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
Fremviser for HDF4 og relaterede formater
Versions of package hdf-compass
ReleaseVersionArchitectures
bullseye0.7~b8-3all
sid0.7~b8-3all
stretch0.6.0-1all
buster0.6.0-1all
Popcon: 14 users (4 upd.)*
Versions and Archs
License: DFSG free
Git

HDF Compass er et eksperimentelt fremviserprogram for HDF5 og relaterede formater, designet til at komplementere andre mere komplekse programmer såsom HDFView. Stærk vægt er lagt på et rent minimalt design og maksimal mulighed for udvidelse via et system for udvidelsesmoduler for nye formater.

Denne pakke tilbyder HDF Compass-programmet.

Openstereogram
Stereogram ("Magic Eye") generator with GUI
Maintainer: Debian Science Team
Versions of package openstereogram
ReleaseVersionArchitectures
wheezy0.1+20080921-2all
stretch0.1+20080921-2all
sid0.1+20080921-3all
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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).

Python3-h5netcdf
netCDF4 support via h5py for Python 3
Versions of package python3-h5netcdf
ReleaseVersionArchitectures
sid0.8.1-1all
bullseye0.8.1-1all
Popcon: 5 users (48 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package python3-h5py
ReleaseVersionArchitectures
jessie2.2.1-1.1amd64,armel,armhf,i386
buster2.8.0-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch2.7.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid2.10.0-8all
bullseye2.10.0-8all
Popcon: 243 users (142 upd.)*
Versions and Archs
License: DFSG free
Git

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 dummy package which depends on the serial or MPI build of h5py.

Python3-hdf5storage
high-level utilities to read from and write to HDF5 (Python 3)
Versions of package python3-hdf5storage
ReleaseVersionArchitectures
stretch0.1.14-1all
sid0.1.15+git20200608.09dfc5f-1all
bullseye0.1.15-2all
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package python3-pybind11
ReleaseVersionArchitectures
sid2.5.0-4all
stretch2.0.1-3all
buster2.2.4-2all
bullseye2.5.0-4all
Popcon: 17 users (23 upd.)*
Versions and Archs
License: DFSG free
Git

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
Værktøj til at reproducere videnskabelige eksperimenter - udpakker
Versions of package reprounzip
ReleaseVersionArchitectures
sid1.0.10-1all
buster1.0.10-1all
upstream1.0.16
Popcon: 4 users (0 upd.)*
Newer upstream!
License: DFSG free
Git

ReproZip er et værktøj rettet mod at forenkle processen med at oprette reproducerbare eksperimenter fra kørsler på kommandolinjen, en ofte anvendt fælles nævner indenfor beregningsvidenskab.

Værktøjet registrerer systemkald fra operativsystemet og opretter en pakke, som indeholder alle de binære filer, filer og afhængigheder krævet for at afvikle en given kommando på forfatterens beregningsmiljø (pakketrin). En korrekturlæser kan så udtrække eksperimentet i sit miljø for at genskabe resultaterne (udpakningstrin).

Denne pakke tilbyder udpakkeren ReproZip.

Reprozip
Værktøj til at reproducere videnskabelige eksperimenter - pakkeprogram
Versions of package reprozip
ReleaseVersionArchitectures
buster1.0.14-2all
sid1.0.14-2all
upstream1.0.16
Popcon: 5 users (0 upd.)*
Newer upstream!
License: DFSG free
Git

ReproZip er et værktøj rettet mod at forenkle processen med at oprette reproducerbare eksperimenter fra kørsler på kommandolinjen, en ofte anvendt fælles nævner indenfor beregningsvidenskab.

Værktøjet registrerer systemkald fra operativsystemet og opretter en pakke, som indeholder alle de binære filer, filer og afhængigheder krævet for at afvikle en given kommando på forfatterens beregningsmiljø (pakketrin). En korrekturlæser kan så udtrække eksperimentet i sit miljø for at genskabe resultaterne (udpakningstrin).

Denne pakke tilbyder pakkeprogrammet ReproZip.

Science-workflow
Håndteringssystem til arbejdsforløb der er nyttig i videnskabelig forskning
Maintainer: Debian Science Team
Versions of package science-workflow
ReleaseVersionArchitectures
buster1.10all
bullseye1.13all
sid1.13all
stretch1.7all
Popcon: 5 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

Denne opgave viser nogle pakker, der tilbyder håndteringssystemer for arbejdsforløb, der er nyttige i videnskabelig forskning.

Xoscope
Digitalt oscilloskop
Versions of package xoscope
ReleaseVersionArchitectures
sid2.2-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye2.2-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.2-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch2.2-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie2.0-3.2amd64,armel,armhf,i386
wheezy2.0-3.2amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc
squeeze2.0-3.1amd64,armel,i386,ia64,mips,mipsel,powerpc,s390,sparc
Debtags of package xoscope:
fieldelectronics
interfacex11
roleprogram
usechecking, learning
x11application
Popcon: 30 users (65 upd.)*
Versions and Archs
License: DFSG free
Git

Xoscope er et oscilloskop, der bruger inddata fra et lydkort eller EsounD- server og/eller COMEDI-udstyr. Inkluderer 8 signalenheder, variabel tidsskala, matematik, hukommelse, målinger og gem/hent fil.

Screenshots of package xoscope

Official Debian packages with lower relevance

Libmemtailor-dev
C++-bibliotek for specielle hukommelsesmålere - udviklerværktøjer
Versions of package libmemtailor-dev
ReleaseVersionArchitectures
bullseye1.0~git20200526-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster1.0~git20160311-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch1.0~git20160302-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.0~git20200526-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream1.0~git20200709
Popcon: 0 users (0 upd.)*
Newer upstream!
License: DFSG free
Git

Memtailer er et C++-bibliotek med specielle hukommelsesmålere. Biblioteket tilbyder i øjeblikket en arena-måler og en hukommelseskø.

Denne pakke indeholder udviklerværktøjerne.

Libmrmpi-dev
Implements MapReduce operation on top of standard MPI message - development
Maintainer: Debian Science Team
Versions of package libmrmpi-dev
ReleaseVersionArchitectures
buster1.0~20140404-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy1.0~20110620.dfsg-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie1.0~20140404-1amd64,armel,armhf,i386
sid1.0~20140404-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.0~20140404-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch1.0~20140404-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package libmrmpi-dev:
devellibrary
roledevel-lib
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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-pweave
scientific report generator for Python
Versions of package python3-pweave
ReleaseVersionArchitectures
sid0.25-3all
bullseye0.25-3all
buster0.25-1all
upstream0.30.3
Popcon: 10 users (0 upd.)*
Newer upstream!
License: DFSG free
Git

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.

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

Python3-pydap
implementation of the Data Access Protocol in Python
Versions of package python3-pydap
ReleaseVersionArchitectures
VCS3.2.2+ds1-1all
Versions and Archs
License: Expat
Debian package not available
Git
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 193646