April 2012
9 posts
4 tags
GSoC 2012
I’m pleased to announce that I will be spending the summer working on Biopython, funded by Google Summer of Code 2012!
OBF announcement: http://news.open-bio.org/news/2012/04/students-selected-for-gsoc/
Project abstract: http://www.google-melange.com/gsoc/project/google/gsoc2012/lenna/23001
3 tags
Fun with git
I currently have three (!) open github pull requests for biopython, and I also pointed out an open issue that had been fixed. Busy busy!
One update was to allow automatic construction of a dict based on a remote file. Someone had already written the conversion script; I just worked on downloading the file. Struggled a bit with urllib etc. and couldn’t figure out how to get a file...
Streamlining workflow
I’ve been reading The Pragmatic Programmer (http://pragprog.com/the-pragmatic-programmer) and one thing they really emphasize (other than Don’t Repeat Yourself) is trying to make sure the computer doesn’t get in your way while programming.
I’ve made a few tweaks that should make my programming life more streamlined.
In my ~/.inputrc, I added set editing-mode vi which...
2 tags
PyPy notes
Decided to test PyPy because the PLY lexer isn’t much use on Python implementations that can use the C module.
Initial tests of the PLY CIF lexer with PyPy show that it’s marginally slower than with CPython.
PyPy can’t import modules from within PDB due to NumPy dependency; however, most modules in PDB are compatible with NumPyPy. Determine least-ugly way to implement this.
...
6 tags
Python segfault!
Background
Biopython has had a C CIF* parser for quite some time (2002 I believe) but it has been commented out of setup.py for a few years because the compiler required a link library and I don’t think Python has a great way to check for C libraries.
The parser is written using flex,* which takes a fairly simple input file and makes generated C (default name lex.yy.c). This file is...
3 tags
Virtualization pt 1: Debian
I finally gave in and made a Debian virtual machine (using VMWare Fusion). Yes, I know, I should use VirtualBox, but I’ve never had good experiences with free software interaction with the OS X windowing system. Qt does an acceptable Cocoa interface, but Tcl/Tk and X window software are both unbearably slow. So when MacUpdate’s latest package included VMWare, I decided to spring for...
8 tags
Finding a libre 2D molecule editor: success!
After much blood, sweat, and tears, I’ve finally gotten gnome-chemistry-utils running on Mac OS X. Yes, really.
Previous tribulations here.
I decided to not make a CMake project because I figured there wouldn’t be Find scripts for most of the dependencies, and I eventually realized that everything I needed had a .pc somewhere.
Major steps to getting it to find the dependencies:
...
6 tags
Finding a libre 2D molecule editor: part 2
Right now, I’m trying to get gnome-chemistry-utils to install. Of course there’s no macport, so I’m currently in the ./configure -> install dependency via macports endless cycle.
At least it’s got screenshots that show the simple line drawings I want, and it was updated in 2012. I’m keeping my fingers crossed.
Fun things so far: requires goffice 0.9.0, macport...
5 tags
Finding a libre 2D molecule editor
So I’ve been having fun trying to find a usable libre 2D molecule editor. I’m just trying to make diagrams of some simple pyridine-based molecules, nothing fancy.
Avogadro seems a bit buggy. Odd graphics glitches (atom labels showing up as white squares, ball rendering very wrong), poor interface (no menus?). It also seems overly 3D oriented for my needs. I couldn’t find a...
