yaml2cli: Script Generator that organizes cli args by YAML

X.Org X11 libXrender runtime library

🌊 Online machine learning in Python

regular expression library

Unittest extensions for Flask

LibThai is a set of Thai language support routines aimed to ease developers' tasks to incorporate Thai language support in their applications. It includes important Thai-specific functions e.g. word breaking, input and output methods as well as basic character and string supports.

amqplib fork

An R interface to the Tiingo stock price API

Microservice to generate Jupyter reports by executing notebook and exporting them to static HTML page combining [papermill](https://papermill.readthedocs.io/en/latest/) and [nbconvert](nbconvert.readthedocs.io/). It can be run as a standalone application or as a JupyterHub service.

Create easy-to-use Query objects that can apply on NumPy structured arrays, astropy Table, and Pandas DataFrame

Python wrapper around cvodes (from the sundials library)

xeus-robot is a Jupyter kernel for the Robot Framework based on the Xeus library, a native implementation of the Jupyter protocol.

Simple wrapper to run a Plotly Dash script inside Tornado

A fully featured logging framework for R

Python package for the PDAL library.

C++ Port of the TurboReg/StackReg ImageJ Plugin. Original code by Philippe Thevenaz (see below). Porting by Gregor Lichtner. This work is based on the following paper: P. Thevenaz, U.E. Ruttimann, M. Unser A Pyramid Approach to Subpixel Registration Based on Intensity IEEE Transactions on Image Processing vol. 7, no. 1, pp. 27-41, January 1998. This paper is available on-line at http://bigwww.epfl.ch/publications/thevenaz9801.html Other relevant on-line publications are available at http://bigwww.epfl.ch/publications/

This package contains the libraries amd header files that are needed for writing applications with the GTK+ widget toolkit. If you plan to develop applications with GTK+, consider installing the gtk2-devel-docs package.

Choose Univariate Class Intervals

Fast and versatile argument checks

Mesa-based DRI drivers.

pyspectral is a package to read and manipulate satellite sensor spectral responses and solar irradiance spectra

SignalR Core python client

C library for the Public Suffix List

MeshPy offers quality triangular and tetrahedral mesh generation for Python. Meshes of this type are chiefly used in finite-element simulation codes, but also have many other applications ranging from computer graphics to robotics. In order to generate 2D and 3D meshes, MeshPy provides Python interfaces to three well-regarded mesh generators, [Triangle](http://www.cs.cmu.edu/~quake/triangle.html) by J. Shewchuk, [TetGen](http://tetgen.berlios.de/) by Hang Si, and [gmsh](http://www.geuz.org/gmsh/) by Christophe Geuzaine and Jean-Francois Remacle. The former two are included in the package in slightly modified versions. A generic mesh reader for the latter is included, as is an easy way to run gmsh from a Python script. As of Version 0.91.2, MeshPy also works with Python 3.

KBookmarks lets you access and manipulate bookmarks stored using the XBEL format. The most common use for bookmarks is web browsers, but this can also be useful in any application where local files or URLs can be saved as bookmarks.

Regularization paths for regression models with grouped covariates

wxWidgets is a C++ library that lets developers create applications for Windows, macOS, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. It's also extensive, free, open-source and mature.

Monitoring filesystems events with inotify on Linux.

Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently, featuring tight integration with NumPy, transparent use of a GPU, efficient symbolic differentiation, speed and stability optimizations and dynamic C code generation.

X.Org X11 libXdamage development package.

PLINK reader for Python.

Community Diagnostics Package

An FTP transport adapter for use with the Python Requests library.

GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.

The newrelic package instruments your application for performance monitoring and advanced performance analytics with New Relic. Pinpoint and solve Python application performance issues down to the line of code. New Relic APM is the only tool you’ll need to see everything in your Python application, from the end user experience to server monitoring. Trace problems down to slow database queries, slow 3rd party APIs and web services, caching layers, and more. Monitor your app in a production environment and make sure your app can stand a big spike in traffic by running scalability reports.

The StaticFrame library defines the Series and Frame, immutable data structures for one- and two-dimensional calculations with self-aligning, labelled axes. StaticFrame meets the need for an immutable, Pandas-like DataFrame with a modern and interface. StaticFrame is suitable for applications in data science, data engineering, finance, scientific computing, and related fields where reducing opportunities for error by prohibiting mutation is critical. While many interfaces are similar to Pandas, StaticFrame deviates from Pandas in many ways: all data is immutable, and all indices are unique; the full range of NumPy data types is preserved, and date-time indices use discrete NumPy types; hierarchical indices are seamlessly integrated; and uniform approaches to element, row, and column iteration and function application are provided. Core StaticFrame depends only on NumPy: Pandas is not a dependency. A wide variety of table storage and representation formats are supported, including input from and output to CSV, TSV, JSON, Excel XLSX, SQLite, HDF5, NumPy, Pandas, Arrow, and Parquet; additionally, output to xarray, HTML, RST, Markdown, and LaTeX is supported, as well as HTML representations in Jupyter notebooks. The Bus, a container of Frames, permits writing to and lazily reading from multi-table storage formats, including zipped pickles, XLSX workbooks, SQLite, and HDF5.

SendGrid Python library. This library allows you to quickly and easily use the SendGrid Web API v3 via Python

The OpenJDK development tools.

This is a backport of the standard library typing module to Python versions older than 3.5. Typing defines a standard notation for Python function and variable type annotations. The notation can be used for documenting code in a concise, standard format, and it has been designed to also be used by static and runtime type checkers, static analyzers, IDEs and other tools.

SQLAlchemy dialect for Turbodbc

This module provides the ConfigParser class which implements a basic configuration language which provides a structure similar to what's found in Microsoft Windows INI files.

Collection of common code that's shared among different research projects in FAIR computer vision team.

Tool to convert geopandas vector data into rasterized xarray data.

Consider TPOT your Data Science Assistant. TPOT is a Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming. TPOT will automate the most tedious part of machine learning by intelligently exploring thousands of possible pipelines to find the best one for your data. Once TPOT is finished searching (or you get tired of waiting), it provides you with the Python code for the best pipeline it found so you can tinker with the pipeline from there. TPOT is built on top of scikit-learn, so all of the code it generates should look familiar... if you're familiar with scikit-learn, anyway. TPOT is still under active development and we encourage you to check back on this repository regularly for updates.

GStreamer Base Plug-ins is a well-groomed and well-maintained collection of GStreamer plug-ins and elements, spanning the range of possible types of elements one would want to write for GStreamer.

Schedule an R function or formula to run after a specified period of time.

🌐 R package: Identify Global Objects in R Expressions

Programmer friendly subprocess wrapper

Package to parse decay files, describe and convert particle decays between digital representations.

This metapackage exists to define the Rubin Observatory common software environment, including version specifications where needed, while allowing users flexibility when installing additional packages into the same environment.

The ATK library provides a set of interfaces for adding accessibility support to applications and graphical user interface toolkits. By supporting the ATK interfaces, an application or toolkit can be used with tools such as screen readers, magnifiers, and alternative input devices.

A text progress bar is typically used to display the progress of a long running operation, providing a visual cue that processing is underway. The ProgressBar class manages the current progress, and the format of the line is given by a number of widgets. A widget is an object that may display differently depending on the state of the progress bar. There are many types of widgets: - `Timer` - `ETA` - `AdaptiveETA` - `FileTransferSpeed` - `AdaptiveTransferSpeed` - `AnimatedMarker` - `Counter` - `Percentage` - `FormatLabel` - `SimpleProgress` - `Bar` - `ReverseBar` - `BouncingBar` - `RotatingMarker` - `DynamicMessage` The progressbar module is very easy to use, yet very powerful. It will also automatically enable features like auto-resizing when the system supports it.

Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. Applications built with NSS can support SSL v3, TLS, PKCS #5, PKCS #7, PKCS #11, PKCS #12, S/MIME, X.509 v3 certificates, and other security standards.

MNELAB - a GUI for MNE

A library for comparing results of predictive models on single or multiple data sets using Bayesian approaches. The libary is in pure Python, and depends on numpy, scipy and matplotlib. The more advanced hierarchical tests require pystan, which needs to be installed separately.

PyEphem provides an ``ephem`` Python package for performing high-precision astronomy computations. The underlying numeric routines are coded in C and are the same ones that drive the popular `XEphem`_ astronomy application, whose author, Elwood Charles Downey, generously gave permission for their use in PyEphem. The name *ephem* is short for the word *ephemeris*, which is the traditional term for a table giving the position of a planet, asteroid, or comet for a series of dates. The design of PyEphem emphasizes convenience and ease of use. Both celestial bodies and the observer's location on Earth are represented by Python objects, while dates and angles automatically print themselves in standard astronomical formats.

Conda environment and package management extension from within Jupyter

Numpy's documentation uses several custom extensions to Sphinx. These are shipped in this numpydoc package, in case you want to make use of them in third-party projects.

Create and publish interactive reports in Python. Datapane is an open source framework which makes it easy to turn scripts and notebooks into interactive reports.

LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. Today, LAME is considered the best MP3 encoder at mid-high bitrates and at VBR, mostly thanks to the dedicated work of its developers and the open source licensing model that allowed the project to tap into engineering resources from all around the world.

This module provides a nearly complete wrapping of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects, and each of these is exposed as a Python type in the bsddb3.db module. The database objects can use various access methods: btree, hash, recno, and queue. Complete support of Berkeley DB distributed transactions. Complete support for Berkeley DB Replication Manager. Complete support for Berkeley DB Base Replication. Support for RPC.

A library to support the Internationalised Domain Names in Applications (IDNA) protocol as specified in RFC 5891. This version of the protocol is often referred to as "IDNA2008".

Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy

Python Binding for xxHash

Jupyter Packaging Utilities

Mesh Data Abstraction Library (MDAL) is a C++ library for handling unstructured mesh data released with MIT license. It provides a single data model for multiple supported data formats. MDAL is used by QGIS for data access for mesh layers.

A conda-smithy repository for conda-forge-build-setup.

PyMongo - the Python driver for MongoDB

A simple Python wrapper around inotify. No fancy bells and whistles, just a literal wrapper with ctypes.

NetScape Portable Runtime (NSPR) provides platform independence for non-GUI operating system facilities. These facilities include threads, thread synchronization, normal file and network I/O, interval timing and calendar time, basic memory management (malloc and free) and shared library linking.

Fontconfig is a library designed to provide system-wide font configuration, customization and application access.

The Fast Conda and Mamba Package Builder

An open source application framework for building scalable, user-friendly scientific applications.

pyScss is a compiler for the Sass language, a superset of CSS3 that adds programming capabilities and some other syntactic sugar.

This package provides a python implementation of the Hierarchichal Veto (hveto) algorithm

A port of Ruby on Rails' inflector to Python

Genozip (available on Conda, Docker Hub and https://github.com/divonlan/genozip) Genozip is a compressor for genomic files - while it can compress any file (i.e. not only genomic files), it is optimized to compress FASTQ, SAM/BAM/CRAM, VCF/BCF, FASTA, GVF and 23andMe files. It can even compress them if they are already compressed with .gz .bz2 .xz (for full list of supported file types see 'genozip --help=input'). The compression ratio depends on the data being compressed, and you can usually expect about a 1.5-3X ratio when compressing .bam, 2X-5X for .fastq.gz files (i.e. compressing already-compressed files), and up to 200X when compressing an uncompressed high-sample-count .vcf file with only GT data. Sign up to receive low-frequency updates related to Genozip: https://tinyurl.com/genozip The compression is lossless - the decompressed file is 100% identical to the original file. Notes: 1. Losslessness when the original file is already compressed (with .gz, .bz2 or .xz as well as .bam) is relative to the underlying uncompressed file. If the original file was compressed with BGZF (as in BAM and most genomic files with a .gz extension) - genounzip will re-compresses the file with BGZF upon decompression (unless --plain is specified), and, further, it will attempt to recover the exact same BGZF compression as in the original file. However, sometimes exact-same BGZF compression is not possible due to different libraries used. 2. The one exception to Genozip's strict losslessness is when using the --optimize option which is lossy (see --help for details) The command line options are similar to gzip and samtools/bcftools, so if you are familiar with these, it works pretty much the same. To get started, try: genozip --help Commands: genozip - compress one or more files genounzip - decompress one or more files genols - show metadata of one or more files or the entire directory genocat - view one or more files Some examples: Creating a reference file: genozip --make-reference myfasta.fa Compressing a FASTQ, SAM/BAM or VCF file(s) with a reference: genozip --reference myfasta.ref.genozip mysample1.fq mysample2.fq mysample3.fq genozip --reference myfasta.ref.genozip mysample.bam genozip --reference myfasta.ref.genozip mysamples.vcf.gz genozip --reference myfasta.ref.genozip * ←compresses all files in the current directory Notes: 1. Genozip can compress with or without a reference - using a reference achieves much better compression when compressing FASTQ or unaligned SAM/BAM, and modestly better compression in other cases 2. SAM/BAM - compression of aligned or unaligned SAM/BAM files is possible. Sorting makes no difference 3. Long reads - compression of long reads (Pac Bio / Nanopore) achieves signficantly better results when compressing an aligned BAM vs an unaligned BAM or FASTQ 4. Compression of CRAM (but not SAM or BAM) files requires samtools to be installed 5. Use --REFERENCE instead of --reference to store the relevant parts of the reference file as part of the compressed file itself, which will then allow decompression with genounzip without need of the reference file. Compressing and uncompressing paired-end reads with --pair - better than compressing FASTQs individually genozip --reference myfasta.ref.genozip --pair mysample-R1.fastq.gz mysample-R2.fastq.gz genounzip --reference myfasta.ref.genozip --unbind mysample-R1+2.fastq.genozip Using genozip in a pipline: genocat mysample.sam.genozip | samtools - ..... my-sam-outputing-method | genozip - --input sam --output mysample.sam.genozip Lookups, downsampling and other subsets: genocat --regions chr1:10000-20000 mysamples.vcf.genozip ←displays a specific region genocat --regions ^Y,MT mysample.bam.genozip ←displays all alignments except Y and MT contigs genocat --regions chrM GRCh38.fa.genozip ←displays the sequence of chrM genocat --samples SMPL1,SMPL2 mysamples.vcf.genozip ←displays 2 samples genocat --grep 1101:2392 myreads.fq.genozip ←displays reads that have "1101:2392" anywhere in the description genocat --downsample 10 mysample.fq.genozip ←displays 1 in 10 reads Notes: 1. --regions works with VCF, SAM/BAM, FASTA, 23andMe, GVF and reference files ; --grep works with FASTQ, FASTA ; --samples works with VCF ; --downsample works with all types 2. There is no need for a separate indexing step or index file 3. Many more options (see --help for full list): --no-header ; --header-only ; --header-one ; --sequential ; --list-chroms ; --drop-genotypes ; --GT-only Binding mutiple files into a single genozip file and unbinding: genozip *.fq.gz -o all-samples.fq.genozip ←binds all .fq.gz files in the current directory genounzip my-project.fq.genozip --unbind Compressing even better, with some minor modifications of the data (therefore not lossless, see --help for details): genozip file.bam --optimize Compressing faster, sacrificing a bit of compression ratio: genozip file.bam --fast Encrypting (256 bit AES): genozip file.vcf --password abc genounzip file.vcf.genozip --password abc Converting SAM/BAM to FASTQ: genounzip file.bam.genozip --fastq Converting 23andMe to VCF: genounzip genome_mydata-Full.txt.genozip --vcf -e GRCh37.ref.genozip Generate a samtools/bcftools index file when uncompressing: genounzip file.bam.genozip --index Calculating the MD5 of the underlying textual file (also included in --test): genozip file.vcf --md5 genounzip file.vcf.genozip --md5 genols file.vcf.genozip Compressing and then verifying that the compressed file decompresses correctly: genozip file.vcf --test Citing Do you find Genozip useful? Please support continued development by citing: Lan, D., et al. Bioinformatics, 36, 4091–4092, July 2020, https://doi.org/10.1093/bioinformatics/btaa290 Feature requests and bug reports: bugs@genozip.com Genozip is free for non-commercial use. For a commercial license, please contact sales@genozip.com Usage is subject to terms and conditions. The non-commercial license can be viewed with genozip --license THIS SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Systematic force field optimization.

Multi-user server for Jupyter notebooks

Python interface for ERDDAP

pyquery allows you to make jquery queries on xml documents. The API is as much as possible the similar to jquery. pyquery uses lxml for fast xml and html manipulation.

NTL is a high-performance, portable C++ library providing data structures and algorithms for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the integers and over finite fields.