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
viewer for HDF5 and related formats
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HDF Compass is an experimental viewer program for HDF5 and related formats, designed to complement other more complex applications like HDFView. Strong emphasis is placed on clean minimal design, and maximum extensibility through a plugin system for new formats.

This package provides the HDF Compass application.

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
Stereogram ("Magic Eye") generator with GUI
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A desktop application written in Java to generate autosterograms, made popular through the book "Magic Eye." Users create images which appear to pop out in 3D when looked at cross-eyed or wall-eyed (parallel vision).

Other screenshots of package openstereogram
VersionURL
0.1+20080921-3https://screenshots.debian.net/shrine/screenshot/simage/large-b4a88455c1875671287804b2209f8d47.png
Screenshots of package openstereogram
python3-h5netcdf
netCDF4 support via h5py for Python 3
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A Python interface for the netCDF4 file-format that reads and writes local or remote HDF5 files directly via h5py or h5pyd, without relying on the Unidata netCDF library.

This package provides the modules for 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
digital oscilloscope
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Xoscope is a oscilloscope using input from a sound card or EsounD server and/or a COMEDI hardware. Includes 8 signal displays, variable time scale, math, memory, measurements, and file save/load.

Screenshots of package xoscope

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
scientific report generator for Python
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Pweave is a scientific report generator and a literate programming tool for Python. Pweave can capture the results and plots from data analysis and works well with NumPy, SciPy and matplotlib. It is able to run Python code from source document and include the results and capture matplotlib plots in the output.

spacenavd
daemon for using 3D input devices from 3Dconnexion
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A regular computer mouse or trackball is cumbersome to use for 3D applications - one dimension is missing, more if one wants to distinguish tilting from moving or wants to perform both operations at the same time, just like one can do it intuitively with a coffee cup. 3Dconnexion's has such six-degree-of-freedom input devices that are known as "space navigator", "space pilot", "space traveller", "space mouse", etc., and once you have them, you likely stop using the mouse and look back in anger about all the time you have wasted in the past to position objects in CAD/CAM or elsewhere.

Spacenavd is a free software replacement user-space driver (daemon) and software development kit for these devices. It is compatible with the original 3dxsrv proprietary daemon provided by 3Dconnexion, and works perfectly with any program that was written for the 3Dconnexion driver. It also offers another method of accessing the device via a new non-X11-dependent protocol.

tiemu-skinedit
skin editor for TiEmu
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skinedit is the skin editor that accompanies TiEmu, the Texas Instruments calculators emulator. By using a different skin, you change the appearance of the emulator.

skinedit can handle VTi (another emulator, running on Windows) skins too, allowing you to convert the skins between the VTi formats and the TiEmu format.

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 237180