scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.

PhenoGraph is a clustering method designed for high-dimensional single-cell data. It works by creating a graph representing phenotypic similarities between cells and then identifying communities in this graph.

pynetdicom is a Python package that implements the DICOM networking protocol. It allows the easy creation of DICOM SCUs and SCPs.

Scikit-opt (or sko) is a Python module implementing swarm intelligence algorithms: genetic algorithm, particle swarm optimization, simulated annealing, ant colony algorithm, immune algorithm, artificial fish swarm algorithm.

Python LiveReload provides a command line utility, livereload, for starting a web server in a directory. It can trigger arbitrary commands and serve updated contents upon changes to the directory.

This library contains the HTTP/2 framing code used in the hyper project. It provides a pure-Python codebase that is capable of decoding a binary stream into HTTP/2 frames.

This module provides a standard interface to extract, format and print stack traces of Python programs. It exactly mimics the behavior of the Python interpreter when it prints a stack trace.

This package provides a pixel-level image comparison library for Python, originally created to compare screenshots in tests. Its features include accurate anti-aliased pixels detection and perceptual color difference metrics.

rst.linker automatically replaces text by a reStructuredText external reference or timestamps. It's primary purpose is to augment the changelog, but it can be used for other documents, too.

This driver is based on black box reverse engineering of the USB behaviour of the proprietary software, and reading the basic data structure layouts in the original python-can canalystii source.

Scripttest is a Python helper library for testing interactive command-line applications. With it you can run a script in a subprocess and see the output as well as any file modifications.

This Python library provides interfaces for parsing and analyzing two binary and library file formats ; the Executable and Linking Format (ELF), and debugging information in the Debugging With Attributed Record Format (DWARF).

Simple, modern file watching and code reload in Python inspired by watchdog. Among the differences are a unified approach for each operating systems and an elegant approach to concurrency using threading.

The linecache module allows one to get any line from any file, while attempting to optimize internally, using a cache, the common case where many lines are read from a single file.

This package provides a library that wraps the traditional Python dictionaries and provides a syntax to access nested dictionaries values using a dot syntax, for example: dictionary['deeply.nested.key'].

Cloud-init is the multi-distribution method for cross-platform cloud instance initialization. It is supported across all major public cloud providers, provisioning systems for private cloud infrastructure, and bare-metal installations.

This package provides a Quart extension to provide Trio support. This is an alternative to using the asyncio event loop present in the Python standard library and supported by default in Quart.

This is a fork of the standard library modules cgi and cgitb. They are slated to be removed from the Python standard library in Python 3.13 by PEP-594.

Ipywidgets are interactive HTML widgets for Jupyter notebooks and the IPython kernel. Notebooks come alive when interactive widgets are used. Users gain control of their data and can visualize changes in the data.

This package provides a framework for working with formal language grammars. The library was originally developed for educational purposes and therefore implements many textbook algorithms regarding the manipulation and interaction with formal grammars.

The SciPy library is one of the core packages that make up the SciPy stack. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.

This package is a Python wrapper for Aaron Quinlan's BEDtools programs, which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python.

This package provides a plugin for Pytest that enables a CSV output mode for Pytest. It can be enabled via the --csv option it adds to the Pytest command line interface (CLI).

asn1crypto is an ASN.1 parser and serializer with definitions for private keys, public keys, certificates, CRL, OCSP, CMS, PKCS#3, PKCS#7, PKCS#8, PKCS#12, PKCS#5, X.509 and TSP.