The nbconvert tool, jupyter nbconvert, converts notebooks to various other formats via Jinja templates. It allows you to convert an .ipynb notebook file into various static formats including:

1. HTML

2. LaTeX

3. PDF

4. Reveal JS

5. Markdown (md)

6. ReStructured Text (rst)

7. executable script

The asttokens module annotates Python abstract syntax trees (ASTs) with the positions of tokens and text in the source code that generated them. It makes it possible for tools that work with logical AST nodes to find the particular text that resulted in those nodes, for example for automated refactoring or highlighting.

pycountry provides the ISO databases for the standards:

1. 639-3 (Languages)

2. 3166 (Countries)

3. 3166-3 (Deleted Countries)

4. 3166-2 (Subdivisions of countries)

5. 4217 (Currencies)

6. 15924 (Scripts)

It includes a copy from Debian’s pkg-isocodes and makes the data accessible through a Python API.

Soup Sieve is a CSS selector library designed to be used with Beautiful Soup 4. It aims to provide selecting, matching, and filtering using modern CSS selectors. Soup Sieve currently provides selectors from the CSS level 1 specifications up through the latest CSS level 4 drafts and beyond (though some are not yet implemented).

pycountry provides the ISO databases for the standards:

1. 639-3 (Languages)

2. 3166 (Countries)

3. 3166-3 (Deleted Countries)

4. 3166-2 (Subdivisions of countries)

5. 4217 (Currencies)

6. 15924 (Scripts)

It includes a copy from Debian’s pkg-isocodes and makes the data accessible through a Python API.

Astrolib PySynphot (hereafter referred to only as pysynphot) is an object-oriented replacement for STSDAS SYNPHOT synthetic photometry package in IRAF. pysynphot simulates photometric data and spectra as they are observed with the Hubble Space Telescope (HST). Passbands for standard photometric systems are available, and users can incorporate their own filters, spectra, and data.

SnapTools can operate on snap files the following types of operations:

• index the reference genome before alignment;

• align reads to the corresponding reference genome;

• pre-process by convert pair-end reads into fragments, checking the mapping quality score, alignment and filtration;

• create the cell-by-bin matrix.

FontTools/TTX is a library to manipulate font files from Python. It supports reading and writing of TrueType/OpenType fonts, reading and writing of AFM files, reading (and partially writing) of PS Type 1 fonts. The package also contains a tool called “TTX” which converts TrueType/OpenType fonts to and from an XML-based format.

This package provides both simple, atomic constructs (such as integers of various sizes), as well as composite ones which allow you form hierarchical and sequential structures of increasing complexity. It features bit and byte granularity, easy debugging and testing, an easy-to-extend subclass system, and lots of primitive constructs to make your work easier.

The main purpose of this package is to provide more complex arithmetic operations on dates/times. Heavy use is made of the relativedelta type from the dateutil library. Much of this package is just a light wrapper on top of this with some added features such as range generation and business day calculation.

The xmlschema library is an implementation of XML Schema for Python. It has full support for the XSD 1.0 and 1.1 standards, an XPath-based API for finding schema's elements and attributes; and can encode and decode XML data to JSON and other formats.

This package includes simulation models for an induction motor, a synchronous reluctance motor, and a permanent-magnet synchronous motor. The motor models are simulated in the continuous-time domain while the control algorithms run in discrete time. The default solver is the explicit Runge-Kutta method of order 5(4) from scipy.integrate.solve_ivp.

The goal of GeoPandas is to make working with geospatial data in Python easier. It combines the capabilities of Pandas and Shapely, providing geospatial operations in Pandas and a high-level interface to multiple geometries to Shapely. GeoPandas enables you to easily do operations in Python that would otherwise require a spatial database such as PostGIS.

specutils is a Python package for representing, loading, manipulating,and analyzing astronomical spectroscopic data. The generic data containers and accompanying modules provide a toolbox that the astronomical community can use to build more domain-specific packages. For more details about the underlying principles, see APE13.

geosketch is a Python package that implements the geometric sketching algorithm described by Brian Hie, Hyunghoon Cho, Benjamin DeMeo, Bryan Bryson, and Bonnie Berger in "Geometric sketching compactly summarizes the single-cell transcriptomic landscape", Cell Systems (2019). This package provides an example implementation of the algorithm as well as scripts necessary for reproducing the experiments in the paper.

HTML to Text is a Python library for extract text from HTML. Contrary to other solution such as LXML or Beautiful Soup, the text extracted with html_text does not contain elements such as JavaScript or inline styles not normally visible to users. It also normalizes white space characters in a smarter, more visually pleasing style.

Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.

Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.

Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Importantly, "informative" is decided based on how well a gene's variation agrees with some cell metric---some similarity mapping between cells. Genes which are informative are those whose expression varies in similar way among cells which are nearby in the given metric.

This package provides an implementation of the Ensemble Slice Sampling method. Features:

• fast & Robust Bayesian Inference

• efficient Markov Chain Monte Carlo (MCMC)

• black-box inference, no hand-tuning

• excellent performance in terms of autocorrelation time and convergence rate

• scale to multiple CPUs without any extra effort

• automated Convergence diagnostics

pyjanitor provides a set of data cleaning routines for pandas DataFrames. These routines extend the method chaining API defined by pandas for a subset of its methods. Originally, this package was a port of the R package by the same name and it is inspired by the ease-of-use and expressiveness of the dplyr package.

This package provides more-reasonable core functionality for numpy.

A lot of numpysane functionality is inspired by PDL (Perl Data Language).

numpysane has:

• easier broadcasting

• nicer array manipulation

• array concatenation

• manipulation of dimensions

• broadcast-aware inner product

• broadcast-aware outer product

• broadcast-aware 2-norm

• broadcast-aware matrix multiplication

Blessings is a pythonic API to manipulate terminal color, styling, and positioning. It provides similar features to curses but avoids some of curses’s limitations: it does not require clearing the whole screen for little changes, provides a scroll-back buffer after the program exits, and avoids styling altogether when the output is redirected to something other than a terminal.

Hatch is a modern, extensible Python project manager. It has features such as:

• Standardized build system with reproducible builds by default

• Robust environment management with support for custom scripts

• Easy publishing to PyPI or other indexes

• Version management

• Configurable project generation with sane defaults

• Responsive CLI, ~2-3x faster than equivalent tools.