Utilities
The following tools are among the software currently tested in NeuroFedora:
| Software | Summary | pip (PyPi) | Notes |
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Efficiently computes derivatives of NumPy code. |
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A Grammar of Graphics for Python |
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Python library for reading files in Axon Binary Format (ABF) |
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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. |
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. |
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