nodepy 0.3 available via easy_install

To facilitate my research and perhaps help someone else out there, I develop a python package based around numerical ODE solvers (Runge-Kutta methods, multistep methods, etc.) as objects. The package is called nodepy, and has somewhat limited functionality. However, it contains a very nice implementation of rooted trees, including the ability to compute all the things necessary for deriving order conditions of general linear methods. It also has a lot of nice functionality for Runge-Kutta methods, including a lot of things related to low-storage methods and embedded methods.

As of today, the package is finally available on the PyPI server, and therefore can be installed using

easy_install nodepy

Hopefully this will encourage interested parties to try it out (or better yet, to contribute!)

Using pylint to clean up Python code

I just recently discovered a very useful package for anyone who writes python code: pylint. It took a little tweaking to get it to do what I wanted. Besides looking for outright errors, it checks all the recommended Python coding style conventions. Since I don't abide by many of those, pylint gave my nodepy code a rating of -4.5/10.0 (yes, that's a NEGATIVE rating) initially. More importantly, I couldn't find the real errors among the thousands of style complaints. To run pylint without checking all the style conventions, just type

pylint -d C xxxx

where "xxxx" is the name of a python package or module. It will still make a lot of subjective judgments about your code (like suggesting that no function should have more than 5 arguments), but to me it's a tolerable level (and sometimes the suggestions really are helpful). More information about pylint's output messages can be found here: http://www.logilab.org/card/pylintfeatures. I was able to uncover several previously unnoticed issues in my package in this way.

"Open Access" and unscrupulous scientific publishers

I received a rather surprising invitation in my inbox the other day:

Dear X,
Greetings from theAmerican Journal of Plant Sciences(AJPS), which is published by the Scientific Research Publishing, USA. The journal dedicates to the latest advancement of plant sciences and the goal is to keep a record of the state-of-the-art research and promote the research work in these fast moving areas. With an open access publication model of this journal, all interested readers around the world can freely access articles online. Now we sincerely invite you to join the editorial board of AJPS.

Surprising, because I'm not a plant scientist. I've never collaborated with a plant scientist, written a plant science paper, or even thought about plant science beyond Biology 101. I've received this invitation twice in the last two months in fact -- both times addressed to my student e-mail address at the University of Washington. Apparently being an applied math grad student is qualification enough to edit articles for this journal.

This isn't the first such invitation of its kind I've received. Previously, I was one of the countless scientists spammed by Bentham Open. That invitation was at least subject-appropriate (the "Open Numerical Methods Journal"). But claiming they had targeted me because of my "eminence in the field" when I didn't yet have a Ph.D. seemed a bit of a stretch. Both Bentham and the publisher of AJPS (Scientific Research Publishing) are establishing large numbers of so-called open-access journals that seem to be, in practice, little more than vanity press (they rely on author-pay funding).

Out of curiosity, I went to the publisher's website and noticed that they have a journal in applied math. I clicked through to the abstract of an article with an intriguing title and found this:

ABSTRACT

Approach to expansion of an opportunity of the reception the guaranteed estimation for a problem of reconstruction the impact within the limits of the dynamical algorithm is considered in the article.

I really can't add anything to that.

SCIRP's 'about us' page contains the following memorable statement:

The company has an outstanding work team as well as the widespread third party relations, enables our customers to obtain great satisfactions and convenience in their publications.

The grammatical hopelessness was no surprise to me at this point -- but notice that their customers are the authors, not the readers. Well, at least they're honest about being vanity press.

For more blog posts on this topic, look here, here, and here.