MySQLdb is an interface to the popular MySQL database server for Python. The design goals are:

• with Python database API version 2.0

• Thread-safety

• Thread-friendliness (threads will not block each other)

• Compatibility with MySQL-3.23 and later

This package provides a Pytest plugin that allows multiple failures per test. This is a fork from pytest-expect which includes the following improvements:

• showlocals support (the Pytest option)

• global usage support (a fixture is not required)

• output refinements and tweaks.

SeaSurf is a Flask extension for preventing cross-site request forgery (CSRF). CSRF attacks are problematic because the mechanism they use is relatively easy to exploit. This extension attempts to aid you in securing your application from such attacks. This extension is based on the Django middleware.

The functions and classes in humanfriendly can be used to make text interfaces more user-friendly. It includes tools to parse and format numbers, file sizes, and timespans, timers for long-running operations, menus to allow the user to choose from a list of options, and terminal interaction helpers.

The h5py package provides both a high- and low-level interface to the HDF5 library from Python. The low-level interface is intended to be a complete wrapping of the HDF5 API, while the high-level component supports access to HDF5 files, datasets and groups using established Python and NumPy concepts.

This is a library to allow the easy creation of Relay-compliant servers using the GraphQL Python reference implementation of a GraphQL server. It should be noted that the code is a exact port of the original graphql-relay js implementation from Facebook.

This is Python port of linkify-it, which is a links recognition library with full Unicode support. It has features like:

• Full unicode support, with astral characters

• International domains support

• Allows rules extension and custom normalizers.

Provides a backport of Python 3's csv module for parsing comma separated values. The API of the csv module in Python 2 is drastically different from the csv module in Python 3. This is due, for the most part, to the difference between str in Python 2 and Python 3.

Scikit-rebate is a scikit-learn-compatible Python implementation of ReBATE, a suite of Relief-based feature selection algorithms for Machine Learning. These algorithms excel at identifying features that are predictive of the outcome in supervised learning problems, and are especially good at identifying feature interactions that are normally overlooked by standard feature selection algorithms.

This package provides line_profiler - a Python module for doing line-by-line profiling of functions. kernprof is a convenient script for running either line_profiler or the Python standard library's cProfile or profile modules, depending on what is available. It's a successor of https://github.com/rkern/line_profiler.

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.

python-secretstorage provides a way for securely storing passwords and other secrets. It uses D-Bus Secret Service API that is supported by GNOME Keyring (since version 2.30) and KSecretsService. SecretStorage supports most of the functions provided by Secret Service, including creating and deleting items and collections, editing items, locking and unlocking collections (asynchronous unlocking is also supported).

The simplegeneric module lets you define simple single-dispatch generic functions, akin to Python’s built-in generic functions like len(), iter() and so on. However, instead of using specially-named methods, these generic functions use simple lookup tables, akin to those used by e.g. pickle.dump() and other generic functions found in the Python standard library.

Six is a Python 2 and 3 compatibility library. It provides utility functions for smoothing over the differences between the Python versions with the goal of writing Python code that is compatible on both Python versions. Six supports every Python version since 2.5. It is contained in only one Python file, so it can be easily copied into your project.

This hook sends emails describing changes introduced by pushes to a Git repository. For each reference that was changed, it emits one ReferenceChange email summarizing how the reference was changed, followed by one Revision email for each new commit that was introduced by the reference change.

This script is designed to be used as a post-receive hook in a Git repository

This package supports the efficient creation of hookable objects, which are callable objects that are meant to be optionally replaced. The idea is that you create a function that does some default thing and make i hookable. Later, someone can modify what it does by calling its sethook method and changing its implementation. All users of the function, including those that imported it, will see the change.

zipstream.py is a zip archive generator based on zipfile.py. It was created to generate a zip file generator for streaming. This is beneficial for when you want to provide a downloadable archive of a large collection of regular files, which would be infeasible to generate the archive prior to downloading or of a very large file that you do not want to store entirely on disk or on memory.

gcvb (generate compute validate benchmark) is a Python 3 module aiming at facilitating non-regression, validation and benchmarking of simulation codes. gcvb is not a complete tool of continuous integration (CI). It is rather a component of the testing part of a CI workflow. It can compare the different metrics of your computation with references that can be a file, depends of the 'configuration' or are absolute. This is the fork of Marek Felšöci.

This package provides Python implementation of ASDF - a proposed next generation interchange format for scientific data. ASDF aims to exist in the same middle ground that made FITS so successful, by being a hybrid text and binary format: containing human editable metadata for interchange, and raw binary data that is fast to load and use. Unlike FITS, the metadata is highly structured and is designed up-front for extensibility.

The purpose of the ufonormalizer command is to provide a standard formatting so that updates to UFO data can be usefully versioned. Examples of formatting applied by ufoNormalizer include:

• Changing floating-point numbers to integers where it doesn't alter the value (e.g. x="95.0" becomes x="95")

• Rounding floating-point numbers to 10 digits

• Formatting XML with tabs rather than spaces.

This is a set of functions for processing raw scDam&T-seq data. scDam&T-seq is a method to simultaneously measure protein-DNA interactions and transcription from single cells (Rooijers et al., 2019). It combines a DamID-based method to measure protein-DNA interactions and an adaptation of CEL-Seq to measure transcription. The starting point of the workflow is raw sequencing data and the end result are tables of UMI-unique DamID and CEL-Seq counts.

Pandoc is a powerful utility to transform various input formats into a wide range of output formats. To alter the exported output document, Pandoc allows the usage of filters, which are pipes that read a JSON serialization of the Pandoc AST from stdin, transform it in some way, and write it to stdout. It allows therefore to alter the processing of Pandoc's supported input formats, for instance one can add new syntax elements to markdown, etc.

This package provides Python bindings.

Deterministically encode JSON.

• Encodes objects and arrays as RFC 7159 JSON.

• Sorts object keys so that you get the same result each time.

• Has no insignificant whitespace to make the output as small as possible.

• Escapes only the characters that must be escaped, U+0000 to U+0019 / U+0022 / U+0056, to keep the output as small as possible.

• Uses the shortest escape sequence for each escaped character.

• Encodes the JSON as UTF-8.

• Can encode frozendict immutable dictionaries.

This package implements a multi-dimensional spatial image data structure for scientific Python.

To facilitate:

• Multi-scale processing and analysis

• Registration

• Resampling

• Subregion parallel processing

• Coupling with meshes, point sets, and annotations

with scientific images, which are typically multi-dimensional with anisotropic sampling, this package provides a spatial-image data structure. In addition to an N-dimensional array of pixel values, spatial metadata defines the location of the pixel sampling grid in space time. It also labels the array dimensions. This metadata is easily utilized and carried through image processing pipelines.