genomepy is designed to provide a simple and straightforward way to download and use genomic data. This includes

1. searching available data,

2. showing the available metadata,

3. automatically downloading, preprocessing and matching data, and

4. generating optional aligner indexes.

All with sensible, yet controllable defaults.

This is a Python library that aims at making tensor learning simple and accessible. It allows performing tensor decomposition, tensor learning and tensor algebra easily. Its backend system allows seamlessly perform computation with NumPy, PyTorch, JAX, MXNet, TensorFlow or CuPy and run methodxs at scale on CPU or GPU.

tinycss2 can parse strings, return Python objects representing tokens and blocks, and generate CSS strings corresponding to these objects.

Based on the CSS Syntax Level 3 specification, tinycss2 knows the grammar of CSS but doesn’t know specific rules, properties or values supported in various CSS modules.

This Python library provides a recursive descent parser with backtracking and memoization (a.k.a. packrat parser). Arpeggio grammars are based on PEG formalism. Arpeggio's main use is a foundation for a toolchain for DSL development but it can be used for all sorts of general purpose parsing.

PETSc, the Portable, Extensible Toolkit for Scientific Computation, is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for all message-passing communication. petsc4py provides Python bindings to almost all functions of PETSc.

This library provides a publish-subscribe API to facilitate event-based or message-based architecture in a single-process application. It is centered on the notion of a topic - senders publish messages of a given topic, and listeners subscribe to messages of a given topic, all inside the same process.

This package provides an implementation of the Web Application Messaging Protocol (WAMP). WAMP connects components in distributed applications using Publish and Subscribe (PubSub) and routed Remote Procedure Calls (rRPC). It is ideal for distributed, multi-client and server applications such as IoT applications or multi-user database-driven business applications.

Billiard is a fork of the Python 2.7 multiprocessing package. The multiprocessing package itself is a renamed and updated version of R Oudkerk's pyprocessing package. This standalone variant is intended to be compatible with Python 2.4 and 2.5, and will draw its fixes/improvements from python-trunk.

This package provides a deconvolution based on Single Nucleotide Position (SNP) for multiplexed scRNA-seq data. The name vireo stand for Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data and follows the clone identification from single-cell data named cardelino.

python-gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. The files are loaded into a SQLite database, allowing much more complex manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone.

pyregion is a python module to parse ds9 region files. It also supports ciao region files. Features:

• ds9 and ciao region files.

• (physical, WCS) coordinate conversion to the image coordinate.

• convert regions to matplotlib patches.

• convert regions to spatial filter (i.e., generate mask images)

Docutils is a modular system for processing documentation into useful formats, such as HTML, XML, and LaTeX. It uses reStructuredText, an easy to use markup language, for input.

This package provides tools for converting .rst files to other formats via commands such as rst2man, as well as supporting Python code.

Jupytext is a plugin for Jupyter that can save Jupyter notebooks as either Markdown files or scripts in many languages. Common use cases for Jupytext are:

• version control on Jupyter Notebooks

• editing, merging or refactoring notebooks in your favorite text editor

• applying Q&A checks on notebooks.

Docutils is a modular system for processing documentation into useful formats, such as HTML, XML, and LaTeX. It uses reStructuredText, an easy to use markup language, for input.

This package provides tools for converting .rst files to other formats via commands such as rst2man, as well as supporting Python code.

The Gurobi Optimizer is a commercial optimization solver for linear programming (LP), quadratic programming (QP), quadratically constrained programming (QCP), mixed integer linear programming (MILP), mixed-integer quadratic programming (MIQP), and mixed-integer quadratically constrained programming (MIQCP). See here for more info: https://www.gurobi.com/documentation/9.0/quickstart_linux/cs_python.html.

This package provides a small library, built on top of pyOpenSSL, which allows for creating a custom certificate authority (CA) certificate, and generating on-demand dynamic host certs using that CA certificate. It is most useful for use with a man-in-the-middle HTTPS proxy, for example, for recording or replaying web content.

If your code lets other people supply callback functions, it's important to specify the function signature you expect, and check that functions support that. Adding extra parameters later would break other peoples code unless you're careful. The backcall package provides a way of specifying the callback signature using a prototype function.

Parallel Python module (PP) provides an easy and efficient way to create parallel-enabled applications for SMP computers and clusters. PP module features cross-platform portability and dynamic load balancing. Thus applications written with PP will parallelize efficiently even on heterogeneous and multi-platform clusters (including clusters running other applications with variable CPU loads).

This Python package is a high-level wrapper for Kerberos (GSSAPI) operations. The goal is to avoid having to build a module that wraps the entire Kerberos.framework, and instead offer a limited set of functions that do what is needed for client/server Kerberos authentication based on <http://www.ietf.org/rfc/rfc4559.txt>.

This package cleans Jupyter notebooks of cell execution counts, metadata, outputs, and empty cells, preparing them for committing to version control. It provides a Git filter to automatically clean notebooks before they're staged, and can also be used with other version control systems, as a command line tool, and as a Python library.

Python is a remarkably powerful dynamic programming language that is used in a wide variety of application domains. Some of its key distinguishing features include: clear, readable syntax; strong introspection capabilities; intuitive object orientation; natural expression of procedural code; full modularity, supporting hierarchical packages; exception-based error handling; and very high level dynamic data types.

Plots, scatter plots, histograms and heatmaps in the terminal using braille dots, and foreground and background colors - with (almost) no dependancies. Make complex figures using the Figure class or make fast and simple plots using graphing function - similar to a very small sibling to matplotlib. Or use the canvas to plot dots, lines and images yourself.

Deepdish is a Python library to load and save HDF5 files. The primary feature of deepdish is its ability to save and load all kinds of data as HDF5. It can save any Python data structure, offering the same ease of use as pickling or numpy.save, but with the language interoperability offered by HDF5.

This package provides a set of handlers for the Python standard library logging package. Some of these handlers are out-of-scope for the standard library, and so they are packaged here. Others are updated versions which have appeared in recent Python releases, but are usable with older versions of Python and so are packaged here.