Cython vs. Python vs. h5py vs. yEd Comparison Chart

Cython is an optimizing static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself. Cython gives you the combined power of Python and C to let you write Python code that calls back and forth from and to C or C++ code natively at any point. Easily tune readable Python code into plain C performance by adding static type declarations, also in Python syntax. Use combined source code level debugging to find bugs in your Python, Cython, and C code. Interact efficiently with large data sets, e.g. using multi-dimensional NumPy arrays. Quickly build your applications within the large, mature, and widely used CPython ecosystem. The Cython language is a superset of the Python language that additionally supports calling C functions and declaring C types on variables and class attributes.

The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want. H5py uses straightforward NumPy and Python metaphors, like dictionary and NumPy array syntax. For example, you can iterate over datasets in a file, or check out the .shape or .dtype attributes of datasets. You don't need to know anything special about HDF5 to get started. In addition to the easy-to-use high level interface, h5py rests on a object-oriented Cython wrapping of the HDF5 C API. Almost anything you can do from C in HDF5, you can do from h5py.