40 Most Popular Python Scientific Libraries

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Python is many things.

Cross-platform. General-purpose. High-level.

As such, the programming language has numerous applications and has been widely
adopted by all sorts of communities, from data science to business.

These communities value Python for its precise and efficient syntax, relatively flat
learning curve, and good integration with other languages (e.g. C/C++).

The language’s popularity has resulted in a wide range of Python packages being
produced for data visualization, machine learning, natural language processing,
complex data analysis, and more.

Learn why Python is the perfect choice for data science and discover 40 best
scientific libraries that Python has to offer.

Why should you use Python libraries for data science?

Python has become the go-to language in data science and it’s one of the first
things recruiters will probably search for in a data scientist’s skill set.

It consistently ranks top in the global data science surveys and its widespread popularity
keeps on increasing. As a matter of fact, a recent survey revealed that roughly 65.8% of
machine learning engineers and data scientists use Python regularly—way more often
than SQL (44%) and R (31%).

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But what makes Python such a good fit for data science?

One of the main reasons why Python is so widely used in the scientific and research
communities is its accessibility, ease of use, and simple syntax. Thanks to that, people
who don’t have any engineering background find it generally easier to adopt.

Python’s popularity also stems from its simplicity, flexibility, and the widespread
community participation. It’s very effective and extremely useful for data analytics
because of the multitude of libraries that programmers have developed for it over the
years.

Libraries are essentially ready-made modules that can be easily inserted into data
science projects without having to write new code. There are around 137,000 Python
libraries for data science available at the moment.

Such tools make data tasks much easier and contain a plethora of functions, extensions,
and methods to manage and analyze data. Each of these libraries has a particular focus
—some on managing image and textual data, and others on data mining, neural
networks, and data visualization.

The best way to make sure that you have everything you need to become a
proficient data scientist is to become familiar with the Python scientific libraries
we’ve provided in this article. So read on to see what we’ve prepared for you!

40 essential Python libraries for data science, machine learning, and more

1. Astropy
Astropy 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 software for astronomy.

2. Biopython
Biopython is a collection of non-commercial Python tools for computational biology and
bioinformatics.

It contains classes to represent biological sequences and sequence annotations. The

library can also read and write to a variety of file formats.

3. Bokeh
Bokeh is a Python interactive visualization library that targets modern web browsers for
presentation.

It can help anyone who wishes to quickly and easily create interactive plots, dashboards,
and data applications.

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The purpose of Bokeh 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.

4. Cubes
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.

5. Dask
Dask is a flexible parallel computing library for analytic computing, composed of two
components:

1. dynamic task scheduling optimized for computation and interactive computational

workloads;
2. Big Data collections like parallel arrays, dataframes, and lists that extend common
interfaces such as NumPy, Pandas, or Python iterators to larger-than-memory or
distributed environments.

6. DEAP
DEAP is an evolutionary computation framework for rapid prototyping and testing of
ideas.

It incorporates the data structures and tools required to implement the most common
evolutionary computation techniques, such as genetic algorithms, genetic programming,
evolution strategies, particle swarm optimization, differential evolution, and estimation of
distribution algorithms.

7. DMelt
DataMelt, or DMelt, is a software for numeric computation, statistics, analysis of large
data volumes (Big Data), and scientific visualization.

It can be used with several scripting languages, including Python/Jython, BeanShell,

Groovy, Ruby, and Java.

The library has numerous applications, such as natural sciences, engineering, modeling,
and analysis of financial markets.

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

9. matplotlib

Matplotlib is a Python 2D plotting library that produces publication-quality figures in a

variety of hard-copy formats and interactive cross-platform environments.

It allows you to generate plots, histograms, power spectra, bar charts, error charts,
scatter plots, and more.

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10. Mlpy
Mlpy is a machine learning library built on top of NumPy/SciPy, the GNU Scientific
Libraries.

It provides a wide range of machine learning methods for supervised and unsupervised
problems, and is aimed at finding a reasonable compromise between modularity,
maintainability, reproducibility, usability, and efficiency.

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

12. Nilearn

Nilearn is a Python module for fast and easy statistical learning on neuroimaging data.

This library makes it easy to use many advanced machine learning, pattern recognition,
and multivariate statistical techniques on neuroimaging data for applications such as
MVPA (Multi-Voxel Pattern Analysis), decoding, predictive modelling, functional
connectivity, brain parcellations, or connectomes.

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

14. Pandas
Pandas is a library for data manipulation and analysis, providing data structures and
operations for manipulating numerical tables and time series.

15. Pipenv
Pipenv is a tool designed to bring the best of all packaging worlds to the Python world.

It automatically creates and manages a virtualenv for your projects, along with adding or
removing packages from your Pipfile as you install or uninstall packages.

Pipenv is primarily meant to provide users and developers of applications with an easy
method to set up a working environment.

16. PsychoPy
PsychoPy is a package for the generation of experiments for neuroscience and
experimental psychology.

It is designed to allow the presentation of stimuli and collection of data for a wide range of
neuroscience, psychology, and psychophysical experiments.

17. PySpark
PySpark is the Python API for Apache Spark.

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Spark is a distributed computing framework for big data processing. It serves as a unified
analytics engine, built with speed, ease of use, and generality in mind.

Spark offers modules for streaming, machine learning, and graph processing. It’s also
completely open-source.

18. python-weka-wrapper
Weka is a suite of machine learning software written in Java, developed at the University
of Waikato, New Zealand.

It contains a collection of visualization tools and algorithms for data analysis and
predictive modeling, together with graphical user interfaces for easy access to these
functions.

The python-weka-wrapper package makes it easy to run Weka algorithms and filters from
within Python.

19. PyTorch
PyTorch is a deep learning framework for fast, flexible experimentation.

This package provides two high-level features: Tensor computation with strong GPU
acceleration and deep neural networks built on a tape-based autodiff system.

It can be used either as a replacement for numpy to use the power of GPUs, or a deep
learning research platform that provides maximum flexibility and speed.

20. SQLAlchemy
SQLAlchemy is an open-source SQL toolkit and Object-Relational Mapper that gives
application developers the full power and flexibility of SQL.

It provides a full suite of well-known enterprise-level persistence patterns, designed for

efficient and high-performing database access, adapted into a simple and Pythonic
domain language.

The main goal of the library is to change the way we approach databases and SQL.

21. SageMath
SageMath is a mathematical software system with features covering multiple aspects of
mathematics, including algebra, combinatorics, numerical mathematics, number theory,
and calculus.

It uses Python to support procedural, functional, and object-oriented constructs.

22. ScientificPython
ScientificPython is a collection of modules for scientific computing.

It contains support for geometry, mathematical functions, statistics, physical units, IO,
visualization, and parallelization.

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23. scikit-image
Scikit-image is an image processing library.

It includes algorithms for segmentation, geometric transformations, color space

manipulation, analysis, filtering, morphology, feature detection, and more.

24. scikit-learn
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.

The library is designed to interoperate with the Python numerical and scientific libraries
NumPy and SciPy.

25. SciPy
SciPy is a library used by scientists, analysts, and engineers doing scientific computing
and technical computing.

It 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.

26. SCOOP

SCOOP is a Python module for distributing concurrent parallel tasks on various

environments, from heterogeneous grids of workstations to supercomputers.

27. SunPy

SunPy is a data analysis environment specializing in providing the software necessary to

analyze solar and heliospheric data in Python.

28. SymPy
SymPy is a library for symbolic computation, offering features ranging from basic
symbolic arithmetic to calculus, algebra, discrete mathematics, and quantum physics.

It provides computer algebra capabilities either as a standalone application, a library to

other applications, or live on the web.

29. TensorFlow
TensorFlow is an open-source software library for machine learning across a range of
tasks, developed by Google to meet their needs for systems capable of building and
training neural networks to detect and decipher patterns and correlations, analogous to
the learning and reasoning employed by humans.

It is currently used for both research and production at Google products,‍often replacing
the role of its closed-source predecessor, DistBelief.

30. Theano

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Theano is a numerical computation Python library, allowing you to define, optimize, and
evaluate mathematical expressions involving multidimensional arrays efficiently.

31. TomoPy
TomoPy is an open-source Python toolbox for performing tomographic data processing
and image reconstruction tasks.

It offers a collaborative framework for the analysis of synchrotron tomographic data, with
the goal to unify the efforts of different facilities and beamlines performing similar tasks.

32. Veusz

Veusz is a scientific plotting and graphing package designed to produce publication-

quality plots in popular vector formats, including PDF, PostScript, and SVG.

33. Beautiful Soup

Beautiful Soup is a powerful tool that can save you hours of work. The library makes it
easy to scrape information from web pages. It pulls data out of HTML and XML files and
works with your favorite parser to provide idiomatic ways of navigating, searching, and
modifying the parse tree.

34. Scrapy

Even though Scrapy was originally designed for web scraping and crawling, it can be
used for a wide range of purposes, from data mining to monitoring and automated testing.

Among many of its powerful features are built-in support for selecting and extracting data
from HTML/XML sources using extended CSS selectors and XPath expressions and an
interactive shell console for trying out the CSS and XPath expressions to scrape data.

35. Plotly

Plotly is an open-source library used to make interactive, web-based visualizations that

can be displayed in Jupyter notebooks, saved to standalone HTML files, or provided as
part of Python-built web applications using Dash. It supports over 4- unique chart types
that can be used to present data in a wide array of areas, including statistics, finance,
geography, and science.

To differentiate it from the JavaScrip library, it’s sometimes referred to as “plotly.py.”

36. Seaborn
Seaborn is a highly popular data visualization library used to make statistical graphics in
Python. It’s based on matplotlib and allows you to use it with the many environments that
matplotlib supports. As opposed to matplotlib, it has a high-level interface.

The library makes it effortless to create stunning, amplified data visuals, and understand
the data better by discovering unobvious correlations between variables and trends.
Seaborn also integrates closely with Pandas data structures.

37. Keras

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Keras is a well-known library that provides extensive pre-labeled datasets. It is used
primarily for deep learning and neural network modules. This library contains various
implemented layers and parameters that can be used for the construction, configuration,
training, and evaluation of neural networks.

Keras supports both the TensorFlow and Theano backends.

38. PyCaret

PyCaret is an open-source scientific library that will help you easily perform end-to-end
machine learning experiments, such as: imputing missing values, encoding categorical
data, feature engineering, hyper-parameter tuning, or building ensemble models.

39. Mahotas

Mahotas is a computer vision library designed for image processing. It uses algorithms
implemented in C++ and operates on top of NumPy for an easy-to-use, clean, and fast
Python interface. Mahotas provides various image processing functions like thresholding,
convolution, and Sobel edge detections.

40. Statsmodels

Statsmodels is a part of the Python scientific stack oriented toward data science, data
analysis, and statistics. It is built on top of NumPy and SciPy, and integrates with Pandas
for data handling. Statsmodels supports users in exploring data, estimating statistical
models, and performing statistical tests.

Final thoughts on most popular Python scientific libraries

Thank you for checking out our list of 40 most popular Python scientific libraries. As we’ve
mentioned, there are around 137,000 other options available at the moment, so please
keep in mind that in no way could this list be exhaustive.

With so many great Python libraries out there to explore, there are surely some exciting
tools that belong on this list and didn’t make the cut, but the ones we’ve provided here
should be more than satisfying at the beginning of your data science journey.

We hope this article made finding the right Python library for data science a lot easier for
you. However, you can always reach out to us if you have any questions—we’ll be glad
to answer them.

And since you’ve gotten through our list of Python libraries, maybe we could interest you
in our other free resources on data science and machine learning, such as:

Python for Data Engineering: Why Do Data Engineers Use Python?

Will Artificial Intelligence Replace Software Developers?

Machine Learning Implementation and Project Management: A How-To Guide

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At STX Next, our goal is to provide high-quality, comprehensive data engineering
development services focused on Python and other modern frameworks to help you
resolve any data-related challenge.

We believe that our experienced data engineers will help you become a truly data-driven
business, so if you’re struggling with any data engineering issues and would like to
receive some support, feel free to drop us a message. We’d be happy to find the best
solution to your problems!

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