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Cython performed inline: compile and run your Cython snippets on the fly.

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cyper

Cython performed inline: compile and run your Cython snippets on the fly.

It is aiming to provide a flexible alternative to the IPython Cython magic command outside the IPython/Jupyter environment.

Features

  • Simple, get rid of the tedious setup files or makefile.
  • Smart, auto-detect and set compiler flags for Numpy and OpenMP.
  • Highly customizable, allow one to set Cython directives, environment variables and compiler options.

Usage

Basic usage

  • Basic usage

    import cyper
    
    code = r'''
    def func(x):
        return 2.0 * x
    '''
    
    pyx = cyper.inline(code)
    pyx.func(1)
    # 2.0

    Raw string is recommended to avoid breaking escape character.

  • It is convenient (though usually not encouraged) to export the variables from compiled module to the current namespace

    cyper.inline(code, globals())
    func(1)
  • Example of using Numpy array and external gsl library, assuming gsl installed at /opt/gsl/

    code = r'''
    import numpy as np
    
    cdef extern from "gsl/gsl_math.h":
        double gsl_pow_int (double x, int n)
    
    def pow(double x, int n):
        y = gsl_pow_int(x, n)
        return y
    
    def pow_array(double[:] x, int n):
        cdef:
            int i, m=len(x)
            double[:] y=np.empty(m, dtype='f8')
        for i in range(m):
            y[i] = gsl_pow_int(x[i], n)
        return y.base
    '''
    
    pyx = cyper.inline(
        code,
        include_dirs=['/opt/gsl/include/'],
        library_dirs=['/opt/gsl/lib'],
        libraries=['gsl', 'gslcblas']
    )
    
    pyx.pow(2, 6)
    # 64.0
    
    import numpy as np
    pyx.pow_array(np.arange(5, dtype='f8'), 2)
    # array([ 0.,  1.,  4.,  9., 16.])
  • Get better performance (at your own risk) with arrays

    cyper.inline(code, fast_indexing=True)
    # it is equivalent to
    cyper.inline(code, directives=dict(boundscheck=False, wraparound=False))

Advanced usage

  • Set the compiler options, e.g., compiling OpenMP codes with gcc

    cyper.inline(openmpcode,
                 extra_compile_args=['-fopenmp'],
                 extra_link_args=['-fopenmp'],
                 )
    # use '-openmp' or '-qopenmp' (>=15.0) for Intel
    # use '/openmp' for Microsoft Visual C++ Compiler
    # use '-fopenmp=libomp' for Clang

    Or equivalently write this for short

    cyper.inline(openmpcode, openmp='-fopenmp')

    The cython directives and distutils extension_args can also be set in a directive comment at the top of the code snippet, e.g.,

    code = r'''
    # cython: boundscheck=False, wraparound=False, cdivision=True
    # distutils: extra_compile_args = -fopenmp
    # distutils: extra_link_args = -fopenmp
    ...<code>...
    '''
    cyper.inline(code)
  • Set environment variables, e.g., using icc to compile

    cyper.inline(code, environ={'CC':'icc', 'LDSHARED':'icc -shared'})

    See https://software.intel.com/en-us/articles/thread-parallelism-in-cython

  • Set directory for searching cimport (.pxd file)

    cyper.inline(code, cimport_dirs=[custom_path]})
    # or equivalently
    cyper.inline(code, cythonize_args={'include_path': [custom_path]})

    Try setting cimport_dirs=sys.path if Cython can not find the installed cimport modules.

Installation

  • Dependencies: Cython

  • Installation:

    pip install cyper

License

Cyper is licensed under the MIT License

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Cython performed inline: compile and run your Cython snippets on the fly.

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