Debian Science typesetting packages

AUCTeX is a comprehensive customizable integrated environment for writing input files for TeX/LaTeX/ConTeXt/Texinfo using GNU Emacs.

It supports processing source files by running TeX and related tools (such as output filters, post processors for generating indices and bibliographies, and viewers) from inside Emacs. AUCTeX allows browsing through the errors reported by TeX, while it moves the cursor directly to the reported error, and displays some documentation for that particular error. This will even work when the document is spread over several files.

AUCTeX can automatically indent LaTeX source, either line by line or for an entire document, and has a special outline feature which can greatly assist in getting an overview of a document.

AUCTeX is written entirely in Emacs Lisp, and may therefore be enhanced with new features for specific needs. It comes with a large range of handy Emacs macros. It is a GNU project, and documentation for all its features is accessible via the Emacs info browser.

The biblatex package by Philipp Lehman is becoming the definitive citation management tool for LaTeX users. Biblatex has relied on the venerable BibTeX program only for sorting and generating a very generic .bbl file without any formatting instruction. Everything else is taken care of by biblatex, which provides a powerful and flexible macro interface for authors of citation styles.

Biber offers a large superset of BibTeX functionality for BibLaTeX users. In addition it offers full UTF-8 (Unicode 6.0) capabilities, fully customisable sorting, output to GraphViz to help visualise complex crossrefs, support for remote data sources, structural validation of the data against the (customisable) data model, and a lot more.

Bibus is a bibliographic database which has been developed with LibreOffice/ OpenOffice.org in mind. It can directly insert citations and format the bibliographic index in an open OpenOffice.org Writer document. The main features are

• hierarchical organization of the references with user-defined keys
• designed for multiuser-environments (share databases between users)
• a search engine supporting live queries
• on-line PubMed access
• import of PubMed (Medline), EndNote/Refer, RIS and BibTeX records.

Bibus will use an SQLite-database by default for storage (via the SQLite3 module available in Python >2.5). But it also supports MySQL-databases. If you want to use a MySQL-database, make sure, that you have the python-mysqldb package installed.

Convert between the following bibliographic data formats: BibTeX, COPAC, EndNote refer, EndNote XML, Pubmed XML, ISI web of science, US Library of Congress MODS XML, RIS, and Word 2007 bibliography.

This package provides command line tools bib2xml, copac2xml, end2xml endx2xml, isi2xml, med2xml, ris2xml which convert to MODS XML format, modsclean which reformats MODS XML, and a matching set of commands xml2ads, xml2bib, xml2end, xml2isi, xml2ris, xml2wordbib which convert from MODS XML.

cb2bib is a program to extract bibliographic references from unformatted and non standard sources, like:

• email alerts;
• journal Web pages;
• and most interestingly PDF files.

Output references are written to BibTeX-formatted files. Other features include:

• article files can be linked and renamed by dragging them onto the cb2Bib window;
• editing and browsing BibTeX files;
• citing references, searching references and the full contents of the referenced documents;
• inserting bibliographic metadata to documents;
• writing short notes that interrelate several references.

Dia är en redigerare för scheman, diagram, tabeller, etc. Det finns stöd för UML statiska strukturdiagram (klassdiagram), enhetsrelaterade diagram, nätverksscheman och mycket mer. Diagram kan exporteras till PostScript och många andra format.

Debian GNU/Linux is widely used at universities to do research and to write papers with LaTeX. The package diploma contains examples which illustrate the possible ways to do this effectively with Debian GNU/Linux. Each example consists of a source tree where you can do "make" in the top level directory and then the source code is compiled, the measurement data are processed, and the results are converted into nice figures. Then the text is processed and combined with the figures to a print file.

FeynMF is a LaTeX package for easy drawing of professional-quality Feynman diagrams, illustrations that depict the fundamental interactions of subatomic particles. The diagrams may be created using either the Metafont or MetaPost programs. FeynMF lays out most diagrams satisfactorily from the structure of the graph without any need for manual intervention. Nevertheless all the power of Metafont or MetaPost is available for more obscure cases.

Note that you will need the texlive-metapost package in order to use the MetaPost-based version of FeynMF.

Gummi is a LaTeX editor based on GTK3. The basic features are:

• Live preview pane for the compiled document,
• BibTeX integration,
• Helpers for tables and matrices,
• Exporting to PDF,
• Error checking,
• Syntax highlighting,
• Spellchecking,
• Document statistics,
• Persistent configuration.

A set of utilities for manipulating DSC compliant postscript. The following programs are included:

impose: A preprocessor to pstops for creating 2-up printouts. It tries to remove white space from the printout by probing the original postscript for the printed area's bounding box. This makes the output more esthetic than a simplistic layout of non-cropped original pages.

bboxx: Extracts the bounding boxes of a postscript file, with the option of entering the bounding box into the file. This program uses the ghostscript bbox device.

fixtd: Sets options in a Postscript file asking the printer to turn on tumbling or duplex printing.

psbl: Rearranges pages in a file to create booklets.

Ipe supports making small figures for inclusion into LaTeX documents as well as making multi-page PDF presentations Ipe's main features are:

• Entry of text as LaTeX source code. This makes it easy to enter mathematical expressions, and to reuse the LaTeX-macros of the main document. In the display text is displayed as it will appear in the figure.
• Produces pure Postscript/PDF, including the text. Ipe converts the LaTeX-source to PDF or Postscript when the file is saved.
• It is easy to align objects with respect to each other (for instance, to place a point on the intersection of two lines, or to draw a circle through three given points) using various snapping modes.
• Users can provide ipelets (Ipe plug-ins) to add functionality to Ipe. This way, Ipe can be extended for each task at hand.
• The text model is based on Unicode, and has been tested with Korean, Chinese, and Japanese.

Package lua5.3 is recommended if using Ipe with LaTeX.

Package texlive-latex-recommended enables unicode text entry (for accented characters).

Converts figures that were made with Ipe 5 to the format understood by Ipe 6. You can then run ipe6upgrade (from package ipe) to convert them to Ipe 7 format. Ipe is a drawing editor for creating figures, provided in package ipe.

JabRef is a graphical Java application for editing BibTeX (.bib) databases. JabRef lets you organize your entries into overlapping logical groups, and with a single click limit your view to a single group or an intersection or union of several groups. You can customize the entry information shown in the main window, and sort by any of the standard BibTeX fields. JabRef can autogenerate BibTeX keys for your entries. JabRef also lets you easily link to PDF or web sources for your reference entries.

JabRef can import from and export to several formats, and you can customize export filters. JabRef can be run as a command line application to convert from any import format to any export format.

JEuclid is a complete MathML rendering solution, consisting of:

• A MathViewer application
• Command line converters from MathML to other formats
• An ant task for automated conversion
• Display components for AWT and Swing
• A component for Apache Cocoon

This package contains the Swing MathViewer application.

An application to manage bibliography databases in the BibTeX format. KBibTeX can be used as a standalone program, but can also be embedded into other KDE applications (e.g. as bibliography editor into Kile).

KBibTeX can query online resources (e.g. Google scholar) via customizable search URLs. It is also able to import complete datasets from NCBI Pubmed. It also supports tagging references with keywords and manages references to local files.

BibTeX files can be exported into HTML, XML, PDF, PS and RTF format using a number of citation styles.

Kile is a user-friendly LaTeX source editor and TeX shell for KDE.

The source editor is a multi-document editor designed for .tex and .bib files. Menus, wizards and auto-completion are provided to assist with tag insertion and code generation. A structural view of the document assists with navigation within source files.

The TeX shell integrates the various tools required for TeX processing. It assists with LaTeX compilation, DVI and postscript document viewing, generation of bibliographies and indices and other common tasks.

Kile can support large projects consisting of several smaller files.

latexdiff compares two LaTeX files and marks up significant differences between them (i.e. a diff for LaTeX files). It generates a new LaTeX file containing the annotated differences.

Various options are available for visual markup using standard LaTeX packages such as 'color.sty'. Changes not directly affecting visible text, for example in formatting commands, are still marked in the LaTeX source.

A rudimentary revision facilility is provided by another Perl script, 'latexrevise', which accepts or rejects all changes. Manual editing of the difference file can be used to override this default behaviour and accept or reject selected changes only.

JLaTeXmath library provides a set of Java classes for displaying (complex) mathematical formulas as part of a Java application. Some use cases are:

• Displaying text with embedded formulas (in an editor pane, a JavaHelp page, ...)
• Make a combo box which provides the user with a choice between various formulas.
• Have a slider with ticks that display their values not as decimal numbers, but as exact values, e.g., fractions, square roots or any combination of these.
• Display the formula together with the graph of a function.

LyX is an almost WYSIWYG-frontend for LaTeX. It makes the power and typesetting quality of LaTeX available for people who are used to word processors. Since LyX supports LaTeX's concept of general mark-ups, it is even easier and faster to create professional quality documents with it than with usual word processors. It is also possible to use LaTeX commands within LyX, so nothing of LaTeX's power is lost.

You can extend the functionality of LyX by installing these packages:

• chktex: check for typographical errors
• gnuhtml2latex: import HTML documents
• groff: improved table formatting in plain text exports
• gnumeric: import spreadsheats
• librsvg2-bin, inkscape: use the SVG image format in LyX documents
• lilypond: support for musical sheets
• maxima: integrated CAS support for equation evaluation
• mythes-*: use the OpenOffice.org/LibreOffice Thesaurus
• noweb, r-cran-knitr: use literate programming
• rcs, cvs, svn, git: integrated version control
• texlive-xetex/luatex: use the XeTeX/LuaTeX typesetting system
• wv: import MS Word documents
• xsltproc (or saxon with openjdk-17-jre), docbook-xsl: ePub export

Mlpost is an OCaml library for scientific drawing. It relies on Metapost, giving the possibility to include (La)TeX fragments. Mlpost users can use the full power of OCaml to generate their diagrams, including static typing and the possibility to use any OCaml library. Moreover, Mlpost promotes a declarative style quite different from existing tools.

This package contains a command-line tool to ease the generation of PostScript or PDF figures directly from .ml files.

Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. The formats it can handle include

• light markup formats (many variants of Markdown, reStructuredText, AsciiDoc, Org-mode, Muse, Textile, txt2tags)
• HTML formats (HTML 4 and 5)
• Ebook formats (EPUB v2 and v3, FB2)
• Documentation formats (GNU TexInfo, Haddock)
• Roff formats (man, ms)
• TeX formats (LaTeX, ConTeXt)
• Typst
• XML formats (DocBook 4 and 5, JATS, TEI Simple, OpenDocument)
• Outline formats (OPML)
• Bibliography formats (BibTeX, BibLaTeX, CSL JSON, CSL YAML, RIS)
• Word processor formats (Docx, RTF, ODT)
• Interactive notebook formats (Jupyter notebook ipynb)
• Page layout formats (InDesign ICML)
• Wiki markup formats (MediaWiki, DokuWiki, TikiWiki, TWiki, Vimwiki, XWiki, ZimWiki, Jira wiki, Creole)
• Slide show formats (LaTeX Beamer, PowerPoint, Slidy, reveal.js, Slideous, S5, DZSlides)
• Data formats (CSV and TSV tables)
• PDF (via external programs such as pdflatex or wkhtmltopdf)

Pandoc can convert mathematical content in documents between TeX, MathML, Word equations, roff eqn, typst, and plain text. It includes a powerful system for automatic citations and bibliographies, and it can be customized extensively using templates, filters, and custom readers and writers written in Lua.

This package contains the pandoc tool.

Some uses of Pandoc require additional packages:

• SVG content in PDF output requires librsvg2-bin.
• YAML metadata in TeX-related output requires texlive-latex-extra.
• *.hs filters not set executable requires ghc.
• *.js filters not set executable requires nodejs.
• *.php filters not set executable requires php.
• *.pl filters not set executable requires perl.
• *.py filters not set executable requires python.
• *.rb filters not set executable requires ruby.
• *.r filters not set executable requires r-base-core.
• LaTeX output, and PDF output via PDFLaTeX, require texlive-latex-recommended.
• XeLaTeX output, and PDF output via XeLaTeX, require texlive-xetex.
• LuaTeX output, and PDF output via LuaTeX, require texlive-luatex.
• ConTeXt output, and PDF output via ConTeXt, require context.
• PDF output via wkhtmltopdf requires wkhtmltopdf.
• Roff man and roff ms output, and PDF output via roff ms, require groff.
• MathJax-rendered equations require libjs-mathjax.
• KaTeX-rendered equations require node-katex.
• option --csl may use styles in citation-style-language-styles.

pandoc-citeproc is a Haskell implementation of the Citation Style Language (CSL).

This package also contains an executable: pandoc-citeproc, which works as a pandoc filter (pandoc >= 1.12), and also has a mode for converting bibliographic databases a YAML format suitable for inclusion in pandoc YAML metadata.

Pybtex reads citation information from a file and produces a formatted bibliography. BibTeX style files are supported. Alternatively it is possible to write styles in Python.

Pybtex currently understands the following bibliography formats:

• BibTeX
• BibTeXML
• YAML-based format

The resulting bibliography may be output in one of the following formats:

• LaTeX
• HTML
• plain text

This package provides the command-line interface.

Pybtex reads citation information from a file and produces a formatted bibliography. Pybtex-docutils provides a plugin which brings support for docutils to pybtex.

This package provides the modules for Python 3.

This extension allows BibTeX citations to be inserted into documentation generated by Sphinx, via a bibliography directive, and a cite role, which work similarly to LaTeX’s thebibliography environment and \cite command.

This package provides the modules for Python 3.

The R package knitr is a general-purpose literate programming engine, with lightweight API's designed to give users full control of the output without heavy coding work. It combines many features into one package with slight tweaks motivated from everyday use of Sweave.

The SageTeX LaTeX package allows you to embed code, results of computations, and plots from the SageMath mathematics software suite into LaTeX documents. SageMath is an open-source Computer Algebra System (CAS).

This package provides the LaTeX package.

Setzer features shortcuts for many LaTeX elements and symbols, a document creation wizard, a dark mode, a high screen to content ratio and a good side-by-side pdf viewer.

Sketch is a simple system for producing line drawings of three-dimensional objects and scenes. Sketch is intended to produce finely wrought, mathematically-based illustrations with no extraneous detail and be able to easily overlay TeX math and text. The input language is reminiscent of PSTricks, so will be easy to learn for current PSTricks users. It generates either PSTricks or TikZ/PGF code as output.

Note that this package is not the interactive vector drawing program now known as skencil.

The TeX Live software distribution offers a complete TeX system. It encompasses programs for typesetting, previewing and printing of TeX documents in many different languages, and a large collection of TeX macros and font libraries. . This metapackage provides a decent selection of the TeX Live packages which should suffice for the most common tasks. . The distribution also includes extensive general documentation about TeX, as well as the documentation accompanying the included software packages.

Texmaker is a clean, highly configurable LaTeX editor with good hot key support and extensive LaTeX documentation. Texmaker integrates many tools needed to develop documents with LaTeX, in just one application. It has some nice features such as syntax highlighting, insertion of 370 mathematical symbols with only one click, and "structure view" of the document for easier navigation.

TeXstudio is an integrated writing environment for creating LaTeX documents. The software aims to simplify and enhance the LaTeX writing process, providing users with a range of features, including:

• Advanced syntax highlighting
• Live reference checking
• An integrated PDF viewer
• Live inline preview
• LaTeX command completion and syntax checking
• Local and global structure view
• Citations checking and completion
• Live grammar checking
• Spellchecking

vim-latexsuite attempts to provide a comprehensive set of tools to view, edit and compile LaTeX documents in Vim. Together, they provide tools starting from macros to speed up editing LaTeX documents to functions for forward searching .dvi documents.

This package also provides help to LaTeX in Vim.

By default, vim-latexsuite is not enabled. Please read /usr/share/doc/vim-latexsuite/README.Debian after installing the package.

XFig is a menu-driven tool that allows the user to draw and manipulate objects interactively in an X window. The resulting pictures can be saved. If the fig2dev program is installed, which is contained in the fig2dev package, the pictures can be printed on postscript printers or converted to a variety of other formats (e.g. to allow inclusion in LaTeX documents or web pages).

This package contains the xfig program itself.

You should think about installing the fig2dev package to export the graphics to several common formats. You should also think about installing xfig-doc, which contains the documentation and xfig-libs, which contains several clip art libraries.

csv2latex is a simple command-line file converter that converts a comma-separated-values file into a LaTeX table. It can guess exotic csv formats.

GtkMathView is a C++ rendering engine for MathML documents. It provides an interactive view that can be used for browsing and editing MathML markup.

GtkMathView reads MathML documents by means of a frontend whose purpose is to traverse the MathML document (or part of it) and to appropriately instantiate GtkMathView's internal data structures that are suitable for rendering it. Currently the following frontends are supported: libxml2 (tree view using libxml2 API), libxml2 reader (event view using libxml2 reader API), GMetaDOM (tree view using DOM API), custom (application-specific view with application-provided callbacks).

GtkMathView renders MathML documents through a backend whose purpose is to provide an interface between the portable rendering engine and the platform-specific capabilities (like retrieving fonts, drawing on the screen, and so on). Currently the following backends are provided: GTK+, GTK+ widget, PostScript, SVG, AbiWord.

This package includes utilities to view and render MathML documents.

QTeXEngine enables Qt based applications to easily export graphics created using the QPainter class to TeX. It is built on top of QPaintEngine and uses the TikZ/Pgf graphic systems for TeX.

This package contains the development and header files for the QTeXEngine library.

This package integrates with LibreOffice to simplify the editing of mathematical and scientific formulas. It also allows you to use your favorite drawing software and include graphs of functions into a document.

This is a transitional package for luasseq to ensure proper upgrade to texlive-luatex. It can be safely removed after the installation is complete.

This GNU R package enables integration of base and grid graphics.

The GNU R package highr provides syntax highlighting for R source code; it natively supports generating LaTeX and HTML output from R source code. Source code of other languages is supported via Andre Simon's highlight package.

This GNU R package creates 'D3' 'JavaScript' scatterplots from 'R' with interactive features : panning, zooming, tooltips, etc.

The scatterD3 package provides an HTML widget based on the htmlwidgets package and allows one to produce interactive scatterplots by using the d3 javascript visualization library.

This GNU R package provides functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...

This R package provides functions returning, displaying or writing to disk the LaTeX or HTML code associated with the supplied object of class xtable. The package also provides functions converting an R object to an xtable object, which can then be printed as a LaTeX or HTML table.

Ipe is a drawing editor for creating figures, provided in package ipe.

This package contains a tool to convert drawings in SVG format to XML that can be used by ipe editor.

Tellico is a collection manager for KDE. It includes default collections for books, bibliographies, comic books, videos, music, coins, stamps, trading cards, and wines.

Tellico capabilities include:

• creation of user-defined custom collections with unlimited fields,
• automatically formatted names,
• sorting and filtering by any field or property,
• ISBN validation,
• full customization for printing or display through XSLT files,
• import and export of CSV, RIS, BibTeX and BibTeXML files,
• import data from Amazon, IMDb, CDDB or any US-MARC compliant z39.50 server.

Tellico files are stored in XML format, avoiding the need for a database server, and allowing other software applications to use the data.

pymarc is a Python library for working with MARC21 bibliographic data loosely based on the MARC/Perl suite of modules (http://marcpm.sf.net).

Quaneko is a tool that allows you to quickly search for keywords in the files and directories on the local hard disk. It creates indexes over the words in those files. For you, this means that a typical search query will only take seconds.

quaneko can not only search for words in plain text files but also in various other file formats, depending on its configuration (e.g. Word doc, pdf, html, xml,...)

Digital library manager. Think of it as an iTunes for your PDFs.