Utilities
Upstream packages
The following tools are among the software currently tested in NeuroFedora and can be installed directly from upstream forges (e.g. PyPi):
Python packages
| Software | Summary | pip (PyPi) | Notes |
|---|---|---|---|
Airspeed is a powerful and easy-to-use templating engine for Python that aims for a high level of compatibility with the popular Velocity library for Java. |
|
||
Efficiently computes derivatives of NumPy code. |
|
||
An implementation of Wilkinson formulas. |
|
||
Robust Hypothesis Testing of Location Parameters using Lq-Likelihood-Ratio-Type Test in Python. |
|
||
An open-source interactive data visualization library for Python. |
|
||
A Grammar of Graphics for Python. |
|
||
Frequent Item Set Mining and Association Rule Induction for Python. |
|
||
A Python library for creating LaTeX files and snippets. |
|
Requires LaTeX |
|
Python library for interfacing with Cedrus XID devices, e.g. StimTracker, Riponda, RB-x40, c-pod, and Lumina. |
|
Requires ftd drivers: https://pypi.org/project/ftd2xx/ |
|
RatInABox: A package for simulating spatial navigation and spatial representation neural data in continuous 2D environments. |
|
||
Read ROI files .zip or .roi generated with ImageJ. |
|
||
Scikit-learn models hyperparameters tuning and features selection, using evolutionary algorithms. |
|
Reference/bibliography managers
Fedora does not currently include any of these tools. However, the developers provide pre-built binaries that are ready to use.
Full featured bibliography manager written in Java. |
|
Zotero client. You can also create an account on the Zotero web-service and use it to sync your bibliography between different machines. |
System packages
The following general purpose utilties are included in the repositories:
| Software | Install with | Notes |
|---|---|---|
|
The Bokeh Visualization Library |
|
|
Blue Brain Python Optimisation Library |
|
|
Numerical tool for performing uncertainty quantification using polynomial. |
|
|
Thread-safe connection pool for python. |
|
|
Keep code, data, containers under control with git and git-annex. |
|
|
Super-fast, efficiently stored Trie for Python. |
|
|
Python package for reading, timeshifting and writing sensor data. |
|
|
C++ port of earcut.js, a fast, header-only polygon triangulation library. |
|
|
C/C++ library to read/write EDF+ and BDF+ files. |
|
|
Directory structure standard for experimental pipelines. |
|
|
An automatic Changelog generator using Jinja2 templates. From git logs to change logs. |
|
|
GNU Octave: Scientific programming language. FOSS, compatible with Matlab scripts. |
|
|
An efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). |
|
|
A single-file header-only version of ISO C++ Guidelines Support Library (GSL) for C++98, C++11, and later. |
|
|
A modern header-only C++11 friendly interface for libhdf5 |
|
|
Library for bio-inspired computational intelligence. |
|
|
Interrogate a codebase for docstring coverage. |
|
|
A JSON/UBJSON/MessagePack encoder/decoder for GNU Octave. |
|
|
A lightweight LLVM-Python binding for writing JIT compilers. |
|
|
Very fast and quite robust triangulation of 2D polygons. |
|
|
Venn diagram plotting routines for Python/Matplotlib. |
|
|
Missing data visualization module for Python. |
|
|
A python and C++ library for reading and writing neuronal morphologies. |
|
|
Python toolkit for the analysis and processing of neuron morphologies. |
|
|
OWL-RL and RDFS based RDF Closure inferencing for Python. |
|
|
Virtual environment manager written in pure Python. |
|
|
An open-source, interactive data visualization library for Python. |
|
|
A friend to fetch your data files. |
|
|
Framework for managing and maintaining multi-language pre-commit hooks. |
|
|
A Progressbar library to provide visual progress to long running operations. |
|
|
A python Linear Programming API. |
|
|
Python library to read/write EDF+/BDF+ files, based on EDFlib. |
|
|
Parameter exploration toolbox. |
|
|
Phase plane analysis of nonlinear systems |
|
|
Python module providing rate limiting. |
|
|
Python rdflib extension adding JSON-LD parser and serializer. |
|
|
Nature-inspired algorithms for hyper-parameter tuning of Scikit-Learn models. |
|
|
Workflow management system to create reproducible and scalable data analyses. |
|
|
A powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts. |
|
|
Timeout control decorator and context managers. |
|
|
Implements a topological sort algorithm. |
|
|
Visualizing categorical data. |
|
|
wxnatpy is a wxPython widget which allows users to browse the contents of a XNAT repository. |
|
|
A new XNAT client that exposes XNAT objects/functions as python objects/functions. |
|
|
A portable data compression/decompression toolbox for GNU Octave. |
|
|
A portable library with easy-to-use data compression/decompression interfaces. |
Python Science Stack
The python-science package group includes commonly used scientific Python libraries.
This can be installed using dnf:
sudo dnf install @python-scienceThe individual packages may also be installed independently:
|
The Python plotting package. |
|
|
Jupyter notebook. |
|
|
Fundamental package for array computing with Python. |
|
|
Python Data Analysis library. |
|
|
The Python Imaging Library. |
|
|
Read ROI files .zip or .roi generated with ImageJ. |
|
|
Collection of algorithms for image processing. |
|
|
Machine learning in Python. |
|
|
Python library for scientific computing. |
|
|
Statistics in Python. |
|
|
Library for symbolic mathematics. |
|
|
An interactive multitool for tabular data. |
Want to help? Learn how to contribute to Fedora Docs ›