Scientific Computing Tools for Python

SciPy refers to several related but distinct entities:

  • The SciPy ecosystem, a collection of open source software for scientific computing in Python.
  • The community of people who use and develop this stack.
  • Several conferences dedicated to scientific computing in Python - SciPy, EuroSciPy and
  • The SciPy library, one component of the SciPy stack, providing many numerical routines.

The SciPy ecosystem

Scientific computing in Python builds upon a small core of packages:

  • Python, a general purpose programming language. It is interpreted and dynamically typed and is very suited for interactive work and quick prototyping, while being powerful enough to write large applications in.
  • NumPy, the fundamental package for numerical computation. It defines the numerical array and matrix types and basic operations on them.
  • The SciPy library, a collection of numerical algorithms and domain-specific toolboxes, including signal processing, optimization, statistics and much more.
  • Matplotlib, a mature and popular plotting package, that provides publication-quality 2D plotting as well as rudimentary 3D plotting

On this base, the SciPy ecosystem includes general and specialised tools for data management and computation, productive experimentation and high-performance computing. Below we overview some key packages, though there are many more relevant packages.

Data and computation:

  • pandas, providing high-performance, easy to use data structures.
  • SymPy, for symbolic mathematics and computer algebra.
  • scikit-image is a collection of algorithms for image processing.
  • scikit-learn is a collection of algorithms and tools for machine learning.
  • h5py and PyTables can both access data stored in the HDF5 format.

Productivity and high-performance computing:

  • IPython, a rich interactive interface, letting you quickly process data and test ideas.
  • The Jupyter notebook provides IPython functionality and more in your web browser, allowing you to document your computation in an easily reproducible form.
  • Cython extends Python syntax so that you can conveniently build C extensions, either to speed up critical code, or to integrate with C/C++ libraries.
  • Dask, Joblib or IPyParallel for distributed processing with a focus on numeric data.

Quality assurance:

  • nose, a framework for testing Python code, being phased out in preference for pytest.
  • numpydoc, a standard and library for documenting Scientific Python libraries.