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

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

Pyro is a Distributed Object Technology system written in Python that is designed to be easy to use. It resembles Java's Remote Method Invocation (RMI). It has less similarity to CORBA, which is a system and language independent Distributed Object Technology and has much more to offer than Pyro or RMI. Pyro 3.x is no longer maintained. New projects should use Pyro4 instead, which is the new Pyro version that is actively developed.

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.

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.

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. Version 1.8 is the last one to contain the numpy.oldnumeric API that includes the compatibility layer numpy.oldnumeric with NumPy's predecessor Numeric.

importlib_metadata is a library which provides an API for accessing an installed Python package's metadata, such as its entry points or its top-level name. This functionality intends to replace most uses of pkg_resources entry point API and metadata API. Along with importlib.resources in Python 3.7 and newer, this can eliminate the need to use the older and less efficient pkg_resources package.

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.

MMTK is a library for molecular simulations with an emphasis on biomolecules. It provides widely used methods such as Molecular Dynamics and normal mode analysis, but also basic routines for implementing new methods for simulation and analysis. The library is currently not actively maintained and works only with Python 2 and NumPy < 1.9.

The pyparsing module is an alternative approach to creating and executing simple grammars, vs. the traditional lex/yacc approach, or the use of regular expressions. The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code.

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 provides an implementation of importlib.resources for older versions of Python.

Python bindings for GLib, GObject, and GIO.

This package provides chardet, a Python module that can automatically detect a wide range of file encodings.

The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.

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.).

Pytest-cov produces coverage reports. It supports centralised testing and distributed testing in both load and each modes. It also supports coverage of subprocesses.

Setuptools_scm handles managing your Python package versions in software configuration management (SCM) metadata instead of declaring them as the version argument or in a SCM managed file.

Pycairo is a set of Python bindings for the Cairo graphics library.

Certifi is a Python library that contains a CA certificate bundle, which is used by the Requests library to verify HTTPS requests.

Pluggy is an extraction of the plugin manager as used by Pytest but stripped of Pytest specific details.

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.

This package provides an implementation of importlib.resources for older versions of Python.

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.).