16 Jan 2016
We have just released MDAnalysis version 0.13.0.
Upgrade
You can upgrade with pip install --upgrade MDAnalysis
Noticable Changes
Usage of openMP
The MDAnalysis.lib.parallel.distances module has been merged into
MDAnalysis.lib.distances. To select the openMP implementation all functions in
that module now accept a backend='openMP' keyword. See
#530.
Reading GRO files has been sped up for large files. Velocities will now also be
written written for GRO files if possible.
Others
This release contains other performance enhancements and fixes. For a detailed
list see the
release notes
15 Dec 2015
MDAnalysis has truly arrived in the 21st century: we now even have a
blog (in addition to a Twitter account
@mdanalysis) and of course,
development occurs on GitHub, the “social
coding platform” (at least that was the tag line a while
back). However, for most of its life (January 2008 – March 2015)
MDAnalysis lived on Google Code and the move to
GitHub was done
more out of necessity (because of Google Code’s
shutdown)
than for any other reasons. After all, we knew, moving a repository,
issue tracker, wiki, and what-not would be painful and what could we
possibly gain?
In turns out, a lot.
As you can see from the image of the commit
history,
moving to GitHub in April 2015 coincided with a flurry of activity and
significant contributions from new developers, two of which are now
also on the
coredevs
team. The graph, of course, does not demonstrate causation, only
correlation. But anecdotally it seems to be the case that the ease
with which one can communicate on GitHub through the issue
tracker and comment
on code through pull
requests helps people
to enjoy open source software development. In addition, the good
integration with continuous integration services such as Travis
CI, coveralls or
quantifiedcode takes care of many
essential but boring tasks and allows people to focus on what they
like doing — writing code that helps them and others to get their
research done.
Given that an open source projects such as MDAnalysis very much
depends on developers offering up their own time and expertise,
working on a platform that makes it (mostly) enjoyable for them, is
rather valuable. And maybe, before trying it, we just slightly
underestimated the social component of writing code.
— @orbeckst