Pysam is a Python module for reading and manipulating files in the SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It also includes an interface for tabix.

This Python library provides functions for converting between Julian dates and Gregorian dates.

Setuptools is a fully-featured, stable library designed to facilitate packaging Python projects, where packaging includes:

• Python package and module definitions

• distribution package metadata

• test hooks

• project installation

• platform-specific details.

This package provides a pathlib-compatible Zipfile object wrapper. It provides a backport of the Path object.

Directory iteration function like os.listdir(), except that instead of returning a list of bare filenames, it yields DirEntry objects that include file type and stat information along with the name. Using scandir() increases the speed of os.walk() by 2-20 times (depending on the platform and file system) by avoiding unnecessary calls to os.stat() in most cases.

This package is part of the Python standard library since version 3.5.

Thin-wrapper around the mock package for easier use with pytest

Pytest is a testing tool that provides auto-discovery of test modules and functions, detailed info on failing assert statements, modular fixtures, and many external plugins.

Beautiful Soup is a Python library designed for rapidly setting up screen-scraping projects. It offers Pythonic idioms for navigating, searching, and modifying a parse tree, providing a toolkit for dissecting a document and extracting what you need. It automatically converts incoming documents to Unicode and outgoing documents to UTF-8.

Python bindings for GLib, GObject, and GIO.

Unittest2 is a replacement for the unittest module in the Python standard library.

Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language. It makes writing C extensions for Python as easy as Python itself.

Library for atomic file writes using platform dependent tools for atomic file system operations.

This is a backport of the subprocess standard library module from Python 3.2 and 3.3 for use on Python 2. It includes bugfixes and some new features. On POSIX systems it is guaranteed to be reliable when used in threaded applications. It includes timeout support from Python 3.3 but otherwise matches 3.2’s API.

Coverage measures code coverage, typically during test execution. It uses the code analysis tools and tracing hooks provided in the Python standard library to determine which lines are executable, and which have been executed.

Enum34 is the new Python stdlib enum module available in Python 3.4 backported for previous versions of Python from 2.4 to 3.3.

Hypothesis is a library for testing your Python code against a much larger range of examples than you would ever want to write by hand. It’s based on the Haskell library, Quickcheck, and is designed to integrate seamlessly into your existing Python unit testing work flow.

Wcwidth measures the number of terminal column cells of wide-character codes. It is useful for those implementing a terminal emulator, or programs that carefully produce output to be interpreted by one. It is a Python implementation of the wcwidth and wcswidth C functions specified in POSIX.1-2001 and POSIX.1-2008.

Python's built-in itertools module implements a number of iterator building blocks inspired by constructs from APL, Haskell, and SML. more-itertools includes additional building blocks for working with iterables.

The goal of pathlib2 is to provide a backport of standard pathlib module which tracks the standard library module, so all the newest features of the standard pathlib can be used also on older Python versions.

Pathlib offers a set of classes to handle file system paths. It offers the following advantages over using string objects:

1. No more cumbersome use of os and os.path functions. Everything can be done easily through operators, attribute accesses, and method calls.

2. Embodies the semantics of different path types. For example, comparing Windows paths ignores casing.

3. Well-defined semantics, eliminating any inconsistencies or ambiguities (forward vs. backward slashes, etc.).

Pandas is a Python package providing fast, flexible, and expressive data structures designed to make working with structured (tabular, multidimensional, potentially heterogeneous) and time series data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python.

python-configparser is a backport of configparser from Python 3.5 so that it can be used directly in other versions.

Qt is a cross-platform application and UI framework for developers using C++ or QML, a CSS & JavaScript like language.

The Georgia Tech Network Simulator (GTNets) is designed to allow network researchers to conduct simulation-based experiments to observe the behavior of moderate to large scale computer networks under a variety of conditions. The GTNets environment allows the creation of simulation network topologies (consisting of nodes and their associated communication links), and end–user applications describing the flow of data over the simulated topology.

SimGrid is a scientific instrument to study the behavior of large-scale distributed systems such as grids, "clouds", HPC, and P2P systems. It can be used to evaluate heuristics, prototype applications or even assess legacy MPI applications.