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
Versions of package hdf-compass
ReleaseVersionArchitectures
sid0.6.0-1all
buster0.6.0-1all
stretch0.6.0-1all
upstream0.6.0.dev1
Popcon: 4 users (7 upd.)*
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License: DFSG free
Git

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.

Openstereogram
Stereogram ("Magic Eye") generator with GUI
Versions of package openstereogram
ReleaseVersionArchitectures
stretch0.1+20080921-2all
sid0.1+20080921-2all
buster0.1+20080921-2all
wheezy0.1+20080921-2all
Popcon: 3 users (1 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
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buster0.5.0-1all
sid0.5.0-1all
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License: DFSG free
Git

A Python interface for the netCDF4 file-format that reads and writes HDF5 files API directly via h5py, without relying on the Unidata netCDF library.

This package provides the modules for Python 3.

Python3-h5py
general-purpose Python interface to hdf5 (Python 3)
Versions of package python3-h5py
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sid2.7.1-2amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x
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Popcon: 116 users (83 upd.)*
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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 package provides the modules for Python 3.

Python3-hdf5storage
high-level utilities to read from and write to HDF5 (Python 3)
Versions of package python3-hdf5storage
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stretch0.1.14-1all
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sid0.1.14-1all
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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
Versions of package python3-pybind11
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buster2.0.1-4all
sid2.0.1-4all
stretch2.0.1-3all
experimental2.2.1-1all
upstream2.2.1
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License: DFSG free
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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)
Versions of package reprounzip
ReleaseVersionArchitectures
sid1.0.10-1all
buster1.0.10-1all
upstream1.0.11
Popcon: 1 users (0 upd.)*
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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)
Versions of package reprozip
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buster1.0.10-1all
sid1.0.10-1all
upstream1.0.11
Popcon: 1 users (0 upd.)*
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License: DFSG free
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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
Versions of package science-workflow
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buster1.7all
sid1.7all
stretch1.7all
Popcon: 5 users (2 upd.)*
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License: DFSG free
Git

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

Xoscope
digital oscilloscope
Maintainer: Bhavani Shankar
Versions of package xoscope
ReleaseVersionArchitectures
wheezy2.0-3.2amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc
stretch2.2-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.2-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
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squeeze2.0-3.1amd64,armel,i386,ia64,mips,mipsel,powerpc,s390,sparc
jessie2.0-3.2amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
Debtags of package xoscope:
fieldelectronics
interfacex11
roleprogram
usechecking, learning
x11application
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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)
Versions of package libmemtailor-dev
ReleaseVersionArchitectures
buster1.0~git20160302-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch1.0~git20160302-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.0~git20160302-1amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,powerpc,ppc64el,s390x
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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.

Libmrmpi-dev
Implements MapReduce operation on top of standard MPI message - development
Versions of package libmrmpi-dev
ReleaseVersionArchitectures
sid1.0~20140404-1amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,powerpc,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,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
stretch1.0~20140404-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.0~20140404-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package libmrmpi-dev:
devellibrary
roledevel-lib
Popcon: 1 users (0 upd.)*
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License: DFSG free
Svn

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 langauges 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.

Python-h5py
general-purpose Python interface to hdf5 (Python 2)
Versions of package python-h5py
ReleaseVersionArchitectures
sid2.6.0-2powerpc
squeeze1.3.0-3amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy2.0.1-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie2.2.1-1.1amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
stretch2.7.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.7.1-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid2.7.1-2amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 355 users (175 upd.)*
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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 package provides the modules for Python 2.

Python-hdf5storage
high-level utilities to read from and write to HDF5 (Python 2)
Versions of package python-hdf5storage
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buster0.1.14-1all
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sid0.1.14-1all
Popcon: 0 users (1 upd.)*
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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 2 interpreter.

Python-mrjob
MapReduce framework for writing and running Hadoop Streaming jobs
Maintainer: Janos Guljas
Versions of package python-mrjob
ReleaseVersionArchitectures
wheezy0.3.3.2-1all
sid0.3.3.2-1all
buster0.3.3.2-1all
stretch0.3.3.2-1all
jessie0.3.3.2-1all
upstream0.6.0
Popcon: 8 users (60 upd.)*
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License: DFSG free
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Mrjob is a Python package that helps you write and run Hadoop Streaming jobs.

Mrjob fully supports Amazon's Elastic MapReduce (EMR) service, which allows you to buy time on a Hadoop cluster on an hourly basis. It also works with your own Hadoop cluster.

Python-pybind11
pybind11 helper module for Python 2
Versions of package python-pybind11
ReleaseVersionArchitectures
buster2.0.1-4all
experimental2.2.1-1all
sid2.0.1-4all
stretch2.0.1-3all
upstream2.2.1
Popcon: 0 users (0 upd.)*
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License: DFSG free
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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 2.

Python3-pweave
scientific report generator for Python
Versions of package python3-pweave
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buster0.25-1all
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upstream0.30.1
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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.

Python3-pydap
implementation of the Data Access Protocol in Python
Versions of package python3-pydap
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buster3.2.2+ds1-1all
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Popcon: 1 users (0 upd.)*
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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 203532