Installing Tioga on Leopard

Written by thomas on April 4th, 2008

Since I do DNA analysis in Ruby, I wanted to be able to make some nice graphs for my data. Enter Tioga, a Ruby library originally created by "Bill Paxton, one of the creators of Adobe PostScript". Needless to say, the graphs look beautiful.

Anyway, I wasn't able to install it on Leopard. Installing via gem didn't produce a workable Tioga, so I had to do it the old fashioned way:

tar zxf tioga-1.7.tar.gz
cd tioga-1.7
cd split
ruby extconf.rb

Now, the last command failed with this error message:

checking for zlib.h... no
Error: you should have zlib (including development files) installed to
build and run Tioga. You can get it there:

  http://www.zlib.net/

If that doesn't solve your problem, please report it on the Tioga tracker:

  http://rubyforge.org/tracker/?group_id=701

After a lot of debugging, the problem was solved by instead running the following:

hdrdir="/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/universal-darwin9.0" \
ARCHFLAGS="-arch i386" ruby extconf.rb

Mind you, this is on a Mac Pro, which should otherwise have ARCHFLAGS="-arch x86_64". Moving on, running the rest of the code is a piece of cake.

make
sudo make install
cd ../tests
ruby ts_Tioga.rb

Ta-da! It should work, and you can start working with Tioga. Enjoy!

Project page for TextMate bundles

Written by thomas on January 30th, 2008

Well, I finally got a project site up and running, which will be hosting all my code. If there are any bug reports or feature requests, please submit an issue notice there. The project page will, in due time, provide you with proper documentation via the built-in Wiki.

Hopefully, this change will be quite useful. The link:

https://projects.ux.uis.no/projects/show/textmate

Temporary Matlab bundle download

Written by thomas on January 9th, 2008

Seems way more people than I thought use this bundle. Yay!

The bad part is that I’ve had a series of problems lately. Firstly, the Leopard upgrade went somewhat awry. Turned out that not only did Macports bork the Apache install (SSL issue), but also nuked my configuration files. After being on vacation, about 2000km away from my computer, I lost connection to the server amidst network upgrades at the university. Anyhow, I’m back at working out the kinks of the server setup. I should have everything up and running in not too long.

In the mean time, here’s revision 140 of the Matlab.bundle. There may be some issues in the “enter in string” command, which turned out to be much more difficult than imagined. Hopefully, I’ll have the new version done fairly soon. There are a number of new features, such as func⇥, more advanced fun⇥, and ⌃⇥ to fill in variable descriptions in the function snippets. I’ll detail these changes later on, when all is back to normal.

For now, please enjoy the bundle, and let me know if you find bugs or if you have any suggestions!

Bugfixes In The TextMate MATLAB Bundle

Written by thomas on June 15th, 2007

As a result of feedback, I have commited a few bug fixes for the MATLAB bundle.

Changelog:

* Added handling of curly brackets.
* Added trigging on Enter in curly brackets.
* Removed automatic conversion of != to ~=. Highlighting as error instead.
* Minor changes

I should also mention that hitting the Return key, or is it the Enter key? Eh, anyway, the enterish key on the numpad should automatically indent and insert a new % if hit within a comment! This can be very useful if you have to write multi-line comments.

Installing the comment notifier plugin in Mephisto

Written by thomas on May 2nd, 2007

After some work, this was what I had to do to install the notifier plugin.

There are two different plugins, and I ended up using the one from agileevolved after struggling for a long time with the other available notifier plugin.

If this is useful to you, read on...

New MATLAB Bundle for TextMate

Written by thomas on March 28th, 2007

Unhappy with the MATLAB bundle that was included in TextMate, I set out to write a new one. The old one was a mashup of Bash, Octave, MATLAB, and some other stuff, which, needless to say, didn't quite measure up. So, without further ado, you can now download the new and improved MATLAB bundle!

New design

Written by thomas on November 21st, 2006

Hurray! My brand, spanking, shining new design is up and running. Hopefully, there won’t be too many bugs. Let me tell you, working around the heap of bugs that constitute the web browser called Internet Explorer, is not fun. In any case, the theme should look decent from IE 6 and up. IE 5.0 is just too broken to bother with, and no sane person should be running that anyway. I’ve tested the design in Opera 9, Firefox 2, Safari 2, ELinks 0.9.2, IE 5, IE 5.5, IE 6, and IE 7.

If you see something that looks like a theme bug, please let me know! Maybe I’ll release this theme some day, if people really want it, but for now, it feels good having a theme that nobody else has. ;-)

In dealing with my new theme, i found that I had to modify the LaTeX plugin somewhat. Here is the updated patch.

Mephisto LaTeX plugin patch

Written by thomas on November 7th, 2006

After a reinstall of Mephisto everything’s back up and running as it should. Now, back on topic.

When researching the available blogging softwares, I ran across Mephisto in an attempt of finding myself a Ruby on Rails based software. One of my primary wishes for my new blog was the ability to easily include [LaTeX] equations in my webpages. The only viable alternative which had LaTeX support was WordPress, which I’ve been told has quite a number of issues. After some inquiring in the #mephisto channel, somebody offered to code up a plugin, and a couple of days later the LatexRenderer plugin was born.

Excellent as it was, I still wanted more ;) A couple of versions later, the LatexRenderer patch was done. The original plugin takes the code as:

< filter : latex >
$x = \frac{-b\pm\sqrt{b^2 - 4ac}}{2a}$
< / filter : latex >

, minus the spaces that is, and renders the equation as an image.

What I added to the plugin was the ability to quickly show the underlying LaTeX source code. Rendering the above equation now gives us:

If you click on the equation, the image disappears and the source code appears. Click again, and you’ll get the image back.

I hope somebody will find this a useful feature, and hopefully Jan will include the patch in the official plugin.

My first post

Written by thomas on November 6th, 2006

ZOMG!!1!one!11!!! FP!!!

OK, the enthusiasm is over now. I’m just happy things are working.