Debian Science Project
Summary
Tools
Debian Science generic tools for scientific work

This task lists Debian Science some packages which are providing some generic tools for sciences and to enhance scientific work.

Note that there is no according metapackage created since the packages might be to different to make sense to install all on one machine.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Science to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Science mailing list

Links to other tasks

Debian Science Tools packages

Official Debian packages with high relevance

hdf-compass
visualisateur pour les formats HDF5 et apparentés
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HDF Compass est un programme expérimental de visualisation pour les formats HDF5 et apparentés, conçu pour compléter d’autres applications plus complexes comme HDFView. Un accent fort a été placé sur une conception minimale épurée et une extensibilité maximale à l’aide d’un système de greffons pour de nouveaux formats.

Ce paquet fournit l’application HDF Compass.

mrcal
Calibration and SFM library
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A photogrammetry toolkit that provides improved methods for making and using camera models (calibration, tracking, mapping, etc). The focus is on calibration and uncertainty propagation to produce the most accurate models possible. This package provides the user-facing tools

openstereogram
générateur de stéréogrammes (« Magic Eye ») avec interface graphique
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Il s’agit d’une application de bureau écrite en Java pour créer des autostéréogrammes, rendus populaires par le livre « Magic Eye ». Des images peuvent être créées qui paraissent surgir en 3D lorsqu’elles sont regardées en louchant (cross-eyed ou wall-eyed, vision parallèle).

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0.1+20080921-3https://screenshots.debian.net/shrine/screenshot/simage/large-c53e9f0957017451d8391d1b419cb2bb.png
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python3-h5netcdf
prise en charge de netCDF4 à l’aide d’h5py pour Python 3
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Il s’agit d’une interface de Python pour le format de fichier netCDF4, qui lit et écrit des fichiers HDF5, locaux ou distants, directement à l’aide de h5py oo h5pyd, sans s’appuyer sur la bibliothèque netCDF d’Unidata.

Ce paquet fournit les modules pour Python⋅3.

python3-h5py
general-purpose Python interface to hdf5
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HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.

From a Python programmer's perspective, HDF5 provides a robust way to store data, organized by name in a tree-like fashion. You can create datasets (arrays on disk) hundreds of gigabytes in size, and perform random-access I/O on desired sections. Datasets are organized in a filesystem-like hierarchy using containers called "groups", and accessed using the tradional POSIX /path/to/resource syntax.

H5py provides a simple, robust read/write interface to HDF5 data from Python. Existing Python and Numpy concepts are used for the interface; for example, datasets on disk are represented by a proxy class that supports slicing, and has dtype and shape attributes. HDF5 groups are presented using a dictionary metaphor, indexed by name.

This is a simple dependency package which depends on the serial or MPI build of h5py and provides test data files.

python3-hdf5plugin
Python library to make HDF5 compression filters usable from h5py
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hdf5plugin provides h5py extensions to control HDF5 compression filters plugins installed in the system.

The package supports providing options to: * blosc * bitshuffle * lz4 * FCIDECOMP * ZFP * zstd

These filter plugins are not provided by this package and need to be installed using their own packages.

python3-hdf5storage
high-level utilities to read from and write to HDF5 (Python 3)
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This package provides high level utilities to read/write a variety of Python types to/from HDF5 (Heirarchal Data Format) formatted files. This package also provides support for MATLAB MAT v7.3 formatted files, which are just HDF5 files with a different extension and some extra meta-data.

This package provides hdf5storage for the Python 3 interpreter.

python3-pybind11
pybind11 helper module for Python 3
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pybind11 is a lightweight header library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. Its goals and syntax are similar to the excellent Boost.Python library by David Abrahams: to minimize boilerplate code in traditional extension modules by inferring type information using compile-time introspection.

This package provides pybind11 for Python 3.

reprounzip
tool for reproducing scientific experiments (unpacker)
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ReproZip is a tool aimed at simplifying the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.

It tracks operating system calls and creates a package that contains all the binaries, files and dependencies required to run a given command on the author’s computational environment (packing step). A reviewer can then extract the experiment in his environment to reproduce the results (unpacking step).

This package provides the ReproZip unpacker.

reprozip
tool for reproducing scientific experiments (packer)
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ReproZip is a tool aimed at simplifying the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.

It tracks operating system calls and creates a package that contains all the binaries, files and dependencies required to run a given command on the author’s computational environment (packing step). A reviewer can then extract the experiment in his environment to reproduce the results (unpacking step).

This package provides the ReproZip packer.

science-workflow
workflow management systems useful for scientific research
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This task lists some packages providing workflow management systems useful for scientific research.

xoscope
oscilloscope numérique
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Xoscope est un oscilloscope utilisant comme entrée une carte audio, un serveur EsounD, et/ou un périphérique COMEDI. Il fournit un affichage de huit canaux, une base de temps variable, des fonctions mathématiques, la fonction mémoire, des mesures et l’enregistrement ou le chargement de fichier.

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Official Debian packages with lower relevance

libmemtailor-dev
C++ library of special purpose memory allocators (developer tools)
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Memtailor is a C++ library of special purpose memory allocators. It currently offers an arena allocator and a memory pool.

This package contains the developer tools.

libmrcal-dev
Calibration and SFM library
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A photogrammetry toolkit that provides improved methods for making and using camera models (calibration, tracking, mapping, etc). The focus is on calibration and uncertainty propagation to produce the most accurate models possible. This package provides the development C libraries

libmrmpi-dev
Implements MapReduce operation on top of standard MPI message - development
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The MapReduce-MPI (MR-MPI) library is open-source software that implements the MapReduce operation popularized by Google on top of standard MPI message passing.

The MR-MPI library is written in C++ and is callable from hi-level languages such as C++, C, Fortran. A Python wrapper is also included, so MapReduce programs can be written in Python, including map() and reduce() user callback methods. A hi-level scripting interface to the MR-MPI library, called OINK, is also included which can be used to develop and chain MapReduce algorithms together in scripts with commands that simplify data management tasks. OINK has its own manual and doc pages.

This package contains development files needed to build MapReduce-MPI applications.

python3-mrcal
Calibration and SFM library
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A photogrammetry toolkit that provides improved methods for making and using camera models (calibration, tracking, mapping, etc). The focus is on calibration and uncertainty propagation to produce the most accurate models possible. This package provides the Python interfaces

python3-opcodes
Database of Processor Instructions/Opcodes (Python 3)
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Newer upstream!
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The project provides descriptions for most user-mode x86, x86-64, and k1om instructions up to AVX-512 and SHA (including 3dnow!+, XOP, FMA3, FMA4, TBM and BMI2).

This package installs the library for Python 3.

python3-pweave
générateur de rapport scientifique pour Python
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Pweave est un générateur de rapport scientifique et un outil de programmation lettrée pour Python. Pweave peut capturer le résultat et réaliser des tracés à partir d’analyse de données et fonctionne parfaitement avec NumPy, SciPy et matplotlib. Il peut exécuter du code Python à partir d’un document source et inclure le résultat et les tracés matplotlib dans sa sortie.

spacenavd
démon pour utiliser les périphériques de saisie de 3Dconnexion
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L’utilisation d’une souris ou d’une boule de commande est laborieuse pour les applications en 3D : il manque une dimension, et plus encore si une distinction doit être faite entre l’inclinaison et le déplacement ou la réalisation des deux opérations en même temps, comme ce qui est fait intuitivement avec une tasse de café. 3Dconnexion produit des périphériques de saisie à six degrés de liberté, vendus comme « space navigator », « space pilot », « space traveller », « space mouse », etc., et l’acquisition d’un de ces produits conduit vraisemblablement à l’abandon de la souris et à regretter tout le temps perdu à positionner des objets en CAD/CAM ou ailleurs.

Spacenavd est un logiciel ouvert de remplacement de pilote en espace utilisateur (démon) pour ces périphériques. Il est compatible avec le démon propriétaire original 3dxsrv fourni par 3Dconnexion, et fonctionne parfaitement avec n’importe quel programme écrit pour le pilote de 3Dconnexion. Il propose aussi une autre méthode d’accès au périphérique à l’aide d’un protocole nouveau non dépendant de X11.

tiemu-skinedit
éditeur d'interface pour TiEmu
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Skinedit est l’éditeur de thème qui accompagne TiEmu, l’émulateur des calculatrices de Texas Instruments. En utilisant un nouveau thème, l’apparence de l’émulateur est changée.

Skinedit peut aussi prendre en charge les thèmes de VTi (un autre émulateur, fonctionnant sur Windows), permettant de convertir les thèmes entre le format de VTi et celui de TiEmu.

Packaging has started and developers might try the packaging code in VCS

python3-pydap
implementation of the Data Access Protocol in Python
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Version: 3.2.2+ds1-1

Pydap is an implementation of the Opendap/DODS protocol, written from scratch. You can use Pydap to access scientific data on the internet without having to download it; instead, you work with special array and iterable objects that download data on-the-fly as necessary, saving bandwidth and time. The module also comes with a robust-but-lightweight Opendap server, implemented as a WSGI application.

This package provides the modules for Python 3.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 237410