deps = create_dependency_tree(ctx, quiet=quiet)
+
+    to_exclude = set()
+    if not isinstance(exclude, list):
+        exclude = [exclude]
+    for pattern in exclude:
+        to_exclude.update(map(os.path.abspath, extended_iglob(pattern)))
+
+    module_list = []
+    module_metadata = {}
+
+    # if no create_extension() function is defined, use a simple
+    # default function.
+    create_extension = ctx.options.create_extension or default_create_extension
+
+    seen = set()
+    for pattern in patterns:
+        if not isinstance(pattern, extension_classes):
+            pattern = encode_filename_in_py2(pattern)
+        if isinstance(pattern, str):
+            filepattern = pattern
+            template = Extension(pattern, [])  # Fake Extension without sources
+            name = '*'
+            base = None
+            ext_language = language
+        elif isinstance(pattern, extension_classes):
+            cython_sources = [s for s in pattern.sources
+                              if os.path.splitext(s)[1] in ('.py', '.pyx')]
+            if cython_sources:
+                filepattern = cython_sources[0]
+                if len(cython_sources) > 1:
+                    print(u"Warning: Multiple cython sources found for extension '%s': %s\n"
+                          u"See https://cython.readthedocs.io/en/latest/src/userguide/sharing_declarations.html "
+                          u"for sharing declarations among Cython files." % (pattern.name, cython_sources))
+            else:
+                # ignore non-cython modules
+                module_list.append(pattern)
+                continue
+            template = pattern
+            name = template.name
+            base = DistutilsInfo(exn=template)
+            ext_language = None  # do not override whatever the Extension says
+        else:
+            msg = str("pattern is not of type str nor subclass of Extension (%s)"
+                      " but of type %s and class %s" % (repr(Extension),
+                                                        type(pattern),
+                                                        pattern.__class__))
+            raise TypeError(msg)
+
+        for file in nonempty(sorted(extended_iglob(filepattern)), "'%s' doesn't match any files" % filepattern):
+            if os.path.abspath(file) in to_exclude:
+                continue
+            module_name = deps.fully_qualified_name(file)
+            if '*' in name:
+                if module_name in explicit_modules:
+                    continue
+            elif name:
+                module_name = name
+
+            Utils.raise_error_if_module_name_forbidden(module_name)
+
+            if module_name not in seen:
+                try:
+                    kwds = deps.distutils_info(file, aliases, base).values
+                except Exception:
+                    if exclude_failures:
+                        continue
+                    raise
+                if base is not None:
+                    for key, value in base.values.items():
+                        if key not in kwds:
+                            kwds[key] = value
+
+                kwds['name'] = module_name
+
+                sources = [file] + [m for m in template.sources if m != filepattern]
+                if 'sources' in kwds:
+                    # allow users to add .c files etc.
+                    for source in kwds['sources']:
+                        source = encode_filename_in_py2(source)
+                        if source not in sources:
+                            sources.append(source)
+                kwds['sources'] = sources
+
+                if ext_language and 'language' not in kwds:
+                    kwds['language'] = ext_language
+
+                np_pythran = kwds.pop('np_pythran', False)
+
+                # Create the new extension
+                m, metadata = create_extension(template, kwds)
+                m.np_pythran = np_pythran or getattr(m, 'np_pythran', False)
+                if m.np_pythran:
+                    update_pythran_extension(m)
+                module_list.append(m)
+
+                # Store metadata (this will be written as JSON in the
+                # generated C file but otherwise has no purpose)
+                module_metadata[module_name] = metadata
+
+                if file not in m.sources:
+                    # Old setuptools unconditionally replaces .pyx with .c/.cpp
+                    target_file = os.path.splitext(file)[0] + ('.cpp' if m.language == 'c++' else '.c')
+                    try:
+                        m.sources.remove(target_file)
+                    except ValueError:
+                        # never seen this in the wild, but probably better to warn about this unexpected case
+                        print(u"Warning: Cython source file not found in sources list, adding %s" % file)
+                    m.sources.insert(0, file)
+                seen.add(name)
+    return module_list, module_metadata
+
+
+# This is the user-exposed entry point.
+def cythonize(module_list, exclude=None, nthreads=0, aliases=None, quiet=False, force=None, language=None,
+              exclude_failures=False, show_all_warnings=False, **options):
+    """
+    Compile a set of source modules into C/C++ files and return a list of distutils
+    Extension objects for them.
+
+    :param module_list: As module list, pass either a glob pattern, a list of glob
+                        patterns or a list of Extension objects.  The latter
+                        allows you to configure the extensions separately
+                        through the normal distutils options.
+                        You can also pass Extension objects that have
+                        glob patterns as their sources. Then, cythonize
+                        will resolve the pattern and create a
+                        copy of the Extension for every matching file.
+
+    :param exclude: When passing glob patterns as ``module_list``, you can exclude certain
+                    module names explicitly by passing them into the ``exclude`` option.
+
+    :param nthreads: The number of concurrent builds for parallel compilation
+                     (requires the ``multiprocessing`` module).
+
+    :param aliases: If you want to use compiler directives like ``# distutils: ...`` but
+                    can only know at compile time (when running the ``setup.py``) which values
+                    to use, you can use aliases and pass a dictionary mapping those aliases
+                    to Python strings when calling :func:`cythonize`. As an example, say you
+                    want to use the compiler
+                    directive ``# distutils: include_dirs = ../static_libs/include/``
+                    but this path isn't always fixed and you want to find it when running
+                    the ``setup.py``. You can then do ``# distutils: include_dirs = MY_HEADERS``,
+                    find the value of ``MY_HEADERS`` in the ``setup.py``, put it in a python
+                    variable called ``foo`` as a string, and then call
+                    ``cythonize(..., aliases={'MY_HEADERS': foo})``.
+
+    :param quiet: If True, Cython won't print error, warning, or status messages during the
+                  compilation.
+
+    :param force: Forces the recompilation of the Cython modules, even if the timestamps
+                  don't indicate that a recompilation is necessary.
+
+    :param language: To globally enable C++ mode, you can pass ``language='c++'``. Otherwise, this
+                     will be determined at a per-file level based on compiler directives.  This
+                     affects only modules found based on file names.  Extension instances passed
+                     into :func:`cythonize` will not be changed. It is recommended to rather
+                     use the compiler directive ``# distutils: language = c++`` than this option.
+
+    :param exclude_failures: For a broad 'try to compile' mode that ignores compilation
+                             failures and simply excludes the failed extensions,
+                             pass ``exclude_failures=True``. Note that this only
+                             really makes sense for compiling ``.py`` files which can also
+                             be used without compilation.
+
+    :param show_all_warnings: By default, not all Cython warnings are printed.
+                              Set to true to show all warnings.
+
+    :param annotate: If ``True``, will produce a HTML file for each of the ``.pyx`` or ``.py``
+                     files compiled. The HTML file gives an indication
+                     of how much Python interaction there is in
+                     each of the source code lines, compared to plain C code.
+                     It also allows you to see the C/C++ code
+                     generated for each line of Cython code. This report is invaluable when
+                     optimizing a function for speed,
+                     and for determining when to :ref:`release the GIL <nogil>`:
+                     in general, a ``nogil`` block may contain only "white" code.
+                     See examples in :ref:`determining_where_to_add_types` or
+                     :ref:`primes`.
+
+
+    :param annotate-fullc: If ``True`` will produce a colorized HTML version of
+                           the source which includes entire generated C/C++-code.
+
+
+    :param compiler_directives: Allow to set compiler directives in the ``setup.py`` like this:
+                                ``compiler_directives={'embedsignature': True}``.
+                                See :ref:`compiler-directives`.
+
+    :param depfile: produce depfiles for the sources if True.
+    """
+    if exclude is None:
+        exclude = []
+    if 'include_path' not in options:
+        options['include_path'] = ['.']
+    if 'common_utility_include_dir' in options:
+        safe_makedirs(options['common_utility_include_dir'])
+
+    depfile = options.pop('depfile', None)
+
+    if pythran is None:
+        pythran_options = None
+    else:
+        pythran_options = CompilationOptions(**options)
+        pythran_options.cplus = True
+        pythran_options.np_pythran = True
+
+    if force is None:
+        force = os.environ.get("CYTHON_FORCE_REGEN") == "1"  # allow global overrides for build systems
+
+    c_options = CompilationOptions(**options)
+    cpp_options = CompilationOptions(**options); cpp_options.cplus = True
+    ctx = Context.from_options(c_options)
+    options = c_options
+    module_list, module_metadata = create_extension_list(
+        module_list,
+        exclude=exclude,
+        ctx=ctx,
+        quiet=quiet,
+        exclude_failures=exclude_failures,
+        language=language,
+        aliases=aliases)
+
+    fix_windows_unicode_modules(module_list)
+
+    deps = create_dependency_tree(ctx, quiet=quiet)
+    build_dir = getattr(options, 'build_dir', None)
+
+    def copy_to_build_dir(filepath, root=os.getcwd()):
+        filepath_abs = os.path.abspath(filepath)
+        if os.path.isabs(filepath):
+            filepath = filepath_abs
+        if filepath_abs.startswith(root):
+            # distutil extension depends are relative to cwd
+            mod_dir = join_path(build_dir,
+                                os.path.dirname(_relpath(filepath, root)))
+            copy_once_if_newer(filepath_abs, mod_dir)
+
+    modules_by_cfile = collections.defaultdict(list)
+    to_compile = []
+    for m in module_list:
+        if build_dir:
+            for dep in m.depends:
+                copy_to_build_dir(dep)
+
+        cy_sources = [
+            source for source in m.sources
+            if os.path.splitext(source)[1] in ('.pyx', '.py')]
+        if len(cy_sources) == 1:
+            # normal "special" case: believe the Extension module name to allow user overrides
+            full_module_name = m.name
+        else:
+            # infer FQMN from source files
+            full_module_name = None
+
+        new_sources = []
+        for source in m.sources:
+            base, ext = os.path.splitext(source)
+            if ext in ('.pyx', '.py'):
+                if m.np_pythran:
+                    c_file = base + '.cpp'
+                    options = pythran_options
+                elif m.language == 'c++':
+                    c_file = base + '.cpp'
+                    options = cpp_options
+                else:
+                    c_file = base + '.c'
+                    options = c_options
+
+                # setup for out of place build directory if enabled
+                if build_dir:
+                    if os.path.isabs(c_file):
+                        c_file = os.path.splitdrive(c_file)[1]
+                        c_file = c_file.split(os.sep, 1)[1]
+                    c_file = os.path.join(build_dir, c_file)
+                    dir = os.path.dirname(c_file)
+                    safe_makedirs_once(dir)
+
+                # write out the depfile, if requested
+                if depfile:
+                    dependencies = deps.all_dependencies(source)
+                    write_depfile(c_file, source, dependencies)
+
+                # Missing files and those generated by other Cython versions should always be recreated.
+                if Utils.file_generated_by_this_cython(c_file):
+                    c_timestamp = os.path.getmtime(c_file)
+                else:
+                    c_timestamp = -1
+
+                # Priority goes first to modified files, second to direct
+                # dependents, and finally to indirect dependents.
+                if c_timestamp < deps.timestamp(source):
+                    dep_timestamp, dep = deps.timestamp(source), source
+                    priority = 0
+                else:
+                    dep_timestamp, dep = deps.newest_dependency(source)
+                    priority = 2 - (dep in deps.immediate_dependencies(source))
+                if force or c_timestamp < dep_timestamp:
+                    if not quiet and not force:
+                        if source == dep:
+                            print(u"Compiling %s because it changed." % Utils.decode_filename(source))
+                        else:
+                            print(u"Compiling %s because it depends on %s." % (
+                                Utils.decode_filename(source),
+                                Utils.decode_filename(dep),
+                            ))
+                    if not force and options.cache:
+                        fingerprint = deps.transitive_fingerprint(source, m, options)
+                    else:
+                        fingerprint = None
+                    to_compile.append((
+                        priority, source, c_file, fingerprint, quiet,
+                        options, not exclude_failures, module_metadata.get(m.name),
+                        full_module_name, show_all_warnings))
+                new_sources.append(c_file)
+                modules_by_cfile[c_file].append(m)
+            else:
+                new_sources.append(source)
+                if build_dir:
+                    copy_to_build_dir(source)
+        m.sources = new_sources
+
+    if options.cache:
+        if not os.path.exists(options.cache):
+            os.makedirs(options.cache)
+    to_compile.sort()
+    # Drop "priority" component of "to_compile" entries and add a
+    # simple progress indicator.
+    N = len(to_compile)
+    progress_fmt = "[{0:%d}/{1}] " % len(str(N))
+    for i in range(N):
+        progress = progress_fmt.format(i+1, N)
+        to_compile[i] = to_compile[i][1:] + (progress,)
+
+    if N <= 1:
+        nthreads = 0
+    if nthreads:
+        import multiprocessing
+        pool = multiprocessing.Pool(
+            nthreads, initializer=_init_multiprocessing_helper)
+        # This is a bit more involved than it should be, because KeyboardInterrupts
+        # break the multiprocessing workers when using a normal pool.map().
+        # See, for example:
+        # https://noswap.com/blog/python-multiprocessing-keyboardinterrupt
+        try:
+            result = pool.map_async(cythonize_one_helper, to_compile, chunksize=1)
+            pool.close()
+            while not result.ready():
+                try:
+                    result.get(99999)  # seconds
+                except multiprocessing.TimeoutError:
+                    pass
+        except KeyboardInterrupt:
+            pool.terminate()
+            raise
+        pool.join()
+    else:
+        for args in to_compile:
+            cythonize_one(*args)
+
+    if exclude_failures:
+        failed_modules = set()
+        for c_file, modules in modules_by_cfile.items():
+            if not os.path.exists(c_file):
+                failed_modules.update(modules)
+            elif os.path.getsize(c_file) < 200:
+                f = io_open(c_file, 'r', encoding='iso8859-1')
+                try:
+                    if f.read(len('#error ')) == '#error ':
+                        # dead compilation result
+                        failed_modules.update(modules)
+                finally:
+                    f.close()
+        if failed_modules:
+            for module in failed_modules:
+                module_list.remove(module)
+            print(u"Failed compilations: %s" % ', '.join(sorted([
+                module.name for module in failed_modules])))
+
+    if options.cache:
+        cleanup_cache(options.cache, getattr(options, 'cache_size', 1024 * 1024 * 100))
+    # cythonize() is often followed by the (non-Python-buffered)
+    # compiler output, flush now to avoid interleaving output.
+    sys.stdout.flush()
+    return module_list
+
+
+def fix_windows_unicode_modules(module_list):
+    # Hack around a distutils 3.[5678] bug on Windows for unicode module names.
+    # https://bugs.python.org/issue39432
+    if sys.platform != "win32":
+        return
+    if sys.version_info < (3, 5) or sys.version_info >= (3, 8, 2):
+        return
+
+    def make_filtered_list(ignored_symbol, old_entries):
+        class FilteredExportSymbols(list):
+            # export_symbols for unicode filename cause link errors on Windows
+            # Cython doesn't need them (it already defines PyInit with the correct linkage)
+            # so use this class as a temporary fix to stop them from being generated
+            def __contains__(self, val):
+                # so distutils doesn't "helpfully" add PyInit_<name>
+                return val == ignored_symbol or list.__contains__(self, val)
+
+        filtered_list = FilteredExportSymbols(old_entries)
+        if old_entries:
+            filtered_list.extend(name for name in old_entries if name != ignored_symbol)
+        return filtered_list
+
+    for m in module_list:
+        # TODO: use m.name.isascii() in Py3.7+
+        try:
+            m.name.encode("ascii")
+            continue
+        except UnicodeEncodeError:
+            pass
+        m.export_symbols = make_filtered_list(
+            "PyInit_" + m.name.rsplit(".", 1)[-1],
+            m.export_symbols,
+        )
+
+
+if os.environ.get('XML_RESULTS'):
+    compile_result_dir = os.environ['XML_RESULTS']
+    def record_results(func):
+        def with_record(*args):
+            t = time.time()
+            success = True
+            try:
+                try:
+                    func(*args)
+                except:
+                    success = False
+            finally:
+                t = time.time() - t
+                module = fully_qualified_name(args[0])
+                name = "cythonize." + module
+                failures = 1 - success
+                if success:
+                    failure_item = ""
+                else:
+                    failure_item = "failure"
+                output = open(os.path.join(compile_result_dir, name + ".xml"), "w")
+                output.write("""
+                    <?xml version="1.0" ?>
+                    <testsuite name="%(name)s" errors="0" failures="%(failures)s" tests="1" time="%(t)s">
+                    <testcase classname="%(name)s" name="cythonize">
+                    %(failure_item)s
+                    </testcase>
+                    </testsuite>
+                """.strip() % locals())
+                output.close()
+        return with_record
+else:
+    def record_results(func):
+        return func
+
+
+# TODO: Share context? Issue: pyx processing leaks into pxd module
+@record_results
+def cythonize_one(pyx_file, c_file, fingerprint, quiet, options=None,
+                  raise_on_failure=True, embedded_metadata=None,
+                  full_module_name=None, show_all_warnings=False,
+                  progress=""):
+    from ..Compiler.Main import compile_single, default_options
+    from ..Compiler.Errors import CompileError, PyrexError
+
+    if fingerprint:
+        if not os.path.exists(options.cache):
+            safe_makedirs(options.cache)
+        # Cython-generated c files are highly compressible.
+        # (E.g. a compression ratio of about 10 for Sage).
+        fingerprint_file_base = join_path(
+            options.cache, "%s-%s" % (os.path.basename(c_file), fingerprint))
+        gz_fingerprint_file = fingerprint_file_base + gzip_ext
+        zip_fingerprint_file = fingerprint_file_base + '.zip'
+        if os.path.exists(gz_fingerprint_file) or os.path.exists(zip_fingerprint_file):
+            if not quiet:
+                print(u"%sFound compiled %s in cache" % (progress, pyx_file))
+            if os.path.exists(gz_fingerprint_file):
+                os.utime(gz_fingerprint_file, None)
+                with contextlib.closing(gzip_open(gz_fingerprint_file, 'rb')) as g:
+                    with contextlib.closing(open(c_file, 'wb')) as f:
+                        shutil.copyfileobj(g, f)
+            else:
+                os.utime(zip_fingerprint_file, None)
+                dirname = os.path.dirname(c_file)
+                with contextlib.closing(zipfile.ZipFile(zip_fingerprint_file)) as z:
+                    for artifact in z.namelist():
+                        z.extract(artifact, os.path.join(dirname, artifact))
+            return
+    if not quiet:
+        print(u"%sCythonizing %s" % (progress, Utils.decode_filename(pyx_file)))
+    if options is None:
+        options = CompilationOptions(default_options)
+    options.output_file = c_file
+    options.embedded_metadata = embedded_metadata
+
+    old_warning_level = Errors.LEVEL
+    if show_all_warnings:
+        Errors.LEVEL = 0
+
+    any_failures = 0
+    try:
+        result = compile_single(pyx_file, options, full_module_name=full_module_name)
+        if result.num_errors > 0:
+            any_failures = 1
+    except (EnvironmentError, PyrexError) as e:
+        sys.stderr.write('%s\n' % e)
+        any_failures = 1
+        # XXX
+        import traceback
+        traceback.print_exc()
+    except Exception:
+        if raise_on_failure:
+            raise
+        import traceback
+        traceback.print_exc()
+        any_failures = 1
+    finally:
+        if show_all_warnings:
+            Errors.LEVEL = old_warning_level
+
+    if any_failures:
+        if raise_on_failure:
+            raise CompileError(None, pyx_file)
+        elif os.path.exists(c_file):
+            os.remove(c_file)
+    elif fingerprint:
+        artifacts = list(filter(None, [
+            getattr(result, attr, None)
+            for attr in ('c_file', 'h_file', 'api_file', 'i_file')]))
+        if len(artifacts) == 1:
+            fingerprint_file = gz_fingerprint_file
+            with contextlib.closing(open(c_file, 'rb')) as f:
+                with contextlib.closing(gzip_open(fingerprint_file + '.tmp', 'wb')) as g:
+                    shutil.copyfileobj(f, g)
+        else:
+            fingerprint_file = zip_fingerprint_file
+            with contextlib.closing(zipfile.ZipFile(
+                    fingerprint_file + '.tmp', 'w', zipfile_compression_mode)) as zip:
+                for artifact in artifacts:
+                    zip.write(artifact, os.path.basename(artifact))
+        os.rename(fingerprint_file + '.tmp', fingerprint_file)
+
+
+def cythonize_one_helper(m):
+    import traceback
+    try:
+        return cythonize_one(*m)
+    except Exception:
+        traceback.print_exc()
+        raise
+
+
+def _init_multiprocessing_helper():
+    # KeyboardInterrupt kills workers, so don't let them get it
+    import signal
+    signal.signal(signal.SIGINT, signal.SIG_IGN)
+
+
+def cleanup_cache(cache, target_size, ratio=.85):
+    try:
+        p = subprocess.Popen(['du', '-s', '-k', os.path.abspath(cache)], stdout=subprocess.PIPE)
+        stdout, _ = p.communicate()
+        res = p.wait()
+        if res == 0:
+            total_size = 1024 * int(stdout.strip().split()[0])
+            if total_size < target_size:
+                return
+    except (OSError, ValueError):
+        pass
+    total_size = 0
+    all = []
+    for file in os.listdir(cache):
+        path = join_path(cache, file)
+        s = os.stat(path)
+        total_size += s.st_size
+        all.append((s.st_atime, s.st_size, path))
+    if total_size > target_size:
+        for time, size, file in reversed(sorted(all)):
+            os.unlink(file)
+            total_size -= size
+            if total_size < target_size * ratio:
+                break

Lib/site-packages/Cython/Build/Distutils.py

@@ -0,0 +1 @@
+from Cython.Distutils.build_ext import build_ext

Lib/site-packages/Cython/Build/Inline.py

@@ -0,0 +1,367 @@
+from __future__ import absolute_import
+
+import hashlib
+import inspect
+import os
+import re
+import sys
+
+from distutils.core import Distribution, Extension
+from distutils.command.build_ext import build_ext
+
+import Cython
+from ..Compiler.Main import Context
+from ..Compiler.Options import (default_options, CompilationOptions,
+    get_directive_defaults)
+
+from ..Compiler.Visitor import CythonTransform, EnvTransform
+from ..Compiler.ParseTreeTransforms import SkipDeclarations
+from ..Compiler.TreeFragment import parse_from_strings
+from ..Compiler.StringEncoding import _unicode
+from .Dependencies import strip_string_literals, cythonize, cached_function
+from ..Compiler import Pipeline
+from ..Utils import get_cython_cache_dir
+import cython as cython_module
+
+
+IS_PY3 = sys.version_info >= (3,)
+
+# A utility function to convert user-supplied ASCII strings to unicode.
+if not IS_PY3:
+    def to_unicode(s):
+        if isinstance(s, bytes):
+            return s.decode('ascii')
+        else:
+            return s
+else:
+    to_unicode = lambda x: x
+
+
+if sys.version_info < (3, 5):
+    import imp
+    def load_dynamic(name, module_path):
+        return imp.load_dynamic(name, module_path)
+else:
+    import importlib.util
+    from importlib.machinery import ExtensionFileLoader
+
+    def load_dynamic(name, path):
+        spec = importlib.util.spec_from_file_location(name, loader=ExtensionFileLoader(name, path))
+        module = importlib.util.module_from_spec(spec)
+        spec.loader.exec_module(module)
+        return module
+
+
+class UnboundSymbols(EnvTransform, SkipDeclarations):
+    def __init__(self):
+        super(EnvTransform, self).__init__(context=None)
+        self.unbound = set()
+    def visit_NameNode(self, node):
+        if not self.current_env().lookup(node.name):
+            self.unbound.add(node.name)
+        return node
+    def __call__(self, node):
+        super(UnboundSymbols, self).__call__(node)
+        return self.unbound
+
+
+@cached_function
+def unbound_symbols(code, context=None):
+    code = to_unicode(code)
+    if context is None:
+        context = Context([], get_directive_defaults(),
+                          options=CompilationOptions(default_options))
+    from ..Compiler.ParseTreeTransforms import AnalyseDeclarationsTransform
+    tree = parse_from_strings('(tree fragment)', code)
+    for phase in Pipeline.create_pipeline(context, 'pyx'):
+        if phase is None:
+            continue
+        tree = phase(tree)
+        if isinstance(phase, AnalyseDeclarationsTransform):
+            break
+    try:
+        import builtins
+    except ImportError:
+        import __builtin__ as builtins
+    return tuple(UnboundSymbols()(tree) - set(dir(builtins)))
+
+
+def unsafe_type(arg, context=None):
+    py_type = type(arg)
+    if py_type is int:
+        return 'long'
+    else:
+        return safe_type(arg, context)
+
+
+def safe_type(arg, context=None):
+    py_type = type(arg)
+    if py_type in (list, tuple, dict, str):
+        return py_type.__name__
+    elif py_type is complex:
+        return 'double complex'
+    elif py_type is float:
+        return 'double'
+    elif py_type is bool:
+        return 'bint'
+    elif 'numpy' in sys.modules and isinstance(arg, sys.modules['numpy'].ndarray):
+        return 'numpy.ndarray[numpy.%s_t, ndim=%s]' % (arg.dtype.name, arg.ndim)
+    else:
+        for base_type in py_type.__mro__:
+            if base_type.__module__ in ('__builtin__', 'builtins'):
+                return 'object'
+            module = context.find_module(base_type.__module__, need_pxd=False)
+            if module:
+                entry = module.lookup(base_type.__name__)
+                if entry.is_type:
+                    return '%s.%s' % (base_type.__module__, base_type.__name__)
+        return 'object'
+
+
+def _get_build_extension():
+    dist = Distribution()
+    # Ensure the build respects distutils configuration by parsing
+    # the configuration files
+    config_files = dist.find_config_files()
+    dist.parse_config_files(config_files)
+    build_extension = build_ext(dist)
+    build_extension.finalize_options()
+    return build_extension
+
+
+@cached_function
+def _create_context(cython_include_dirs):
+    return Context(
+        list(cython_include_dirs),
+        get_directive_defaults(),
+        options=CompilationOptions(default_options)
+    )
+
+
+_cython_inline_cache = {}
+_cython_inline_default_context = _create_context(('.',))
+
+
+def _populate_unbound(kwds, unbound_symbols, locals=None, globals=None):
+    for symbol in unbound_symbols:
+        if symbol not in kwds:
+            if locals is None or globals is None:
+                calling_frame = inspect.currentframe().f_back.f_back.f_back
+                if locals is None:
+                    locals = calling_frame.f_locals
+                if globals is None:
+                    globals = calling_frame.f_globals
+            if symbol in locals:
+                kwds[symbol] = locals[symbol]
+            elif symbol in globals:
+                kwds[symbol] = globals[symbol]
+            else:
+                print("Couldn't find %r" % symbol)
+
+
+def _inline_key(orig_code, arg_sigs, language_level):
+    key = orig_code, arg_sigs, sys.version_info, sys.executable, language_level, Cython.__version__
+    return hashlib.sha1(_unicode(key).encode('utf-8')).hexdigest()
+
+
+def cython_inline(code, get_type=unsafe_type,
+                  lib_dir=os.path.join(get_cython_cache_dir(), 'inline'),
+                  cython_include_dirs=None, cython_compiler_directives=None,
+                  force=False, quiet=False, locals=None, globals=None, language_level=None, **kwds):
+
+    if get_type is None:
+        get_type = lambda x: 'object'
+    ctx = _create_context(tuple(cython_include_dirs)) if cython_include_dirs else _cython_inline_default_context
+
+    cython_compiler_directives = dict(cython_compiler_directives) if cython_compiler_directives else {}
+    if language_level is None and 'language_level' not in cython_compiler_directives:
+        language_level = '3str'
+    if language_level is not None:
+        cython_compiler_directives['language_level'] = language_level
+
+    key_hash = None
+
+    # Fast path if this has been called in this session.
+    _unbound_symbols = _cython_inline_cache.get(code)
+    if _unbound_symbols is not None:
+        _populate_unbound(kwds, _unbound_symbols, locals, globals)
+        args = sorted(kwds.items())
+        arg_sigs = tuple([(get_type(value, ctx), arg) for arg, value in args])
+        key_hash = _inline_key(code, arg_sigs, language_level)
+        invoke = _cython_inline_cache.get((code, arg_sigs, key_hash))
+        if invoke is not None:
+            arg_list = [arg[1] for arg in args]
+            return invoke(*arg_list)
+
+    orig_code = code
+    code = to_unicode(code)
+    code, literals = strip_string_literals(code)
+    code = strip_common_indent(code)
+    if locals is None:
+        locals = inspect.currentframe().f_back.f_back.f_locals
+    if globals is None:
+        globals = inspect.currentframe().f_back.f_back.f_globals
+    try:
+        _cython_inline_cache[orig_code] = _unbound_symbols = unbound_symbols(code)
+        _populate_unbound(kwds, _unbound_symbols, locals, globals)
+    except AssertionError:
+        if not quiet:
+            # Parsing from strings not fully supported (e.g. cimports).
+            print("Could not parse code as a string (to extract unbound symbols).")
+
+    cimports = []
+    for name, arg in list(kwds.items()):
+        if arg is cython_module:
+            cimports.append('\ncimport cython as %s' % name)
+            del kwds[name]
+    arg_names = sorted(kwds)
+    arg_sigs = tuple([(get_type(kwds[arg], ctx), arg) for arg in arg_names])
+    if key_hash is None:
+        key_hash = _inline_key(orig_code, arg_sigs, language_level)
+    module_name = "_cython_inline_" + key_hash
+
+    if module_name in sys.modules:
+        module = sys.modules[module_name]
+
+    else:
+        build_extension = None
+        if cython_inline.so_ext is None:
+            # Figure out and cache current extension suffix
+            build_extension = _get_build_extension()
+            cython_inline.so_ext = build_extension.get_ext_filename('')
+
+        lib_dir = os.path.abspath(lib_dir)
+        module_path = os.path.join(lib_dir, module_name + cython_inline.so_ext)
+
+        if not os.path.exists(lib_dir):
+            os.makedirs(lib_dir)
+        if force or not os.path.isfile(module_path):
+            cflags = []
+            define_macros = []
+            c_include_dirs = []
+            qualified = re.compile(r'([.\w]+)[.]')
+            for type, _ in arg_sigs:
+                m = qualified.match(type)
+                if m:
+                    cimports.append('\ncimport %s' % m.groups()[0])
+                    # one special case
+                    if m.groups()[0] == 'numpy':
+                        import numpy
+                        c_include_dirs.append(numpy.get_include())
+                        define_macros.append(("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION"))
+                        # cflags.append('-Wno-unused')
+            module_body, func_body = extract_func_code(code)
+            params = ', '.join(['%s %s' % a for a in arg_sigs])
+            module_code = """
+%(module_body)s
+%(cimports)s
+def __invoke(%(params)s):
+%(func_body)s
+    return locals()
+            """ % {'cimports': '\n'.join(cimports),
+                   'module_body': module_body,
+                   'params': params,
+                   'func_body': func_body }
+            for key, value in literals.items():
+                module_code = module_code.replace(key, value)
+            pyx_file = os.path.join(lib_dir, module_name + '.pyx')
+            fh = open(pyx_file, 'w')
+            try:
+                fh.write(module_code)
+            finally:
+                fh.close()
+            extension = Extension(
+                name=module_name,
+                sources=[pyx_file],
+                include_dirs=c_include_dirs or None,
+                extra_compile_args=cflags or None,
+                define_macros=define_macros or None,
+            )
+            if build_extension is None:
+                build_extension = _get_build_extension()
+            build_extension.extensions = cythonize(
+                [extension],
+                include_path=cython_include_dirs or ['.'],
+                compiler_directives=cython_compiler_directives,
+                quiet=quiet)
+            build_extension.build_temp = os.path.dirname(pyx_file)
+            build_extension.build_lib  = lib_dir
+            build_extension.run()
+
+        if sys.platform == 'win32' and sys.version_info >= (3, 8):
+            with os.add_dll_directory(os.path.abspath(lib_dir)):
+                module = load_dynamic(module_name, module_path)
+        else:
+            module = load_dynamic(module_name, module_path)
+
+    _cython_inline_cache[orig_code, arg_sigs, key_hash] = module.__invoke
+    arg_list = [kwds[arg] for arg in arg_names]
+    return module.__invoke(*arg_list)
+
+
+# Cached suffix used by cython_inline above.  None should get
+# overridden with actual value upon the first cython_inline invocation
+cython_inline.so_ext = None
+
+_find_non_space = re.compile('[^ ]').search
+
+
+def strip_common_indent(code):
+    min_indent = None
+    lines = code.splitlines()
+    for line in lines:
+        match = _find_non_space(line)
+        if not match:
+            continue  # blank
+        indent = match.start()
+        if line[indent] == '#':
+            continue  # comment
+        if min_indent is None or min_indent > indent:
+            min_indent = indent
+    for ix, line in enumerate(lines):
+        match = _find_non_space(line)
+        if not match or not line or line[indent:indent+1] == '#':
+            continue
+        lines[ix] = line[min_indent:]
+    return '\n'.join(lines)
+
+
+module_statement = re.compile(r'^((cdef +(extern|class))|cimport|(from .+ cimport)|(from .+ import +[*]))')
+def extract_func_code(code):
+    module = []
+    function = []
+    current = function
+    code = code.replace('\t', ' ')
+    lines = code.split('\n')
+    for line in lines:
+        if not line.startswith(' '):
+            if module_statement.match(line):
+                current = module
+            else:
+                current = function
+        current.append(line)
+    return '\n'.join(module), '    ' + '\n    '.join(function)
+
+
+def get_body(source):
+    ix = source.index(':')
+    if source[:5] == 'lambda':
+        return "return %s" % source[ix+1:]
+    else:
+        return source[ix+1:]
+
+
+# Lots to be done here... It would be especially cool if compiled functions
+# could invoke each other quickly.
+class RuntimeCompiledFunction(object):
+
+    def __init__(self, f):
+        self._f = f
+        self._body = get_body(inspect.getsource(f))
+
+    def __call__(self, *args, **kwds):
+        all = inspect.getcallargs(self._f, *args, **kwds)
+        if IS_PY3:
+            return cython_inline(self._body, locals=self._f.__globals__, globals=self._f.__globals__, **all)
+        else:
+            return cython_inline(self._body, locals=self._f.func_globals, globals=self._f.func_globals, **all)

Lib/site-packages/Cython/Build/IpythonMagic.py

@@ -0,0 +1,572 @@
+# -*- coding: utf-8 -*-
+"""
+=====================
+Cython related magics
+=====================
+
+Magic command interface for interactive work with Cython
+
+.. note::
+
+  The ``Cython`` package needs to be installed separately. It
+  can be obtained using ``easy_install`` or ``pip``.
+
+Usage
+=====
+
+To enable the magics below, execute ``%load_ext cython``.
+
+``%%cython``
+
+{CYTHON_DOC}
+
+``%%cython_inline``
+
+{CYTHON_INLINE_DOC}
+
+``%%cython_pyximport``
+
+{CYTHON_PYXIMPORT_DOC}
+
+Author:
+* Brian Granger
+
+Code moved from IPython and adapted by:
+* Martín Gaitán
+
+Parts of this code were taken from Cython.inline.
+"""
+#-----------------------------------------------------------------------------
+# Copyright (C) 2010-2011, IPython Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file ipython-COPYING.rst, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from __future__ import absolute_import, print_function
+
+import io
+import os
+import re
+import sys
+import time
+import copy
+import distutils.log
+import textwrap
+
+IO_ENCODING = sys.getfilesystemencoding()
+IS_PY2 = sys.version_info[0] < 3
+
+import hashlib
+from distutils.core import Distribution, Extension
+from distutils.command.build_ext import build_ext
+
+from IPython.core import display
+from IPython.core import magic_arguments
+from IPython.core.magic import Magics, magics_class, cell_magic
+try:
+    from IPython.paths import get_ipython_cache_dir
+except ImportError:
+    # older IPython version
+    from IPython.utils.path import get_ipython_cache_dir
+from IPython.utils.text import dedent
+
+from ..Shadow import __version__ as cython_version
+from ..Compiler.Errors import CompileError
+from .Inline import cython_inline, load_dynamic
+from .Dependencies import cythonize
+from ..Utils import captured_fd, print_captured
+
+
+PGO_CONFIG = {
+    'gcc': {
+        'gen': ['-fprofile-generate', '-fprofile-dir={TEMPDIR}'],
+        'use': ['-fprofile-use', '-fprofile-correction', '-fprofile-dir={TEMPDIR}'],
+    },
+    # blind copy from 'configure' script in CPython 3.7
+    'icc': {
+        'gen': ['-prof-gen'],
+        'use': ['-prof-use'],
+    }
+}
+PGO_CONFIG['mingw32'] = PGO_CONFIG['gcc']
+
+
+if IS_PY2:
+    def encode_fs(name):
+        return name if isinstance(name, bytes) else name.encode(IO_ENCODING)
+else:
+    def encode_fs(name):
+        return name
+
+
+@magics_class
+class CythonMagics(Magics):
+
+    def __init__(self, shell):
+        super(CythonMagics, self).__init__(shell)
+        self._reloads = {}
+        self._code_cache = {}
+        self._pyximport_installed = False
+
+    def _import_all(self, module):
+        mdict = module.__dict__
+        if '__all__' in mdict:
+            keys = mdict['__all__']
+        else:
+            keys = [k for k in mdict if not k.startswith('_')]
+
+        for k in keys:
+            try:
+                self.shell.push({k: mdict[k]})
+            except KeyError:
+                msg = "'module' object has no attribute '%s'" % k
+                raise AttributeError(msg)
+
+    @cell_magic
+    def cython_inline(self, line, cell):
+        """Compile and run a Cython code cell using Cython.inline.
+
+        This magic simply passes the body of the cell to Cython.inline
+        and returns the result. If the variables `a` and `b` are defined
+        in the user's namespace, here is a simple example that returns
+        their sum::
+
+            %%cython_inline
+            return a+b
+
+        For most purposes, we recommend the usage of the `%%cython` magic.
+        """
+        locs = self.shell.user_global_ns
+        globs = self.shell.user_ns
+        return cython_inline(cell, locals=locs, globals=globs)
+
+    @cell_magic
+    def cython_pyximport(self, line, cell):
+        """Compile and import a Cython code cell using pyximport.
+
+        The contents of the cell are written to a `.pyx` file in the current
+        working directory, which is then imported using `pyximport`. This
+        magic requires a module name to be passed::
+
+            %%cython_pyximport modulename
+            def f(x):
+                return 2.0*x
+
+        The compiled module is then imported and all of its symbols are
+        injected into the user's namespace. For most purposes, we recommend
+        the usage of the `%%cython` magic.
+        """
+        module_name = line.strip()
+        if not module_name:
+            raise ValueError('module name must be given')
+        fname = module_name + '.pyx'
+        with io.open(fname, 'w', encoding='utf-8') as f:
+            f.write(cell)
+        if 'pyximport' not in sys.modules or not self._pyximport_installed:
+            import pyximport
+            pyximport.install()
+            self._pyximport_installed = True
+        if module_name in self._reloads:
+            module = self._reloads[module_name]
+            # Note: reloading extension modules is not actually supported
+            # (requires PEP-489 reinitialisation support).
+            # Don't know why this should ever have worked as it reads here.
+            # All we really need to do is to update the globals below.
+            #reload(module)
+        else:
+            __import__(module_name)
+            module = sys.modules[module_name]
+            self._reloads[module_name] = module
+        self._import_all(module)
+
+    @magic_arguments.magic_arguments()
+    @magic_arguments.argument(
+        '-a', '--annotate', action='store_const', const='default', dest='annotate',
+        help="Produce a colorized HTML version of the source."
+    )
+    @magic_arguments.argument(
+        '--annotate-fullc', action='store_const', const='fullc', dest='annotate',
+        help="Produce a colorized HTML version of the source "
+             "which includes entire generated C/C++-code."
+    )
+    @magic_arguments.argument(
+        '-+', '--cplus', action='store_true', default=False,
+        help="Output a C++ rather than C file."
+    )
+    @magic_arguments.argument(
+        '-3', dest='language_level', action='store_const', const=3, default=None,
+        help="Select Python 3 syntax."
+    )
+    @magic_arguments.argument(
+        '-2', dest='language_level', action='store_const', const=2, default=None,
+        help="Select Python 2 syntax."
+    )
+    @magic_arguments.argument(
+        '-f', '--force', action='store_true', default=False,
+        help="Force the compilation of a new module, even if the source has been "
+             "previously compiled."
+    )
+    @magic_arguments.argument(
+        '-c', '--compile-args', action='append', default=[],
+        help="Extra flags to pass to compiler via the `extra_compile_args` "
+             "Extension flag (can be specified  multiple times)."
+    )
+    @magic_arguments.argument(
+        '--link-args', action='append', default=[],
+        help="Extra flags to pass to linker via the `extra_link_args` "
+             "Extension flag (can be specified  multiple times)."
+    )
+    @magic_arguments.argument(
+        '-l', '--lib', action='append', default=[],
+        help="Add a library to link the extension against (can be specified "
+             "multiple times)."
+    )
+    @magic_arguments.argument(
+        '-n', '--name',
+        help="Specify a name for the Cython module."
+    )
+    @magic_arguments.argument(
+        '-L', dest='library_dirs', metavar='dir', action='append', default=[],
+        help="Add a path to the list of library directories (can be specified "
+             "multiple times)."
+    )
+    @magic_arguments.argument(
+        '-I', '--include', action='append', default=[],
+        help="Add a path to the list of include directories (can be specified "
+             "multiple times)."
+    )
+    @magic_arguments.argument(
+        '-S', '--src', action='append', default=[],
+        help="Add a path to the list of src files (can be specified "
+             "multiple times)."
+    )
+    @magic_arguments.argument(
+        '--pgo', dest='pgo', action='store_true', default=False,
+        help=("Enable profile guided optimisation in the C compiler. "
+              "Compiles the cell twice and executes it in between to generate a runtime profile.")
+    )
+    @magic_arguments.argument(
+        '--verbose', dest='quiet', action='store_false', default=True,
+        help=("Print debug information like generated .c/.cpp file location "
+              "and exact gcc/g++ command invoked.")
+    )
+    @cell_magic
+    def cython(self, line, cell):
+        """Compile and import everything from a Cython code cell.
+
+        The contents of the cell are written to a `.pyx` file in the
+        directory `IPYTHONDIR/cython` using a filename with the hash of the
+        code. This file is then cythonized and compiled. The resulting module
+        is imported and all of its symbols are injected into the user's
+        namespace. The usage is similar to that of `%%cython_pyximport` but
+        you don't have to pass a module name::
+
+            %%cython
+            def f(x):
+                return 2.0*x
+
+        To compile OpenMP codes, pass the required  `--compile-args`
+        and `--link-args`.  For example with gcc::
+
+            %%cython --compile-args=-fopenmp --link-args=-fopenmp
+            ...
+
+        To enable profile guided optimisation, pass the ``--pgo`` option.
+        Note that the cell itself needs to take care of establishing a suitable
+        profile when executed. This can be done by implementing the functions to
+        optimise, and then calling them directly in the same cell on some realistic
+        training data like this::
+
+            %%cython --pgo
+            def critical_function(data):
+                for item in data:
+                    ...
+
+            # execute function several times to build profile
+            from somewhere import some_typical_data
+            for _ in range(100):
+                critical_function(some_typical_data)
+
+        In Python 3.5 and later, you can distinguish between the profile and
+        non-profile runs as follows::
+
+            if "_pgo_" in __name__:
+                ...  # execute critical code here
+        """
+        args = magic_arguments.parse_argstring(self.cython, line)
+        code = cell if cell.endswith('\n') else cell + '\n'
+        lib_dir = os.path.join(get_ipython_cache_dir(), 'cython')
+        key = (code, line, sys.version_info, sys.executable, cython_version)
+
+        if not os.path.exists(lib_dir):
+            os.makedirs(lib_dir)
+
+        if args.pgo:
+            key += ('pgo',)
+        if args.force:
+            # Force a new module name by adding the current time to the
+            # key which is hashed to determine the module name.
+            key += (time.time(),)
+
+        if args.name:
+            module_name = str(args.name)  # no-op in Py3
+        else:
+            module_name = "_cython_magic_" + hashlib.sha1(str(key).encode('utf-8')).hexdigest()
+        html_file = os.path.join(lib_dir, module_name + '.html')
+        module_path = os.path.join(lib_dir, module_name + self.so_ext)
+
+        have_module = os.path.isfile(module_path)
+        need_cythonize = args.pgo or not have_module
+
+        if args.annotate:
+            if not os.path.isfile(html_file):
+                need_cythonize = True
+
+        extension = None
+        if need_cythonize:
+            extensions = self._cythonize(module_name, code, lib_dir, args, quiet=args.quiet)
+            if extensions is None:
+                # Compilation failed and printed error message
+                return None
+            assert len(extensions) == 1
+            extension = extensions[0]
+            self._code_cache[key] = module_name
+
+            if args.pgo:
+                self._profile_pgo_wrapper(extension, lib_dir)
+
+        def print_compiler_output(stdout, stderr, where):
+            # On windows, errors are printed to stdout, we redirect both to sys.stderr.
+            print_captured(stdout, where, u"Content of stdout:\n")
+            print_captured(stderr, where, u"Content of stderr:\n")
+
+        get_stderr = get_stdout = None
+        try:
+            with captured_fd(1) as get_stdout:
+                with captured_fd(2) as get_stderr:
+                    self._build_extension(
+                        extension, lib_dir, pgo_step_name='use' if args.pgo else None, quiet=args.quiet)
+        except (distutils.errors.CompileError, distutils.errors.LinkError):
+            # Build failed, print error message from compiler/linker
+            print_compiler_output(get_stdout(), get_stderr(), sys.stderr)
+            return None
+
+        # Build seems ok, but we might still want to show any warnings that occurred
+        print_compiler_output(get_stdout(), get_stderr(), sys.stdout)
+
+        module = load_dynamic(module_name, module_path)
+        self._import_all(module)
+
+        if args.annotate:
+            try:
+                with io.open(html_file, encoding='utf-8') as f:
+                    annotated_html = f.read()
+            except IOError as e:
+                # File could not be opened. Most likely the user has a version
+                # of Cython before 0.15.1 (when `cythonize` learned the
+                # `force` keyword argument) and has already compiled this
+                # exact source without annotation.
+                print('Cython completed successfully but the annotated '
+                      'source could not be read.', file=sys.stderr)
+                print(e, file=sys.stderr)
+            else:
+                return display.HTML(self.clean_annotated_html(annotated_html))
+
+    def _profile_pgo_wrapper(self, extension, lib_dir):
+        """
+        Generate a .c file for a separate extension module that calls the
+        module init function of the original module.  This makes sure that the
+        PGO profiler sees the correct .o file of the final module, but it still
+        allows us to import the module under a different name for profiling,
+        before recompiling it into the PGO optimised module.  Overwriting and
+        reimporting the same shared library is not portable.
+        """
+        extension = copy.copy(extension)  # shallow copy, do not modify sources in place!
+        module_name = extension.name
+        pgo_module_name = '_pgo_' + module_name
+        pgo_wrapper_c_file = os.path.join(lib_dir, pgo_module_name + '.c')
+        with io.open(pgo_wrapper_c_file, 'w', encoding='utf-8') as f:
+            f.write(textwrap.dedent(u"""
+            #include "Python.h"
+            #if PY_MAJOR_VERSION < 3
+            extern PyMODINIT_FUNC init%(module_name)s(void);
+            PyMODINIT_FUNC init%(pgo_module_name)s(void); /*proto*/
+            PyMODINIT_FUNC init%(pgo_module_name)s(void) {
+                PyObject *sys_modules;
+                init%(module_name)s();  if (PyErr_Occurred()) return;
+                sys_modules = PyImport_GetModuleDict();  /* borrowed, no exception, "never" fails */
+                if (sys_modules) {
+                    PyObject *module = PyDict_GetItemString(sys_modules, "%(module_name)s");  if (!module) return;
+                    PyDict_SetItemString(sys_modules, "%(pgo_module_name)s", module);
+                    Py_DECREF(module);
+                }
+            }
+            #else
+            extern PyMODINIT_FUNC PyInit_%(module_name)s(void);
+            PyMODINIT_FUNC PyInit_%(pgo_module_name)s(void); /*proto*/
+            PyMODINIT_FUNC PyInit_%(pgo_module_name)s(void) {
+                return PyInit_%(module_name)s();
+            }
+            #endif
+            """ % {'module_name': module_name, 'pgo_module_name': pgo_module_name}))
+
+        extension.sources = extension.sources + [pgo_wrapper_c_file]  # do not modify in place!
+        extension.name = pgo_module_name
+
+        self._build_extension(extension, lib_dir, pgo_step_name='gen')
+
+        # import and execute module code to generate profile
+        so_module_path = os.path.join(lib_dir, pgo_module_name + self.so_ext)
+        load_dynamic(pgo_module_name, so_module_path)
+
+    def _cythonize(self, module_name, code, lib_dir, args, quiet=True):
+        pyx_file = os.path.join(lib_dir, module_name + '.pyx')
+        pyx_file = encode_fs(pyx_file)
+
+        c_include_dirs = args.include
+        c_src_files = list(map(str, args.src))
+        if 'numpy' in code:
+            import numpy
+            c_include_dirs.append(numpy.get_include())
+        with io.open(pyx_file, 'w', encoding='utf-8') as f:
+            f.write(code)
+        extension = Extension(
+            name=module_name,
+            sources=[pyx_file] + c_src_files,
+            include_dirs=c_include_dirs,
+            library_dirs=args.library_dirs,
+            extra_compile_args=args.compile_args,
+            extra_link_args=args.link_args,
+            libraries=args.lib,
+            language='c++' if args.cplus else 'c',
+        )
+        try:
+            opts = dict(
+                quiet=quiet,
+                annotate=args.annotate,
+                force=True,
+                language_level=min(3, sys.version_info[0]),
+            )
+            if args.language_level is not None:
+                assert args.language_level in (2, 3)
+                opts['language_level'] = args.language_level
+            return cythonize([extension], **opts)
+        except CompileError:
+            return None
+
+    def _build_extension(self, extension, lib_dir, temp_dir=None, pgo_step_name=None, quiet=True):
+        build_extension = self._get_build_extension(
+            extension, lib_dir=lib_dir, temp_dir=temp_dir, pgo_step_name=pgo_step_name)
+        old_threshold = None
+        try:
+            if not quiet:
+                old_threshold = distutils.log.set_threshold(distutils.log.DEBUG)
+            build_extension.run()
+        finally:
+            if not quiet and old_threshold is not None:
+                distutils.log.set_threshold(old_threshold)
+
+    def _add_pgo_flags(self, build_extension, step_name, temp_dir):
+        compiler_type = build_extension.compiler.compiler_type
+        if compiler_type == 'unix':
+            compiler_cmd = build_extension.compiler.compiler_so
+            # TODO: we could try to call "[cmd] --version" for better insights
+            if not compiler_cmd:
+                pass
+            elif 'clang' in compiler_cmd or 'clang' in compiler_cmd[0]:
+                compiler_type = 'clang'
+            elif 'icc' in compiler_cmd or 'icc' in compiler_cmd[0]:
+                compiler_type = 'icc'
+            elif 'gcc' in compiler_cmd or 'gcc' in compiler_cmd[0]:
+                compiler_type = 'gcc'
+            elif 'g++' in compiler_cmd or 'g++' in compiler_cmd[0]:
+                compiler_type = 'gcc'
+        config = PGO_CONFIG.get(compiler_type)
+        orig_flags = []
+        if config and step_name in config:
+            flags = [f.format(TEMPDIR=temp_dir) for f in config[step_name]]
+            for extension in build_extension.extensions:
+                orig_flags.append((extension.extra_compile_args, extension.extra_link_args))
+                extension.extra_compile_args = extension.extra_compile_args + flags
+                extension.extra_link_args = extension.extra_link_args + flags
+        else:
+            print("No PGO %s configuration known for C compiler type '%s'" % (step_name, compiler_type),
+                  file=sys.stderr)
+        return orig_flags
+
+    @property
+    def so_ext(self):
+        """The extension suffix for compiled modules."""
+        try:
+            return self._so_ext
+        except AttributeError:
+            self._so_ext = self._get_build_extension().get_ext_filename('')
+            return self._so_ext
+
+    def _clear_distutils_mkpath_cache(self):
+        """clear distutils mkpath cache
+
+        prevents distutils from skipping re-creation of dirs that have been removed
+        """
+        try:
+            from distutils.dir_util import _path_created
+        except ImportError:
+            pass
+        else:
+            _path_created.clear()
+
+    def _get_build_extension(self, extension=None, lib_dir=None, temp_dir=None,
+                             pgo_step_name=None, _build_ext=build_ext):
+        self._clear_distutils_mkpath_cache()
+        dist = Distribution()
+        config_files = dist.find_config_files()
+        try:
+            config_files.remove('setup.cfg')
+        except ValueError:
+            pass
+        dist.parse_config_files(config_files)
+
+        if not temp_dir:
+            temp_dir = lib_dir
+        add_pgo_flags = self._add_pgo_flags
+
+        if pgo_step_name:
+            base_build_ext = _build_ext
+            class _build_ext(_build_ext):
+                def build_extensions(self):
+                    add_pgo_flags(self, pgo_step_name, temp_dir)
+                    base_build_ext.build_extensions(self)
+
+        build_extension = _build_ext(dist)
+        build_extension.finalize_options()
+        if temp_dir:
+            temp_dir = encode_fs(temp_dir)
+            build_extension.build_temp = temp_dir
+        if lib_dir:
+            lib_dir = encode_fs(lib_dir)
+            build_extension.build_lib = lib_dir
+        if extension is not None:
+            build_extension.extensions = [extension]
+        return build_extension
+
+    @staticmethod
+    def clean_annotated_html(html):
+        """Clean up the annotated HTML source.
+
+        Strips the link to the generated C or C++ file, which we do not
+        present to the user.
+        """
+        r = re.compile('<p>Raw output: <a href="(.*)">(.*)</a>')
+        html = '\n'.join(l for l in html.splitlines() if not r.match(l))
+        return html
+
+__doc__ = __doc__.format(
+    # rST doesn't see the -+ flag as part of an option list, so we
+    # hide it from the module-level docstring.
+    CYTHON_DOC=dedent(CythonMagics.cython.__doc__\
+                                  .replace('-+, --cplus', '--cplus    ')),
+    CYTHON_INLINE_DOC=dedent(CythonMagics.cython_inline.__doc__),
+    CYTHON_PYXIMPORT_DOC=dedent(CythonMagics.cython_pyximport.__doc__),
+)

Lib/site-packages/Cython/Build/Tests/TestCyCache.py

@@ -0,0 +1,119 @@
+import difflib
+import glob
+import gzip
+import os
+import sys
+import tempfile
+import unittest
+
+import Cython.Build.Dependencies
+import Cython.Utils
+from Cython.TestUtils import CythonTest
+
+
+class TestCyCache(CythonTest):
+
+    def setUp(self):
+        CythonTest.setUp(self)
+        self.temp_dir = tempfile.mkdtemp(
+            prefix='cycache-test',
+            dir='TEST_TMP' if os.path.isdir('TEST_TMP') else None)
+        self.src_dir = tempfile.mkdtemp(prefix='src', dir=self.temp_dir)
+        self.cache_dir = tempfile.mkdtemp(prefix='cache', dir=self.temp_dir)
+
+    def cache_files(self, file_glob):
+        return glob.glob(os.path.join(self.cache_dir, file_glob))
+
+    def fresh_cythonize(self, *args, **kwargs):
+        Cython.Utils.clear_function_caches()
+        Cython.Build.Dependencies._dep_tree = None  # discard method caches
+        Cython.Build.Dependencies.cythonize(*args, **kwargs)
+
+    def test_cycache_switch(self):
+        content1 = 'value = 1\n'
+        content2 = 'value = 2\n'
+        a_pyx = os.path.join(self.src_dir, 'a.pyx')
+        a_c = a_pyx[:-4] + '.c'
+
+        with open(a_pyx, 'w') as f:
+            f.write(content1)
+        self.fresh_cythonize(a_pyx, cache=self.cache_dir)
+        self.fresh_cythonize(a_pyx, cache=self.cache_dir)
+        self.assertEqual(1, len(self.cache_files('a.c*')))
+        with open(a_c) as f:
+            a_contents1 = f.read()
+        os.unlink(a_c)
+
+        with open(a_pyx, 'w') as f:
+            f.write(content2)
+        self.fresh_cythonize(a_pyx, cache=self.cache_dir)
+        with open(a_c) as f:
+            a_contents2 = f.read()
+        os.unlink(a_c)
+
+        self.assertNotEqual(a_contents1, a_contents2, 'C file not changed!')
+        self.assertEqual(2, len(self.cache_files('a.c*')))
+
+        with open(a_pyx, 'w') as f:
+            f.write(content1)
+        self.fresh_cythonize(a_pyx, cache=self.cache_dir)
+        self.assertEqual(2, len(self.cache_files('a.c*')))
+        with open(a_c) as f:
+            a_contents = f.read()
+        self.assertEqual(
+            a_contents, a_contents1,
+            msg='\n'.join(list(difflib.unified_diff(
+                a_contents.split('\n'), a_contents1.split('\n')))[:10]))
+
+    def test_cycache_uses_cache(self):
+        a_pyx = os.path.join(self.src_dir, 'a.pyx')
+        a_c = a_pyx[:-4] + '.c'
+        with open(a_pyx, 'w') as f:
+            f.write('pass')
+        self.fresh_cythonize(a_pyx, cache=self.cache_dir)
+        a_cache = os.path.join(self.cache_dir, os.listdir(self.cache_dir)[0])
+        with gzip.GzipFile(a_cache, 'wb') as gzipfile:
+            gzipfile.write('fake stuff'.encode('ascii'))
+        os.unlink(a_c)
+        self.fresh_cythonize(a_pyx, cache=self.cache_dir)
+        with open(a_c) as f:
+            a_contents = f.read()
+        self.assertEqual(a_contents, 'fake stuff',
+                         'Unexpected contents: %s...' % a_contents[:100])
+
+    def test_multi_file_output(self):
+        a_pyx = os.path.join(self.src_dir, 'a.pyx')
+        a_c = a_pyx[:-4] + '.c'
+        a_h = a_pyx[:-4] + '.h'
+        a_api_h = a_pyx[:-4] + '_api.h'
+        with open(a_pyx, 'w') as f:
+            f.write('cdef public api int foo(int x): return x\n')
+        self.fresh_cythonize(a_pyx, cache=self.cache_dir)
+        expected = [a_c, a_h, a_api_h]
+        for output in expected:
+            self.assertTrue(os.path.exists(output), output)
+            os.unlink(output)
+        self.fresh_cythonize(a_pyx, cache=self.cache_dir)
+        for output in expected:
+            self.assertTrue(os.path.exists(output), output)
+
+    def test_options_invalidation(self):
+        hash_pyx = os.path.join(self.src_dir, 'options.pyx')
+        hash_c = hash_pyx[:-len('.pyx')] + '.c'
+
+        with open(hash_pyx, 'w') as f:
+            f.write('pass')
+        self.fresh_cythonize(hash_pyx, cache=self.cache_dir, cplus=False)
+        self.assertEqual(1, len(self.cache_files('options.c*')))
+
+        os.unlink(hash_c)
+        self.fresh_cythonize(hash_pyx, cache=self.cache_dir, cplus=True)
+        self.assertEqual(2, len(self.cache_files('options.c*')))
+
+        os.unlink(hash_c)
+        self.fresh_cythonize(hash_pyx, cache=self.cache_dir, cplus=False, show_version=False)
+        self.assertEqual(2, len(self.cache_files('options.c*')))
+
+        os.unlink(hash_c)
+        self.fresh_cythonize(hash_pyx, cache=self.cache_dir, cplus=False, show_version=True)
+        self.assertEqual(2, len(self.cache_files('options.c*')))

Lib/site-packages/Cython/Build/Tests/TestCythonizeArgsParser.py

@@ -0,0 +1,482 @@
+from Cython.Build.Cythonize import (
+    create_args_parser, parse_args_raw, parse_args,
+    parallel_compiles
+)
+
+from Cython.Compiler import Options
+from Cython.Compiler.Tests.Utils import backup_Options, restore_Options, check_global_options
+
+from unittest import TestCase
+
+import sys
+try:
+    from StringIO import StringIO
+except ImportError:
+    from io import StringIO  # doesn't accept 'str' in Py2
+
+
+class TestCythonizeArgsParser(TestCase):
+
+    def setUp(self):
+        TestCase.setUp(self)
+        self.parse_args = lambda x, parser=create_args_parser() : parse_args_raw(parser, x)
+
+
+    def are_default(self, options, skip):
+        # empty containers
+        empty_containers = ['directives', 'compile_time_env', 'options', 'excludes']
+        are_none = ['language_level', 'annotate', 'build', 'build_inplace', 'force', 'quiet', 'lenient', 'keep_going', 'no_docstrings']
+        for opt_name in empty_containers:
+            if len(getattr(options, opt_name))!=0 and (opt_name not in skip):
+                self.assertEqual(opt_name,"", msg="For option "+opt_name)
+                return False
+        for opt_name in are_none:
+            if (getattr(options, opt_name) is not None) and (opt_name not in skip):
+                self.assertEqual(opt_name,"", msg="For option "+opt_name)
+                return False
+        if options.parallel!=parallel_compiles and ('parallel' not in skip):
+            return False
+        return True
+
+    # testing directives:
+    def test_directive_short(self):
+        options, args =  self.parse_args(['-X', 'cdivision=True'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['directives']))
+        self.assertEqual(options.directives['cdivision'], True)
+
+    def test_directive_long(self):
+        options, args =  self.parse_args(['--directive', 'cdivision=True'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['directives']))
+        self.assertEqual(options.directives['cdivision'], True)
+
+    def test_directive_multiple(self):
+        options, args =  self.parse_args(['-X', 'cdivision=True', '-X', 'c_string_type=bytes'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['directives']))
+        self.assertEqual(options.directives['cdivision'], True)
+        self.assertEqual(options.directives['c_string_type'], 'bytes')
+
+    def test_directive_multiple_v2(self):
+        options, args =  self.parse_args(['-X', 'cdivision=True,c_string_type=bytes'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['directives']))
+        self.assertEqual(options.directives['cdivision'], True)
+        self.assertEqual(options.directives['c_string_type'], 'bytes')
+
+    def test_directive_value_yes(self):
+        options, args =  self.parse_args(['-X', 'cdivision=YeS'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['directives']))
+        self.assertEqual(options.directives['cdivision'], True)
+
+    def test_directive_value_no(self):
+        options, args =  self.parse_args(['-X', 'cdivision=no'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['directives']))
+        self.assertEqual(options.directives['cdivision'], False)
+
+    def test_directive_value_invalid(self):
+        with self.assertRaises(ValueError) as context:
+            options, args =  self.parse_args(['-X', 'cdivision=sadfasd'])
+
+    def test_directive_key_invalid(self):
+        with self.assertRaises(ValueError) as context:
+            options, args =  self.parse_args(['-X', 'abracadabra'])
+
+    def test_directive_no_value(self):
+        with self.assertRaises(ValueError) as context:
+            options, args =  self.parse_args(['-X', 'cdivision'])
+
+    def test_directives_types(self):
+        directives = {
+                'auto_pickle': True,
+                'c_string_type': 'bytearray',
+                'c_string_type': 'bytes',
+                'c_string_type': 'str',
+                'c_string_type': 'bytearray',
+                'c_string_type': 'unicode',
+                'c_string_encoding' : 'ascii',
+                'language_level' : 2,
+                'language_level' : 3,
+                'language_level' : '3str',
+                'set_initial_path' : 'my_initial_path',
+        }
+        for key, value in directives.items():
+            cmd = '{key}={value}'.format(key=key, value=str(value))
+            options, args =  self.parse_args(['-X', cmd])
+            self.assertFalse(args)
+            self.assertTrue(self.are_default(options, ['directives']), msg = "Error for option: "+cmd)
+            self.assertEqual(options.directives[key], value, msg = "Error for option: "+cmd)
+
+    def test_directives_wrong(self):
+        directives = {
+                'auto_pickle': 42,        # for bool type
+                'auto_pickle': 'NONONO',  # for bool type
+                'c_string_type': 'bites',
+                #'c_string_encoding' : 'a',
+                #'language_level' : 4,
+        }
+        for key, value in directives.items():
+            cmd = '{key}={value}'.format(key=key, value=str(value))
+            with self.assertRaises(ValueError, msg = "Error for option: "+cmd) as context:
+                options, args =  self.parse_args(['-X', cmd])
+
+    def test_compile_time_env_short(self):
+        options, args =  self.parse_args(['-E', 'MYSIZE=10'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['compile_time_env']))
+        self.assertEqual(options.compile_time_env['MYSIZE'], 10)
+
+    def test_compile_time_env_long(self):
+        options, args =  self.parse_args(['--compile-time-env', 'MYSIZE=10'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['compile_time_env']))
+        self.assertEqual(options.compile_time_env['MYSIZE'], 10)
+
+    def test_compile_time_env_multiple(self):
+        options, args =  self.parse_args(['-E', 'MYSIZE=10', '-E', 'ARRSIZE=11'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['compile_time_env']))
+        self.assertEqual(options.compile_time_env['MYSIZE'], 10)
+        self.assertEqual(options.compile_time_env['ARRSIZE'], 11)
+
+    def test_compile_time_env_multiple_v2(self):
+        options, args =  self.parse_args(['-E', 'MYSIZE=10,ARRSIZE=11'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['compile_time_env']))
+        self.assertEqual(options.compile_time_env['MYSIZE'], 10)
+        self.assertEqual(options.compile_time_env['ARRSIZE'], 11)
+
+    #testing options
+    def test_option_short(self):
+        options, args =  self.parse_args(['-s', 'docstrings=True'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['options']))
+        self.assertEqual(options.options['docstrings'], True)
+
+    def test_option_long(self):
+        options, args =  self.parse_args(['--option', 'docstrings=True'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['options']))
+        self.assertEqual(options.options['docstrings'], True)
+
+    def test_option_multiple(self):
+        options, args =  self.parse_args(['-s', 'docstrings=True', '-s', 'buffer_max_dims=8'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['options']))
+        self.assertEqual(options.options['docstrings'], True)
+        self.assertEqual(options.options['buffer_max_dims'], True)  #  really?
+
+    def test_option_multiple_v2(self):
+        options, args =  self.parse_args(['-s', 'docstrings=True,buffer_max_dims=8'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['options']))
+        self.assertEqual(options.options['docstrings'], True)
+        self.assertEqual(options.options['buffer_max_dims'], True)  #  really?
+
+    def test_option_value_yes(self):
+        options, args =  self.parse_args(['-s', 'docstrings=YeS'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['options']))
+        self.assertEqual(options.options['docstrings'], True)
+
+    def test_option_value_4242(self):
+        options, args =  self.parse_args(['-s', 'docstrings=4242'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['options']))
+        self.assertEqual(options.options['docstrings'], True)
+
+    def test_option_value_0(self):
+        options, args =  self.parse_args(['-s', 'docstrings=0'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['options']))
+        self.assertEqual(options.options['docstrings'], False)
+
+    def test_option_value_emptystr(self):
+        options, args =  self.parse_args(['-s', 'docstrings='])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['options']))
+        self.assertEqual(options.options['docstrings'], True)
+
+    def test_option_value_a_str(self):
+        options, args =  self.parse_args(['-s', 'docstrings=BB'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['options']))
+        self.assertEqual(options.options['docstrings'], True)
+
+    def test_option_value_no(self):
+        options, args =  self.parse_args(['-s', 'docstrings=nO'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['options']))
+        self.assertEqual(options.options['docstrings'], False)
+
+    def test_option_no_value(self):
+        options, args =  self.parse_args(['-s', 'docstrings'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['options']))
+        self.assertEqual(options.options['docstrings'], True)
+
+    def test_option_any_key(self):
+        options, args =  self.parse_args(['-s', 'abracadabra'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['options']))
+        self.assertEqual(options.options['abracadabra'], True)
+
+    def test_language_level_2(self):
+        options, args =  self.parse_args(['-2'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['language_level']))
+        self.assertEqual(options.language_level, 2)
+
+    def test_language_level_3(self):
+        options, args =  self.parse_args(['-3'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['language_level']))
+        self.assertEqual(options.language_level, 3)
+
+    def test_language_level_3str(self):
+        options, args =  self.parse_args(['--3str'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['language_level']))
+        self.assertEqual(options.language_level, '3str')
+
+    def test_annotate_short(self):
+        options, args =  self.parse_args(['-a'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['annotate']))
+        self.assertEqual(options.annotate, 'default')
+
+    def test_annotate_long(self):
+        options, args =  self.parse_args(['--annotate'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['annotate']))
+        self.assertEqual(options.annotate, 'default')
+
+    def test_annotate_fullc(self):
+        options, args =  self.parse_args(['--annotate-fullc'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['annotate']))
+        self.assertEqual(options.annotate, 'fullc')
+
+    def test_annotate_and_positional(self):
+        options, args =  self.parse_args(['-a', 'foo.pyx'])
+        self.assertEqual(args, ['foo.pyx'])
+        self.assertTrue(self.are_default(options, ['annotate']))
+        self.assertEqual(options.annotate, 'default')
+
+    def test_annotate_and_optional(self):
+        options, args =  self.parse_args(['-a', '--3str'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['annotate', 'language_level']))
+        self.assertEqual(options.annotate, 'default')
+        self.assertEqual(options.language_level, '3str')
+
+    def test_exclude_short(self):
+        options, args =  self.parse_args(['-x', '*.pyx'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['excludes']))
+        self.assertTrue('*.pyx' in options.excludes)
+
+    def test_exclude_long(self):
+        options, args =  self.parse_args(['--exclude', '*.pyx'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['excludes']))
+        self.assertTrue('*.pyx' in options.excludes)
+
+    def test_exclude_multiple(self):
+        options, args =  self.parse_args(['--exclude', '*.pyx', '--exclude', '*.py', ])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['excludes']))
+        self.assertEqual(options.excludes, ['*.pyx', '*.py'])
+
+    def test_build_short(self):
+        options, args =  self.parse_args(['-b'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['build']))
+        self.assertEqual(options.build, True)
+
+    def test_build_long(self):
+        options, args =  self.parse_args(['--build'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['build']))
+        self.assertEqual(options.build, True)
+
+    def test_inplace_short(self):
+        options, args =  self.parse_args(['-i'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['build_inplace']))
+        self.assertEqual(options.build_inplace, True)
+
+    def test_inplace_long(self):
+        options, args =  self.parse_args(['--inplace'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['build_inplace']))
+        self.assertEqual(options.build_inplace, True)
+
+    def test_parallel_short(self):
+        options, args =  self.parse_args(['-j', '42'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['parallel']))
+        self.assertEqual(options.parallel, 42)
+
+    def test_parallel_long(self):
+        options, args =  self.parse_args(['--parallel', '42'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['parallel']))
+        self.assertEqual(options.parallel, 42)
+
+    def test_force_short(self):
+        options, args =  self.parse_args(['-f'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['force']))
+        self.assertEqual(options.force, True)
+
+    def test_force_long(self):
+        options, args =  self.parse_args(['--force'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['force']))
+        self.assertEqual(options.force, True)
+
+    def test_quite_short(self):
+        options, args =  self.parse_args(['-q'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['quiet']))
+        self.assertEqual(options.quiet, True)
+
+    def test_quite_long(self):
+        options, args =  self.parse_args(['--quiet'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['quiet']))
+        self.assertEqual(options.quiet, True)
+
+    def test_lenient_long(self):
+        options, args =  self.parse_args(['--lenient'])
+        self.assertTrue(self.are_default(options, ['lenient']))
+        self.assertFalse(args)
+        self.assertEqual(options.lenient, True)
+
+    def test_keep_going_short(self):
+        options, args =  self.parse_args(['-k'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['keep_going']))
+        self.assertEqual(options.keep_going, True)
+
+    def test_keep_going_long(self):
+        options, args =  self.parse_args(['--keep-going'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['keep_going']))
+        self.assertEqual(options.keep_going, True)
+
+    def test_no_docstrings_long(self):
+        options, args =  self.parse_args(['--no-docstrings'])
+        self.assertFalse(args)
+        self.assertTrue(self.are_default(options, ['no_docstrings']))
+        self.assertEqual(options.no_docstrings, True)
+
+    def test_file_name(self):
+        options, args =  self.parse_args(['file1.pyx', 'file2.pyx'])
+        self.assertEqual(len(args), 2)
+        self.assertEqual(args[0], 'file1.pyx')
+        self.assertEqual(args[1], 'file2.pyx')
+        self.assertTrue(self.are_default(options, []))
+
+    def test_option_first(self):
+        options, args =  self.parse_args(['-i', 'file.pyx'])
+        self.assertEqual(args, ['file.pyx'])
+        self.assertEqual(options.build_inplace, True)
+        self.assertTrue(self.are_default(options, ['build_inplace']))
+
+    def test_file_inbetween(self):
+        options, args =  self.parse_args(['-i', 'file.pyx', '-a'])
+        self.assertEqual(args, ['file.pyx'])
+        self.assertEqual(options.build_inplace, True)
+        self.assertEqual(options.annotate, 'default')
+        self.assertTrue(self.are_default(options, ['build_inplace', 'annotate']))
+
+    def test_option_trailing(self):
+        options, args =  self.parse_args(['file.pyx', '-i'])
+        self.assertEqual(args, ['file.pyx'])
+        self.assertEqual(options.build_inplace, True)
+        self.assertTrue(self.are_default(options, ['build_inplace']))
+
+    def test_interspersed_positional(self):
+        options, sources = self.parse_args([
+             'file1.pyx', '-a',
+             'file2.pyx'
+        ])
+        self.assertEqual(sources, ['file1.pyx', 'file2.pyx'])
+        self.assertEqual(options.annotate, 'default')
+        self.assertTrue(self.are_default(options, ['annotate']))
+
+    def test_interspersed_positional2(self):
+        options, sources = self.parse_args([
+             'file1.pyx', '-a',
+             'file2.pyx', '-a', 'file3.pyx'
+        ])
+        self.assertEqual(sources, ['file1.pyx', 'file2.pyx', 'file3.pyx'])
+        self.assertEqual(options.annotate, 'default')
+        self.assertTrue(self.are_default(options, ['annotate']))
+
+    def test_interspersed_positional3(self):
+        options, sources = self.parse_args([
+             '-f', 'f1', 'f2', '-a',
+             'f3', 'f4', '-a', 'f5'
+        ])
+        self.assertEqual(sources, ['f1', 'f2', 'f3', 'f4', 'f5'])
+        self.assertEqual(options.annotate, 'default')
+        self.assertEqual(options.force, True)
+        self.assertTrue(self.are_default(options, ['annotate', 'force']))
+
+    def test_wrong_option(self):
+        old_stderr = sys.stderr
+        stderr = sys.stderr = StringIO()
+        try:
+            self.assertRaises(SystemExit, self.parse_args,
+                              ['--unknown-option']
+                              )
+        finally:
+            sys.stderr = old_stderr
+        self.assertTrue(stderr.getvalue())
+
+
+class TestParseArgs(TestCase):
+    def setUp(self):
+        self._options_backup = backup_Options()
+
+    def tearDown(self):
+        restore_Options(self._options_backup)
+
+    def check_default_global_options(self, white_list=[]):
+        self.assertEqual(check_global_options(self._options_backup, white_list), "")
+
+    def test_build_set_for_inplace(self):
+        options, args = parse_args(['foo.pyx', '-i'])
+        self.assertEqual(options.build, True)
+        self.check_default_global_options()
+
+    def test_lenient(self):
+        options, sources = parse_args(['foo.pyx', '--lenient'])
+        self.assertEqual(sources, ['foo.pyx'])
+        self.assertEqual(Options.error_on_unknown_names, False)
+        self.assertEqual(Options.error_on_uninitialized, False)
+        self.check_default_global_options(['error_on_unknown_names', 'error_on_uninitialized'])
+
+    def test_annotate(self):
+        options, sources = parse_args(['foo.pyx', '--annotate'])
+        self.assertEqual(sources, ['foo.pyx'])
+        self.assertEqual(Options.annotate, 'default')
+        self.check_default_global_options(['annotate'])
+
+    def test_annotate_fullc(self):
+        options, sources = parse_args(['foo.pyx', '--annotate-fullc'])
+        self.assertEqual(sources, ['foo.pyx'])
+        self.assertEqual(Options.annotate, 'fullc')
+        self.check_default_global_options(['annotate'])
+
+    def test_no_docstrings(self):
+        options, sources = parse_args(['foo.pyx', '--no-docstrings'])
+        self.assertEqual(sources, ['foo.pyx'])
+        self.assertEqual(Options.docstrings, False)
+        self.check_default_global_options(['docstrings'])

Lib/site-packages/Cython/Build/Tests/TestDependencies.py

@@ -0,0 +1,142 @@
+import contextlib
+import os.path
+import sys
+import tempfile
+import unittest
+from io import open
+from os.path import join as pjoin
+
+from ..Dependencies import extended_iglob
+
+
+@contextlib.contextmanager
+def writable_file(dir_path, filename):
+    with open(pjoin(dir_path, filename), "w", encoding="utf8") as f:
+        yield f
+
+
+class TestGlobbing(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        cls._orig_dir = os.getcwd()
+        if sys.version_info[0] < 3:
+            temp_path = cls._tmpdir = tempfile.mkdtemp()
+        else:
+            cls._tmpdir = tempfile.TemporaryDirectory()
+            temp_path = cls._tmpdir.name
+        os.chdir(temp_path)
+
+        for dir1 in "abcd":
+            for dir1x in [dir1, dir1 + 'x']:
+                for dir2 in "xyz":
+                    dir_path = pjoin(dir1x, dir2)
+                    os.makedirs(dir_path)
+                    with writable_file(dir_path, "file2_pyx.pyx") as f:
+                        f.write(u'""" PYX """')
+                    with writable_file(dir_path, "file2_py.py") as f:
+                        f.write(u'""" PY """')
+
+                with writable_file(dir1x, "file1_pyx.pyx") as f:
+                    f.write(u'""" PYX """')
+                with writable_file(dir1x, "file1_py.py") as f:
+                    f.write(u'""" PY """')
+
+    @classmethod
+    def tearDownClass(cls):
+        os.chdir(cls._orig_dir)
+        if sys.version_info[0] < 3:
+            import shutil
+            shutil.rmtree(cls._tmpdir)
+        else:
+            cls._tmpdir.cleanup()
+
+    def files_equal(self, pattern, expected_files):
+        expected_files = sorted(expected_files)
+        # It's the users's choice whether '/' will appear on Windows.
+        matched_files = sorted(path.replace('/', os.sep) for path in extended_iglob(pattern))
+        self.assertListEqual(matched_files, expected_files)  # /
+
+        # Special case for Windows: also support '\' in patterns.
+        if os.sep == '\\' and '/' in pattern:
+            matched_files = sorted(extended_iglob(pattern.replace('/', '\\')))
+            self.assertListEqual(matched_files, expected_files)  # \
+
+    def test_extended_iglob_simple(self):
+        ax_files = [pjoin("a", "x", "file2_pyx.pyx"), pjoin("a", "x", "file2_py.py")]
+        self.files_equal("a/x/*", ax_files)
+        self.files_equal("a/x/*.c12", [])
+        self.files_equal("a/x/*.{py,pyx,c12}", ax_files)
+        self.files_equal("a/x/*.{py,pyx}", ax_files)
+        self.files_equal("a/x/*.{pyx}", ax_files[:1])
+        self.files_equal("a/x/*.pyx", ax_files[:1])
+        self.files_equal("a/x/*.{py}", ax_files[1:])
+        self.files_equal("a/x/*.py", ax_files[1:])
+
+    def test_extended_iglob_simple_star(self):
+        for basedir in "ad":
+            files = [
+                pjoin(basedir, dirname, filename)
+                for dirname in "xyz"
+                for filename in ["file2_pyx.pyx", "file2_py.py"]
+            ]
+            self.files_equal(basedir + "/*/*", files)
+            self.files_equal(basedir + "/*/*.c12", [])
+            self.files_equal(basedir + "/*/*.{py,pyx,c12}", files)
+            self.files_equal(basedir + "/*/*.{py,pyx}", files)
+            self.files_equal(basedir + "/*/*.{pyx}", files[::2])
+            self.files_equal(basedir + "/*/*.pyx", files[::2])
+            self.files_equal(basedir + "/*/*.{py}", files[1::2])
+            self.files_equal(basedir + "/*/*.py", files[1::2])
+
+            for subdir in "xy*":
+                files = [
+                    pjoin(basedir, dirname, filename)
+                    for dirname in "xyz"
+                    if subdir in ('*', dirname)
+                    for filename in ["file2_pyx.pyx", "file2_py.py"]
+                ]
+                path = basedir + '/' + subdir + '/'
+                self.files_equal(path + "*", files)
+                self.files_equal(path + "*.{py,pyx}", files)
+                self.files_equal(path + "*.{pyx}", files[::2])
+                self.files_equal(path + "*.pyx", files[::2])
+                self.files_equal(path + "*.{py}", files[1::2])
+                self.files_equal(path + "*.py", files[1::2])
+
+    def test_extended_iglob_double_star(self):
+        basedirs = os.listdir(".")
+        files = [
+            pjoin(basedir, dirname, filename)
+            for basedir in basedirs
+            for dirname in "xyz"
+            for filename in ["file2_pyx.pyx", "file2_py.py"]
+        ]
+        all_files = [
+            pjoin(basedir, filename)
+            for basedir in basedirs
+            for filename in ["file1_pyx.pyx", "file1_py.py"]
+        ] + files
+        self.files_equal("*/*/*", files)
+        self.files_equal("*/*/**/*", files)
+        self.files_equal("*/**/*.*", all_files)
+        self.files_equal("**/*.*", all_files)
+        self.files_equal("*/**/*.c12", [])
+        self.files_equal("**/*.c12", [])
+        self.files_equal("*/*/*.{py,pyx,c12}", files)
+        self.files_equal("*/*/**/*.{py,pyx,c12}", files)
+        self.files_equal("*/**/*/*.{py,pyx,c12}", files)
+        self.files_equal("**/*/*/*.{py,pyx,c12}", files)
+        self.files_equal("**/*.{py,pyx,c12}", all_files)
+        self.files_equal("*/*/*.{py,pyx}", files)
+        self.files_equal("**/*/*/*.{py,pyx}", files)
+        self.files_equal("*/**/*/*.{py,pyx}", files)
+        self.files_equal("**/*.{py,pyx}", all_files)
+        self.files_equal("*/*/*.{pyx}", files[::2])
+        self.files_equal("**/*.{pyx}", all_files[::2])
+        self.files_equal("*/**/*/*.pyx", files[::2])
+        self.files_equal("*/*/*.pyx", files[::2])
+        self.files_equal("**/*.pyx", all_files[::2])
+        self.files_equal("*/*/*.{py}", files[1::2])
+        self.files_equal("**/*.{py}", all_files[1::2])
+        self.files_equal("*/*/*.py", files[1::2])
+        self.files_equal("**/*.py", all_files[1::2])

Lib/site-packages/Cython/Build/Tests/TestInline.py

@@ -0,0 +1,112 @@
+import os
+import tempfile
+import unittest
+from Cython.Shadow import inline
+from Cython.Build.Inline import safe_type
+from Cython.TestUtils import CythonTest
+
+try:
+    import numpy
+    has_numpy = True
+except:
+    has_numpy = False
+
+test_kwds = dict(force=True, quiet=True)
+
+global_value = 100
+
+class TestInline(CythonTest):
+    def setUp(self):
+        CythonTest.setUp(self)
+        self._call_kwds = dict(test_kwds)
+        if os.path.isdir('TEST_TMP'):
+            lib_dir = os.path.join('TEST_TMP','inline')
+        else:
+            lib_dir = tempfile.mkdtemp(prefix='cython_inline_')
+        self._call_kwds['lib_dir'] = lib_dir
+
+    def test_simple(self):
+        self.assertEqual(inline("return 1+2", **self._call_kwds), 3)
+
+    def test_types(self):
+        self.assertEqual(inline("""
+            cimport cython
+            return cython.typeof(a), cython.typeof(b)
+        """, a=1.0, b=[], **self._call_kwds), ('double', 'list object'))
+
+    def test_locals(self):
+        a = 1
+        b = 2
+        self.assertEqual(inline("return a+b", **self._call_kwds), 3)
+
+    def test_globals(self):
+        self.assertEqual(inline("return global_value + 1", **self._call_kwds), global_value + 1)
+
+    def test_no_return(self):
+        self.assertEqual(inline("""
+            a = 1
+            cdef double b = 2
+            cdef c = []
+        """, **self._call_kwds), dict(a=1, b=2.0, c=[]))
+
+    def test_def_node(self):
+        foo = inline("def foo(x): return x * x", **self._call_kwds)['foo']
+        self.assertEqual(foo(7), 49)
+
+    def test_class_ref(self):
+        class Type(object):
+            pass
+        tp = inline("Type")['Type']
+        self.assertEqual(tp, Type)
+
+    def test_pure(self):
+        import cython as cy
+        b = inline("""
+        b = cy.declare(float, a)
+        c = cy.declare(cy.pointer(cy.float), &b)
+        return b
+        """, a=3, **self._call_kwds)
+        self.assertEqual(type(b), float)
+
+    def test_compiler_directives(self):
+        self.assertEqual(
+            inline('return sum(x)',
+                   x=[1, 2, 3],
+                   cython_compiler_directives={'boundscheck': False}),
+            6
+        )
+
+    def test_lang_version(self):
+        # GH-3419. Caching for inline code didn't always respect compiler directives.
+        inline_divcode = "def f(int a, int b): return a/b"
+        self.assertEqual(
+            inline(inline_divcode, language_level=2)['f'](5,2),
+            2
+        )
+        self.assertEqual(
+            inline(inline_divcode, language_level=3)['f'](5,2),
+            2.5
+        )
+        self.assertEqual(
+            inline(inline_divcode, language_level=2)['f'](5,2),
+            2
+        )
+
+    def test_repeated_use(self):
+        inline_mulcode = "def f(int a, int b): return a * b"
+        self.assertEqual(inline(inline_mulcode)['f'](5, 2), 10)
+        self.assertEqual(inline(inline_mulcode)['f'](5, 3), 15)
+        self.assertEqual(inline(inline_mulcode)['f'](6, 2), 12)
+        self.assertEqual(inline(inline_mulcode)['f'](5, 2), 10)
+
+        f = inline(inline_mulcode)['f']
+        self.assertEqual(f(5, 2), 10)
+        self.assertEqual(f(5, 3), 15)
+
+    @unittest.skipIf(not has_numpy, "NumPy is not available")
+    def test_numpy(self):
+        import numpy
+        a = numpy.ndarray((10, 20))
+        a[0,0] = 10
+        self.assertEqual(safe_type(a), 'numpy.ndarray[numpy.float64_t, ndim=2]')
+        self.assertEqual(inline("return a[0,0]", a=a, **self._call_kwds), 10.0)

Lib/site-packages/Cython/Build/Tests/TestIpythonMagic.py

@@ -0,0 +1,295 @@
+# -*- coding: utf-8 -*-
+# tag: ipython
+
+"""Tests for the Cython magics extension."""
+
+from __future__ import absolute_import
+
+import os
+import io
+import sys
+from contextlib import contextmanager
+from unittest import skipIf
+
+from Cython.Build import IpythonMagic
+from Cython.TestUtils import CythonTest
+from Cython.Compiler.Annotate import AnnotationCCodeWriter
+
+try:
+    import IPython.testing.globalipapp
+except ImportError:
+    # Disable tests and fake helpers for initialisation below.
+    def skip_if_not_installed(_):
+        return None
+else:
+    def skip_if_not_installed(c):
+        return c
+
+# not using IPython's decorators here because they depend on "nose"
+skip_win32 = skipIf(sys.platform == 'win32', "Skip on Windows")
+skip_py27 = skipIf(sys.version_info[:2] == (2,7), "Disabled in Py2.7")
+
+try:
+    # disable IPython history thread before it gets started to avoid having to clean it up
+    from IPython.core.history import HistoryManager
+    HistoryManager.enabled = False
+except ImportError:
+    pass
+
+
+@contextmanager
+def capture_output():
+    backup = sys.stdout, sys.stderr
+    try:
+        replacement = [
+             io.TextIOWrapper(io.BytesIO(), encoding=sys.stdout.encoding),
+             io.TextIOWrapper(io.BytesIO(), encoding=sys.stderr.encoding),
+        ]
+        sys.stdout, sys.stderr = replacement
+        output = []
+        yield output
+    finally:
+        sys.stdout, sys.stderr = backup
+        for wrapper in replacement:
+            wrapper.seek(0)  # rewind
+            output.append(wrapper.read())
+            wrapper.close()
+
+
+code = u"""\
+def f(x):
+    return 2*x
+"""
+
+cython3_code = u"""\
+def f(int x):
+    return 2 / x
+
+def call(x):
+    return f(*(x,))
+"""
+
+pgo_cython3_code = cython3_code + u"""\
+def main():
+    for _ in range(100): call(5)
+main()
+"""
+
+compile_error_code = u'''\
+cdef extern from *:
+    """
+    xxx a=1;
+    """
+    int a;
+def doit():
+    return a
+'''
+
+compile_warning_code = u'''\
+cdef extern from *:
+    """
+    #pragma message ( "CWarning" )
+    int a = 42;
+    """
+    int a;
+def doit():
+    return a
+'''
+
+
+@skip_if_not_installed
+class TestIPythonMagic(CythonTest):
+
+    @classmethod
+    def setUpClass(cls):
+        CythonTest.setUpClass()
+        cls._ip = IPython.testing.globalipapp.get_ipython()
+
+    def setUp(self):
+        CythonTest.setUp(self)
+        self._ip.extension_manager.load_extension('cython')
+
+    def test_cython_inline(self):
+        ip = self._ip
+        ip.ex('a=10; b=20')
+        result = ip.run_cell_magic('cython_inline', '', 'return a+b')
+        self.assertEqual(result, 30)
+
+    @skip_win32
+    def test_cython_pyximport(self):
+        ip = self._ip
+        module_name = '_test_cython_pyximport'
+        ip.run_cell_magic('cython_pyximport', module_name, code)
+        ip.ex('g = f(10)')
+        self.assertEqual(ip.user_ns['g'], 20.0)
+        ip.run_cell_magic('cython_pyximport', module_name, code)
+        ip.ex('h = f(-10)')
+        self.assertEqual(ip.user_ns['h'], -20.0)
+        try:
+            os.remove(module_name + '.pyx')
+        except OSError:
+            pass
+
+    def test_cython(self):
+        ip = self._ip
+        ip.run_cell_magic('cython', '', code)
+        ip.ex('g = f(10)')
+        self.assertEqual(ip.user_ns['g'], 20.0)
+
+    def test_cython_name(self):
+        # The Cython module named 'mymodule' defines the function f.
+        ip = self._ip
+        ip.run_cell_magic('cython', '--name=mymodule', code)
+        # This module can now be imported in the interactive namespace.
+        ip.ex('import mymodule; g = mymodule.f(10)')
+        self.assertEqual(ip.user_ns['g'], 20.0)
+
+    def test_cython_language_level(self):
+        # The Cython cell defines the functions f() and call().
+        ip = self._ip
+        ip.run_cell_magic('cython', '', cython3_code)
+        ip.ex('g = f(10); h = call(10)')
+        if sys.version_info[0] < 3:
+            self.assertEqual(ip.user_ns['g'], 2 // 10)
+            self.assertEqual(ip.user_ns['h'], 2 // 10)
+        else:
+            self.assertEqual(ip.user_ns['g'], 2.0 / 10.0)
+            self.assertEqual(ip.user_ns['h'], 2.0 / 10.0)
+
+    def test_cython3(self):
+        # The Cython cell defines the functions f() and call().
+        ip = self._ip
+        ip.run_cell_magic('cython', '-3', cython3_code)
+        ip.ex('g = f(10); h = call(10)')
+        self.assertEqual(ip.user_ns['g'], 2.0 / 10.0)
+        self.assertEqual(ip.user_ns['h'], 2.0 / 10.0)
+
+    def test_cython2(self):
+        # The Cython cell defines the functions f() and call().
+        ip = self._ip
+        ip.run_cell_magic('cython', '-2', cython3_code)
+        ip.ex('g = f(10); h = call(10)')
+        self.assertEqual(ip.user_ns['g'], 2 // 10)
+        self.assertEqual(ip.user_ns['h'], 2 // 10)
+
+    def test_cython_compile_error_shown(self):
+        ip = self._ip
+        with capture_output() as out:
+            ip.run_cell_magic('cython', '-3', compile_error_code)
+        captured_out, captured_err = out
+
+        # it could be that c-level output is captured by distutil-extension
+        # (and not by us) and is printed to stdout:
+        captured_all = captured_out + "\n" + captured_err
+        self.assertTrue("error" in captured_all, msg="error in " + captured_all)
+
+    def test_cython_link_error_shown(self):
+        ip = self._ip
+        with capture_output() as out:
+            ip.run_cell_magic('cython', '-3 -l=xxxxxxxx', code)
+        captured_out, captured_err = out
+
+        # it could be that c-level output is captured by distutil-extension
+        # (and not by us) and is printed to stdout:
+        captured_all = captured_out + "\n!" + captured_err
+        self.assertTrue("error" in captured_all, msg="error in " + captured_all)
+
+    def test_cython_warning_shown(self):
+        ip = self._ip
+        with capture_output() as out:
+            # force rebuild, otherwise no warning as after the first success
+            # no build step is performed
+            ip.run_cell_magic('cython', '-3 -f', compile_warning_code)
+        captured_out, captured_err = out
+
+        # check that warning was printed to stdout even if build hasn't failed
+        self.assertTrue("CWarning" in captured_out)
+
+    @skip_py27  # Not strictly broken in Py2.7 but currently fails in CI due to C compiler issues.
+    @skip_win32
+    def test_cython3_pgo(self):
+        # The Cython cell defines the functions f() and call().
+        ip = self._ip
+        ip.run_cell_magic('cython', '-3 --pgo', pgo_cython3_code)
+        ip.ex('g = f(10); h = call(10); main()')
+        self.assertEqual(ip.user_ns['g'], 2.0 / 10.0)
+        self.assertEqual(ip.user_ns['h'], 2.0 / 10.0)
+
+    @skip_win32
+    def test_extlibs(self):
+        ip = self._ip
+        code = u"""
+from libc.math cimport sin
+x = sin(0.0)
+        """
+        ip.user_ns['x'] = 1
+        ip.run_cell_magic('cython', '-l m', code)
+        self.assertEqual(ip.user_ns['x'], 0)
+
+
+    def test_cython_verbose(self):
+        ip = self._ip
+        ip.run_cell_magic('cython', '--verbose', code)
+        ip.ex('g = f(10)')
+        self.assertEqual(ip.user_ns['g'], 20.0)
+
+    def test_cython_verbose_thresholds(self):
+        @contextmanager
+        def mock_distutils():
+            class MockLog:
+                DEBUG = 1
+                INFO = 2
+                thresholds = [INFO]
+
+                def set_threshold(self, val):
+                    self.thresholds.append(val)
+                    return self.thresholds[-2]
+
+
+            new_log = MockLog()
+            old_log = IpythonMagic.distutils.log
+            try:
+                IpythonMagic.distutils.log = new_log
+                yield new_log
+            finally:
+                IpythonMagic.distutils.log = old_log
+
+        ip = self._ip
+        with mock_distutils() as verbose_log:
+            ip.run_cell_magic('cython', '--verbose', code)
+            ip.ex('g = f(10)')
+        self.assertEqual(ip.user_ns['g'], 20.0)
+        self.assertEqual([verbose_log.INFO, verbose_log.DEBUG, verbose_log.INFO],
+                          verbose_log.thresholds)
+
+        with mock_distutils() as normal_log:
+            ip.run_cell_magic('cython', '', code)
+            ip.ex('g = f(10)')
+        self.assertEqual(ip.user_ns['g'], 20.0)
+        self.assertEqual([normal_log.INFO], normal_log.thresholds)
+
+    def test_cython_no_annotate(self):
+        ip = self._ip
+        html = ip.run_cell_magic('cython', '', code)
+        self.assertTrue(html is None)
+
+    def test_cython_annotate(self):
+        ip = self._ip
+        html = ip.run_cell_magic('cython', '--annotate', code)
+        # somewhat brittle way to differentiate between annotated htmls
+        # with/without complete source code:
+        self.assertTrue(AnnotationCCodeWriter.COMPLETE_CODE_TITLE not in html.data)
+
+    def test_cython_annotate_default(self):
+        ip = self._ip
+        html = ip.run_cell_magic('cython', '-a', code)
+        # somewhat brittle way to differentiate between annotated htmls
+        # with/without complete source code:
+        self.assertTrue(AnnotationCCodeWriter.COMPLETE_CODE_TITLE not in html.data)
+
+    def test_cython_annotate_complete_c_code(self):
+        ip = self._ip
+        html = ip.run_cell_magic('cython', '--annotate-fullc', code)
+        # somewhat brittle way to differentiate between annotated htmls
+        # with/without complete source code:
+        self.assertTrue(AnnotationCCodeWriter.COMPLETE_CODE_TITLE in html.data)

Lib/site-packages/Cython/Build/Tests/TestRecythonize.py

@@ -0,0 +1,212 @@
+import shutil
+import os
+import tempfile
+import time
+
+import Cython.Build.Dependencies
+import Cython.Utils
+from Cython.TestUtils import CythonTest
+
+
+def fresh_cythonize(*args, **kwargs):
+    Cython.Utils.clear_function_caches()
+    Cython.Build.Dependencies._dep_tree = None  # discard method caches
+    Cython.Build.Dependencies.cythonize(*args, **kwargs)
+
+class TestRecythonize(CythonTest):
+
+    def setUp(self):
+        CythonTest.setUp(self)
+        self.temp_dir = (
+            tempfile.mkdtemp(
+                prefix='recythonize-test',
+                dir='TEST_TMP' if os.path.isdir('TEST_TMP') else None
+            )
+        )
+
+    def tearDown(self):
+        CythonTest.tearDown(self)
+        shutil.rmtree(self.temp_dir)
+
+    def test_recythonize_pyx_on_pxd_change(self):
+
+        src_dir = tempfile.mkdtemp(prefix='src', dir=self.temp_dir)
+
+        a_pxd = os.path.join(src_dir, 'a.pxd')
+        a_pyx = os.path.join(src_dir, 'a.pyx')
+        a_c = os.path.join(src_dir, 'a.c')
+        dep_tree = Cython.Build.Dependencies.create_dependency_tree()
+
+        with open(a_pxd, 'w') as f:
+            f.write('cdef int value\n')
+
+        with open(a_pyx, 'w') as f:
+            f.write('value = 1\n')
+
+
+        # The dependencies for "a.pyx" are "a.pxd" and "a.pyx".
+        self.assertEqual({a_pxd, a_pyx}, dep_tree.all_dependencies(a_pyx))
+
+        # Cythonize to create a.c
+        fresh_cythonize(a_pyx)
+
+        # Sleep to address coarse time-stamp precision.
+        time.sleep(1)
+
+        with open(a_c) as f:
+            a_c_contents1 = f.read()
+
+        with open(a_pxd, 'w') as f:
+            f.write('cdef double value\n')
+
+        fresh_cythonize(a_pyx)
+
+        with open(a_c) as f:
+            a_c_contents2 = f.read()
+
+        self.assertTrue("__pyx_v_1a_value = 1;" in a_c_contents1)
+        self.assertFalse("__pyx_v_1a_value = 1;" in a_c_contents2)
+        self.assertTrue("__pyx_v_1a_value = 1.0;" in a_c_contents2)
+        self.assertFalse("__pyx_v_1a_value = 1.0;" in a_c_contents1)
+
+
+    def test_recythonize_py_on_pxd_change(self):
+
+        src_dir = tempfile.mkdtemp(prefix='src', dir=self.temp_dir)
+
+        a_pxd = os.path.join(src_dir, 'a.pxd')
+        a_py = os.path.join(src_dir, 'a.py')
+        a_c = os.path.join(src_dir, 'a.c')
+        dep_tree = Cython.Build.Dependencies.create_dependency_tree()
+
+        with open(a_pxd, 'w') as f:
+            f.write('cdef int value\n')
+
+        with open(a_py, 'w') as f:
+            f.write('value = 1\n')
+
+
+        # The dependencies for "a.py" are "a.pxd" and "a.py".
+        self.assertEqual({a_pxd, a_py}, dep_tree.all_dependencies(a_py))
+
+        # Cythonize to create a.c
+        fresh_cythonize(a_py)
+
+        # Sleep to address coarse time-stamp precision.
+        time.sleep(1)
+
+        with open(a_c) as f:
+            a_c_contents1 = f.read()
+
+        with open(a_pxd, 'w') as f:
+            f.write('cdef double value\n')
+
+        fresh_cythonize(a_py)
+
+        with open(a_c) as f:
+            a_c_contents2 = f.read()
+
+
+        self.assertTrue("__pyx_v_1a_value = 1;" in a_c_contents1)
+        self.assertFalse("__pyx_v_1a_value = 1;" in a_c_contents2)
+        self.assertTrue("__pyx_v_1a_value = 1.0;" in a_c_contents2)
+        self.assertFalse("__pyx_v_1a_value = 1.0;" in a_c_contents1)
+
+    def test_recythonize_pyx_on_dep_pxd_change(self):
+        src_dir = tempfile.mkdtemp(prefix='src', dir=self.temp_dir)
+
+        a_pxd = os.path.join(src_dir, 'a.pxd')
+        a_pyx = os.path.join(src_dir, 'a.pyx')
+        b_pyx = os.path.join(src_dir, 'b.pyx')
+        b_c = os.path.join(src_dir, 'b.c')
+        dep_tree = Cython.Build.Dependencies.create_dependency_tree()
+
+        with open(a_pxd, 'w') as f:
+            f.write('cdef int value\n')
+
+        with open(a_pyx, 'w') as f:
+            f.write('value = 1\n')
+
+        with open(b_pyx, 'w') as f:
+            f.write('cimport a\n' + 'a.value = 2\n')
+
+
+        # The dependencies for "b.pyx" are "a.pxd" and "b.pyx".
+        self.assertEqual({a_pxd, b_pyx}, dep_tree.all_dependencies(b_pyx))
+
+
+        # Cythonize to create b.c
+        fresh_cythonize([a_pyx, b_pyx])
+
+        # Sleep to address coarse time-stamp precision.
+        time.sleep(1)
+
+        with open(b_c) as f:
+            b_c_contents1 = f.read()
+
+        with open(a_pxd, 'w') as f:
+            f.write('cdef double value\n')
+
+        fresh_cythonize([a_pyx, b_pyx])
+
+        with open(b_c) as f:
+            b_c_contents2 = f.read()
+
+
+
+        self.assertTrue("__pyx_v_1a_value = 2;" in b_c_contents1)
+        self.assertFalse("__pyx_v_1a_value = 2;" in b_c_contents2)
+        self.assertTrue("__pyx_v_1a_value = 2.0;" in b_c_contents2)
+        self.assertFalse("__pyx_v_1a_value = 2.0;" in b_c_contents1)
+
+
+
+    def test_recythonize_py_on_dep_pxd_change(self):
+
+        src_dir = tempfile.mkdtemp(prefix='src', dir=self.temp_dir)
+
+        a_pxd = os.path.join(src_dir, 'a.pxd')
+        a_pyx = os.path.join(src_dir, 'a.pyx')
+        b_pxd = os.path.join(src_dir, 'b.pxd')
+        b_py = os.path.join(src_dir, 'b.py')
+        b_c = os.path.join(src_dir, 'b.c')
+        dep_tree = Cython.Build.Dependencies.create_dependency_tree()
+
+        with open(a_pxd, 'w') as f:
+            f.write('cdef int value\n')
+
+        with open(a_pyx, 'w') as f:
+            f.write('value = 1\n')
+
+        with open(b_pxd, 'w') as f:
+            f.write('cimport a\n')
+
+        with open(b_py, 'w') as f:
+            f.write('a.value = 2\n')
+
+
+        # The dependencies for b.py are "a.pxd", "b.pxd" and "b.py".
+        self.assertEqual({a_pxd, b_pxd, b_py}, dep_tree.all_dependencies(b_py))
+
+
+        # Cythonize to create b.c
+        fresh_cythonize([a_pyx, b_py])
+
+        # Sleep to address coarse time-stamp precision.
+        time.sleep(1)
+
+        with open(b_c) as f:
+            b_c_contents1 = f.read()
+
+        with open(a_pxd, 'w') as f:
+            f.write('cdef double value\n')
+
+        fresh_cythonize([a_pyx, b_py])
+
+        with open(b_c) as f:
+            b_c_contents2 = f.read()
+
+        self.assertTrue("__pyx_v_1a_value = 2;" in b_c_contents1)
+        self.assertFalse("__pyx_v_1a_value = 2;" in b_c_contents2)
+        self.assertTrue("__pyx_v_1a_value = 2.0;" in b_c_contents2)
+        self.assertFalse("__pyx_v_1a_value = 2.0;" in b_c_contents1)

Lib/site-packages/Cython/Build/Tests/TestStripLiterals.py

@@ -0,0 +1,56 @@
+from Cython.Build.Dependencies import strip_string_literals
+
+from Cython.TestUtils import CythonTest
+
+class TestStripLiterals(CythonTest):
+
+    def t(self, before, expected):
+        actual, literals = strip_string_literals(before, prefix="_L")
+        self.assertEqual(expected, actual)
+        for key, value in literals.items():
+            actual = actual.replace(key, value)
+        self.assertEqual(before, actual)
+
+    def test_empty(self):
+        self.t("", "")
+
+    def test_single_quote(self):
+        self.t("'x'", "'_L1_'")
+
+    def test_double_quote(self):
+        self.t('"x"', '"_L1_"')
+
+    def test_nested_quotes(self):
+        self.t(""" '"' "'" """, """ '_L1_' "_L2_" """)
+
+    def test_triple_quote(self):
+        self.t(" '''a\n''' ", " '''_L1_''' ")
+
+    def test_backslash(self):
+        self.t(r"'a\'b'", "'_L1_'")
+        self.t(r"'a\\'", "'_L1_'")
+        self.t(r"'a\\\'b'", "'_L1_'")
+
+    def test_unicode(self):
+        self.t("u'abc'", "u'_L1_'")
+
+    def test_raw(self):
+        self.t(r"r'abc\\'", "r'_L1_'")
+
+    def test_raw_unicode(self):
+        self.t(r"ru'abc\\'", "ru'_L1_'")
+
+    def test_comment(self):
+        self.t("abc # foo", "abc #_L1_")
+
+    def test_comment_and_quote(self):
+        self.t("abc # 'x'", "abc #_L1_")
+        self.t("'abc#'", "'_L1_'")
+
+    def test_include(self):
+        self.t("include 'a.pxi' # something here",
+               "include '_L1_' #_L2_")
+
+    def test_extern(self):
+        self.t("cdef extern from 'a.h': # comment",
+               "cdef extern from '_L1_': #_L2_")

Lib/site-packages/Cython/Build/Tests/__init__.py

@@ -0,0 +1 @@
+# empty file

Lib/site-packages/Cython/Build/__init__.py

@@ -0,0 +1,14 @@
+from .Dependencies import cythonize
+
+import sys
+if sys.version_info < (3, 7):
+    from .Distutils import build_ext
+del sys
+
+
+def __getattr__(name):
+    if name == 'build_ext':
+        # Lazy import, fails if distutils is not available (in Python 3.12+).
+        from .Distutils import build_ext
+        return build_ext
+    raise AttributeError("module '%s' has no attribute '%s'" % (__name__, name))

Lib/site-packages/Cython/CodeWriter.py

@@ -0,0 +1,820 @@
+"""
+Serializes a Cython code tree to Cython code. This is primarily useful for
+debugging and testing purposes.
+The output is in a strict format, no whitespace or comments from the input
+is preserved (and it could not be as it is not present in the code tree).
+"""
+
+from __future__ import absolute_import, print_function
+
+from .Compiler.Visitor import TreeVisitor
+from .Compiler.ExprNodes import *
+from .Compiler.Nodes import CSimpleBaseTypeNode
+
+
+class LinesResult(object):
+    def __init__(self):
+        self.lines = []
+        self.s = u""
+
+    def put(self, s):
+        self.s += s
+
+    def newline(self):
+        self.lines.append(self.s)
+        self.s = u""
+
+    def putline(self, s):
+        self.put(s)
+        self.newline()
+
+
+class DeclarationWriter(TreeVisitor):
+    """
+    A Cython code writer that is limited to declarations nodes.
+    """
+
+    indent_string = u"    "
+
+    def __init__(self, result=None):
+        super(DeclarationWriter, self).__init__()
+        if result is None:
+            result = LinesResult()
+        self.result = result
+        self.numindents = 0
+        self.tempnames = {}
+        self.tempblockindex = 0
+
+    def write(self, tree):
+        self.visit(tree)
+        return self.result
+
+    def indent(self):
+        self.numindents += 1
+
+    def dedent(self):
+        self.numindents -= 1
+
+    def startline(self, s=u""):
+        self.result.put(self.indent_string * self.numindents + s)
+
+    def put(self, s):
+        self.result.put(s)
+
+    def putline(self, s):
+        self.result.putline(self.indent_string * self.numindents + s)
+
+    def endline(self, s=u""):
+        self.result.putline(s)
+
+    def line(self, s):
+        self.startline(s)
+        self.endline()
+
+    def comma_separated_list(self, items, output_rhs=False):
+        if len(items) > 0:
+            for item in items[:-1]:
+                self.visit(item)
+                if output_rhs and item.default is not None:
+                    self.put(u" = ")
+                    self.visit(item.default)
+                self.put(u", ")
+            self.visit(items[-1])
+            if output_rhs and items[-1].default is not None:
+                self.put(u" = ")
+                self.visit(items[-1].default)
+
+    def _visit_indented(self, node):
+        self.indent()
+        self.visit(node)
+        self.dedent()
+
+    def visit_Node(self, node):
+        raise AssertionError("Node not handled by serializer: %r" % node)
+
+    def visit_ModuleNode(self, node):
+        self.visitchildren(node)
+
+    def visit_StatListNode(self, node):
+        self.visitchildren(node)
+
+    def visit_CDefExternNode(self, node):
+        if node.include_file is None:
+            file = u'*'
+        else:
+            file = u'"%s"' % node.include_file
+        self.putline(u"cdef extern from %s:" % file)
+        self._visit_indented(node.body)
+
+    def visit_CPtrDeclaratorNode(self, node):
+        self.put('*')
+        self.visit(node.base)
+
+    def visit_CReferenceDeclaratorNode(self, node):
+        self.put('&')
+        self.visit(node.base)
+
+    def visit_CArrayDeclaratorNode(self, node):
+        self.visit(node.base)
+        self.put(u'[')
+        if node.dimension is not None:
+            self.visit(node.dimension)
+        self.put(u']')
+
+    def visit_CFuncDeclaratorNode(self, node):
+        # TODO: except, gil, etc.
+        self.visit(node.base)
+        self.put(u'(')
+        self.comma_separated_list(node.args)
+        self.endline(u')')
+
+    def visit_CNameDeclaratorNode(self, node):
+        self.put(node.name)
+
+    def visit_CSimpleBaseTypeNode(self, node):
+        # See Parsing.p_sign_and_longness
+        if node.is_basic_c_type:
+            self.put(("unsigned ", "", "signed ")[node.signed])
+            if node.longness < 0:
+                self.put("short " * -node.longness)
+            elif node.longness > 0:
+                self.put("long " * node.longness)
+        if node.name is not None:
+            self.put(node.name)
+
+    def visit_CComplexBaseTypeNode(self, node):
+        self.visit(node.base_type)
+        self.visit(node.declarator)
+
+    def visit_CNestedBaseTypeNode(self, node):
+        self.visit(node.base_type)
+        self.put(u'.')
+        self.put(node.name)
+
+    def visit_TemplatedTypeNode(self, node):
+        self.visit(node.base_type_node)
+        self.put(u'[')
+        self.comma_separated_list(node.positional_args + node.keyword_args.key_value_pairs)
+        self.put(u']')
+
+    def visit_CVarDefNode(self, node):
+        self.startline(u"cdef ")
+        self.visit(node.base_type)
+        self.put(u" ")
+        self.comma_separated_list(node.declarators, output_rhs=True)
+        self.endline()
+
+    def _visit_container_node(self, node, decl, extras, attributes):
+        # TODO: visibility
+        self.startline(decl)
+        if node.name:
+            self.put(u' ')
+            self.put(node.name)
+            if node.cname is not None:
+                self.put(u' "%s"' % node.cname)
+        if extras:
+            self.put(extras)
+        self.endline(':')
+        self.indent()
+        if not attributes:
+            self.putline('pass')
+        else:
+            for attribute in attributes:
+                self.visit(attribute)
+        self.dedent()
+
+    def visit_CStructOrUnionDefNode(self, node):
+        if node.typedef_flag:
+            decl = u'ctypedef '
+        else:
+            decl = u'cdef '
+        if node.visibility == 'public':
+            decl += u'public '
+        if node.packed:
+            decl += u'packed '
+        decl += node.kind
+        self._visit_container_node(node, decl, None, node.attributes)
+
+    def visit_CppClassNode(self, node):
+        extras = ""
+        if node.templates:
+            extras = u"[%s]" % ", ".join(node.templates)
+        if node.base_classes:
+            extras += "(%s)" % ", ".join(node.base_classes)
+        self._visit_container_node(node, u"cdef cppclass", extras, node.attributes)
+
+    def visit_CEnumDefNode(self, node):
+        self._visit_container_node(node, u"cdef enum", None, node.items)
+
+    def visit_CEnumDefItemNode(self, node):
+        self.startline(node.name)
+        if node.cname:
+            self.put(u' "%s"' % node.cname)
+        if node.value:
+            self.put(u" = ")
+            self.visit(node.value)
+        self.endline()
+
+    def visit_CClassDefNode(self, node):
+        assert not node.module_name
+        if node.decorators:
+            for decorator in node.decorators:
+                self.visit(decorator)
+        self.startline(u"cdef class ")
+        self.put(node.class_name)
+        if node.base_class_name:
+            self.put(u"(")
+            if node.base_class_module:
+                self.put(node.base_class_module)
+                self.put(u".")
+            self.put(node.base_class_name)
+            self.put(u")")
+        self.endline(u":")
+        self._visit_indented(node.body)
+
+    def visit_CTypeDefNode(self, node):
+        self.startline(u"ctypedef ")
+        self.visit(node.base_type)
+        self.put(u" ")
+        self.visit(node.declarator)
+        self.endline()
+
+    def visit_FuncDefNode(self, node):
+        # TODO: support cdef + cpdef functions
+        self.startline(u"def %s(" % node.name)
+        self.comma_separated_list(node.args)
+        self.endline(u"):")
+        self._visit_indented(node.body)
+
+    def visit_CFuncDefNode(self, node):
+        self.startline(u'cpdef ' if node.overridable else u'cdef ')
+        if node.modifiers:
+            self.put(' '.join(node.modifiers))
+            self.put(' ')
+        if node.visibility != 'private':
+            self.put(node.visibility)
+            self.put(u' ')
+        if node.api:
+            self.put(u'api ')
+
+        if node.base_type:
+            self.visit(node.base_type)
+            if node.base_type.name is not None:
+                self.put(u' ')
+
+        # visit the CFuncDeclaratorNode, but put a `:` at the end of line
+        self.visit(node.declarator.base)
+        self.put(u'(')
+        self.comma_separated_list(node.declarator.args)
+        self.endline(u'):')
+
+        self._visit_indented(node.body)
+
+    def visit_CArgDeclNode(self, node):
+        # For "CSimpleBaseTypeNode", the variable type may have been parsed as type.
+        # For other node types, the "name" is always None.
+        if not isinstance(node.base_type, CSimpleBaseTypeNode) or \
+                node.base_type.name is not None:
+            self.visit(node.base_type)
+
+            # If we printed something for "node.base_type", we may need to print an extra ' '.
+            #
+            # Special case: if "node.declarator" is a "CNameDeclaratorNode",
+            # its "name" might be an empty string, for example, for "cdef f(x)".
+            if node.declarator.declared_name():
+                self.put(u" ")
+        self.visit(node.declarator)
+        if node.default is not None:
+            self.put(u" = ")
+            self.visit(node.default)
+
+    def visit_CImportStatNode(self, node):
+        self.startline(u"cimport ")
+        self.put(node.module_name)
+        if node.as_name:
+            self.put(u" as ")
+            self.put(node.as_name)
+        self.endline()
+
+    def visit_FromCImportStatNode(self, node):
+        self.startline(u"from ")
+        self.put(node.module_name)
+        self.put(u" cimport ")
+        first = True
+        for pos, name, as_name, kind in node.imported_names:
+            assert kind is None
+            if first:
+                first = False
+            else:
+                self.put(u", ")
+            self.put(name)
+            if as_name:
+                self.put(u" as ")
+                self.put(as_name)
+        self.endline()
+
+    def visit_NameNode(self, node):
+        self.put(node.name)
+
+    def visit_DecoratorNode(self, node):
+        self.startline("@")
+        self.visit(node.decorator)
+        self.endline()
+
+    def visit_PassStatNode(self, node):
+        self.startline(u"pass")
+        self.endline()
+
+
+class StatementWriter(DeclarationWriter):
+    """
+    A Cython code writer for most language statement features.
+    """
+
+    def visit_SingleAssignmentNode(self, node):
+        self.startline()
+        self.visit(node.lhs)
+        self.put(u" = ")
+        self.visit(node.rhs)
+        self.endline()
+
+    def visit_CascadedAssignmentNode(self, node):
+        self.startline()
+        for lhs in node.lhs_list:
+            self.visit(lhs)
+            self.put(u" = ")
+        self.visit(node.rhs)
+        self.endline()
+
+    def visit_PrintStatNode(self, node):
+        self.startline(u"print ")
+        self.comma_separated_list(node.arg_tuple.args)
+        if not node.append_newline:
+            self.put(u",")
+        self.endline()
+
+    def visit_ForInStatNode(self, node):
+        self.startline(u"for ")
+        if node.target.is_sequence_constructor:
+            self.comma_separated_list(node.target.args)
+        else:
+            self.visit(node.target)
+        self.put(u" in ")
+        self.visit(node.iterator.sequence)
+        self.endline(u":")
+        self._visit_indented(node.body)
+        if node.else_clause is not None:
+            self.line(u"else:")
+            self._visit_indented(node.else_clause)
+
+    def visit_IfStatNode(self, node):
+        # The IfClauseNode is handled directly without a separate match
+        # for clariy.
+        self.startline(u"if ")
+        self.visit(node.if_clauses[0].condition)
+        self.endline(":")
+        self._visit_indented(node.if_clauses[0].body)
+        for clause in node.if_clauses[1:]:
+            self.startline("elif ")
+            self.visit(clause.condition)
+            self.endline(":")
+            self._visit_indented(clause.body)
+        if node.else_clause is not None:
+            self.line("else:")
+            self._visit_indented(node.else_clause)
+
+    def visit_WhileStatNode(self, node):
+        self.startline(u"while ")
+        self.visit(node.condition)
+        self.endline(u":")
+        self._visit_indented(node.body)
+        if node.else_clause is not None:
+            self.line("else:")
+            self._visit_indented(node.else_clause)
+
+    def visit_ContinueStatNode(self, node):
+        self.line(u"continue")
+
+    def visit_BreakStatNode(self, node):
+        self.line(u"break")
+
+    def visit_SequenceNode(self, node):
+        self.comma_separated_list(node.args)  # Might need to discover whether we need () around tuples...hmm...
+
+    def visit_ExprStatNode(self, node):
+        self.startline()
+        self.visit(node.expr)
+        self.endline()
+
+    def visit_InPlaceAssignmentNode(self, node):
+        self.startline()
+        self.visit(node.lhs)
+        self.put(u" %s= " % node.operator)
+        self.visit(node.rhs)
+        self.endline()
+
+    def visit_WithStatNode(self, node):
+        self.startline()
+        self.put(u"with ")
+        self.visit(node.manager)
+        if node.target is not None:
+            self.put(u" as ")
+            self.visit(node.target)
+        self.endline(u":")
+        self._visit_indented(node.body)
+
+    def visit_TryFinallyStatNode(self, node):
+        self.line(u"try:")
+        self._visit_indented(node.body)
+        self.line(u"finally:")
+        self._visit_indented(node.finally_clause)
+
+    def visit_TryExceptStatNode(self, node):
+        self.line(u"try:")
+        self._visit_indented(node.body)
+        for x in node.except_clauses:
+            self.visit(x)
+        if node.else_clause is not None:
+            self.visit(node.else_clause)
+
+    def visit_ExceptClauseNode(self, node):
+        self.startline(u"except")
+        if node.pattern is not None:
+            self.put(u" ")
+            self.visit(node.pattern)
+        if node.target is not None:
+            self.put(u", ")
+            self.visit(node.target)
+        self.endline(":")
+        self._visit_indented(node.body)
+
+    def visit_ReturnStatNode(self, node):
+        self.startline("return")
+        if node.value is not None:
+            self.put(u" ")
+            self.visit(node.value)
+        self.endline()
+
+    def visit_ReraiseStatNode(self, node):
+        self.line("raise")
+
+    def visit_ImportNode(self, node):
+        self.put(u"(import %s)" % node.module_name.value)
+
+    def visit_TempsBlockNode(self, node):
+        """
+        Temporaries are output like $1_1', where the first number is
+        an index of the TempsBlockNode and the second number is an index
+        of the temporary which that block allocates.
+        """
+        idx = 0
+        for handle in node.temps:
+            self.tempnames[handle] = "$%d_%d" % (self.tempblockindex, idx)
+            idx += 1
+        self.tempblockindex += 1
+        self.visit(node.body)
+
+    def visit_TempRefNode(self, node):
+        self.put(self.tempnames[node.handle])
+
+
+class ExpressionWriter(TreeVisitor):
+    """
+    A Cython code writer that is intentionally limited to expressions.
+    """
+
+    def __init__(self, result=None):
+        super(ExpressionWriter, self).__init__()
+        if result is None:
+            result = u""
+        self.result = result
+        self.precedence = [0]
+
+    def write(self, tree):
+        self.visit(tree)
+        return self.result
+
+    def put(self, s):
+        self.result += s
+
+    def remove(self, s):
+        if self.result.endswith(s):
+            self.result = self.result[:-len(s)]
+
+    def comma_separated_list(self, items):
+        if len(items) > 0:
+            for item in items[:-1]:
+                self.visit(item)
+                self.put(u", ")
+            self.visit(items[-1])
+
+    def visit_Node(self, node):
+        raise AssertionError("Node not handled by serializer: %r" % node)
+
+    def visit_IntNode(self, node):
+        self.put(node.value)
+
+    def visit_FloatNode(self, node):
+        self.put(node.value)
+
+    def visit_NoneNode(self, node):
+        self.put(u"None")
+
+    def visit_NameNode(self, node):
+        self.put(node.name)
+
+    def visit_EllipsisNode(self, node):
+        self.put(u"...")
+
+    def visit_BoolNode(self, node):
+        self.put(str(node.value))
+
+    def visit_ConstNode(self, node):
+        self.put(str(node.value))
+
+    def visit_ImagNode(self, node):
+        self.put(node.value)
+        self.put(u"j")
+
+    def emit_string(self, node, prefix=u""):
+        repr_val = repr(node.value)
+        if repr_val[0] in 'ub':
+            repr_val = repr_val[1:]
+        self.put(u"%s%s" % (prefix, repr_val))
+
+    def visit_BytesNode(self, node):
+        self.emit_string(node, u"b")
+
+    def visit_StringNode(self, node):
+        self.emit_string(node)
+
+    def visit_UnicodeNode(self, node):
+        self.emit_string(node, u"u")
+
+    def emit_sequence(self, node, parens=(u"", u"")):
+        open_paren, close_paren = parens
+        items = node.subexpr_nodes()
+        self.put(open_paren)
+        self.comma_separated_list(items)
+        self.put(close_paren)
+
+    def visit_ListNode(self, node):
+        self.emit_sequence(node, u"[]")
+
+    def visit_TupleNode(self, node):
+        self.emit_sequence(node, u"()")
+
+    def visit_SetNode(self, node):
+        if len(node.subexpr_nodes()) > 0:
+            self.emit_sequence(node, u"{}")
+        else:
+            self.put(u"set()")
+
+    def visit_DictNode(self, node):
+        self.emit_sequence(node, u"{}")
+
+    def visit_DictItemNode(self, node):
+        self.visit(node.key)
+        self.put(u": ")
+        self.visit(node.value)
+
+    unop_precedence = {
+        'not': 3, '!': 3,
+        '+': 11, '-': 11, '~': 11,
+    }
+    binop_precedence = {
+        'or': 1,
+        'and': 2,
+        # unary: 'not': 3, '!': 3,
+        'in': 4, 'not_in': 4, 'is': 4, 'is_not': 4, '<': 4, '<=': 4, '>': 4, '>=': 4, '!=': 4, '==': 4,
+        '|': 5,
+        '^': 6,
+        '&': 7,
+        '<<': 8, '>>': 8,
+        '+': 9, '-': 9,
+        '*': 10, '@': 10, '/': 10, '//': 10, '%': 10,
+        # unary: '+': 11, '-': 11, '~': 11
+        '**': 12,
+    }
+
+    def operator_enter(self, new_prec):
+        old_prec = self.precedence[-1]
+        if old_prec > new_prec:
+            self.put(u"(")
+        self.precedence.append(new_prec)
+
+    def operator_exit(self):
+        old_prec, new_prec = self.precedence[-2:]
+        if old_prec > new_prec:
+            self.put(u")")
+        self.precedence.pop()
+
+    def visit_NotNode(self, node):
+        op = 'not'
+        prec = self.unop_precedence[op]
+        self.operator_enter(prec)
+        self.put(u"not ")
+        self.visit(node.operand)
+        self.operator_exit()
+
+    def visit_UnopNode(self, node):
+        op = node.operator
+        prec = self.unop_precedence[op]
+        self.operator_enter(prec)
+        self.put(u"%s" % node.operator)
+        self.visit(node.operand)
+        self.operator_exit()
+
+    def visit_BinopNode(self, node):
+        op = node.operator
+        prec = self.binop_precedence.get(op, 0)
+        self.operator_enter(prec)
+        self.visit(node.operand1)
+        self.put(u" %s " % op.replace('_', ' '))
+        self.visit(node.operand2)
+        self.operator_exit()
+
+    def visit_BoolBinopNode(self, node):
+        self.visit_BinopNode(node)
+
+    def visit_PrimaryCmpNode(self, node):
+        self.visit_BinopNode(node)
+
+    def visit_IndexNode(self, node):
+        self.visit(node.base)
+        self.put(u"[")
+        if isinstance(node.index, TupleNode):
+            if node.index.subexpr_nodes():
+                self.emit_sequence(node.index)
+            else:
+                self.put(u"()")
+        else:
+            self.visit(node.index)
+        self.put(u"]")
+
+    def visit_SliceIndexNode(self, node):
+        self.visit(node.base)
+        self.put(u"[")
+        if node.start:
+            self.visit(node.start)
+        self.put(u":")
+        if node.stop:
+            self.visit(node.stop)
+        if node.slice:
+            self.put(u":")
+            self.visit(node.slice)
+        self.put(u"]")
+
+    def visit_SliceNode(self, node):
+        if not node.start.is_none:
+            self.visit(node.start)
+        self.put(u":")
+        if not node.stop.is_none:
+            self.visit(node.stop)
+        if not node.step.is_none:
+            self.put(u":")
+            self.visit(node.step)
+
+    def visit_CondExprNode(self, node):
+        self.visit(node.true_val)
+        self.put(u" if ")
+        self.visit(node.test)
+        self.put(u" else ")
+        self.visit(node.false_val)
+
+    def visit_AttributeNode(self, node):
+        self.visit(node.obj)
+        self.put(u".%s" % node.attribute)
+
+    def visit_SimpleCallNode(self, node):
+        self.visit(node.function)
+        self.put(u"(")
+        self.comma_separated_list(node.args)
+        self.put(")")
+
+    def emit_pos_args(self, node):
+        if node is None:
+            return
+        if isinstance(node, AddNode):
+            self.emit_pos_args(node.operand1)
+            self.emit_pos_args(node.operand2)
+        elif isinstance(node, TupleNode):
+            for expr in node.subexpr_nodes():
+                self.visit(expr)
+                self.put(u", ")
+        elif isinstance(node, AsTupleNode):
+            self.put("*")
+            self.visit(node.arg)
+            self.put(u", ")
+        else:
+            self.visit(node)
+            self.put(u", ")
+
+    def emit_kwd_args(self, node):
+        if node is None:
+            return
+        if isinstance(node, MergedDictNode):
+            for expr in node.subexpr_nodes():
+                self.emit_kwd_args(expr)
+        elif isinstance(node, DictNode):
+            for expr in node.subexpr_nodes():
+                self.put(u"%s=" % expr.key.value)
+                self.visit(expr.value)
+                self.put(u", ")
+        else:
+            self.put(u"**")
+            self.visit(node)
+            self.put(u", ")
+
+    def visit_GeneralCallNode(self, node):
+        self.visit(node.function)
+        self.put(u"(")
+        self.emit_pos_args(node.positional_args)
+        self.emit_kwd_args(node.keyword_args)
+        self.remove(u", ")
+        self.put(")")
+
+    def emit_comprehension(self, body, target,
+                           sequence, condition,
+                           parens=(u"", u"")):
+        open_paren, close_paren = parens
+        self.put(open_paren)
+        self.visit(body)
+        self.put(u" for ")
+        self.visit(target)
+        self.put(u" in ")
+        self.visit(sequence)
+        if condition:
+            self.put(u" if ")
+            self.visit(condition)
+        self.put(close_paren)
+
+    def visit_ComprehensionAppendNode(self, node):
+        self.visit(node.expr)
+
+    def visit_DictComprehensionAppendNode(self, node):
+        self.visit(node.key_expr)
+        self.put(u": ")
+        self.visit(node.value_expr)
+
+    def visit_ComprehensionNode(self, node):
+        tpmap = {'list': u"[]", 'dict': u"{}", 'set': u"{}"}
+        parens = tpmap[node.type.py_type_name()]
+        body = node.loop.body
+        target = node.loop.target
+        sequence = node.loop.iterator.sequence
+        condition = None
+        if hasattr(body, 'if_clauses'):
+            # type(body) is Nodes.IfStatNode
+            condition = body.if_clauses[0].condition
+            body = body.if_clauses[0].body
+        self.emit_comprehension(body, target, sequence, condition, parens)
+
+    def visit_GeneratorExpressionNode(self, node):
+        body = node.loop.body
+        target = node.loop.target
+        sequence = node.loop.iterator.sequence
+        condition = None
+        if hasattr(body, 'if_clauses'):
+            # type(body) is Nodes.IfStatNode
+            condition = body.if_clauses[0].condition
+            body = body.if_clauses[0].body.expr.arg
+        elif hasattr(body, 'expr'):
+            # type(body) is Nodes.ExprStatNode
+            body = body.expr.arg
+        self.emit_comprehension(body, target, sequence, condition, u"()")
+
+
+class PxdWriter(DeclarationWriter, ExpressionWriter):
+    """
+    A Cython code writer for everything supported in pxd files.
+    (currently unused)
+    """
+
+    def __call__(self, node):
+        print(u'\n'.join(self.write(node).lines))
+        return node
+
+    def visit_CFuncDefNode(self, node):
+        if node.overridable:
+            self.startline(u'cpdef ')
+        else:
+            self.startline(u'cdef ')
+        if node.modifiers:
+            self.put(' '.join(node.modifiers))
+            self.put(' ')
+        if node.visibility != 'private':
+            self.put(node.visibility)
+            self.put(u' ')
+        if node.api:
+            self.put(u'api ')
+        self.visit(node.declarator)
+
+    def visit_StatNode(self, node):
+        pass
+
+
+class CodeWriter(StatementWriter, ExpressionWriter):
+    """
+    A complete Cython code writer.
+    """

Lib/site-packages/Cython/Compiler/AnalysedTreeTransforms.py

@@ -0,0 +1,99 @@
+from __future__ import absolute_import
+
+from .Visitor import ScopeTrackingTransform
+from .Nodes import StatListNode, SingleAssignmentNode, CFuncDefNode, DefNode
+from .ExprNodes import DictNode, DictItemNode, NameNode, UnicodeNode
+from .PyrexTypes import py_object_type
+from .StringEncoding import EncodedString
+from . import Symtab
+
+class AutoTestDictTransform(ScopeTrackingTransform):
+    # Handles autotestdict directive
+
+    excludelist = ['__cinit__', '__dealloc__', '__richcmp__',
+                   '__nonzero__', '__bool__',
+                   '__len__', '__contains__']
+
+    def visit_ModuleNode(self, node):
+        if node.is_pxd:
+            return node
+        self.scope_type = 'module'
+        self.scope_node = node
+
+        if not self.current_directives['autotestdict']:
+            return node
+        self.all_docstrings = self.current_directives['autotestdict.all']
+        self.cdef_docstrings = self.all_docstrings or self.current_directives['autotestdict.cdef']
+
+        assert isinstance(node.body, StatListNode)
+
+        # First see if __test__ is already created
+        if u'__test__' in node.scope.entries:
+            # Do nothing
+            return node
+
+        pos = node.pos
+
+        self.tests = []
+        self.testspos = node.pos
+
+        test_dict_entry = node.scope.declare_var(EncodedString(u'__test__'),
+                                                 py_object_type,
+                                                 pos,
+                                                 visibility='public')
+        create_test_dict_assignment = SingleAssignmentNode(pos,
+            lhs=NameNode(pos, name=EncodedString(u'__test__'),
+                         entry=test_dict_entry),
+            rhs=DictNode(pos, key_value_pairs=self.tests))
+        self.visitchildren(node)
+        node.body.stats.append(create_test_dict_assignment)
+        return node
+
+    def add_test(self, testpos, path, doctest):
+        pos = self.testspos
+        keystr = u'%s (line %d)' % (path, testpos[1])
+        key = UnicodeNode(pos, value=EncodedString(keystr))
+        value = UnicodeNode(pos, value=doctest)
+        self.tests.append(DictItemNode(pos, key=key, value=value))
+
+    def visit_ExprNode(self, node):
+        # expressions cannot contain functions and lambda expressions
+        # do not have a docstring
+        return node
+
+    def visit_FuncDefNode(self, node):
+        if not node.doc or (isinstance(node, DefNode) and node.fused_py_func):
+            return node
+        if not self.cdef_docstrings:
+            if isinstance(node, CFuncDefNode) and not node.py_func:
+                return node
+        if not self.all_docstrings and '>>>' not in node.doc:
+            return node
+
+        pos = self.testspos
+        if self.scope_type == 'module':
+            path = node.entry.name
+        elif self.scope_type in ('pyclass', 'cclass'):
+            if isinstance(node, CFuncDefNode):
+                if node.py_func is not None:
+                    name = node.py_func.name
+                else:
+                    name = node.entry.name
+            else:
+                name = node.name
+            if self.scope_type == 'cclass' and name in self.excludelist:
+                return node
+            if self.scope_type == 'pyclass':
+                class_name = self.scope_node.name
+            else:
+                class_name = self.scope_node.class_name
+            if isinstance(node.entry.scope, Symtab.PropertyScope):
+                property_method_name = node.entry.scope.name
+                path = "%s.%s.%s" % (class_name, node.entry.scope.name,
+                                     node.entry.name)
+            else:
+                path = "%s.%s" % (class_name, node.entry.name)
+        else:
+            assert False
+        self.add_test(node.pos, path, node.doc)
+        return node

Lib/site-packages/Cython/Compiler/Annotate.py

@@ -0,0 +1,341 @@
+# Note: Work in progress
+
+from __future__ import absolute_import
+
+import os
+import os.path
+import re
+import codecs
+import textwrap
+from datetime import datetime
+from functools import partial
+from collections import defaultdict
+from xml.sax.saxutils import escape as html_escape
+try:
+    from StringIO import StringIO
+except ImportError:
+    from io import StringIO  # does not support writing 'str' in Py2
+
+from . import Version
+from .Code import CCodeWriter
+from .. import Utils
+
+
+class AnnotationCCodeWriter(CCodeWriter):
+
+    # also used as marker for detection of complete code emission in tests
+    COMPLETE_CODE_TITLE = "Complete cythonized code"
+
+    def __init__(self, create_from=None, buffer=None, copy_formatting=True, show_entire_c_code=False, source_desc=None):
+        CCodeWriter.__init__(self, create_from, buffer, copy_formatting=copy_formatting)
+        self.show_entire_c_code = show_entire_c_code
+        if create_from is None:
+            self.annotation_buffer = StringIO()
+            self.last_annotated_pos = None
+            # annotations[filename][line] -> [(column, AnnotationItem)*]
+            self.annotations = defaultdict(partial(defaultdict, list))
+            # code[filename][line] -> str
+            self.code = defaultdict(partial(defaultdict, str))
+            # scopes[filename][line] -> set(scopes)
+            self.scopes = defaultdict(partial(defaultdict, set))
+        else:
+            # When creating an insertion point, keep references to the same database
+            self.annotation_buffer = create_from.annotation_buffer
+            self.annotations = create_from.annotations
+            self.code = create_from.code
+            self.scopes = create_from.scopes
+            self.last_annotated_pos = create_from.last_annotated_pos
+
+    def create_new(self, create_from, buffer, copy_formatting):
+        return AnnotationCCodeWriter(create_from, buffer, copy_formatting)
+
+    def _write_to_buffer(self, s):
+        self.buffer.write(s)
+        self.annotation_buffer.write(s)
+
+    def mark_pos(self, pos, trace=True):
+        if pos is not None:
+            CCodeWriter.mark_pos(self, pos, trace)
+            if self.funcstate and self.funcstate.scope:
+                # lambdas and genexprs can result in multiple scopes per line => keep them in a set
+                self.scopes[pos[0].filename][pos[1]].add(self.funcstate.scope)
+        if self.last_annotated_pos:
+            source_desc, line, _ = self.last_annotated_pos
+            pos_code = self.code[source_desc.filename]
+            pos_code[line] += self.annotation_buffer.getvalue()
+        self.annotation_buffer = StringIO()
+        self.last_annotated_pos = pos
+
+    def annotate(self, pos, item):
+        self.annotations[pos[0].filename][pos[1]].append((pos[2], item))
+
+    def _css(self):
+        """css template will later allow to choose a colormap"""
+        css = [self._css_template]
+        for i in range(255):
+            color = u"FFFF%02x" % int(255.0 // (1.0 + i/10.0))
+            css.append('.cython.score-%d {background-color: #%s;}' % (i, color))
+        try:
+            from pygments.formatters import HtmlFormatter
+        except ImportError:
+            pass
+        else:
+            css.append(HtmlFormatter().get_style_defs('.cython'))
+        return '\n'.join(css)
+
+    _css_template = textwrap.dedent("""
+        body.cython { font-family: courier; font-size: 12; }
+
+        .cython.tag  {  }
+        .cython.line { color: #000000; margin: 0em }
+        .cython.code { font-size: 9; color: #444444; display: none; margin: 0px 0px 0px 8px; border-left: 8px none; }
+
+        .cython.line .run { background-color: #B0FFB0; }
+        .cython.line .mis { background-color: #FFB0B0; }
+        .cython.code.run  { border-left: 8px solid #B0FFB0; }
+        .cython.code.mis  { border-left: 8px solid #FFB0B0; }
+
+        .cython.code .py_c_api  { color: red; }
+        .cython.code .py_macro_api  { color: #FF7000; }
+        .cython.code .pyx_c_api  { color: #FF3000; }
+        .cython.code .pyx_macro_api  { color: #FF7000; }
+        .cython.code .refnanny  { color: #FFA000; }
+        .cython.code .trace  { color: #FFA000; }
+        .cython.code .error_goto  { color: #FFA000; }
+
+        .cython.code .coerce  { color: #008000; border: 1px dotted #008000 }
+        .cython.code .py_attr { color: #FF0000; font-weight: bold; }
+        .cython.code .c_attr  { color: #0000FF; }
+        .cython.code .py_call { color: #FF0000; font-weight: bold; }
+        .cython.code .c_call  { color: #0000FF; }
+    """)
+
+    # on-click toggle function to show/hide C source code
+    _onclick_attr = ' onclick="{0}"'.format((
+        "(function(s){"
+        "    s.display =  s.display === 'block' ? 'none' : 'block'"
+        "})(this.nextElementSibling.style)"
+        ).replace(' ', '')  # poor dev's JS minification
+    )
+
+    def save_annotation(self, source_filename, target_filename, coverage_xml=None):
+        with Utils.open_source_file(source_filename) as f:
+            code = f.read()
+        generated_code = self.code.get(source_filename, {})
+        c_file = Utils.decode_filename(os.path.basename(target_filename))
+        html_filename = os.path.splitext(target_filename)[0] + ".html"
+
+        with codecs.open(html_filename, "w", encoding="UTF-8") as out_buffer:
+            out_buffer.write(self._save_annotation(code, generated_code, c_file, source_filename, coverage_xml))
+
+    def _save_annotation_header(self, c_file, source_filename, coverage_timestamp=None):
+        coverage_info = ''
+        if coverage_timestamp:
+            coverage_info = u' with coverage data from {timestamp}'.format(
+                timestamp=datetime.fromtimestamp(int(coverage_timestamp) // 1000))
+
+        outlist = [
+            textwrap.dedent(u'''\
+            <!DOCTYPE html>
+            <!-- Generated by Cython {watermark} -->
+            <html>
+            <head>
+                <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+                <title>Cython: {filename}</title>
+                <style type="text/css">
+                {css}
+                </style>
+            </head>
+            <body class="cython">
+            <p><span style="border-bottom: solid 1px grey;">Generated by Cython {watermark}</span>{more_info}</p>
+            <p>
+                <span style="background-color: #FFFF00">Yellow lines</span> hint at Python interaction.<br />
+                Click on a line that starts with a "<code>+</code>" to see the C code that Cython generated for it.
+            </p>
+            ''').format(css=self._css(), watermark=Version.watermark,
+                        filename=os.path.basename(source_filename) if source_filename else '',
+                        more_info=coverage_info)
+        ]
+        if c_file:
+            outlist.append(u'<p>Raw output: <a href="%s">%s</a></p>\n' % (c_file, c_file))
+        return outlist
+
+    def _save_annotation_footer(self):
+        return (u'</body></html>\n',)
+
+    def _save_annotation(self, code, generated_code, c_file=None, source_filename=None, coverage_xml=None):
+        """
+        lines : original cython source code split by lines
+        generated_code : generated c code keyed by line number in original file
+        target filename : name of the file in which to store the generated html
+        c_file : filename in which the c_code has been written
+        """
+        if coverage_xml is not None and source_filename:
+            coverage_timestamp = coverage_xml.get('timestamp', '').strip()
+            covered_lines = self._get_line_coverage(coverage_xml, source_filename)
+        else:
+            coverage_timestamp = covered_lines = None
+        annotation_items = dict(self.annotations[source_filename])
+        scopes = dict(self.scopes[source_filename])
+
+        outlist = []
+        outlist.extend(self._save_annotation_header(c_file, source_filename, coverage_timestamp))
+        outlist.extend(self._save_annotation_body(code, generated_code, annotation_items, scopes, covered_lines))
+        outlist.extend(self._save_annotation_footer())
+        return ''.join(outlist)
+
+    def _get_line_coverage(self, coverage_xml, source_filename):
+        coverage_data = None
+        for entry in coverage_xml.iterfind('.//class'):
+            if not entry.get('filename'):
+                continue
+            if (entry.get('filename') == source_filename or
+                    os.path.abspath(entry.get('filename')) == source_filename):
+                coverage_data = entry
+                break
+            elif source_filename.endswith(entry.get('filename')):
+                coverage_data = entry  # but we might still find a better match...
+        if coverage_data is None:
+            return None
+        return dict(
+            (int(line.get('number')), int(line.get('hits')))
+            for line in coverage_data.iterfind('lines/line')
+        )
+
+    def _htmlify_code(self, code, language):
+        try:
+            from pygments import highlight
+            from pygments.lexers import CythonLexer, CppLexer
+            from pygments.formatters import HtmlFormatter
+        except ImportError:
+            # no Pygments, just escape the code
+            return html_escape(code)
+
+        if language == "cython":
+            lexer = CythonLexer(stripnl=False, stripall=False)
+        elif language == "c/cpp":
+            lexer = CppLexer(stripnl=False, stripall=False)
+        else:
+            # unknown language, use fallback
+            return html_escape(code)
+        html_code = highlight(
+            code, lexer,
+            HtmlFormatter(nowrap=True))
+        return html_code
+
+    def _save_annotation_body(self, cython_code, generated_code, annotation_items, scopes, covered_lines=None):
+        outlist = [u'<div class="cython">']
+        pos_comment_marker = u'/* \N{HORIZONTAL ELLIPSIS} */\n'
+        new_calls_map = dict(
+            (name, 0) for name in
+            'refnanny trace py_macro_api py_c_api pyx_macro_api pyx_c_api error_goto'.split()
+        ).copy
+
+        self.mark_pos(None)
+
+        def annotate(match):
+            group_name = match.lastgroup
+            calls[group_name] += 1
+            return u"<span class='%s'>%s</span>" % (
+                group_name, match.group(group_name))
+
+        lines = self._htmlify_code(cython_code, "cython").splitlines()
+        lineno_width = len(str(len(lines)))
+        if not covered_lines:
+            covered_lines = None
+
+        for k, line in enumerate(lines, 1):
+            try:
+                c_code = generated_code[k]
+            except KeyError:
+                c_code = ''
+            else:
+                c_code = _replace_pos_comment(pos_comment_marker, c_code)
+                if c_code.startswith(pos_comment_marker):
+                    c_code = c_code[len(pos_comment_marker):]
+                c_code = html_escape(c_code)
+
+            calls = new_calls_map()
+            c_code = _parse_code(annotate, c_code)
+            score = (5 * calls['py_c_api'] + 2 * calls['pyx_c_api'] +
+                     calls['py_macro_api'] + calls['pyx_macro_api'])
+
+            if c_code:
+                onclick = self._onclick_attr
+                expandsymbol = '+'
+            else:
+                onclick = ''
+                expandsymbol = '&#xA0;'
+
+            covered = ''
+            if covered_lines is not None and k in covered_lines:
+                hits = covered_lines[k]
+                if hits is not None:
+                    covered = 'run' if hits else 'mis'
+
+            outlist.append(
+                u'<pre class="cython line score-{score}"{onclick}>'
+                # generate line number with expand symbol in front,
+                # and the right  number of digit
+                u'{expandsymbol}<span class="{covered}">{line:0{lineno_width}d}</span>: {code}</pre>\n'.format(
+                    score=score,
+                    expandsymbol=expandsymbol,
+                    covered=covered,
+                    lineno_width=lineno_width,
+                    line=k,
+                    code=line.rstrip(),
+                    onclick=onclick,
+                ))
+            if c_code:
+                outlist.append(u"<pre class='cython code score-{score} {covered}'>{code}</pre>".format(
+                    score=score, covered=covered, code=c_code))
+        outlist.append(u"</div>")
+
+        # now the whole c-code if needed:
+        if self.show_entire_c_code:
+            outlist.append(u'<p><div class="cython">')
+            onclick_title = u"<pre class='cython line'{onclick}>+ {title}</pre>\n"
+            outlist.append(onclick_title.format(
+                              onclick=self._onclick_attr,
+                              title=AnnotationCCodeWriter.COMPLETE_CODE_TITLE,
+                           ))
+            complete_code_as_html = self._htmlify_code(self.buffer.getvalue(), "c/cpp")
+            outlist.append(u"<pre class='cython code'>{code}</pre>".format(code=complete_code_as_html))
+            outlist.append(u"</div></p>")
+
+        return outlist
+
+
+_parse_code = re.compile((
+    br'(?P<refnanny>__Pyx_X?(?:GOT|GIVE)REF|__Pyx_RefNanny[A-Za-z]+)|'
+    br'(?P<trace>__Pyx_Trace[A-Za-z]+)|'
+    br'(?:'
+    br'(?P<pyx_macro_api>__Pyx_[A-Z][A-Z_]+)|'
+    br'(?P<pyx_c_api>(?:__Pyx_[A-Z][a-z_][A-Za-z_]*)|__pyx_convert_[A-Za-z_]*)|'
+    br'(?P<py_macro_api>Py[A-Z][a-z]+_[A-Z][A-Z_]+)|'
+    br'(?P<py_c_api>Py[A-Z][a-z]+_[A-Z][a-z][A-Za-z_]*)'
+    br')(?=\()|'       # look-ahead to exclude subsequent '(' from replacement
+    br'(?P<error_goto>(?:(?<=;) *if [^;]* +)?__PYX_ERR\([^)]+\))'
+).decode('ascii')).sub
+
+
+_replace_pos_comment = re.compile(
+    # this matches what Cython generates as code line marker comment
+    br'^\s*/\*(?:(?:[^*]|\*[^/])*\n)+\s*\*/\s*\n'.decode('ascii'),
+    re.M
+).sub
+
+
+class AnnotationItem(object):
+
+    def __init__(self, style, text, tag="", size=0):
+        self.style = style
+        self.text = text
+        self.tag = tag
+        self.size = size
+
+    def start(self):
+        return u"<span class='cython tag %s' title='%s'>%s" % (self.style, self.text, self.tag)
+
+    def end(self):
+        return self.size, u"</span>"