cogent3 is a Python library for the analysis of biological sequence data. We endeavour to provide a first-class experience within Jupyter notebooks, but the algorithms also support parallel execution on compute systems with 1000’s of processors.
This is a Python package for performing representational similarity analysis (RSA) using MNE-Python data structures. The main use-case is to perform RSA using a “searchlight” approach through time and/or a volumetric or surface source space.
This package provides a library implementing the Mapper algorithm in Python. KeplerMapper can be used for visualization of high-dimensional data and 3D point cloud data. KeplerMapper can make use of Scikit-Learn API compatible cluster and scaling algorithms.
This package implements functionality for hierarchical analysis of strong lensing systems to infer lens properties and cosmological parameters simultaneously. It allows fitting lenses with measured time delays, imaging information, kinematics constraints and standardizable magnifications with parameters described on the ensemble level.
python-scanrbp is a Python package that provides the scanRBP tool that loads RNA-protein binding motif PWM and computes the log-odds scores for all the loaded RBPs across a given genomic sequence and draws a heatmap of the scores.
Chaospy is a numerical toolbox for performing uncertainty quantification using polynomial chaos expansions, advanced Monte Carlo methods implemented in Python. It also include a full suite of tools for doing low-discrepancy sampling, quadrature creation, polynomial manipulations, and a lot more.
Equinox is a comprehensive JAX library that provides a wide range of tools and features not found in core JAX, including neural networks with PyTorch-like syntax, filtered APIs for transformations, PyTree manipulation routines, and advanced features like runtime errors.
Pybox2d is a 2D physics library for your games and simple simulations. It's based on the Box2D library, written in C++. It supports several shape types (circle, polygon, thin line segments), and quite a few joint types (revolute, prismatic, wheel, etc.).
Slixmpp is a XMPP library for Python 3.11+. It is a fork of SleekXMPP. Its goal is to only rewrite the core of the library (the low level socket handling, the timers, the events dispatching) in order to remove all threads.
python-portend can be used to monitor TCP ports for bound or unbound states. For example, waiting for a port to be occupied or freed within a set timeout. python-portend can also be used directly from the command line.
Seaborn is a library for making attractive and informative statistical graphics in Python. It is built on top of matplotlib and tightly integrated with the PyData stack, including support for numpy and pandas data structures and statistical routines from scipy and statsmodels.
Tree is a python library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows you to apply a function to each leaf preserving the overall structure.
NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities.
NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities.
NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities.
tsinfer is a Python package to infer an ARG in tree sequence format from large quantities of phased DNA sequence data in VCF Zarr format (see the usage documentation for how to convert data from a VCF into a suitable input format).
It helps developers working in continuous integration (CI) environments by providing essential information about the CI server. It can determine if the code is running on a CI server,identify the specific server,and detect if a pull request is being tested.
Pretend is a library to make stubbing with Python easier. Stubbing is a technique for writing tests. You may hear the term mixed up with mocks,fakes, or doubles. Basically, a stub is an object that returns pre-canned responses, rather than doing any computation.
wsproto is a pure-Python implementation of a WebSocket protocol stack. It's written from the ground up to be embeddable in whatever program you choose to use, ensuring that you can communicate via WebSockets, as defined in RFC6455, regardless of your programming paradigm.
Pexpect is a pure Python module for spawning child applications; controlling them; and responding to expected patterns in their output. Pexpect works like Don Libes’ Expect. Pexpect allows your script to spawn a child application and control it as if a human were typing commands.
WORLD Vocoder is a fast and high-quality vocoder which parameterizes speech into three components:
f0: Pitch contoursp: Harmonic spectral envelopeap: Aperiodic spectral envelope
It can also (re)synthesize speech using these features.
Pythran is an ahead of time compiler for a subset of the Python language, with a focus on scientific computing. It takes a Python module annotated with a few interface descriptions and turns it into a native Python module with the same interface, but (hopefully) faster.
kitchen module provides a python API for all sorts of little useful snippets of code that everybody ends up writing for their projects but never seem big enough to build an independent release. Use kitchen and stop cutting and pasting that code over and over.
bashlex is a Python port of the parser used internally by GNU bash.
For the most part it's transliterated from C, the major differences are:
it does not execute anything
it is reentrant
it generates a complete AST