LaTeX

JabRef and xmonad

I use JabRef for BibTeX reference management. It has a handy GUI and a nice web search feature so you don’t have to manually type in entries. But it apparently doesn’t like to work with tiling window managers like xmonad. If you start JabRef in xmonad, you just get a blank white/gray box with only a File > Close menu option and nothing else. This makes it completely unusable.

It took me a while to google up a solution since there were a few false starts with some sort of MToolkit vs XToolkit option in Java but it turns out you can just set the environmental variable _JAVA_AWT_WM_NONREPARENTING=1 and things will start working correctly.

So if jabref is in your path you could make an alias for jabref like:
alias jabref="_JAVA_AWT_WM_NONREPARENTING=1 jabref"
and then just type jabref and it should work normally.

LaTeX
Programmer

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Displaying Code in LaTeX

gioby of Bioinfo Blog! (an interesting read by the way) left a comment asking about displaying code in LaTeX documents. I’ve sort of been cludging around using \hspace‘s and \textcolor but I’ve always meant to figure out the right way to do things so this seemed like a good chance to figure out how to do it right.

LaTeX tends to ignore white space. This is good when you’re writing papers but not so good when you’re trying to show code where white space is an essential part (e.g. Python). Luckily there’s a builtin verbatim environment in LaTeX that is equivalent to html’s <pre>. So something like the following should preserve white space.

Code in LaTeX using verbatim
\begin{verbatim}
for i in range(1, 5):
  print i
else:
  print "The for loop is over"
\end{verbatim}

Unfortunately, you can’t use any normal LaTeX commands inside verbatim (since they’re displayed verbatim). But luckily there a handy package called fancyvrb that fixes this (the color package is also useful for adding colors). For example, if you wanted to highlight “for” in the above code, you can use the Verbatim (note the capital V) environment from fancyvrb:

Code in LaTeX using fancyvrb
\newcommand\codeHighlight[1]{\textcolor[rgb]{1,0,0}{\textbf{#1}}}
\begin{Verbatim}[commandchars=\\\{\}]
\codeHighlight{for} i in range(1, 5):
  print i
else:
  print "The for loop is over"
\end{Verbatim}
Code in LaTeX using pygmentize

If you really want to get fancy, the Pygments package in Python will output syntax highlighted latex code with a command like: pygmentize -f latex -O full test.py >py.tex The LaTeX it outputs is a bit hard to read but it’s not too bad (it helped me figure out the fancyvrb package) and it does make nice syntax highlighted output.

Here’s an example LaTeX file with the three examples above and the pdf it generates if you’re curious.

LaTeX
Programmer

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LaTeX: Document Creation Alternative

I’ve been using LaTeX a lot recently and I thought I would write a quick post since I wish I would have found out about it earlier. LaTeX is a really powerful document (pdf and others) creation program. It’s sort of like HTML and CSS for paper publishing. As a first warning, LaTeX, like HTML, is not WYSIWYG. You have to code in things like \textbf{This will be bold}. This takes some getting used to after programs like MS Word but after using LaTeX, I really can’t stand working in Word for anything longer than a page or two.

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Grad Student
LaTeX
Programmer

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