Gyselalib++ is a collection of C++ components for writing gyrokinetic semi-lagrangian codes and similar as well as a collection of such codes.

ROOT is a data analysis framework developed by CERN for tasks such as data storage, processing, and visualization. It provides tools for histograms, statistical tests, fitting, simulations, and machine learning. It can handle large datasets and uses a specialized file format.

FCLIB is an open source collection of Frictional Contact (FC) problems stored in a specific HDF5 format with a light implementation in C Language of Input/Output functions to read and write those problems.

Stand-alone application and Python tools for interactive and/or batch processing analysis of X-Ray Fluorescence Spectra.

FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, …), for a total of 30 different file formats (like CBF, EDF, TIFF, …) and offers an unified interface to their headers (as a Python dictionary) and datasets (as a numpy ndarray of integers or floats).

This package provides a Zarr I/O backend for the HDMF.

Chaco is a Python package for building interactive and custom 2-D plots and visualizations. Chaco facilitates writing plotting applications at all levels of complexity, from simple scripts with hard-coded data to large plotting programs with complex data interrelationships and a multitude of interactive tools. While Chaco generates attractive static plots for publication and presentation, Chaco differs from tools like Matplotlib in that it also works well for dynamic interactive data visualization and exploration.

This package provides a Python library for generating word clouds.

This inspector is meant as a companion to the PyNWB validator, which checks for strict schema compliance. This tool attempts to apply some common sense to find components of the file that are technically compliant, but possibly incorrect, suboptimal in their representation, or deviate from best practices.

nwb2bids reorganizes NWB files into a BIDS directory layout.

Features:

• Automatically renames NWB files and their directories to conform to BIDS conventions.

• Extracts relevant metadata from NWB files to populate BIDS sidecar TSV & JSON files.

• Currently supports BEP32 (micro-electrode electrophysiology) data types, such as extracellular (ecephys) and intracellular (icephys) electrophysiology, as well as associated behavioral events.

Paste provides a variety of web development tools and middleware which can be nested together to build web applications. Paste's design closely follows ideas flowing from WSGI (Web Standard Gateway Interface).

Table logger using Rich, aimed at PyTorch Lightning logging.

Features

• display your training logs with pretty rich tables

• describe your fields with goal, format and name

• a field descriptor can be matched with any regex

• a field name can be computed as a regex substitution

• works in Jupyter notebooks as well as in a command line

• integrates easily with Pytorch Lightning

The TraitsUI project provides a toolkit-independent GUI abstraction layer, which is used to support the “visualization” features of the Traits package. You can write a model using the Traits API and specify a GUI using the TraitsUI API (views, items, editors, etc.), and let TraitsUI and your selected toolkit back-end (Qt or Wx) take care of the details of displaying them.

The Traits library is designed to enhance object-oriented programming in Python by providing a way to define and manage attributes of objects more effectively.

This package provides a flexible utility for flattening and unflattening dict-like objects in Python.

Click is a package for creating powerful and beautiful command line interfaces (CLI) in Python, but it has no the functionality for creating option groups. The aim of this package is to provide group options with extensible functionality using canonical and clean API (Click-like API as far as possible).

This package provides common CLI patterns on top of Click.

Easily pick a place to store data for your Python code.

This package provides an implementation of chunked, compressed, N-dimensional arrays for Python.

colourmap is a Python package which generates N unique colors from the specified input colormap.

bezier is a Python helper for Bézier curves and surfaces. Bézier curves (and surfaces) are parametric curves with polynomial components, but they are expressed in terms of the Bernstein basis rather than the traditional power basis.

This package provides a hierarchical data modeling framework for modern science data standards.

This package provides a library to find out what is still holding a reference to an object that should be dead. It is used to track down reference leaks in MNE-Python, PyVista and pyvistaqt.

scitrack is a simple package aimed at researchers writing scripts, or more substantial scientific software, to support the tracking of scientific computation. The package provides elementary functionality to support logging. The primary capabilities concern generating checksums on input and output files and facilitating logging of the computational environment.