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

Search:

Software Summary pip (PyPi) Notes

Software	Summary	pip (PyPi)	Notes
airspeed	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.	`airspeed`
autograd	Efficiently computes derivatives of NumPy code.	`autograd`
duecredit	Publications (and donations) tracer.	`duecredit`
editdistance	Fast implementation of the edit distance (Levenshtein distance).	`editdistance`
formulaic	An implementation of Wilkinson formulas.	`formulaic`
hl7	Python library parsing HL7 v2.x messages.	`hl7`
lazyarray	A Python package that provides a lazily-evaluated numerical array class, larray, based on and compatible with NumPy arrays.	`lazyarray`
lqrt	Robust Hypothesis Testing of Location Parameters using Lq-Likelihood-Ratio-Type Test in Python.	`lqrt`
papermill	Parameterize and run Jupyter and nteract Notebooks.	`papermill`
plotly	An open-source interactive data visualization library for Python.	`plotly`	Use in a jupyter notebook requires `jupyter` and `anywidget`
plotnine	A Grammar of Graphics for Python.	`plotnine`
pydeps	Display module dependencies.	`pydeps`
pyemd	A Python wrapper for Ofir Pele and Michael Werman’s implementation of the Earth Mover’s Distance.	`pyemd`	Unmaintained upstream
pyfim	Frequent Item Set Mining and Association Rule Induction for Python.	`pyfim`
pylatex	A Python library for creating LaTeX files and snippets.	`pylatex`	Requires LaTeX
pyplane	Interface to INI’s CoACH class-chip via Teensy based PLANE (Platform for Learning About Neuromorphic Engineering).	`pyplane`	Unmaintained upstream, does not install
pyxid2	Python library for interfacing with Cedrus XID devices, e.g. StimTracker, Riponda, RB-x40, c-pod, and Lumina.	`pyxid2`	Requires ftd drivers: https://pypi.org/project/ftd2xx/
ratinabox	RatInABox: A package for simulating spatial navigation and spatial representation neural data in continuous 2D environments.	`ratinabox`
read-roi	Read ROI files .zip or .roi generated with ImageJ.	`read-roi`
sklearn-genetic-opt	Scikit-learn models hyperparameters tuning and features selection, using evolutionary algorithms.	`sklearn-genetic-opt`
sklearn-nature-inspired-algorithms	Search using nature inspired algorithms over specified parameter values for an sklearn estimator.	`sklearn-nature-inspired-algorithms`	Does not install in Py3.12+. No module named 'numpy.distutils'. No module named 'numpy.distutils'

airspeed

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.

airspeed

autograd

Efficiently computes derivatives of NumPy code.

autograd

duecredit

Publications (and donations) tracer.

duecredit

editdistance

Fast implementation of the edit distance (Levenshtein distance).

editdistance

formulaic

An implementation of Wilkinson formulas.

formulaic

hl7

Python library parsing HL7 v2.x messages.

hl7

lazyarray

A Python package that provides a lazily-evaluated numerical array class, larray, based on and compatible with NumPy arrays.

lazyarray

lqrt

Robust Hypothesis Testing of Location Parameters using Lq-Likelihood-Ratio-Type Test in Python.

lqrt

papermill

Parameterize and run Jupyter and nteract Notebooks.

papermill

plotly

An open-source interactive data visualization library for Python.

plotly

Use in a jupyter notebook requires jupyter and anywidget

plotnine

A Grammar of Graphics for Python.

plotnine

pydeps

Display module dependencies.

pydeps

pyemd

A Python wrapper for Ofir Pele and Michael Werman’s implementation of the Earth Mover’s Distance.

pyemd

Unmaintained upstream

pyfim

Frequent Item Set Mining and Association Rule Induction for Python.

pyfim

pylatex

A Python library for creating LaTeX files and snippets.

pylatex

Requires LaTeX

pyplane

Interface to INI’s CoACH class-chip via Teensy based PLANE (Platform for Learning About Neuromorphic Engineering).

pyplane

Unmaintained upstream, does not install

pyxid2

Python library for interfacing with Cedrus XID devices, e.g. StimTracker, Riponda, RB-x40, c-pod, and Lumina.

pyxid2

Requires ftd drivers: https://pypi.org/project/ftd2xx/

ratinabox

RatInABox: A package for simulating spatial navigation and spatial representation neural data in continuous 2D environments.

ratinabox

read-roi

Read ROI files .zip or .roi generated with ImageJ.

read-roi

sklearn-genetic-opt

Scikit-learn models hyperparameters tuning and features selection, using evolutionary algorithms.

sklearn-genetic-opt

sklearn-nature-inspired-algorithms

Search using nature inspired algorithms over specified parameter values for an sklearn estimator.

sklearn-nature-inspired-algorithms

Does not install in Py3.12+. No module named 'numpy.distutils'. No module named 'numpy.distutils'

Showing 1 to 21 of 21 entries

Reference/bibliography managers

Fedora does not currently include any of these tools. However, the developers provide pre-built binaries that are ready to use.

JabRef

Full featured bibliography manager written in Java.

Zotero

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:

Search:

Software Install with Notes

Software	Install with	Notes
bioread	`sudo dnf install python3-bioread`	Utilities to work with files from BIOPAC’s AcqKnowlege software
BluePyOpt	`sudo dnf install python3-bluepyopt python3-bluepyopt-doc`	Blue Brain Python Optimisation Library
Bokeh	`sudo dnf install python3-bokeh`	The Bokeh Visualization Library
chaospy	`sudo dnf install python3-chaospy`	Numerical tool for performing uncertainty quantification using polynomial.
connection_pool	`sudo dnf install python3-connection_pool`	Thread-safe connection pool for python.
datalad	`sudo dnf install datalad python3-datalad`	Keep code, data, containers under control with git and git-annex.
datrie	`sudo dnf install python3-datrie`	Super-fast, efficiently stored Trie for Python.
devicely	`sudo dnf install python3-devicely`	Python package for reading, timeshifting and writing sensor data.
earcut.hpp	`sudo dnf install earcut-hpp-devel`	C++ port of earcut.js, a fast, header-only polygon triangulation library.
edflib	`sudo dnf install edflib`	C/C++ library to read/write EDF+ and BDF+ files.
exdir	`sudo dnf install python3-exdir`	Directory structure standard for experimental pipelines.
Git-changelog	`sudo dnf install python3-git-changelog`	An automatic Changelog generator using Jinja2 templates. From git logs to change logs.
GNU Octave	`sudo dnf install octave`	GNU Octave: Scientific programming language. FOSS, compatible with Matlab scripts.
Graph Tool	`sudo dnf install python3-graph-tool`	An efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks).
gsl-lite	`sudo dnf install gsl-lite-devel`	A single-file header-only version of ISO C++ Guidelines Support Library (GSL) for C++98, C++11, and later.
HighFive	`sudo dnf install highfive-devel`	A modern header-only C++11 friendly interface for libhdf5
inspyred	`sudo dnf install python3-inspyred`	Library for bio-inspired computational intelligence.
interrogate	`sudo dnf install python3-interrogate`	Interrogate a codebase for docstring coverage.
JSONLab	`sudo dnf install octave-jsonlab`	A JSON/UBJSON/MessagePack encoder/decoder for GNU Octave.
llvmlite	`sudo dnf install python3-llvmlite`	A lightweight LLVM-Python binding for writing JIT compilers.
mapbox-earcut	`sudo dnf install python3-mapbox-earcut`	Very fast and quite robust triangulation of 2D polygons.
matplotlib-venn	`sudo dnf install python3-matplotlib-venn`	Venn diagram plotting routines for Python/Matplotlib.
missingno	`sudo dnf install python3-missingno`	Missing data visualization module for Python.
MorphIO	`sudo dnf install python3-morphio morphio-devel`	A python and C++ library for reading and writing neuronal morphologies.
NeuroM	`sudo dnf install python3-neurom`	Python toolkit for the analysis and processing of neuron morphologies.
OWL_RL	`sudo dnf install python3-owl_rl`	OWL-RL and RDFS based RDF Closure inferencing for Python.
Pew	`sudo dnf install python3-pew`	Virtual environment manager written in pure Python.
Plotly	`sudo dnf install python3-plotly`	An open-source, interactive data visualization library for Python.
Pooch	`sudo dnf install python3-pooch`	A friend to fetch your data files.
pre-commit	`sudo dnf install pre-commit`	Framework for managing and maintaining multi-language pre-commit hooks.
progressbar2	`sudo dnf install python3-progressbar2`	A Progressbar library to provide visual progress to long running operations.
PuLP	`sudo dnf install python3-pulp`	A python Linear Programming API.
pyedflib	`sudo dnf install python3-pyedflib`	Python library to read/write EDF+/BDF+ files, based on EDFlib.
pypet	`sudo dnf install python3-pypet`	Parameter exploration toolbox.
pyplane	`sudo dnf install pyplane`	Phase plane analysis of nonlinear systems
ratelimiter	`sudo dnf install python3-ratelimiter`	Python module providing rate limiting.
RDFlib-JSON-LD	`sudo dnf install python3-rdflib-jsonld`	Python rdflib extension adding JSON-LD parser and serializer.
Sklearn-nature-inspired-algorithms	`sudo dnf install python3-sklearn-nature-inspired-algorithms`	Nature-inspired algorithms for hyper-parameter tuning of Scikit-Learn models.
snakemake	`sudo dnf install snakemake`	Workflow management system to create reproducible and scalable data analyses.
spyder	`sudo dnf install spyder`	A powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.
stopit	`sudo dnf install python3-stopit`	Timeout control decorator and context managers.
toposort	`sudo dnf install python3-toposort`	Implements a topological sort algorithm.
vcd	`sudo dnf install R-vcd`	Visualizing categorical data.
wxnatpy	`sudo dnf install python3-wxnatpy`	wxnatpy is a wxPython widget which allows users to browse the contents of a XNAT repository.
xnat	`sudo dnf install python3-xnat`	A new XNAT client that exposes XNAT objects/functions as python objects/functions.
ZMat	`sudo dnf install octave-zmat`	A portable data compression/decompression toolbox for GNU Octave.
ZMat Library	`sudo dnf install zmat`	A portable library with easy-to-use data compression/decompression interfaces.

bioread

sudo dnf install python3-bioread

Utilities to work with files from BIOPAC’s AcqKnowlege software

BluePyOpt

sudo dnf install python3-bluepyopt python3-bluepyopt-doc

Blue Brain Python Optimisation Library

Bokeh

sudo dnf install python3-bokeh

The Bokeh Visualization Library

chaospy

sudo dnf install python3-chaospy

Numerical tool for performing uncertainty quantification using polynomial.

connection_pool

sudo dnf install python3-connection_pool

Thread-safe connection pool for python.

datalad

sudo dnf install datalad python3-datalad

Keep code, data, containers under control with git and git-annex.

datrie

sudo dnf install python3-datrie

Super-fast, efficiently stored Trie for Python.

devicely

sudo dnf install python3-devicely

Python package for reading, timeshifting and writing sensor data.

earcut.hpp

sudo dnf install earcut-hpp-devel

C++ port of earcut.js, a fast, header-only polygon triangulation library.

edflib

sudo dnf install edflib

C/C++ library to read/write EDF+ and BDF+ files.

exdir

sudo dnf install python3-exdir

Directory structure standard for experimental pipelines.

Git-changelog

sudo dnf install python3-git-changelog

An automatic Changelog generator using Jinja2 templates. From git logs to change logs.

GNU Octave

sudo dnf install octave

GNU Octave: Scientific programming language. FOSS, compatible with Matlab scripts.

Graph Tool

sudo dnf install python3-graph-tool

An efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks).

gsl-lite

sudo dnf install gsl-lite-devel

A single-file header-only version of ISO C++ Guidelines Support Library (GSL) for C++98, C++11, and later.

HighFive

sudo dnf install highfive-devel

A modern header-only C++11 friendly interface for libhdf5

inspyred

sudo dnf install python3-inspyred

Library for bio-inspired computational intelligence.

interrogate

sudo dnf install python3-interrogate

Interrogate a codebase for docstring coverage.

JSONLab

sudo dnf install octave-jsonlab

A JSON/UBJSON/MessagePack encoder/decoder for GNU Octave.

llvmlite

sudo dnf install python3-llvmlite

A lightweight LLVM-Python binding for writing JIT compilers.

mapbox-earcut

sudo dnf install python3-mapbox-earcut

Very fast and quite robust triangulation of 2D polygons.

matplotlib-venn

sudo dnf install python3-matplotlib-venn

Venn diagram plotting routines for Python/Matplotlib.

missingno

sudo dnf install python3-missingno

Missing data visualization module for Python.

MorphIO

sudo dnf install python3-morphio morphio-devel

A python and C++ library for reading and writing neuronal morphologies.

NeuroM

sudo dnf install python3-neurom

Python toolkit for the analysis and processing of neuron morphologies.

OWL_RL

sudo dnf install python3-owl_rl

OWL-RL and RDFS based RDF Closure inferencing for Python.

Pew

sudo dnf install python3-pew

Virtual environment manager written in pure Python.

Plotly

sudo dnf install python3-plotly

An open-source, interactive data visualization library for Python.

Pooch

sudo dnf install python3-pooch

A friend to fetch your data files.

pre-commit

sudo dnf install pre-commit

Framework for managing and maintaining multi-language pre-commit hooks.

progressbar2

sudo dnf install python3-progressbar2

A Progressbar library to provide visual progress to long running operations.

PuLP

sudo dnf install python3-pulp

A python Linear Programming API.

pyedflib

sudo dnf install python3-pyedflib

Python library to read/write EDF+/BDF+ files, based on EDFlib.

pypet

sudo dnf install python3-pypet

Parameter exploration toolbox.

pyplane

sudo dnf install pyplane

Phase plane analysis of nonlinear systems

ratelimiter

sudo dnf install python3-ratelimiter

Python module providing rate limiting.

RDFlib-JSON-LD

sudo dnf install python3-rdflib-jsonld

Python rdflib extension adding JSON-LD parser and serializer.

Sklearn-nature-inspired-algorithms

sudo dnf install python3-sklearn-nature-inspired-algorithms

Nature-inspired algorithms for hyper-parameter tuning of Scikit-Learn models.

snakemake

sudo dnf install snakemake

Workflow management system to create reproducible and scalable data analyses.

spyder

sudo dnf install spyder

A powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.

stopit

sudo dnf install python3-stopit

Timeout control decorator and context managers.

toposort

sudo dnf install python3-toposort

Implements a topological sort algorithm.

vcd

sudo dnf install R-vcd

Visualizing categorical data.

wxnatpy

sudo dnf install python3-wxnatpy

wxnatpy is a wxPython widget which allows users to browse the contents of a XNAT repository.

xnat

sudo dnf install python3-xnat

A new XNAT client that exposes XNAT objects/functions as python objects/functions.

ZMat

sudo dnf install octave-zmat

A portable data compression/decompression toolbox for GNU Octave.

ZMat Library

sudo dnf install zmat

A portable library with easy-to-use data compression/decompression interfaces.

Showing 1 to 47 of 47 entries

Python Science Stack

The python-science package group includes commonly used scientific Python libraries. This can be installed using dnf:

sudo dnf install @python-science

bash

The individual packages may also be installed independently:

matplotlib

sudo dnf install python3-matplotlib

The Python plotting package.

Jupyter Notebook

sudo dnf install python3-notebook

Jupyter notebook.

numpy

sudo dnf install python3-numpy

Fundamental package for array computing with Python.

pandas

sudo dnf install python3-pandas

Python Data Analysis library.

pillow

sudo dnf install python3-pillow

The Python Imaging Library.

read-roi

sudo dnf install python3-read-roi

Read ROI files .zip or .roi generated with ImageJ.

scikit-image

sudo dnf install python3-scikit-image

Collection of algorithms for image processing.

scikit-learn

sudo dnf install python3-scikit-learn

Machine learning in Python.

scipy

sudo dnf install python3-scipy

Python library for scientific computing.

statsmodels

sudo dnf install python3-statsmodels

Statistics in Python.

sympy

sudo dnf install python3-sympy

Library for symbolic mathematics.

visidata

sudo dnf install visidata

An interactive multitool for tabular data.

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