在Jupyter与Spyder中导入.pyx文件失败，寻求解决方法

正在将Python 2代码迁移至Python 3，其中包含一个.pyx扩展名的Cython模块。尝试使用以下代码在Jupyter Notebook和Spyder中导入该模块时均出现错误：Jupyter提示option -f not recognized，Spyder提示no commands supplied。

用户使用的代码：

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])) 

Jupyter Notebook报错信息 #

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'

Spyder报错信息 #

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

方法1：命令行编译安装 #

将上述代码保存为setup.py，打开终端（命令提示符）切换到该文件所在目录，执行以下命令：

python setup.py build_ext --inplace

命令执行后会在当前目录生成编译好的扩展模块（Windows为.pyd文件，Linux/macOS为.so文件），之后即可直接在Python代码中导入deepnovo_cython_modules。

方法2：在Jupyter/Spyder中直接编译（规避参数冲突） #

Jupyter和Spyder运行时会自动传入命令行参数，导致setup()函数解析错误。可以手动指定编译命令参数解决：

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()])
# 手动指定编译命令，避免读取环境参数
setup(ext_modules=cythonize([package]), script_args=['build_ext', '--inplace'])

运行代码后会自动生成编译模块，之后就能正常导入使用。

方法3：使用pyximport快速导入 #

如果只是临时测试，无需编写完整setup脚本，可以用Cython的pyximport工具自动编译导入：

import pyximport
import numpy
# 指定numpy头文件路径，避免编译报错
pyximport.install(pyimport=True, setup_args={'include_dirs': [numpy.get_include()]})
import deepnovo_cython_modules

这种方式会自动完成编译并导入模块，适合快速验证功能。

内容的提问来源于stack exchange，提问作者Minto Mathew