The most popular Python scientific libraries

STX Next | 6 min read, Python

Being a free, cross-platform, general-purpose and high-level programming language, Python has been widely adopted by the scientific community. Scientists value Python for its precise and efficient syntax, relatively flat learning curve and the fact that it integrates well with other languages (e.g. C/C++).

As a result of this popularity there are plenty of Python scientific packages for data visualization, machine learning, natural language processing, complex data analysis and more. All of these factors make Python a great tool for scientific computing and a solid alternative for commercial packages such as MatLab.

Here’s our list of the most popular Python scientific libraries and tools:


The Astropy Project is a collection of packages designed for use in astronomy. The core astropy package contains functionality aimed at professional astronomers and astrophysicists, but may be useful to anyone developing astronomy software.


Biopython is a collection of non-commercial Python tools for computational biology and bioinformatics. It contains classes to represent biological sequences and sequence annotations, and it is able to read and write to a variety of file formats.


Cubes is a light-weight Python framework and set of tools for the development of reporting and analytical applications, Online Analytical Processing (OLAP), multidimensional analysis and browsing of aggregated data.


DEAP is an evolutionary computation framework for rapid prototyping and testing of ideas. It incorporates the data structures and tools required to implement most common evolutionary computation techniques such as genetic algorithm, genetic programming, evolution strategies, particle swarm optimization, differential evolution and estimation of distribution algorithm.


SCOOP is a Python module for distributing concurrent parallel tasks on various environments, from heterogeneous grids of workstations to supercomputers.


PsychoPy is a package for the generation of experiments for neuroscience and experimental psychology. PsychoPy is designed to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments.


Pandas is a library for data manipulation and analysis. The library provides data structures and operations for manipulating numerical tables and time series.


Mlpy is a machine learning library built on top of NumPy/SciPy, the GNU Scientific Libraries. Mlpy provides a wide range of machine learning methods for supervised and unsupervised problems and it is aimed at finding a reasonable compromise between modularity, maintainability, reproducibility, usability and efficiency.


Matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. Matplotlib allows you to generate plots, histograms, power spectra, bar charts, errorcharts, scatterplots, and more.


NumPy is the fundamental package for scientific computing with Python, adding support for large, multi-dimensional arrays and matrices, along with a large library of high-level mathematical functions to operate on these arrays.


NetworkX is a library for studying graphs which helps you create, manipulate, and study the structure, dynamics, and functions of complex networks.


TomoPy is an open-sourced Python toolbox to perform tomographic data processing and image reconstruction tasks. TomoPy provides a collaborative framework for the analysis of synchrotron tomographic data with the goal to unify the effort of different facilities and beamlines performing similar tasks.


Theano is a numerical computation Python library. Theano allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.


SymPy is a library for symbolic computation and includes features ranging from basic symbolic arithmetic to calculus, algebra, discrete mathematics and quantum physics. It provides computer algebra capabilities either as a standalone application, as a library to other applications, or live on the web.


SciPy is a library used by scientists, analysts, and engineers doing scientific computing and technical computing. SciPy contains modules for optimization, linear algebra, integration, interpolation, special functions, FFT, signal and image processing, ODE solvers and other tasks common in science and engineering.


scikit-learn is a machine learning library. It features various classification, regression and clustering algorithms including support vector machines, random forests, gradient boosting, k-means and DBSCAN, and is designed to interoperate with the Python numerical and scientific libraries NumPy and SciPy.


scikit-image is a image processing library. It includes algorithms for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more.


ScientificPython is a collection of modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization.


SageMath is mathematical software with features covering many aspects of mathematics, including algebra, combinatorics, numerical mathematics, number theory, and calculus. SageMath uses the Python, supporting procedural, functional and object-oriented constructs.


Veusz is a scientific plotting and graphing package designed to produce publication-quality plots in popular vector formats, including PDF, PostScript and SVG.


Graph-tool is a module for the manipulation and statistical analysis of graphs.


SunPy is a data-analysis environment specializing in providing the software necessary to analyze solar and heliospheric data in Python.


Bokeh is a Python interactive visualization library that targets modern web browsers for presentation. Bokeh can help anyone who would like to quickly and easily create interactive plots, dashboards, and data applications. Its goal is to provide elegant, concise construction of novel graphics in the style of D3.js, but also deliver this capability with high-performance interactivity over very large or streaming datasets.


Did We Miss Anything?

Is there any tool we missed? With so many Python packages and tools to explore, there’s a good chance you know some exciting new Python libraries that belong on this list. Feel free to add any additional tool or software you feel is relevant in the comment section.

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