I’m going in circles trying to figure out a fairly basic question in Cython. On the Python side, I have a list of variable-length strings. I need to pass these to a C++ function that will process this list and return some calculations (a vector of floats of same length as the input, if that matters). I …
Tag: cython
How to compile python script importing modules to executable using cython
Maybe this is a duplicate, but I couldn’t find an answer for this particular situation: I want to compile and distribute my python Code to c and then to a binary using gcc. For distribution, I use appimagetool to include libraries. I use the command cython3 -3 myapp.py –embed to create the C code,…
Is there a better way to use cython when looking to speed up Python?
I have a large numpy array with the following structure: I’m using cython to try and speed up the processing as much as possible. The argument dataset in the code below is the above array. However, when running the above code with and without cython I get the following times: without cython: 0:00:00.945…
Poetry doesn`t use system-global Cython for compiling dependencies from source
I have a dependency package hdbscan that is compiled from source and requires a Cython to be present. Now, the dependencies are managed through Poetry, and it seems that while compiling hdbscan it uses a dedicated virtualenv with no Cython available in it. I tried installing cython3 in apt before poetry insta…
Do I need to use `nogil` in Cython
I have some Cython code that I’d like to run as quickly as possible. Do I need to release the GIL in order to do this? Let’s suppose my code is similar to this: I get a whole load of error messages from the np.zeros_like line similar to: Do I need to find a way of calling np.zeros_like without the
Importing cython generated *.so-module with another python-version or on another OS
How should a file myModule.cpython-35m-x86_64-linux-gnu.so be imported in python? Is it possible? I tried the regular way: and the interpreter says: This is a software that I can’t install in the cluster that I am working at so I just extracted the .deb package and it does not have a wheel file or struc…
PyCharm CE does not recognize .pyx files
PyCharm Community Edition (CE) does not recognize few Cython files as shown in the picture below (with PyCharm red mark under the file name). Could you please advise me on what can I do ? Answer The PyCharm Community Edition does not support Cython. You should get PyCharm Professional Edition to get that feat…
Cython class AttributeError
I have started to experiment with Cython and ran into the following problem. Consider the following class representing a vertex in the 3D space: Now I try to create an object from the Python console: which works fine. However, when I’m trying to access the class attributes, I’m getting an Attribut…
Translating python function with boolean indexing within loop to cython
Below I’ll write a function in pure python that I want to Cythonize. Suppose that I know how to Cythonize the function do_stuff. The actual do_stuff function I’m interested in is more complicated than the one above but I thought I’d provide an example. The real do_stuff function computes det…
Passing C++ vector to Numpy through Cython without copying and taking care of memory management automatically
Dealing with processing large matrices (NxM with 1K <= N <= 20K & 10K <= M <= 200K), I often need to pass Numpy matrices to C++ through Cython to get the job done and this works as expected & without copying. However, there are times when I need to initiate and preprocess a matrix in C++ a…