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RE: some useful tools


I also used rubber in past for LaTeX compilation, but there is 'texi2dvi',
which is part of most TeX distributions. It's easy to use and I do not know 
why it is so "hidden" It seems that there is quite some redundancy for this 
task, since I once also found an 'lc' command man page, where lc stands for 
LaTeX compiler. If one does not like LaTeX, LyX <http://www.lyx.org> might be 
a very good replacement or at least neat intro into TeX world. And it does not
crash every 5 minutes as MS Word. This is really evident with long files, such
as thesis or similar.

When talking about LaTeX and science I would really like to point to Sweave
<http://www.ci.tuwien.ac.at/~leisch/Sweave/>, which is part of R and provides 
very powerfull combination of LaTeX and R in one file. This is based on Noweb
ideology. You just take LaTeX file and add some code "chunks" like on bellow 
and after your process file (.Rnw) with Sweave you get LaTeX file with results
and figures linked.


some text in \LaTeX, some text in \LaTeX, some text in \LaTeX

<<example, echo=true, results=verbatim, fig=true>>=
tmp <- rnorm(n = 100)
tmp1 <- mean(tmp)

some text in \LaTeX with mixture of some results i.e. \Sexpr{tmp1}


Again one can use LyX in Noweb mode with R to get Sweave power to
LyX. If you are writting reports, thesis, papers, presentations with LaTeX 
Sweave can help you a lot. Actually, LaTeX driver is default, but one can 
also get HTML via R2HTML R package.

with regards, Gregor

-----Original Message-----
From: Yaroslav Halchenko on behalf of Yaroslav Halchenko
Sent: ned 2005-08-07 01:06
To: debian-science@lists.debian.org
Cc: frank@kuesterei.ch
Subject: Re: some useful tools
Hi Jukka (and Frank)

Nice references! 
I think I will give rubber a spin. Not that I am lost in my makefiles
but indeed there might be something better.

jabref sounds cool too. Indeed Java GUI probably is quite nasty but your
description gives some nice features which I think are not present in
pybliographer which I'm using at the moment and which I really like.
if only someone packaged it for debian
well -- there was ITP

Frank, how is packaging going or did you abandoned the idea?


On Sat, Aug 06, 2005 at 01:01:38PM +0300, Jukka Suomela wrote:
> Hi all,

> Here is a list of some tools which I find useful and noone else has mentioned 
> yet. (Sorry if I missed someone's email.)

> - glpk:

> An LP and MILP solver library.

> I can't say I like the API that much. The header files pollute the name space 
> by defining macros like "print". There are useful functions for printing LP 
> problems in human and machine readable formats but those functions can only 
> print to a named file, not to an open file handle or such. There are problems 
> with const correctness. C arrays which are indexed from element 1 instead of 
> 0 make your C code look nonidiomatic and thus error-prone.

> However, the thing seems to do what I want, and the reference manual is great. 
> Just don't say I didn't warn you. The lp-solve (i.e. lp_solve) library seemed 
> to be an even worse mess, YMMV.

> - rubber:

> I always use this tool to build my Latex documents. Thanks to it, Latex is now 
> a productive tool instead of a PITA.

> One simple command "rubber -Wall foo.tex" automatically performs all steps to 
> build up-to-date dvi, ps, pdf, etc. versions of the Latex document, including 
> things like running bibtex and converting images to eps or pstex format if 
> needed. It hides all garbage printed by Latex, parses error messages, and 
> prints relevant messages in a human-readable format. Thanks to the -Wall 
> switch, it can even print warnings when there was no need to re-run Latex 
> this time.

> Magic "% rubber: ..." comments inside the Latex source can be used to specify 
> paths for Latex class files, bibliography files, bibtex style files, etc.; 
> you can also specify if and how you want to create ps and pdf versions. You 
> don't need to maintain any external Makefiles or worry about your build 
> environment; one Latex source file is enough. This is important when more 
> than one people are working on the same document: checkout the document from 
> the version control system, run rubber, and you've got the most up-to-date 
> version of the paper.

> - jabref:

> A GUI for maintaining a bibliography in a bibtex file. (Not in Debian as far 
> as I know; see http://jabref.sourceforge.net/ ; written in Java, so 
> installation is relatively easy if you have a working Java environment.)

> Naturally, there are many similar tools. I don't know if there is anything 
> better; JabRef is far from perfect, but at least the following aspects are, 
> in my opinion, useful: First of all, it is not just a bibtex editor, it is 
> also useful for storing interesting articles and browsing and reading them. 
> The current version works fine in a group work model where the bibliography 
> file and the corresponding PDF files of the articles are kept in a version 
> control system. JabRef supports things like maintaining a tree-like hierarchy 
> of categories and storing one article in multiple categories. It supports 
> Latin-1 characters nowadays quite well. It can automatically generate bibtex 
> entry keys by using a customisable key generation rule. It runs in Windows, 
> too, which can be an important aspect in group work.

> If you are looking for a tool like this, you might want to give it a try. Just 
> don't give up immediately when you notice that the usability of the GUI is 
> far from what one sees in commercial software. One can get used to it.

> Best regards,
> Jukka Suomela
=------------------------------   /v\  ----------------------------=
Keep in touch                    // \\     (yoh@|www.)onerussian.com
Yaroslav Halchenko              /(   )\               ICQ#: 60653192
                   Linux User    ^^-^^    [175555]

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