Michele's wiki/blog

→ Back to programming languages

Meetings:

→ SciPy2006, SciPy2007, SciPy2008

Columns:

→ Charming Python

→ Discover Python

Language:

→ Python Reference Card

→ tidbits of Python

→ installing packages

→ extracting source-embedded comments

→ function decorators

→ Python idioms and efficiency

→ regular expressions

→ SetupTools

→ embedding Python in C

Interaction:

→ TeXmacs plugin

→ IPython

Science:

→ Software Carpentry (excellent!)

→ scientific tools with Python

→ complex numbers

→ normalizing FFTs in Numeric

→ Nelder-Mead optimizer

→ using weave to inline C++ code in Python

→ parallel Python

Graphics:

→ g2 wrappers

→ Tkinter reference

→ Python Imaging Library

→ PyX (see this trick)reference

→ Back to Python, conferences

Tutorials

→ Pyraf and Cython

→ numpy, traits, Chaco

Day 1

→ Plenaries

Day 2

→ Plenaries

→ Back to Python, conferences

General

→ Conference website

→ Useful scientific Python computing resources

→ Schrodinger evolution simulation by Nagel/Perez (from scipy.org cookbook)

→ Installing numpy and scipy: in recent versions, edit site.cfg (in dist directories) for location of blas, lapack, fftw… OS X (with devtools) has accelerated blas and lapack (note a BLAS Altivec bug in OS X 10.4). Note that numpy release 1.0.3 breaks scipy build (it may be enough to link scipy/scipy to scipy/Lib).

→ New traits and ets repository; uses EasyInstall, very nice installation engine

→ Considered the NVIDA G8800 GTX as a platform for CUDA

→ Mac: building universal libraries

→ Notebook progress in ipython?

Tutorials

→ IPython tutorial

→ Idiomatic Python (see also Goodger)

→ Wrapping tutorial: slides, Graph.i, all materials

Day 1

→ Lots about the One Laptop per Child project; talked to Ivan Krstic about hypercard-like educational stacks wtih scientific data and its analysis. Perhaps SAGE?

→ Plenary talks

→ Lightning talks

Day 2

→ Plenary talks

The standard installation procedure for packages built with distutils is python setup.py install. If you want to install in a nonstandard directory, add something like --prefix=/Users/vallis/…. But then the path to the library needs to be added to PYTHONPATH (colon separated), or the library won't be accessible to import without changing sys.path.

Python eggs are a nice innovation that can simplify installs involving C extensions. After installing easy_install and setting up a ~/.pydistutils.cfg specifying something like

[install]
install_lib = ~/lib/python2.4/site-packages
install_scripts = ~/bin

you simply need to run easy_install on the egg (or the tar.gz, or the package name… the tool is a veritable Swiss army knife).

By the way, a good install_lib location on OS X is ~/Library/Python/$py_version_short/site-packages, since Python will then recognize .pth files (which does not happen elsewhere)…

Note that the location specified in ~/.pydistutils.cfg may override other install locations given as --prefix parameters to setup.py. You're warned!

Under default preferences, svn will not edit timestamps in newly added archive files. To allow that, use something like

svn propset svn:keywords Id,Date,Author,Revision lisasim/lisasim-retard.cpp

→ Back to Programming Tricks home

Unix:

→ SVN keyword management

→ if-then in shell scripts

→ redirecting stderr to stdout

→ setting environment variables

→ Make tricks

→ locating unresolved linking dependencies

→ changing file dates

→ adding line numbers

→ removing files by inode number

→ The Art of Unix Programming

Other:

→ CR and LF

→ SynthLISA on SunOS

Numerics:

→ Nelder-Mead optimizer

→ high-precision floating-point arithmetic

Philosophy:

→ The Art of Unix Programming

→ The Jargon File

→ Code as Design

→ Design Patterns

→ Back to Programming Tricks home

C/C++:

→ printing out filename and location in error messages

→ when virtual destructors?

→ extracting source-embedded comments

Java/Processing:

→ creating a standalone application

LaTeX:

→ A survey of free math fonts.

→ STIX fonts project

→ Illustrator and LaTeX fonts

→ slimming down EPS figures

→ comprehensive symbol list

→ Hey, it works! (on TugBoat)

→ Creating sparklines in LaTeX

Mathematica:

→ fixing fonts

MATLAB:

→ normalizing FFTs

→ previewing figures in PDF

→ Mathworks programming contest

→ A figure command that does not raise plot windows

Python:

→ all tricks

→ Python on OS X

→ Back to Python

General

→ Conference website

Day 1: tutorials

→ Travis Oliphant, NumPy tutorial (NumPy website)

→ Fernando Perez, IPython tutorial (IPython website)

Day 2, morning

→ Guido Van Rossum, keynote (Python 3000 PEP)

→ Travis Oliphant, state of Numpy

→ Fernando Perez, doing science with Python

→ Michael Aivazis, Pyre

Day 2, afternoon

→ Eric Jones, Enthought Tool Suite

→ Christopher Mueller, Synthetic programming

→ Prabhu Ramachandran, MayaVi

→ Andrew Straw, realtime computing

→ William Stein, SAGE (uses very cool jsmath for TeX display)

→ Greg Wilson, software carpentry (look at Trac and DrProject, check recommended reading at his homepage)

Day 3, morning

→ Benjamin Eitzen, GpuPy

→ …

→ Bill Spotz, parallel PDE solvers in Python

→ Back to the wiki root

Sections:

→ Generic

→ Languages (direct link to Python)

→ Tools

→ See all tricks

→ See also programming on OS X

Get the inode number using

ls -il

and then remove using the incantation

find . -inum [inode # here] -exec rm -i {} \;

→ Back to Programming Tricks home

Emacs:

→ rerouting backup files

→ setting tab length

→ adding Python mode

Graphics:

→ Fast Light Toolkit

→ Tioga

→ Making cartograms

→ Mini Course on Color

→ The Color Brewer

→ Color Mixer

→ Color Scheme Generator

Literate Programming:

→ Amrita

Presentations:

→ Wink

→ CSS-based presentations: S5

→ LaTeX-based presentations: Prosper, Seminar, PdfScreen, PPower4, Tutorial

PyX 0.8.1 chokes on the stock psfonts.map installed by i-Installer on OS X Tiger (the TeX itself is TeXLive 2006 or something similar). A simple solution is to set

fontmaps = psfonts.cmz

in /etc/pyxrc. This seems to give PyX all the fonts it needs.

→ MPI: PyMPI (not actively maintained, difficult to install), Pypar (poorly maintained?), Scientific.MPI (confusing doc!), MMPI (new, seems simple), myMPI (also new, seems good approach)

→ Shared objects: Pyre, Dopy, Pyro

#!/bin/bash
T1="foo"
T2="bar"
if [ "$T1" = "$T2" ]; then
    echo expression evaluated as true
else
    echo expression evaluated as false
fi

In C mode, add the line

(setq c-basic-offset 4)

to your .emacs file. In Python, it is py-indent-offset. More generally, the tab-length variable is tab-width (if you want to set this in your .emacs file, use setq-default. When working interactively, use ESC-x set-variable.

→ In sh/bash: prog > logfile 2>&1; (to separate files) prog > logfile 2> errfile; (pipe) prog 2>&1 |.

→ In csh/tcsh: prog >& logfile; (to separate files) (prog > logfile) >& errfile; (pipe) prog |&.

For some reason I always seem to forget this.

Using Proce55ing (v. greater than 91) and OS X /Developer/Applications/Java Tools/Java Bundler, it's easy to create a standalone OS X application from a Proce55ing applet. Among other things, this allows use of the very fast OpenGL graphics routines.

Just "Export" the applet under Proce55ing; if you're using any external files (such as fonts), copy them back to the Applet directory, since Proce55ing does not do this by itself (in fact, it repeatedly deletes the files that you put in).

Then open the Jar Bundler, select your main class from the jar file, and under "Classpath and Files", add all additional files and libraries that appear in the Proce55ing-created applet directory. (If you have OpenGL libraries, you should need only those that end in .jnilib; the .so files should be linux, and the .dll files should be Windows. But don't quote me on this. Under "Properties", check "Set Working Directory to Inside Application Package". Don't forget to select a catchy icon under "Build Information" (this is the "running" icon; you'll need to change the "file" icon for the application bundle in the Finder).

A compressed disk image (dmg) can be made with Disk Utility by first creating an image large enough to contain the bundle as it is, and then converting to a read-only compressed image.

I use Mathematica and Adobe Illustrator to create the EPS figures in my papers, but the resulting EPS files often end up enormous. A quick, and usually harmless way to slim them down is to filter them through Ghostscript. I use this script.

Also, when I have multiple versions of a figure, I usually need to find out which version is being used in the current LaTeX file. This script will do that. For good measure, this other script will also find out which other TeX files are being \input into the main LaTeX.

Can be a powerful tool. To look into.

link

From macosxhints: "The following example piece of Matlab code makes Matlab convert a figure to PDF and display it in TeXShop, which auto-refreshes the PDF (unlike Preview):"

figure(1);
set(gcf, 'Visible', 'off');
plot(x, y);
print(gcf, '-dpdf', 'figure1.pdf');
system('open -a Texshop figure1.pdf');