Implement in Cython? about superstring.py HOT 6 OPEN

Cython creates an .so file that can easily be used as a regular library from Python. Cython is a very mature project used by some of the most popular and important libraries in the Python ecosystem, such as pandas. You run files created with Cython in Python. It basically lets you combine C and or C++ and Python to create a library or function that can be used as a regular Python library. Here you can get a feel for what Cython looks like (it is not an example of good code XD): https://github.com/biocore-ntnu/ncls/blob/master/ncls/src/ncls.pyx You can see: - you are allowed to import C libraries and use C code (I do so there) - you can also use regular Python libraries in the same file, together with the C/C++ libraries! - the code looks pretty similar to Python, but with annotations. And the usage of the NCLS library is as if it were any other Python library: ``` # regular_script.py from ncls import NCLS ... ``` Of course, I cannot know how much your library would be sped up by using Cython. But in the example above my implementation is more than a 1000 times faster than the pure python version. It works best if you have contiguous data (i.e. data in arrays) represented with basic data types.