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).

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0.1+20080921-3https://screenshots.debian.net/shrine/screenshot/simage/large-b4a88455c1875671287804b2209f8d47.png
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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
디지탈 오실로스코프
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Xoscope는 사운드카드 또는 EsounD 서버 및/또는 COMEDI 하드웨어의 값을 입력으로 하는 오실로스코프입니다. 8개의 신호 디스플레이, 가변 타임 스케일, 수학, 메모리, 측정, 파일 save/load를 포함합니다.

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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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
3Dconnexion에서 3D 입력 장치를 사용하기 위한 데몬
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일반적인 컴퓨터 마우스 또는 트랙볼은, 일차원이 부족하기 때문에 3D 애플리케이션에서 사용하기가 번거롭습니다. 커피컵에서 직관적으로 할 수 있는 것들, 기울어지는 것과 움직이는 것을 구별하거나 두 가지 작업을 동시에 수행하려는 경우 더 많은 것을 필요로 합니다. 3Dconnexion은 "space navigator", "space pilot", "space traveller", "space mouse" 등으로 알려진 6가지 자유도 입력 장치를 가지며, 일단 이 입력장치를 사용하게 되면, 사용자는 마우스 사용을 중지하고 과거 CAD/CAM 또는 다른 것들에 개체를 배치하기 위해 낭비했던 시간을 분노로 되돌아 보게 됩니다.

Spacenavd는 이러한 장치들을 위한 자유 소프트웨어 대체 사용자 공간 드라이버 (데몬) 및 소프트웨어 개발 킷입니다. 3Dconnecion에서 제공하는 원래의 3dxsrv 독점 데몬과 호환되며, 3Dconnecion 드라이버용으로 개발된 임의 프로그램과 완벽하게 호환됩니다. 또한 새로운 비 X11 종속 프로토콜을 통해 장치에 액세스하는 또 다른 방법을 제공합니다.

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.

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