I was trying to convert a code from python 2 to python 3 but one module has a .pyx extension. I tried to import the below code to import a .pyx extension file in jupyter notebook but its throwing an error. Tried the same in spyder too but then it shows no commands supplied. Is there any easy method to import the file as a module in my python code?
from distutils.core import setup, Extension
from Cython.Build import cythonize
import numpy
package = Extension('deepnovo_cython_modules', ['deepnovo_cython_modules.pyx'], include_dirs=[numpy.get_include()])
setup(ext_modules=cythonize([package]))
the error thrown is
Traceback (most recent call last):
File "C:\Users\minto\anaconda3\envs\tf_env\lib\distutils\fancy_getopt.py", line 233, in getopt
opts, args = getopt.getopt(args, short_opts, self.long_opts)
File "C:\Users\minto\anaconda3\envs\tf_env\lib\getopt.py", line 95, in getopt
opts, args = do_shorts(opts, args[0][1:], shortopts, args[1:])
File "C:\Users\minto\anaconda3\envs\tf_env\lib\getopt.py", line 195, in do_shorts
if short_has_arg(opt, shortopts):
File "C:\Users\minto\anaconda3\envs\tf_env\lib\getopt.py", line 211, in short_has_arg
raise GetoptError(_('option -%s not recognized') % opt, opt)
getopt.GetoptError: option -f not recognized
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\minto\anaconda3\envs\tf_env\lib\distutils\core.py", line 134, in setup
ok = dist.parse_command_line()
File "C:\Users\minto\anaconda3\envs\tf_env\lib\distutils\dist.py", line 475, in parse_command_line
args = parser.getopt(args=self.script_args, object=self)
File "C:\Users\minto\anaconda3\envs\tf_env\lib\distutils\fancy_getopt.py", line 235, in getopt
raise DistutilsArgError(msg)
distutils.errors.DistutilsArgError: option -f not recognized
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\minto\anaconda3\envs\tf_env\lib\site-packages\IPython\core\interactiveshell.py", line 3552, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "C:\Users\minto\AppData\Local\Temp\ipykernel_19296\1354990193.py", line 6, in <cell line: 6>
setup(ext_modules=cythonize([package]))
File "C:\Users\minto\anaconda3\envs\tf_env\lib\distutils\core.py", line 136, in setup
raise SystemExit(gen_usage(dist.script_name) + "\nerror: %s" % msg)
SystemExit: usage: ipykernel_launcher.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: ipykernel_launcher.py --help [cmd1 cmd2 ...]
or: ipykernel_launcher.py --help-commands
or: ipykernel_launcher.py cmd --help
error: option -f not recognized
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\minto\anaconda3\envs\tf_env\lib\site-packages\IPython\core\ultratb.py", line 1101, in get_records
return _fixed_getinnerframes(etb, number_of_lines_of_context, tb_offset)
File "C:\Users\minto\anaconda3\envs\tf_env\lib\site-packages\IPython\core\ultratb.py", line 248, in wrapped
return f(*args, **kwargs)
File "C:\Users\minto\anaconda3\envs\tf_env\lib\site-packages\IPython\core\ultratb.py", line 281, in _fixed_getinnerframes
records = fix_frame_records_filenames(inspect.getinnerframes(etb, context))
File "C:\Users\minto\anaconda3\envs\tf_env\lib\inspect.py", line 1541, in getinnerframes
frameinfo = (tb.tb_frame,) + getframeinfo(tb, context)
AttributeError: 'tuple' object has no attribute 'tb_frame'
I tried to run the same file in spyder and this error occurred
runfile('C:/Users/minto/Desktop/DeepNovo-DIA-master/deepnovo_cython_setup.py', wdir='C:/Users/minto/Desktop/DeepNovo-DIA-master')
An exception has occurred, use %tb to see the full traceback.
Traceback (most recent call last):
File "C:\Users\minto\anaconda3\envs\tf_env\lib\distutils\core.py", line 134, in setup
ok = dist.parse_command_line()
File "C:\Users\minto\anaconda3\envs\tf_env\lib\distutils\dist.py", line 501, in parse_command_line
raise DistutilsArgError("no commands supplied")
DistutilsArgError: no commands supplied
During handling of the above exception, another exception occurred:
SystemExit: usage: deepnovo_cython_setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: deepnovo_cython_setup.py --help [cmd1 cmd2 ...]
or: deepnovo_cython_setup.py --help-commands
or: deepnovo_cython_setup.py cmd --help
error: no commands supplied
