def cython_ann(line, cell):
from Cython.Compiler.Main import compile as cy_compile
from Cython.Compiler.CmdLine import parse_command_line
from IPython.core import display
import re
with open("demo.pyx","wb") as f:
f.write(cell.strip().encode("utf8"))
options, sources = parse_command_line(["-a", "demo.pyx"])
cy_compile(sources, options)
with open("demo.html") as f:
html = f.read().decode("utf8")
html = u"\n".join([line for line in html.split("\n") if not line.startswith("<p>")])
html = html.replace(u"display: none;", u"")
html= re.sub(u"/\*.+?\*/.", u"", html, flags=re.DOTALL | re.MULTILINE)
javascript = u"""
<script>
$("pre.code").css("background-color", "#ffffff").hide()
.css("border-left", "2px solid #cccccc")
.css("margin-left", "10px");
$("pre.line").attr("onclick", "").click(function(){$(this).next().slideToggle();return 0;})
.css("border-bottom", "1px solid #cccccc");
$("span.error_goto").hide();
</script>
"""
display.display(display.HTML(html))
display.display(display.HTML(javascript))
def simple_cythonize(src, destdir=None, cwd=None, **cy_kwargs):
""" Generates a C file from a Cython source file.
Parameters
==========
src: str
Path to Cython source.
destdir: str (optional)
Path to output directory (default: '.').
cwd: path string (optional)
Root of relative paths (default: '.').
**cy_kwargs:
Second argument passed to cy_compile. Generates a .cpp file if ``cplus=True`` in ``cy_kwargs``,
else a .c file.
"""
from Cython.Compiler.Main import (
default_options, CompilationOptions
)
from Cython.Compiler.Main import compile as cy_compile
assert src.lower().endswith('.pyx') or src.lower().endswith('.py')
cwd = cwd or '.'
destdir = destdir or '.'
ext = '.cpp' if cy_kwargs.get('cplus', False) else '.c'
c_name = os.path.splitext(os.path.basename(src))[0] + ext
dstfile = os.path.join(destdir, c_name)
if cwd:
ori_dir = os.getcwd()
else:
ori_dir = '.'
os.chdir(cwd)
try:
cy_options = CompilationOptions(default_options)
cy_options.__dict__.update(cy_kwargs)
# Set language_level if not set by cy_kwargs
# as not setting it is deprecated
if 'language_level' not in cy_kwargs:
cy_options.__dict__['language_level'] = 3
cy_result = cy_compile([src], cy_options)
if cy_result.num_errors > 0:
raise ValueError("Cython compilation failed.")
if os.path.realpath(os.path.dirname(src)) != os.path.realpath(destdir):
if os.path.exists(dstfile):
os.unlink(dstfile)
shutil.move(os.path.join(os.path.dirname(src), c_name), destdir)
finally:
os.chdir(ori_dir)
return dstfile
def simple_cythonize(src, destdir=None, cwd=None, **cy_kwargs):
""" Generates a C file from a Cython source file.
Parameters
==========
src: str
Path to Cython source.
destdir: str (optional)
Path to output directory (default: '.').
cwd: path string (optional)
Root of relative paths (default: '.').
**cy_kwargs:
Second argument passed to cy_compile. Generates a .cpp file if ``cplus=True`` in ``cy_kwargs``,
else a .c file.
"""
from Cython.Compiler.Main import (
default_options, CompilationOptions
)
from Cython.Compiler.Main import compile as cy_compile
assert src.lower().endswith('.pyx') or src.lower().endswith('.py')
cwd = cwd or '.'
destdir = destdir or '.'
ext = '.cpp' if cy_kwargs.get('cplus', False) else '.c'
c_name = os.path.splitext(os.path.basename(src))[0] + ext
dstfile = os.path.join(destdir, c_name)
if cwd:
ori_dir = os.getcwd()
else:
ori_dir = '.'
os.chdir(cwd)
try:
cy_options = CompilationOptions(default_options)
cy_options.__dict__.update(cy_kwargs)
cy_result = cy_compile([src], cy_options)
if cy_result.num_errors > 0:
raise ValueError("Cython compilation failed.")
if os.path.abspath(os.path.dirname(src)) != os.path.abspath(destdir):
if os.path.exists(dstfile):
os.unlink(dstfile)
shutil.move(os.path.join(os.path.dirname(src), c_name), destdir)
finally:
os.chdir(ori_dir)
return dstfile
def simple_cythonize(src, destdir=None, cwd=None, **cy_kwargs):
""" Generates a C file from a Cython source file.
Parameters
==========
src: str
Path to Cython source.
destdir: str (optional)
Path to output directory (default: '.').
cwd: path string (optional)
Root of relative paths (default: '.').
**cy_kwargs:
Second argument passed to cy_compile. Generates a .cpp file if ``cplus=True`` in ``cy_kwargs``,
else a .c file.
"""
from Cython.Compiler.Main import default_options, CompilationOptions
from Cython.Compiler.Main import compile as cy_compile
assert src.lower().endswith(".pyx") or src.lower().endswith(".py")
cwd = cwd or "."
destdir = destdir or "."
ext = ".cpp" if cy_kwargs.get("cplus", False) else ".c"
c_name = os.path.splitext(os.path.basename(src))[0] + ext
dstfile = os.path.join(destdir, c_name)
if cwd:
ori_dir = os.getcwd()
else:
ori_dir = "."
os.chdir(cwd)
try:
cy_options = CompilationOptions(default_options)
cy_options.__dict__.update(cy_kwargs)
cy_result = cy_compile([src], cy_options)
if cy_result.num_errors > 0:
raise ValueError("Cython compilation failed.")
if os.path.abspath(os.path.dirname(src)) != os.path.abspath(destdir):
if os.path.exists(dstfile):
os.unlink(dstfile)
shutil.move(os.path.join(os.path.dirname(src), c_name), destdir)
finally:
os.chdir(ori_dir)
return dstfile
def simple_cythonize(src, destdir=None, cwd=None, logger=None,
full_module_name=None, only_update=False,
**cy_kwargs):
"""
Generates a C file from a Cython source file.
Parameters
----------
src: path string
path to Cython source
destdir: path string (optional)
Path to output directory (default: '.')
cwd: path string (optional)
Root of relative paths (default: '.')
logger: logging.Logger
info level used.
full_module_name: string
passed to cy_compile (default: None)
only_update: bool
Only cythonize if source is newer. default: False
**cy_kwargs:
second argument passed to cy_compile.
Generates a .cpp file if cplus=True in cy_kwargs, else a .c file.
"""
from Cython.Compiler.Main import (
default_options, CompilationOptions
)
from Cython.Compiler.Main import compile as cy_compile
assert src.lower().endswith('.pyx') or src.lower().endswith('.py')
cwd = cwd or '.'
destdir = destdir or '.'
ext = '.cpp' if cy_kwargs.get('cplus', False) else '.c'
c_name = os.path.splitext(os.path.basename(src))[0] + ext
dstfile = os.path.join(destdir, c_name)
if only_update:
if not missing_or_other_newer(dstfile, src, cwd=cwd):
msg = '{0} newer than {1}, did not re-cythonize.'.format(
dstfile, src)
if logger:
logger.info(msg)
else:
print(msg)
return dstfile
if cwd:
ori_dir = os.getcwd()
else:
ori_dir = '.'
os.chdir(cwd)
try:
cy_options = CompilationOptions(default_options)
cy_options.__dict__.update(cy_kwargs)
if logger:
logger.info("Cythonizing {0} to {1}".format(
src, dstfile))
cy_result = cy_compile([src], cy_options, full_module_name=full_module_name)
if cy_result.num_errors > 0:
raise ValueError("Cython compilation failed.")
if os.path.abspath(os.path.dirname(
src)) != os.path.abspath(destdir):
if os.path.exists(dstfile):
os.unlink(dstfile)
shutil.move(os.path.join(os.path.dirname(src), c_name),
destdir)
finally:
os.chdir(ori_dir)
return dstfile
# It can be run in the build process of pyopenms when manual changes to the pyx
# files need to be made (not recommended!).
#
# == taken from autowrap/Main.py run(), lower part
from __future__ import print_function
infile = "pyopenms/pyopenms.pyx"
import cPickle
persisted_data_path = "include_dir.bin"
autowrap_include_dirs = cPickle.load(open(persisted_data_path, "rb"))
# autowrap_include_dirs = ['/usr/local/lib/python2.7/dist-packages/autowrap/data_files/boost', '/usr/local/lib/python2.7/dist-packages/autowrap/data_files', '/path/to/pyOpenMS/pxds', 'from Map cimport Map as _Map']
from Cython.Compiler.Main import compile as cy_compile, CompilationOptions
from Cython.Compiler.Options import directive_defaults
directive_defaults["boundscheck"] = False
directive_defaults["wraparound"] = False
options = dict(
include_path=autowrap_include_dirs,
compiler_directives=directive_defaults,
#output_dir=".",
#gdb_debug=True,
cplus=True)
print("Compiling with Cython the file", infile)
print("Using include_path", autowrap_include_dirs)
options = CompilationOptions(**options)
cy_compile(infile, options=options)
print("Success!")
