Debian Science Project
Summary
Numerical computation
Debian Science Numerical Computation-pakker

Denne metapakke vil installere Debian Science-pakker nyttige til numerisk beregning. Pakkerne tilbyder en tabelorienteret beregning og et visualiseringssystem til videnskabelig beregning og dataanalyse. Disse pakker svarer til kommercielle systemer såsom Matlab og IDL.

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 Numerical computation packages

Official Debian packages with high relevance

Admesh
Værktøj til at behandle triangulerede solide gitre - binær fil
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Aktuelt læser ADMesh alene STL-filformatet, som anvendes til hurtig fremstilling af applikationsprototyper, selv om det kan skrive STL-, VRML-, OFF- og DXF-filer. Nogle egenskaber for admesh er: Fyld huller i gitteret ved at tilføje facetter. Reparer facetter ved at forbinde til nærtliggende facetter. Reparer normale retninger (dvs. facetter skal være mod uret). Fjern fejlgenererede facetter (dvs. facetter lig med 2 eller flere hjørnepunkter).

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Algotutor
Program for observering af de mellemliggende trin for algoritmer
Maintainer: Georges Khaznadar
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Algotutor er et interaktivt program for observering af de mellemliggende trin i algoritmer (»algoritmeanimation«). Målgruppen er studenter indenfor computervidenskab og/eller alle som studier algoritmer og/eller datastrukturer. Man kan oprette datafiler i klarttekstformat (i Perl-anonyme hash'er, men den detalje skal man ikke tænke over) og lade algotutor kører igennem nogle foruddefinerede algoritmer. Man kan så gå frem og tilbage igennem kørselssekvensen for algoritmen på forskellige detaljeniveauer.

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Calculix-ccx
Tredimensionalt strukturelt finitte elementprogram
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Calculix er et frit finitte elementanalyseprogram, udviklet i åben kildekode, som bruger et lignende inddataformat som Abaqus. Det har en implicit og eksplicit løser og en for- og efterbrænder (CGX). Denne pakke indeholder løseren CalculiX CrunchiX (cxx).

Calculix-cgx
Calculix cgx er en 3-dimensionel for- og efterbrænder for fem
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Calculix GraphiX (cgx) er en 3-dimensionel for- og efterbrænder for finitte elementer. CalculiX CrunchiX Finite Element Models kan bygges, beregnes og efterbehandles. For- og efterbrænderen er et interaktivt 3D-værktøj, der bruger openGL API'en.

Udover Calculix CrunchiX-resultatfiler (frd) kan resultater fra OpenFoam, Duns (2D og 3D), Isaac (2D og 3D) og Nastran (f06) læses. For forbrænderens Netgen-standardformat kan STEP og STL importeres.

Coinor-cbc
Coin-or branch-and-cut blandet heltals programmeringsløser
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Cbc (Coin-or branch and cut) er en blandet heltals programmeringsløser udviklet i åben kildekode og skrevet i C++. Den kan bruges som et bibliotek, der kan kaldes eller som en uafhængig kørbar fil.

Denne pakke indeholder kørbare filer for cbc.

Coinor-clp
Coin-or lineær programmeringsløser
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Clp (Coin-or lineær programmering) er en lineær programmeringsløser udviklet i åben kildekode og skrevet i C++. Den er primært lavet for at blive brugt som et kaldbart bibliotek, men en grundlæggende, uafhængig version er også tilgængelig. Den er designet til at finde løsninger indenfor begrænsede lineære matematiske optimeringsproblemer.

Coinor-symphony
COIN-OR-løser for blandede-heltals lineære programmer
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SYMPHONY er en generisk blandet-heltals lineær programløser (MILP). Udviklet i åben kildekode som et kaldbart bibliotek og med en udvidelig ramme for implementering af tilpassede løsere. SYMPHONY har et antal avancerede funktioner, inklusiv evnen til at løse fler-objektive MILP'er, evnen til at forvarme sine løsningsprocedure og evnen til at udføre grundlæggende følsomhedsanalyser.

SYMPHONY er en del af det større COIN-OR-initiativ (Computational Infrastructure for Operations Research).

Denne pakke indeholder symphony's kørbare fil.

Esys-particle
Program til partikelbaserete numerisk modellering - MPI-version
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ESyS-Particle er et program, udviklet i åben kildekode, til partikelbaseret numerisk modellering. Programmet implementerer Discrete Element Method (DEM), en almindeligt anvendt teknik til modellering af processer, der involverer store deformationer, kornet forløb og/eller fragmentering. ESyS-Particle er designet til udførelse på parallelle supercomputere, klynger eller pc'er med flere kerner, der kører et Linux- baseret operativsystem. C++-simulationsmotoren implementerer en rumlig domænenedbrydning via Message Passing Interface (MPI). En Pythonomslags- API giver fleksibilitet i udformningen af ​​numeriske modeller, specifikation af modelleringsparametre og kontaktlogik samt analyse af simulationsdata. ESyS-Particle har været anvendt til at simulere jordskælv kimdannelse, findeling i »shear-celler«, siloforløb, stenfragmentering, og »fault gouge«-evolution, for blot at nævne nogle anvendelsesområder.

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Freemat
Matematisk ramme - hovedsagelig matlab-kompatibel
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FreeMat er et frit miljø for hurtig ingeniørmæssig og videnskabelig prototype- og databehandling. Programmet ligner kommercielle systemer såsom MATLAB fra Mathworks og IDL fra Research Systems, men er udarbejdet i åben kildekode. FreeMat er tilgængelig under GPL-licensen.

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Gnudatalanguage
Fri IDL-kompatibel trinvis kompiler
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GNU Data Language (DGL) er en fri IDL-kompatibel (Interactive Data Language) trinvis kompiler. Den har fuld syntakskompatibilitet med IDL 7.1. IDL er et registreret varemærke for ITT Visual Information Solutions. Fra IDL 8.0 er de følgende sprogelementer understøttet:

  • FOREACH-loop
  • negative tabelindekser
  • affaldssamlingspegere og objekter
  • kald-metoder på et objekt via ».« (f.eks. »object.aMemberProcedure,arg1«)

Filinddatasystemet er fuldt implementeret. GUI-understøttelse (kontroller) er officielt tilbudt, men ikke helt færdig endnu.

Denne pakke indeholder hovedbrugerfladen for kommandolinjen og fortolkeren.

Please cite: A. Coulais, M. Schellens, J. Gales, S. Arabas, M. Boquien, P. Chanial, P. Messmer, D. Fillmore, O. Poplawski, S. Maret, G. Marchal, N. Galmiche and T. Mermet: Status of GDL - GNU Data Language. (eprint) Astronomical Data Analysis Software and Systems XIX 434:187 (2010)
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Iep
Tom overgangspakke for IEP
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Pyzo er en Python IDE for flere platforme fokuseret på interaktivitet og introspektion, som gør den meget egnet for videnskabelig beregning. Dens praktiske design er rettet mod enkelhed og effektivitet.

Den består af to hovedkomponenter, redigeringsprogrammet og skallen, og bruger et sæt af værktøjer, der kan tilkobles, for at hjælpe programmøren på forskellig måde. Nogle eksempler er kildestruktur, projekthåndtering, interaktiv hjælp, arbejdsrum ...

Pyzo er skrevet i (ren) Python 3 og bruger Qt GUI-værktøjssættet. Binære filer tilbydes for alle væsentlige operativsystemer. Efter installation af Pyzo kan det bruges til at køre kode på enhver Pythonversion tilgængelig på dit system (Python 2.4 - 3.x, inklusiv Pypy).

Dette er en tom overgangspakke, der aktiverer opgraderingen fra IEP til Pyzo. Den kan fjernes igen.

Ipython3
Forbedret interaktiv Python 3-skal
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IPython kan bruges som en erstatning for standardskallen for Python, eller den kan bruges som et fuldstændig arbejdsmiljø for videnskabelig beregning (såsom Matlab eller Mathematica) når parret med de videnskabelige og numeriske standardværktøjer for Python. Pakken understøtter dynamiske objektintrospektioner, nummererede input/output prompter, et makrosystem, sessionslogning, gendannelse af session, fuldstændig skaladgang for systemet, uddybende og farvelagte sporingsrapporter, automatiske parenteser, automatisk citation og er indlejret i andre Pythonprogrammer.

Denne pakke indeholder den faktiske terminalskal for Python 3.

The package is enhanced by the following packages: isympy3 python3-matplotlib
Julia
Højtydende programmeringssprog for teknisk beregning
Maintainer: Debian Julia Team (Mo Zhou)
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Julia er et højtydende dynamisk programmeringssprog på højt niveau for teknisk beregning, med syntaks som er kendt af brugere fra andre tekniske beregningsmiljøer. Det tilbyder en sofistikeret kompiler, distribueret parallel kørsel, numerisk præcision, og et omfattende matematisk funktionsbibliotek. Biblioteket, hovedsagelig skrevet i selve Julia, integrerer også de modne samt bedste C- og Fortranbiblioteker for lineær algebra, vilkårlig taloprettelse, FFT'er og strengbehandling. Juliaprogrammer er organiseret omkring definering af funktioner og overbelastning af dem for forskellige kombinationer af parametertyper (som også kan være brugerdefineret).

Denne pakke tilbyder en fuldstændig Juliainstallation (JIT-kompiler, standardbibliotek, tekstbaseret brugergrænseflade).

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Lammps
Molekylær dynamisk simulator
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LAMMPS er en klassisk molekylær dynamisk kode, og et akronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS har potentiale for bløde materialer (biomolekyler, polymerer) og faste materialer (metaller, semikonduktører) og grovkornede eller mesoskopiske systemer. Programmet kan bruges til at opbygge atomer eller, mere generisk, som en parallel partikelsimulator på skalaerne atomar, meso eller kontinuum.

LAMMpS kører på enkelte processorer eller parallelt via teknikker for beskedfortolkning og en delvis-dekomponering af simuleringsdomænet. Koden er designet til at være nemt at ændre eller udvide med ny funktionalitet.

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Libadolc-dev
ADOLC - udviklingsbiblioteker og teksthoveder
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ADOLC-systemet beregner automatisk præcise derivater for en C/C++- funktion. Systemet bruger C++-overbelastning til at registrere aritmetiske operationer, som det afspiller senere på forskellige måder for at beregne de ønskede værdier.

Denne pakke indeholder udviklingsbiblioteket, teksthovedfiler og brugermanualen.

Libarrayfire-unified-dev
Development files for ArrayFire (unified backend)
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ArrayFire is a high performance software library for parallel computing with an easy-to-use API. Its array based function set makes parallel programming simple.

ArrayFire's multiple backends (CUDA, OpenCL and native CPU) make it platform independent and highly portable.

A few lines of code in ArrayFire can replace dozens of lines of parallel computing code, saving you valuable time and lowering development costs.

This package provides the development files for the unified backend of the ArrayFire library.

Please cite: P. Yalamanchili, U. Arshad, Z. Mohammed, P. Garigipati, P. Entschev, B. Kloppenborg, J. Malcolm and J. Melonakos: ArrayFire - A high performance software library for parallel computing with an easy-to-use API (2015)
Libceres-dev
nonlinear least squares minimizer (development files)
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Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems. It is a feature rich, mature and performant library which has been used in production at Google since 2010.

Ceres Solver can solve two kinds of problems.

  • Non-linear Least Squares problems with bounds constraints.
  • General unconstrained optimization problems.

This package contains the development header files.

Libclblas-dev
development files for clBLAS
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This library provides an implementation of the Basic Linear Algebra Subprograms levels 1, 2 and 3, using OpenCL and optimized for AMD GPU hardware.

This package provides the development files.

Libclfft-dev
development files for clFFT
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The clFFT library is an open source OpenCL library implementation of discrete Fast Fourier Transforms, which:

  • Provides a fast and accurate platform for calculating discrete FFTs.
  • Works on CPU or GPU backends.
  • Supports in-place or out-of-place transforms.
  • Supports 1D, 2D, and 3D transforms with a batch size that can be greater than 1.
  • Supports planar (real and complex components in separate arrays) and interleaved (real and complex components as a pair contiguous in memory) formats.
  • Supports dimension lengths that can be any mix of powers of 2, 3, and 5.
  • Supports single and double precision floating point formats.

This package provides the development files.

Libclsparse-dev
development files for clSPARSE
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clSPARSE provides fundamental sparse operations for OpenCL, including:

  • Sparse Matrix - dense Vector multiply (SpM-dV)
  • Sparse Matrix - dense Matrix multiply (SpM-dM)
  • Iterative conjugate gradient solver (CG)
  • Iterative biconjugate gradient stabilized solver (BiCGStab)
  • Dense to CSR conversions (& converse)
  • COO to CSR conversions (& converse)
  • Functions to read matrix market files in COO or CSR format

This package provides the development files.

Libcolpack-dev
Specialized graph vertex coloring library, development files
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ColPack is a package comprising of implementation of algorithms for specialized vertex coloring problems that arise in sparse derivative computation. It is written in an object-oriented fashion heavily using the Standard Template Library (STL). It is designed to be simple, modular, extenable and efficient. Its primary application has been for use in automatic differentiation.

This package contains the development library, header files, and documentation.

Libdune-grid-dev
toolbox for solving PDEs -- grid interface (development files)
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DUNE, the Distributed and Unified Numerics Environment is a modular toolbox for solving partial differential equations (PDEs) with grid-based methods. It supports the easy implementation of methods like Finite Elements (FE), Finite Volumes (FV), and also Finite Differences (FD).

This package contains the development files for the grid interface.

Libopengm-dev
C++ template library for discrete factor graph models
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OpenGM is a C++ template library for discrete factor graph models and distributive operations on these models.

It includes state-of-the-art optimization and inference algorithms beyond message passing. OpenGM handles large models efficiently, is modular and extendible. The graphical model data structure, inference algorithms and different encodings of functions inter-operate through well-defined interfaces. The binary OpenGM file format is based on the HDF5 standard and incorporates user extensions automatically.

This package contains the development headers for the OpenGM library.

Please cite: B. Andres, T. Beier and J.H. Kappes: OpenGM: A C++ Library for Discrete Graphical Models. (eprint) CoRR abs/1206.0111 (2012)
Libppl-dev
Parma Polyhedra Library - udvikling
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Parma Polyhedra Library (PPL) er et C++-bibliotek for manipulation af (ikke nødvendigvis lukket) konvekse polyeder og andre numeriske abstraktioner. Programmerne for konvekse polyeder inkluderer programanalyse, optimeret kompilering, heltal og kombinatoriel optimering og statistisk dataredigering. Parma Polyhedra Library er brugervenlig (du skriver »x + 2y + 5z <= 7« når du skal bruge det), fuld dynamisk (tilgængelig virtuel hukommelse er den eneste begrænsning for dimensionerne på alt), skrevet i standard C++, undtagelsessikker, ret så effektiv og veldokumenteret.

Denne pakke tilbyder teksthovedfiler og statiske biblioteker for C- og C++- grænseflader.

Libqsopt-ex-dev
Exact linear programming solver -- development files
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QSopt-ex is an implementation of a simplex-based algorithm that returns exact rational solutions, taking advantage of the speed of floating-point calculations and attempting to minimize the operations performed in rational arithmetic.

This package contains the header files and static library.

Please cite: David L Applegate, William Cook, Sanjeeb Dash and Daniel G Espinoza: Exact solutions to linear programming problems. Operations Research Letters 35(6):693-699 (2007)
Librsb-dev
recursive sparse blocks matrix computations library (development)
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This is a library for sparse matrix computations featuring the Recursive Sparse Blocks (RSB) matrix format. This format allows cache efficient and multi-threaded (that is, shared memory parallel) operations on large sparse matrices. It provides the most common operations necessary to iterative solvers, like matrix-vector multiplication, triangular solution, rows/columns scaling, diagonal extraction / setting, blocks extraction, norm computation, formats conversion. The RSB format is especially well suited for symmetric and transposed multiplication variants.

This package contains the static libraries for development with librsb, including examples.

Please cite: Michele Martone, Marcin Paprzycki and Salvatore Filippone: An Improved Sparse Matrix-Vector Multiply Based on Recursive Sparse Blocks Layout. :606-613 (2012)
Libsuitesparse-dev
libraries for sparse matrices computations (development files)
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Suitesparse is a collection of libraries for computations involving sparse matrices. This package includes the following libraries:

AMD approximate minimum degree ordering

CAMD symmetric approximate minimum degree

BTF permutation to block triangular form (beta)

COLAMD column approximate minimum degree ordering

CCOLAMD constrained column approximate minimum degree ordering

CHOLMOD sparse Cholesky factorization

CXSparse a concise sparse matrix package

KLU sparse LU factorization, primarily for circuit simulation

LDL a simple LDL' factorization

UMFPACK sparse LU factorization

RBio read/write sparse matrices in Rutherford/Boeing format

SPQR sparse QR factorization

GraphBLAS graph algorithms via sparse matrix operations on semirings

Mongoose graph partitioning library that can quickly compute edge cuts

SuiteSparse_config configuration routines for all the above packages.

This package contains the static libraries and header files.

Liggghts
Open Source DEM Particle Simulation Software
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LIGGGHTS står for LAMMPS forbedret for generel granulering og granuleret varmeoverførselssimulationer (LAMMPS improved for general granular and granular heat transfer simulations).

LAMMPS er en simulator for klassisk molekylær dynamik. Den er udbredt indenfor molekylær dynamik. Takket være fysiske analogier og algoritmeanalogier er LAMMPS en særdeles god platform til DEM-simulationer. LAMMPS tilbyder en GRANULAR-pakke til at udføre denne slags simulationer. LIGGGHTS forsøger at forbedre denne evne med det mål at pakken kan bruges i industrielle programmer. Udviklingsversion.

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Metis
Serial Graph Partitioning and Fill-reducing Matrix Ordering - binære filer
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METIS er et sæt af serielle programmer for partitionering af grafer, partitionering af finitte elementmesher og fremstilling af fyldte reducerende ordninger for tynde matricer. Algoritmerne implementeret i METIS er baseret på flere niveauer af rekursiv-bisektion, flere niveauer af k-way og flere begrænsninger for partitioneringsskemaer. Pakken indeholder nogle binære filer for grafanalyse.

Octave
GNU Octave-sprog til talberegninger
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Octave er et (for det meste Matlab (R)-kompatibelt) højtniveausprog, primært beregnet til numeriske beregninger. Programmet tilbyder en nem brugerflade fra kommandolinjen til løsning af lineære og ikkelineære problemer numerisk.

Octave kan udvides dynamisk med filer i C++ som leveres af brugeren.

The package is enhanced by the following packages: liboctave-dev octave-doc texmacs
Please cite: John W. Eaton, David Bateman, Søren Hauberg and Rik Wehbring: GNU Octave version 4.2.0 manual: a high-level interactive language for numerical computations. (2016)
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Pdl
Perl-datasprog: Perludvidelser for numeriske tal
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PDL giver standard-Perl mulighed for at COMPACTLY lagre og SPEEDILY manipulere de store N-dimensionelle dataarrayer, som er smørret og brødet indenfor videnskabelig beregning. Ideen er at omdanne Perl til et frit, array-orienteret, numerisk sprog på samme måde som kommercielle pakker såsom IDL og MatLab. Man kan skrive simple Perludtryk for at manipulere hele numeriske arrayer på en gang. For eksempel kan Perlvariablen $a, der bruger PDL, indeholde et 1024x1024 flydende heltals billede, det kræver kun 4 Mb hukommelse at lagre det og udtryk såsom $a=sqrt($a)+2 vil manipulere hele billedet på få sekunder.

En simpel interaktiv skal (perldl) tilbydes for kommandolinjen sammen med et modul (PDL) for brug i Perlskripter.

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Psurface
piecewise linear bijections between triangulated surfaces -- utilities
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Psurface is a C++ library that handles piecewise linear bijections between triangulated surfaces. These surfaces can be of arbitrary shape and need not even be manifolds.

This package contains several utilities for working with psurface.

Python3-arrayfire
ArrayFire bindings for Python 3
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ArrayFire is a high performance library for parallel computing with an easy-to-use API. It enables users to write scientific computing code that is portable across CUDA, OpenCL and CPU devices. This project provides Python bindings for the ArrayFire library.

This package provides the bindings for Python 3.

Python3-bitstring
Python module for manipulation of binary data (Python 3)
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Bitstring is a pure Python module designed to help make the creation and analysis of binary data as simple and natural as possible.

Bitstrings can be constructed from integers (big and little endian), hex, octal, binary, strings or files. They can be sliced, joined, reversed, inserted into, overwritten, etc. with simple functions or slice notation. They can also be read from, searched and replaced, and navigated in, similar to a file or stream.

This package provides the Python 3 version of the module.

Python3-deap
Distributed Evolutionary Algorithms in Python3
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DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. It seeks to make algorithms explicit and data structures transparent. It works in perfect harmony with parallelisation mechanism such as multiprocessing and SCOOP.

This package contains the modules for Python3.

Python3-escript
Escript/Finley finite elements Python3 system (with OpenMP)
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Escript is a programming tool for implementing mathematical models in Python using the finite element method (FEM). Because users do not access the data structures it is very easy to use and scripts can run on desktop computers as well as highly parallel supercomputer without changes. Application areas for escript include earth mantle convection, geophysical inversion, earthquakes, porous media flow, reactive transport, plate subduction, erosion, and tsunamis.

Scripts can be executed in parallel (on varying numbers of threads or nodes) without any special modifications.

Escript now includes the esys.downunder module for 3D inversion of geophysical data sets. The current version supports gravity, magnetic and joint inversion.

This package contains the commands and libraries for Python3 with OpenMP threading and MPI multiprocess support.

Python3-escript-mpi
Escript/Finley finitte elementer Python 3-system - OpenMP + MPI
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Escript er et programmeringsværktøj til at implementere matematiske modeller i Python via den finitte element metode (FEM). DA brugere ikke tilgår datastrukturerne er det meget nemt at bruge og skripter kan køre på skrivebordscomputere samt store parallelle supercomputere uden ændringer. Programområder for escript inkluderer jordmantelkonvektion, geofysisk inversion, jordskælv, porøse væskeløb, reaktiv transport, pladesubduktion, erosion og tsunamier.

Skripter kan køres parallelt (på varierende antal tråde eller knuder) uden nogen specielle ændringer.

Escript inkluderer nu modulet esys.downunder for 3D-inversion af geofysiske datasæt. Den nuværende version understøtter tyngdekraft, magnetisk og fælles inversion.

Denne pakke indeholder kommandoerne og bibliotekerne for Python 3 med både OpenMP-tråde og understøttelse af MPI-flerproces.

Python3-guiqwt
efficient 2D data-plotting library - Python 3
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The guiqwt Python library provides efficient 2D data-plotting features (curve/image visualization and related tools) for signal/image processing application development and interactive computing. It's based on the scientific modules NumPy and SciPy, and the PyQwt plotting widgets for PyQt4 graphical user interfaces.

This is the Python 3 version of the package.

Python3-lmfit
Least-Squares Minimization with Constraints - Python 3
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Pakken lmfit tilbyder en simpel, fleksibel grænseflade til ikkelineær optimering af kurvetilpasningsproblemer. Pakken udvider optimeringsfunktionerne i scipy.optimize ved at erstatte flydende kommatalsværdier for variablerne til optimering med parameterobjekterne. Disse parametre kan være faste eller varierende, have øvre og/eller lavere grænser placeret på deres værdi, eller skrevet som et algebraisk udtryk for andre parametre.

The principal advantage of using Parameters instead of simple variables is that the objective function does not have to be rewritten to reflect every change of what is varied in the fit, or what relationships or constraints are placed on the Parameters. This means a scientific programmer can write a general model that encapsulates the phenomenon to be optimized, and then allow user of that model to change what is varied and fixed, what range of values is acceptable for Parameters, and what constraints are placed on the model. The ease with which the model can be changed also allows one to easily test the significance of certain Parameters in a fitting model.

The lmfit package allows a choice of several optimization methods available from scipy.optimize. The default, and by far best tested optimization method used is the Levenberg-Marquardt algorithm from MINPACK-1 as implemented in scipy.optimize.leastsq. This method is by far the most tested and best support method in lmfit, and much of this document assumes this algorithm is used unless explicitly stated. An important point for many scientific analysis is that this is only method that automatically estimates uncertainties and correlations between fitted variables from the covariance matrix calculated during the fit.

A few other optimization routines are also supported, including Nelder-Mead simplex downhill, Powell's method, COBYLA, Sequential Least Squares methods as implemented in scipy.optimize.fmin, and several others from scipy.optimize. In their native form, some of these methods setting allow upper or lower bounds on parameter variables, or adding constraints on fitted variables. By using Parameter objects, lmfit allows bounds and constraints for all of these methods, and makes it easy to swap between methods without hanging the objective function or set of Parameters.

Finally, because the approach derived from MINPACK-1 usin the covariance matrix to determine uncertainties is sometimes questioned (and sometimes rightly so), lmfit supports methods to do a brute force search of the confidence intervals and correlations for sets of parameters.

Dette er Python 3-versionen af pakken.

Python3-matplotlib
Pythonbaseret plotsystem i en stil svarende til Matlab - Python 3
Maintainer: Sandro Tosi
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Matplotlib er et rent Python-plotbibliotek designet til plot i udgivelseskvalitet for Python, med en syntaks der er kendt af Matlab- brugere. Alle plotkommandoerne i pylab-grænsefladen kan tilgås enten via en funktionel grænseflade kendt af Matlab-brugere eller en objektorienteret grænseflade der er kendt af Pythonbrugere.

Denne pakke indeholder Python 3-versionen af matplotlib.

Python3-numpy
Hurtig tabelfacilitet til Python 3-sproget
Maintainer: Sandro Tosi
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Numpy indeholder et kraftfuldt n-dimensionelt vektor-/array-objekt, sofistikerede (udsendelser) funktioner, værktøjer til integrering af kode i C/C++ og Fortran og brugbare lineære algebra, Fourieromdannelse og vilkårlig talevner.

Numpy erstatter modulerne python-numeric og python-numarray, som nu er forældede og ikke bør bruges undtagen for at understøtte ældre programmer.

Denne pakke indeholder Numpy for Python 3.

The package is enhanced by the following packages: python3-shapely
Python3-pysph
open source framework for Smoothed Particle Hydrodynamics
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It is implemented in Python and the performance critical parts are implemented in Cython.

PySPH is implemented in a way that allows a user to specify the entire SPH simulation in pure Python. High-performance code is generated from this high-level Python code, compiled on the fly and executed. PySPH also features optional automatic parallelization using mpi4py and Zoltan.

Python3-scipy
Videnskabelige værktøjer for Python 3
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SciPy er et supplement til det populære NumPy-modul (pakken python-numpy), der samler en række af videnskabelige og ingeniørmæssige moduler på højt niveau i en pakke.

SciPy er et sæt af åben kildekode videnskabelige og numeriske værktøjer for Python. Den understøtter aktuelt specielle funktioner, integration, ordinære løsere af differentialligninger (ODE), gradoptimering, genetiske algoritmer, parallelle programmeringsværktøjer, en udtryk-til-C++ kompiler for hurtig udførelse og andre.

Python3-sfepy
Simple Finite Elements in Python
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SfePy is a software for solving systems of coupled partial differential equations (PDEs) by the finite element method in 1D, 2D and 3D. It can be viewed both as black-box PDE solver, and as a Python package which can be used for building custom applications. The word “simple” means that complex FEM problems can be coded very easily and rapidly.

Python3-sparse
multidimensional sparse arrays for Python
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This package implements sparse multidimensional arrays on top of NumPy and scipy.sparse. It generalizes the scipy.sparse.coo_matrix layout but extends beyond just rows and columns to an arbitrary number of dimensions. The original motivation is for machine learning algorithms, but it is intended for somewhat general use.

It supports:

  • NumPy ufuncs (where zeros are preserved)
  • Arithmetic with scalars (where zeros are preserved)
  • Reductions (sum, max)
  • Reshape
  • Transpose
  • Tensordot
  • Slicing with integers, lists, and slices (with no step value)
  • Concatenation and stacking
  • Addition with other sparse arrays of the same shape

This package provides the modules for Python 3.

Python3-tables
hierarchical database for Python3 based on HDF5
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PyTables is a package for managing hierarchical datasets and designed to efficiently cope with extremely large amounts of data.

It is built on top of the HDF5 library and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively save and retrieve very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that they take much less space (between a factor 3 to 5, and more if the data is compressible) than other solutions, like for example, relational or object oriented databases.

  • Compound types (records) can be used entirely from Python (i.e. it is not necessary to use C for taking advantage of them).
  • The tables are both enlargeable and compressible.
  • I/O is buffered, so you can get very fast I/O, specially with large tables.
  • Very easy to select data through the use of iterators over the rows in tables. Extended slicing is supported as well.
  • It supports the complete set of NumPy objects.

This is the Python 3 version of the package.

Python3-theano
CPU/GPU-matematikudtrykskompiler for Python 3
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Theano er et Pythonbibliotek, som giver mulighed for at definere og evaluere matematiske udtryk, der involverer flerdimensionale tabeller effektivt. Det tilbyder et Numpy-lignende udtrykssprog på højt niveau for funktionel beskrivelse af beregning, arrangerer om på udtryk for hastighed og stabilitet og opretter maskininstruktioner for hurtig beregning. Valgfrit så kan accelererede beregninger udføret på grafikkortprocessorer.

Denne pakke indeholder Theano for Python 3.

Theano-udvikling er ved sin afslutning: overvej at bruge Caffe eller Torch i stedet for.

Please cite: Theano Development Team: Theano: A Python framework for fast computation of mathematical expressions (eprint) (2016)
Python3-woo
Diskrete dynamiske beregninger, esp. granulerede mekanik - python 3
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Ramme, der kan udvides og flyttes, primært til mekanisk granulerede materialer. Beregningsdele er skrevet i C++ paralleliseret ved hjælp af OpenMP, fuldt tilgængelige og ændringsklare fra Python (ipython-konsol eller skripter). Vilkårlig kompleks scene kan opbygges med skripter. En Qt-baseret brugergrænseflade tilbydes, der byder på en fleksibel OpenGL-visning, inspektion af alle objekter og kørselstidsmodifikation. Parametriske forbrændere kan skrives i ren Python og et jobsystem kan anvendes til at drive parametriske undersøgelser. Nye materielle modeller og partikelfigurer kan tilføjes (i c++) uden at ændre eksisterende klasser.

Woo er en videreudvikling af pakken Yade (http://www.launchpad.net/yade), der sigter mod større fleksibilitet, udvidelsesmuligheder, tættere integration med Python og brugervenlighed.

Denne version er bygget med OpenMP aktiveret, og er rettet mod Python 3.x.

Python3-xarray
N-D labeled arrays and datasets in Python 3
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xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures.

It provides a pandas-like and pandas-compatible toolkit for analytics on multi-dimensional arrays, rather than the tabular data for which pandas excels.

This package provides the Python 3 library

Pyzo
interactive editor for scientific Python
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Pyzo is a cross-platform Python IDE focused on interactivity and introspection, which makes it very suitable for scientific computing. Its practical design is aimed at simplicity and efficiency.

It consists of two main components, the editor and the shell, and uses a set of pluggable tools to help the programmer in various ways. Some example tools are source structure, project manager, interactive help, workspace...

Pyzo is written in (pure) Python 3 and uses the Qt GUI toolkit. Binaries are provided for all major operating system. After installing Pyzo, it can be used to execute code on any Python version available on your system (Python 2.4 - 3.x, including Pypy).

This package provides the Pyzo IDE.

Qsopt-ex
Præcis lineær programmeringsløser
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QSopt-ex er en implementering af en simplex-baseret algoritme, som returnerer præcise rationelle løsninger, har fordel af hastigheden for flydende kommatalsberegninger og forsøger at minimere operationerne udført i rationel aritmetik.

Denne pakke indeholder redskaberne for kommandolinjen.

Please cite: David L Applegate, William Cook, Sanjeeb Dash and Daniel G Espinoza: Exact solutions to linear programming problems. Operations Research Letters 35(6):693-699 (2007)
R-base
GNU R statistisk beregning og grafiksystem
Maintainer: Dirk Eddelbuettel
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R er et system til statistisk beregning og grafik. Det består af et sprog plus et afviklingsmiljø med grafik, et aflusningsredskab, adgang til særlige systemfunktioner, samt evnen til at køre programmer som er gemt som skriptfiler.

Designet af R er tungt påvirket af to eksisterende sprog: Becker, Chambers & Wilks' S og Sussman's Scheme. Hvor sprogudformningen i sin fremtræden i høj grad ligner S, så er den underliggende implementering og semantik afledt fra Scheme.

Kernen i R er et fortolket programmeringssprog som tillader forgrening og løkker, så vel som modulær programmering med brug af funktioner. De fleste funktioner som er synlige for brugeren i R er skrevet i R. Det er muligt for brugeren at tilgå procedurer skrevet i C, C++ eller FORTRAN sprogene for effektivitet, og mange af R's kernefunktioner gør dette. Distributionen R indeholder funktionalitet til et stort antal statistiske procedurer og underliggende anvendte matematiske beregninger. Der er også et stort sæt af funktioner, der tilbyder et grafisk miljø til oprettelse af adskillige slags datarepræsentationer.

Derudover er flere tusinde udvidelsespakker tilgængelige fra CRAN (Comprehensive R Archive Network), mange også som Debianpakker, der er navngivet »r-cran-«.

Disse pakker er en metapakke, som letter overgangen fra pre-1.5.0-pakkestrukturen med dennes store r-base-pakke. Så snart den er installeret, kan den uden videre fjernes og apt-get vil automatisk opgradere dens komponenter under fremtidige opgraderinger. Denne pakke gør det muligt for brugerne kun at installere r-base-core, hvis de ønsker det.

The package is enhanced by the following packages: texmacs
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R-cran-nleqslv
GNU R-pakke til at løse systemer med ikkelineære ligninger
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Denne R-pakke løser et system med ikkelineære ligninger via en Broyden- eller en Newton-metode med et valg af globale strategier såsom linjesøgning og trust-region. Der er indstillinger for brug af en numerisk eller brugerangivet Jacobian, for angivelse af en banded numerisk Jacobian og for en singular eller ill-conditioned Jacobian.

Scilab
Videnskabelig softwarepakke til numeriske beregninger
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Scilab er en matricebaseret videnskabelig softwarepakke. Scilab indeholder hundreder af indbyggede matematiske funktioner, rige datastrukturer (inklusive polynomier, rationelle lineære systemer, lister etc...) og der medfølger et antal videnskabelige værktøjsbokse for kontrol, signalprocessering...

Denne pakke tilbyder også Xcos, et grafisk redigeringsprogram til at designe hybride dynamiske systemmodeller. Modeller kan designes, indlæses, gemmes, kompileres og simuleres. Stabil og effektiv løsning for industribehov og akademiske behov, Xcos tilbyder funktionaliteter for modellering af mekaniske systemer (bilproduktion, flyproduktion...), hydrauliske kredsløb (dæmning, datakanalmodeller...), kontrolsystemer etc. Mulighed for Modelica tilbydes også.

Installer pakken »scilab-cli« for en minimal version af scilab.

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Scilab-ann
Scilab module for artificial neural networks
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This module implements artificial neural networks capabilities into the Scilab language. Current features are:

  • Only layered feedforward networks are supported directly at the moment (for others use the "hooks" provided)
  • Unlimited number of layers
  • Unlimited number of neurons per each layer separately
  • User defined activation function (defaults to logistic)
  • User defined error function (defaults to SSE)
  • Algorithms implemented so far:
  • standard (vanilla) with or without bias, on-line or batch
  • momentum with or without bias, on-line or batch
  • SuperSAB with or without bias, on-line or batch
  • Conjugate gradients
  • Jacobian computation
  • Computation of result of multiplication between "vector" and Hessian
  • Some helper functions provided
Scilab-scimax
Symbolic computations for Scilab based on Maxima
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This toolbox is providing symbolic capabilities with the Scilab languages.

It is based on Maxima which is a fully symbolic computation program. It is full featured doing symbolic manipulation of polynomials, matrices, rational functions, integration, Todd-coxeter methods for finite group analysis, graphing, multiple precision floating point computation.

Spyder
Python IDE for videnskabsmænd
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Spyder (tidligere kendt som Pydee) er et frit udviklingsmiljø for Python, der tilbyder MATLAB-lignende funktioner i et simpelt program.

Denne pakke tilbyder programmet for Python 3.

Toulbar2
Præcis kombinatorisk optimering for grafiske modeller
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Toulbar2 er et præcist diskret optimeringsværktøj for grafiske modeller såsom Cost Function Networks, Markov Random Fields, Weighted Constraint Satisfaction Problems og Bayesian Nets.

Vitables
grafisk værktøj til at gennemse og redigere PyTables og HDF5-filer
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ViTables er en komponent i PyTables-familien. Det er et grafisk værktøj til at gennemse og redigere filer i både PyTables- og HDF5-formaterne.

Funktionerne i ViTables inkluderer nem navigering via datahierarki, visning af reelle data og dets associerede metadata, en simpel men stadig funktionsrig måde at gennemse flerdimensionelle data og meget mere.

En af de største styrker i ViTables er dets evne til at vise meget store tabeller. Tabeller med tusind millioner rækker (og mere) navigeres igennem imponerende hurtigt og med meget små hukommelseskrav. Så hvis du på et tidspunkt skal gennemse meget store tabeller, så tøv ikke, ViTables er dit bedste valg.

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Yade
Platform for diskret elementmodellering
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Yet Another Dynamic Engine.

Ramme, der er udviklet i åben kildekode og som kan udvides, for diskrete numeriske modeller, fokuseret på den diskret elementmetode. Beregningsdelene er skrevet i C++ med brug af en fleksibel objektmodel, der giver mulighed for uafhængig implementering af nye algoritmer og grænseflader. Python bruges for hurtig og præcis scenekonstruktion, simuleringskontrol, efterbehandling og fejlsøgning.

Denne pakke indeholder en hastighedsoptimeret bygning af yade.

Please cite: V.ŠMilauer, E. Catalano, B. Chareyre, S. Dorofeenko, J. Duriez, A. Gladky, J. Kozicki, C. Modenese, L. Scholtès, L. Sibille, J. Stránský and K. Thoeni: Yade Documentation (V. Šmilauer, ed.),. The Yade Project, 2nd ed. (2015)
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Yorick
Fortolket sprog og videnskabelig grafik
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Yorick er et tolket sprog til:

  • videnskabelige simuleringer eller beregninger
  • forbehandling eller styring af store simuleringskoder
  • interaktiv videnskabelig grafik
  • læsning, skrivning og oversættelse af store filer med tal

Sproget har en kompakt syntaks for mange almindelige vektoroperationer, så det håndterer store tal-vektorer meget hurtigt og effektivt. Yorick-kode ligner C-kode på overfladen, men yorick-variable bliver aldrig erklæret eksplicit og har dynamiske miljøer (scoping) svarende til mange lisp-dialekter. Yorick-sproget er lavet til at blive skrevet interaktivt på et tastatur, så vel som skrevet i filer til senere brug.

Denne pakke indeholder også et emacs-baseret udviklingsmiljø, som du kan starte ved at trykke M-x yorick i emacs.

Mange udvidelsespakker og udvidelsesmoduler er tilgængelige for Yorick (pakkenavnene begynder med »yorick-«). Du kan eventuelt installere metapakken yorick-full, som afhænger af den største del af dem.

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Official Debian packages with lower relevance

Calculix-ccx-doc
Tredimensionalt strukturelt finitte elementprogram - dokumentationsfiler
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Calculix er et frit finitte elementanalyseprogram, udviklet i åben kildekode, som bruger et lignende inddataformat som Abaqus. Det har en implicit og eksplicit løser og en for- og efterbrænder (CGX).

Denne pakke indeholder dokumentationen i html-format for CalculiX CrunchiX.

Calculix-ccx-test
Tredimensionalt strukturelt finitte elementprogram - dokumentationsfiler
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Calculix er et frit finitte elementanalyseprogram, udviklet i åben kildekode, som bruger et lignende inddataformat som Abaqus. Det har en implicit og eksplicit løser og en for- og efterbrænder (CGX).

Denne pakke indeholder eksempelfiler for Calculix CrunchiX.

Calculix-cgx-examples
Eksempelfiler for Calculix GraphiX
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Calculix GraphiX (cgx) er en 3-dimensionel for- og efterbrænder for finitte elementer. CalculiX CrunchiX Finite Element Models kan bygges, beregnes og efterbehandles. For- og efterbrænderen er et interaktivt 3D-værktøj, der bruger openGL API'en.

Udover Calculix CrunchiX-resultatfiler (frd) kan resultater fra OpenFoam, Duns (2D og 3D), Isaac (2D og 3D) og Nastran (f06) læses. For forbrænderens Netgen-standardformat kan STEP og STL importeres.

Denne pakke indeholder eksemplerne.

Ceres-solver-doc
Dokumentation for ceres-solver
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Ceres Solver er et C++-bibliotek, udviklet i åben kildekode, for modellering og løsning af store og komplicerede optimeringsproblemer. Det er et modent og ydende bibliotek med mange funktioner, som er blevet brugt i produktionen hos Google siden 2010.

Ceres Solver kan løse to slags problemer.

  • Ikkelineær »Least Squares«-problemer med begrænsninger
  • Generelle ubegrænsede optimeringsproblemer

Denne pakke indholder dokumentationen fundet på http://ceres-solver.org/ og eksemplerne, som blev inkluderet i denne udgivelse.

Coinor-libcoinmp-dev
Simpel C-API for COIN-OR Solvers Clp and Cbc - udvikling
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Coin-MP-optimeringsprogrammet er en løser, udviklet i åben kildekode, som er en del af COIN-OR-projektet, som er et initiativ der skal øge udvikling af programmer udviklet i åben kildekode for forskningsfællesskabet indenfor operation.

CoinMP er et C-API-bibliotek, som understøtter det meste af funktionalitetet i CLP (Coin LP)-, CBC (Coin Branch-and-Cut)- og CGL (Cut Generation Library)-projekter.

Denne pakke indeholder filerne krævet for at bygge programmer, der bruger libCoinMP.

Evolver-nox
Surface Evolver - uden X-understøttelse
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Surface Evolver er et interaktivt program for modelopbygning af væskeoverflader formet af forskellige energier og begrænsninger.

Denne pakke indeholder evolver-varianter bygget med forskellige kommatalsformater (dobbelt, lang dobbelt, firdobbelt) men uden X-understøttelse.

The package is enhanced by the following packages: evolver-doc
Evolver-ogl
Surface Evolver - med OpenGL-visning
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Surface Evolver er et interaktivt program for modelopbygning af væskeoverflader formet af forskellige energier og begrænsninger.

Denne pakke tilbyder evolvervarianter bygget med forskellige kommatalsformater (dobbelt, lang dobbelt, firdobbelt) og med en OpenGL/GLUT-visning.

The package is enhanced by the following packages: evolver-doc
Hpcc
HPC Challenge benchmark
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High Performance Computing (HPC) Challenge benchmark kører en programpakke med 7 test, som måler ydelsen for CPU, hukommelse og netværk for HPC- klynger. Blandt andet er Performance LINPACK (HPL) benchmark inkluderet, brugt af Top500 ranking (http://www.top500.org/).

Libcneartree-dev
Library and headers for solving the Nearest Neighbor Problem
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Neartree is an API and a library for finding nearest neighbors among points in spaces of arbitrary dimensions. This package provides a C++ template, TNear.h, and C library and header files for compiling programs using Neartree.

The library uses the Nearest Neighbor algorithm after Kalantari and McDonald, (IEEE Transactions on Software Engineering, v. SE-9, pp. 631-634,1983) modified to use recursion instead of a double-linked tree and simplified so that it does less checking for things like is the distance to the right less than the distance to the left; it was found that these checks make little to no difference.

Libpsurface-dev
piecewise linear bijections between triangulated surfaces -- development files
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Psurface is a C++ library that handles piecewise linear bijections between triangulated surfaces. These surfaces can be of arbitrary shape and need not even be manifolds.

There are two main uses for psurface. When doing adaptive finite element simulations on grids with parametrized boundaries, psurface can store the parametrization. Boundary parametrizations are practically mappings from the coarse grid boundary to the actual boundary, and if that actual boundary is a triangulated surface then psurface can handle it. This is implemented, for example, in the dune-grid module of Dune.

Secondly, when doing domain decomposition methods with nonconforming interfaces, you need to relate the two interface grids to each other. Psurface can do this for you, even if your interfaces do not match geometrically. Such is the case, e.g., in contact problems. This second functionality is also available for 1d surfaces in 2d space.

The easiest way to use psurface for domain decomposition is to get the dune-grid-glue module and use it to drive psurface.

This package contains the development files.

Libquantum-dev
library for the simulation of a quantum computer (development files)
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libquantum is a C library for the simulation of a quantum computer. Based on the principles of quantum mechanics, it provides an implementation of a quantum register. Basic operations for register manipulation such as the Hadamard gate or the Controlled-NOT gate are available through an easy-to-use interface. Measurements can be performed on either single qubits or the whole quantum register.

Features:

  • Simulation of arbitrary quantum algorithms is possible
  • High performance and low memory consumption
  • Decoherence support for realistic quantum computation
  • Interface for quantum error correction (QEC)
  • Supports the density operator formalism
  • Implementations of Shor's factoring algorithm and Grover's search algorithm are included

This package contains the header files and static libraries which are needed to develop applications based on libquantum.

Libscirenderer-java
Java rendering library based on JOGL
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This Java API allows 2-D or 3-D plotting from simple 2-D graph to complex scenes.

While this library has been developed in the context of Scilab, it can be used in any context.

Libsundials-serial-dev
SUNDIALS development files
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The family of solvers referred to as SUNDIALS (SUit of Nonlinear and DIfferential/ALgebraic equation Solvers) consists of solvers CVODE (for ODE systems), CVODES (ODE with sensitivity analysis capabilities), IDA (for differential-algebraic systems), and KINSOL (for nonlinear algebraic systems).

This package contains files necessary for development applications using SUNDIALS in C and, in case of FCVODE and FKINSOL, Fortran. It also contains various example programs distributed by the upstream authors.

Python3-agate
data analysis library optimized for human readability
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Agate is a Python data analysis library that is optimized for humans instead of machines. It is an alternative to numpy and pandas that solves real-world problems with readable code.

Why agate?

  • A readable and user-friendly API.
  • A complete set of SQL-like operations.
  • Unicode support everywhere.
  • Decimal precision everywhere.
  • Exhaustive user documentation.
  • Pluggable extensions that add SQL integration, Excel support, and more.
  • Designed with iPython, Jupyter and atom/hydrogen in mind.
  • Pure Python. No C dependencies to compile.
  • Exhaustive test coverage.
  • MIT licensed and free for all purposes.
  • Zealously zen.
  • Made with love.

This package provides the modules for Python 3.

Python3-agatedbf
support for dbf files in agate
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Agate-dbf adds read support for dbf files to agate. It uses a monkey patching pattern to add read methods for dbf files to all agate.Table instances after import of the corresponding agatedbf module.

This package provides the modules for Python 3.

Python3-agateexcel
support for Excel files in agate
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Agate-excel adds read support for Excel files (xls and xlsx) to agate. It uses a monkey patching pattern to add read methods for xls and xlsx files to all agate.Table instances after import of the corresponding agateexcel module.

This package provides the modules for Python 3.

Python3-agatesql
support for SQL read/write in agate
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Agate-sql adds read/write support for SQL to agate. It uses a monkey patching pattern to add read and write methods for SQL to all agate.Table instances after import of the corresponding agatesql module.

This package provides the modules for Python 3.

Python3-bcolz
high performant compressed data container based on NumPy (Python 3)
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bcolz provides columnar, chunked data containers that can be compressed in-memory and on-disk. Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, but it also comes with support for import/export facilities to/from HDF5/PyTables tables and Pandas dataframes.

This package contains the modules for Python 3.

Python3-dbfread
Læs DBF-filer med Python
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DBF er et filformat brugt af databaser såsom dBase, Visual FoxPro og FoxBase+. Dette bibliotek læser DBF-filer og returnerer dataene som Pythondatatyper for yderligere behandling. Det er primært lavet for batchjob og engangsskripter.

Denne pakke tilbyder modulerne for Python 3.

Python3-leather
charting library for Python
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Leather is the Python charting library for those who need charts now and don’t care if they’re perfect.

Why leather?

  • A readable and user-friendly API.
  • Optimized for exploratory charting.
  • Produces scale-independent SVG charts.
  • Completely type-agnostic. Chart your data, whatever it is.
  • Designed with iPython, Jupyter and atom/hydrogen in mind.
  • Pure Python. No C dependencies to compile.
  • MIT licensed and free for all purposes.
  • Zealously zen.
  • Made with love.

This package provides the modules for Python 3.

Python3-numcodecs
buffer compression and transformation codecs for Python
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Numcodecs is a Python package providing buffer compression and transformation codecs for use in data storage and communication applications. These include:

  • Compression codecs, e.g., Zlib, BZ2, LZMA and Blosc.
  • Pre-compression filters, e.g., Delta, Quantize, FixedScaleOffset, PackBits, Categorize.
  • Integrity checks, e.g., CRC32, Adler32.

All codecs implement the same API, allowing codecs to be organized into pipelines in a variety of ways.

Python3-spyder-line-profiler
line profiling plugin for the Spyder IDE
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This is a plugin for the Spyder IDE that integrates the Python line profiler.

Add a @profile decorator to the functions that you wish to profile then press Shift+F10 (line profiler default) to run the profiler on the current script, or go to Run > Profile line by line.

The results will be shown in a dockwidget, grouped by function. Lines with a stronger color take more time to run.

Python3-spyder-memory-profiler
memory profiling plugin for the Spyder IDE
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This is a plugin for the Spyder IDE that integrates the Python memory profiler. It allows you to see the memory usage in every line.

Add a @profile decorator to the functions that you wish to profile then press Ctrl+Shift+F10 to run the profiler on the current script, or go to Run > Profile memory line by line.

The results will be shown in a dockwidget, grouped by function. Lines with a stronger color have the largest increments in memory usage.

Python3-spyder-reports
plugin to render scientific reports within the Spyder IDE
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Spyder-reports is a plugin for the Spyder IDE which renders scientific reports written in Markdown. The preview is displayed on a separate pannel and uses pandoc and Pweave in the backend to perform the conversion from Markdown to HTML.

Python3-spyder-unittest
plugin to run tests within the Spyder IDE
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This is a plugin for the Spyder IDE that integrates popular unit test frameworks. It allows you to run tests and view the results.

The plugin adds an item Run unit tests to the Run menu in Spyder. Click on this to run the unit tests. After you specify the testing framework and the directory under which the tests are stored, the tests are run. The Unit testing window pane (displayed at the top of this file) will pop up with the results.

Python3-zarr
chunked, compressed, N-dimensional arrays for Python
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Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing. Some highlights:

  • Create N-dimensional arrays with any NumPy dtype.
  • Chunk arrays along any dimension.
  • Compress chunks using the fast Blosc meta-compressor or alternatively using zlib, BZ2 or LZMA.
  • Store arrays in memory, on disk, inside a Zip file, on S3, ...
  • Read an array concurrently from multiple threads or processes.
  • Write to an array concurrently from multiple threads or processes.
  • Organize arrays into hierarchies via groups.
  • Use filters to preprocess data and improve compression.
Scilab-jims
Binds Java from the Scilab engine
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JIMS is an effort to allow Scilab programs full access to Java class libraries. This is achieved by interfacing at the native level in both Virtual Machines.

From Scilab, JIMS allows the capability to load and manage Java objects from the Scilab interpreter.

Thanks to this module, Scilab can access to complex and advanced Java objects with Scilab classical data types.

Theano-doc
CPU/GPU-matematikudtrykskompiler for Python - dokumentation
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Theano er et Pythonbibliotek, som giver mulighed for at definere og evaluere matematiske udtryk, der involverer flerdimensionale tabeller effektivt. Det tilbyder et Numpy-lignende udtrykssprog på højt niveau for funktionel beskrivelse af beregning, arrangerer om på udtryk for hastighed og stabilitet og opretter maskininstruktioner for hurtig beregning. Valgfrit så kan accelererede beregninger udføret på grafikkortprocessorer.

Denne pakke indeholder dokumentationen for Theano.

Please cite: Theano Development Team: Theano: A Python framework for fast computation of mathematical expressions (eprint) (2016)

Debian packages in contrib or non-free

Libsuitesparse-metis-dev
collection of libraries for computations for sparse matrices
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Suitesparse is a collection of libraries for computations involving sparse matrices. libsuitesparse-metis-dev is a replacement for libsuitesparse-dev compiled with libmetis support. The package includes the following libraries:

AMD approximate minimum degree ordering

CAMD symmetric approximate minimum degree

BTF permutation to block triangular form (beta)

COLAMD column approximate minimum degree ordering

CCOLAMD constrained column approximate minimum degree ordering

CHOLMOD sparse Cholesky factorization

CSparse a concise sparse matrix package

CXSparse CSparse extended: complex matrix, int and long int support

KLU sparse LU factorization, primarily for circuit simulation

LDL a simple LDL' factorization

UMFPACK sparse LU factorization

UFconfig configuration file for all the above packages.

This package contains the static libraries and header files.

Matlab-support
distro integration for local MATLAB installations
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This package does not provide MATLAB. Instead, it configures an existing MATLAB installation to integrate more comfortably in a Debian installation.

Currently it provides /usr/bin/matlab through the alternatives system, offers to work around incompatibilities between the libraries bundled with MATLAB and system libraries, and provides a helper utility meant to be used by other packages to compile MEX extensions.

Install this if you would like your MATLAB installation to behave more like an ordinary Debian package. Other packages may depend on this one if they install MATLAB code, for example in order to compile MEX extensions.

Metis-edf
Family of Multilevel Partitioning Algorithms
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METIS: A Family of Multilevel Partitioning Algorithms

This is a collection of serial and parallel programs & libraries that can be used to partitioning unstructured graphs, finite element meshes, and hypergraphs, both on serial as well as on parallel computers.

Adaptation of METIS for Code_Aster purpose

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

Libcblas-dev
Basic Linear Algebra Subroutines 3, static library
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This package is a binary incompatible upgrade to the blas-dev package. Several minor changes to the C interface have been incorporated.

BLAS (Basic Linear Algebra Subroutines) is a set of efficient routines for most of the basic vector and matrix operations. They are widely used as the basis for other high quality linear algebra software, for example lapack and linpack. This implementation is the Fortran 77 reference implementation found at netlib.

This implementation of the library belongs to the CLAPACK distribution.

This package contains a static version of the library.

Libgismo-dev
Geometry plus simulatiom modules development files
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G+Smo (Geometry + Simulation Modules, pronounced "gismo") is a new open-source C++ library that brings together mathematical tools for geometric design and numerical simulation. This package contains inlude headers, cmake configuration files and other development utils.

Python3-pydap
implementation of the Data Access Protocol in Python
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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.

Xtensor-dev
multi-dimensional arrays with broadcasting and lazy computing
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xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions.

xtensor provides:

  • an extensible expression system enabling lazy broadcasting.
  • an API following the idioms of the C++ standard library.
  • tools to manipulate array expressions and build upon xtensor.

Containers of xtensor are inspired by NumPy, the Python array programming library. In fact, xtensor can be used to process numpy data structures inplace using Python's buffer protocol. For more details on the numpy bindings, check out the xtensor-python project.

This package provides the header-only library.

Xtensor-python-dev
Python bindings for the xtensor library
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xtensor is a C++ library for multi-dimensional arrays enabling numpy-style broadcasting and lazy computing.

xtensor-python enables inplace use of numpy arrays in C++ with all the benefits from xtensor:

  • C++ universal function and broadcasting
  • STL - compliant APIs.
  • A broad coverage of numpy APIs (see the numpy to xtensor cheat sheet).

The Python bindings for xtensor are based on the pybind11 C++ library, which enables seemless interoperability between C++ and Python.

This package provides the header-only library.

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