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). You can see the tests results here.
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. |
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Efficiently computes derivatives of NumPy code. |
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An implementation of Wilkinson formulas. |
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Python library parsing HL7 v2.x messages. |
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Robust Hypothesis Testing of Location Parameters using Lq-Likelihood-Ratio-Type Test in Python. |
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Parameterize and run Jupyter and nteract Notebooks. |
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An open-source interactive data visualization library for Python. |
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Use in a jupyter notebook requires |
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A Grammar of Graphics for Python. |
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Frequent Item Set Mining and Association Rule Induction for Python. |
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A Python library for creating LaTeX files and snippets. |
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Requires LaTeX |
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Python library for interfacing with Cedrus XID devices, e.g. StimTracker, Riponda, RB-x40, c-pod, and Lumina. |
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Requires ftd drivers: https://pypi.org/project/ftd2xx/ |
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RatInABox: A package for simulating spatial navigation and spatial representation neural data in continuous 2D environments. |
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Read ROI files .zip or .roi generated with ImageJ. |
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Scikit-learn models hyperparameters tuning and features selection, using evolutionary algorithms. |
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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. |
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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 |
|---|---|---|
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The Bokeh Visualization Library |
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Blue Brain Python Optimisation Library |
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Numerical tool for performing uncertainty quantification using polynomial. |
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Thread-safe connection pool for python. |
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Keep code, data, containers under control with git and git-annex. |
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Super-fast, efficiently stored Trie for Python. |
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Python package for reading, timeshifting and writing sensor data. |
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C++ port of earcut.js, a fast, header-only polygon triangulation library. |
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C/C++ library to read/write EDF+ and BDF+ files. |
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Directory structure standard for experimental pipelines. |
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An automatic Changelog generator using Jinja2 templates. From git logs to change logs. |
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GNU Octave: Scientific programming language. FOSS, compatible with Matlab scripts. |
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An efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). |
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A single-file header-only version of ISO C++ Guidelines Support Library (GSL) for C++98, C++11, and later. |
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A modern header-only C++11 friendly interface for libhdf5 |
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Library for bio-inspired computational intelligence. |
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Interrogate a codebase for docstring coverage. |
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A JSON/UBJSON/MessagePack encoder/decoder for GNU Octave. |
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A lightweight LLVM-Python binding for writing JIT compilers. |
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Very fast and quite robust triangulation of 2D polygons. |
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Venn diagram plotting routines for Python/Matplotlib. |
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Missing data visualization module for Python. |
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A python and C++ library for reading and writing neuronal morphologies. |
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Python toolkit for the analysis and processing of neuron morphologies. |
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OWL-RL and RDFS based RDF Closure inferencing for Python. |
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Virtual environment manager written in pure Python. |
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An open-source, interactive data visualization library for Python. |
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A friend to fetch your data files. |
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Framework for managing and maintaining multi-language pre-commit hooks. |
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A Progressbar library to provide visual progress to long running operations. |
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A python Linear Programming API. |
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Python library to read/write EDF+/BDF+ files, based on EDFlib. |
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Parameter exploration toolbox. |
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Phase plane analysis of nonlinear systems |
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Python module providing rate limiting. |
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Python rdflib extension adding JSON-LD parser and serializer. |
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Nature-inspired algorithms for hyper-parameter tuning of Scikit-Learn models. |
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Workflow management system to create reproducible and scalable data analyses. |
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A powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts. |
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Timeout control decorator and context managers. |
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Implements a topological sort algorithm. |
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Visualizing categorical data. |
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wxnatpy is a wxPython widget which allows users to browse the contents of a XNAT repository. |
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A new XNAT client that exposes XNAT objects/functions as python objects/functions. |
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A portable data compression/decompression toolbox for GNU Octave. |
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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:
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The Python plotting package. |
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Jupyter notebook. |
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Fundamental package for array computing with Python. |
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Python Data Analysis library. |
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The Python Imaging Library. |
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Read ROI files .zip or .roi generated with ImageJ. |
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Collection of algorithms for image processing. |
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Machine learning in Python. |
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Python library for scientific computing. |
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Statistics in Python. |
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Library for symbolic mathematics. |
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An interactive multitool for tabular data. |
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