Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.

Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.

This package provides an implementation of the Ensemble Slice Sampling method. Features:

• fast & Robust Bayesian Inference

• efficient Markov Chain Monte Carlo (MCMC)

• black-box inference, no hand-tuning

• excellent performance in terms of autocorrelation time and convergence rate

• scale to multiple CPUs without any extra effort

• automated Convergence diagnostics

pyjanitor provides a set of data cleaning routines for pandas DataFrames. These routines extend the method chaining API defined by pandas for a subset of its methods. Originally, this package was a port of the R package by the same name and it is inspired by the ease-of-use and expressiveness of the dplyr package.

This package provides more-reasonable core functionality for numpy.

A lot of numpysane functionality is inspired by PDL (Perl Data Language).

numpysane has:

• easier broadcasting

• nicer array manipulation

• array concatenation

• manipulation of dimensions

• broadcast-aware inner product

• broadcast-aware outer product

• broadcast-aware 2-norm

• broadcast-aware matrix multiplication

Hatch is a modern, extensible Python project manager. It has features such as:

• Standardized build system with reproducible builds by default

• Robust environment management with support for custom scripts

• Easy publishing to PyPI or other indexes

• Version management

• Configurable project generation with sane defaults

• Responsive CLI, ~2-3x faster than equivalent tools.

Hatch is a modern, extensible Python project manager. It has features such as:

• Standardized build system with reproducible builds by default

• Robust environment management with support for custom scripts

• Easy publishing to PyPI or other indexes

• Version management

• Configurable project generation with sane defaults

• Responsive CLI, ~2-3x faster than equivalent tools.

Py-BOBYQA is a flexible package for solving bound-constrained general objective minimization, without requiring derivatives of the objective. At its core, it is a Python implementation of the BOBYQA algorithm by Powell,but Py-BOBYQA has extra features improving its performance on some problems. Py-BOBYQA is particularly useful when evaluations of the objective function are expensive and/or noisy.

GitPython is a python library used to interact with Git repositories, high-level like git-porcelain, or low-level like git-plumbing.

It provides abstractions of Git objects for easy access of repository data, and additionally allows you to access the Git repository more directly using either a pure Python implementation, or the faster, but more resource intensive git command implementation.

Traitlets is a framework that lets Python classes have attributes with type checking, dynamically calculated default values, and ‘on change’ callbacks. The package also includes a mechanism to use traitlets for configuration, loading values from files or from command line arguments. This is a distinct layer on top of traitlets, so you can use traitlets in your code without using the configuration machinery.

Fakeredis is a pure-Python implementation of the redis-py Python client that simulates talking to a redis server. It was created for a single purpose: to write unit tests.

Setting up redis is not hard, but one often wants to write unit tests that don't talk to an external server such as redis. This module can be used as a reasonable substitute.

Easy ANSI is a terminal framework API to give you an easy way to use colors, cursor control movements, and line/box drawing. It is not meant as a replacement to more full-featured frameworks (such as curses or urwid), but as a tool to quickly create nice-looking screens in your terminal window. You can even create animations with the cursor controls.

The iniconfig package provides a small and simple INI-file parser module having a unique set of features ; iniconfig

• maintains the order of sections and entries ;

• supports multi-line values with or without line-continuations ;

• supports "#" comments everywhere ;

• raises errors with proper line-numbers ;

• raises an error when two sections have the same name.

Easy ANSI is a terminal framework API to give you an easy way to use colors, cursor control movements, and line/box drawing. It is not meant as a replacement to more full-featured frameworks (such as curses or urwid), but as a tool to quickly create nice-looking screens in your terminal window. You can even create animations with the cursor controls.

duniterpy is an implementation of duniter API. Its main features are:

• Support Duniter's Basic Merkle API and protocol

• Asynchronous/synchronous without threads

• Support HTTP, HTTPS and Web Socket transport for Basic Merkle API

• Support Elasticsearch Duniter4j API

• Duniter signing key

• Sign/verify and encrypt/decrypt messages with the Duniter credentials

This package implements a functionality for creating, editing and loading COLLADA,which is a COLLAborative Design Activity for establishing an interchange file format for interactive 3D applications.

The library allows you to load a COLLADA file and interact with it as a python object. In addition, it supports creating a collada python object from scratch, as well as in-place editing.

FastRLock is a C-level implementation of an optimistic lock for CPython which can be used as a replacement for threading.RLock. It is implemented in Cython and offers a C-API for direct use from Cython code. The lock is 10x faster than threading.RLock under normal conditions and 10% faster under congestion, making it a faster option than the revised RLock implementation in Python 3.2.

This package implements a functionality to tell whether two images look nearly identical. The image hash algorithms (average, perceptual, difference, wavelet) analyse the image structure on luminance (without color information). The color hash algorithm analyses the color distribution and black & gray fractions (without position information).

Features:

• average hashing

• perceptual hashing

• difference hashing

• wavelet hashing

• HSV color hashing (colorhash)

• crop-resistant hashing

python-webcolors is a module for working with HTML/CSS color definitions. Normalizing and converting between the following formats is supported.

• Specification-defined color names

• Six-digit hexadecimal

• Three-digit hexadecimal

• Integer rgb() triplet

• Percentage rgb() triplet

Only the RGB colorspace is supported. Conversion to/from the HSL colorspace can be handled by the colorsys module in the Python standard library.

Python makes loading code dynamically easy, allowing you to configure and extend your application by discovering and loading extensions ("plugins") at runtime. Many applications implement their own library for doing this, using __import__ or importlib. Stevedore avoids creating yet another extension mechanism by building on top of setuptools entry points. The code for managing entry points tends to be repetitive, though, so stevedore provides manager classes for implementing common patterns for using dynamically loaded extensions.

Python makes loading code dynamically easy, allowing you to configure and extend your application by discovering and loading extensions ("plugins") at runtime. Many applications implement their own library for doing this, using __import__ or importlib. Stevedore avoids creating yet another extension mechanism by building on top of setuptools entry points. The code for managing entry points tends to be repetitive, though, so stevedore provides manager classes for implementing common patterns for using dynamically loaded extensions.

This package addresses the challenge of handling large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files. Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.

This package is a stand-alone implementation of several NumPy dtype extensions used in machine learning libraries, including:

• bfloat16: an alternative to the standard float16 format

• float8_*: several experimental 8-bit floating point representations including:

  • float8_e4m3b11fnuz

  • float8_e4m3fn

  • float8_e4m3fnuz

  • float8_e5m2

  • float8_e5m2fnuz

• int4 and uint4: low precision integer types.

POLIASTRO is a Python library for interactive Astrodynamics and Orbital Mechanics, with a focus on ease of use, speed, and quick visualization. It provides a simple and intuitive API, and handles physical quantities with units.

Some features include orbit propagation, solution of the Lambert's problem, conversion between position and velocity vectors and classical orbital elements and orbit plotting, among others. It focuses on interplanetary applications, but can also be used to analyze artificial satellites in Low-Earth Orbit (LEO).