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
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Debian Science Tools packages
Official Debian packages with high relevance
hdf-compass
viewer for HDF5 and related formats
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Versions of package hdf-compass |
Release | Version | Architectures |
buster | 0.6.0-1 | all |
bullseye | 0.7~b8-3 | all |
bookworm | 0.7~b8-3 | all |
trixie | 0.7~b15-1 | all |
stretch | 0.6.0-1 | all |
sid | 0.7~b15-1 | all |
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License: DFSG free
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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.
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mrcal
Calibration and SFM library
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Versions of package mrcal |
Release | Version | Architectures |
bookworm | 2.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.4.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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
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openstereogram
Stereogram ("Magic Eye") generator with GUI
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Versions of package openstereogram |
Release | Version | Architectures |
bookworm | 0.1+20080921-3 | all |
trixie | 0.1+20080921-3 | all |
sid | 0.1+20080921-3 | all |
stretch | 0.1+20080921-2 | all |
bullseye | 0.1+20080921-3 | all |
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License: DFSG free
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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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python3-h5netcdf
netCDF4 support via h5py for Python 3
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Versions of package python3-h5netcdf |
Release | Version | Architectures |
sid | 1.4.1-1 | all |
trixie | 1.4.1-1 | all |
bullseye | 0.8.1-2 | all |
bookworm | 1.1.0-1 | all |
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License: DFSG free
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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.
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python3-h5py
general-purpose Python interface to hdf5
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Versions of package python3-h5py |
Release | Version | Architectures |
trixie | 3.12.1-1 | all |
bullseye | 2.10.0-9 | all |
buster | 2.8.0-3 | amd64,arm64,armhf,i386 |
stretch | 2.7.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.2.1-1.1 | amd64,armel,armhf,i386 |
sid | 3.12.1-1 | all |
bookworm | 3.7.0-8 | all |
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License: DFSG free
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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.
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python3-hdf5plugin
Python library to make HDF5 compression filters usable from h5py
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Versions of package python3-hdf5plugin |
Release | Version | Architectures |
bookworm | 4.0.1-3 | all |
trixie | 4.0.1-3 | all |
sid | 4.0.1-3 | all |
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License: DFSG free
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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.
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python3-hdf5storage
high-level utilities to read from and write to HDF5 (Python 3)
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Versions of package python3-hdf5storage |
Release | Version | Architectures |
sid | 0.1.19-2 | all |
stretch | 0.1.14-1 | all |
bookworm | 0.1.19-1 | all |
trixie | 0.1.19-2 | all |
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License: DFSG free
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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.
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python3-pybind11
pybind11 helper module for Python 3
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Versions of package python3-pybind11 |
Release | Version | Architectures |
trixie | 2.13.6-1 | all |
sid | 2.13.6-1 | all |
bookworm | 2.10.3-1 | all |
buster | 2.2.4-2 | all |
bullseye | 2.6.2-1 | all |
stretch | 2.0.1-3 | all |
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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.
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reprounzip
tool for reproducing scientific experiments (unpacker)
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Versions of package reprounzip |
Release | Version | Architectures |
sid | 1.3-2 | all |
bullseye | 1.0.16-2 | all |
bookworm | 1.0.16-2 | all |
buster | 1.0.10-1 | all |
trixie | 1.3-2 | all |
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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 unpacker.
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reprozip
tool for reproducing scientific experiments (packer)
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Versions of package reprozip |
Release | Version | Architectures |
buster | 1.0.14-2 | all |
bullseye | 1.0.16-1 | all |
sid | 1.3-3 | amd64,i386 |
bookworm | 1.1-2 | all |
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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.
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science-workflow
workflow management systems useful for scientific research
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Versions of package science-workflow |
Release | Version | Architectures |
trixie | 1.14.7 | all |
stretch | 1.7 | all |
buster | 1.10 | all |
bullseye | 1.14.2 | all |
bookworm | 1.14.5 | all |
sid | 1.14.7 | all |
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License: DFSG free
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This task lists some packages providing workflow management
systems useful for scientific research.
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xoscope
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Versions of package xoscope |
Release | Version | Architectures |
trixie | 2.3-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.2-1 | amd64,arm64,armhf,i386 |
stretch | 2.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.0-3.2 | amd64,armel,armhf,i386 |
sid | 2.3-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.2-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package xoscope: |
field | electronics |
interface | x11 |
role | program |
use | checking, learning |
x11 | application |
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License: DFSG free
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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.
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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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Versions of package libmemtailor-dev |
Release | Version | Architectures |
trixie | 1.0~git20230916-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0~git20220104-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0~git20200526-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0~git20160311-2 | amd64,arm64,armhf,i386 |
stretch | 1.0~git20160302-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.0~git20230916-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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.
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libmrcal-dev
Calibration and SFM library
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Versions of package libmrcal-dev |
Release | Version | Architectures |
sid | 2.4.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.4.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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
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libmrmpi-dev
Implements MapReduce operation on top of standard MPI message - development
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Versions of package libmrmpi-dev |
Release | Version | Architectures |
stretch | 1.0~20140404-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.0~20140404-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.0~20140404-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0~20140404-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0~20140404-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0~20140404-2 | amd64,arm64,armhf,i386 |
jessie | 1.0~20140404-1 | amd64,armel,armhf,i386 |
Debtags of package libmrmpi-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
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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.
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python3-mrcal
Calibration and SFM library
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Versions of package python3-mrcal |
Release | Version | Architectures |
trixie | 2.4.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.4.1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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
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python3-opcodes
Database of Processor Instructions/Opcodes (Python 3)
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Versions of package python3-opcodes |
Release | Version | Architectures |
bullseye | 0.0~git20180424.6e2b0cd-3 | all |
bookworm | 0.0~git20180424.6e2b0cd-3 | all |
trixie | 0.0~git20180424.6e2b0cd-3 | all |
sid | 0.0~git20180424.6e2b0cd-3 | all |
upstream | 0.0~git20240108.b606dde |
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License: DFSG free
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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.
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python3-pweave
scientific report generator for Python
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Versions of package python3-pweave |
Release | Version | Architectures |
sid | 0.30.3-1 | all |
buster | 0.25-1 | all |
bullseye | 0.25-3 | all |
bookworm | 0.30.3-1 | all |
trixie | 0.30.3-1 | all |
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License: DFSG free
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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.
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spacenavd
daemon for using 3D input devices from 3Dconnexion
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Versions of package spacenavd |
Release | Version | Architectures |
bullseye | 0.7.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.5-1 | amd64,armel,armhf,i386 |
bookworm | 1.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.6-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.2-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.2-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package spacenavd: |
hardware | input |
interface | daemon |
role | program |
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License: DFSG free
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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.
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tiemu-skinedit
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Versions of package tiemu-skinedit |
Release | Version | Architectures |
sid | 1.28~git20220826.cda2db4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.28~git20220826.cda2db4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.28~git20220826.cda2db4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.28~20200818-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.27-3 | amd64,arm64,armhf,i386 |
stretch | 1.27-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.27-2 | amd64,armel,armhf,i386 |
upstream | 1.28~git20240908.2b8df92 |
Debtags of package tiemu-skinedit: |
hardware | emulation |
interface | x11 |
role | program |
scope | application |
uitoolkit | gtk |
use | editing |
x11 | application |
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License: DFSG free
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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.
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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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Versions of package python3-pydap |
Release | Version | Architectures |
VCS | 3.2.2+ds1-1 | all |
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License: Expat
Debian package not available
Version: 3.2.2+ds1-1
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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.
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