06 Jun 2017
We have just released MDAnalysis version 0.16.1. This release is dedicated to
purely fixing bugs, thank you to everyone who helped us identify these!
For full details of the bugs fixed, see the release notes.
Thank you also to our four new contributors, Jon Kapla, Sang Young Noh,
Andrew William King and Kathleen Clark.
Besides the bug fixes we updated the style
(PR 1126) of our docs so that they match with the website.
Upgrade
You can upgrade with pip install --upgrade MDAnalysis . If you use the conda
package manager run conda update -c conda-forge mdanalysis
04 Jun 2017
We are happy to anounce that MDAnalysis is hosting a GSoC student for
NumFOCUS this year, Utkarsh Bansal (@utkbansal
on GitHub), with his project “Port to pytest”.
Utkarsh Bansal: Port unit tests to pytest
Utkarsh will port our complete unit tests
from nose
to pytest. This is a massive undertaking
for MDAnalysis with over 4000 individual tests. But we have great confidence in
him and he has started work already to ensure that we don’t have a drop in code
coverage during the transition. Newer projects under the MDAnalysis umbrella all
use pytests and we are happy to see the switch happening for MDAnalysis as well.
Utkarsh will blog continuously during the summer to let you know
how far the transition has come and how to best write unit-tests in python.
Utkarsh is currently pursuing a bachelors in Computer Science and Engineering
and will be graduating this summer. He hopes to learn new things about python
and testing in general this summer and is planning to continue his career as a
software developer.
Other NumFOCUS students
NumFOCUS is hosting 12 students this year for several of their supported and
affiliated projects. You can find out about the other
students
here.
03 Jun 2017
We have generously been awarded a small development grant by
NumFOCUS to fully support Python 3. To do this Richard Gowers
and Tyler Reddy will be hosted at Oliver
Beckstein’s lab at Arizona State University in the summer for
a week of hacking.
MDAnalysis started almost 10 years ago
when Python was around version 2.4 and interfacing with existing C code was
mostly done by writing C-wrappers that directly used CPython. This legacy code
has hampered a speedy full transition to Python 3 and consequently MDAnalysis
lags behind the rest of the scientific Python community in fully supporting
Python 3.
Although about 80% of code passes unit tests in Python 3, we urgently need to
close the remaining 20% gap in order to support our user base and to safeguard
the long term viability of the project.
In the meantime we are busy porting our last Python 2.7 only C-extension, the
DCD Reader and Writer, to Cython. We now have a working Cython version that can
be used without MDAnalysis, similar to our XTC and TRR readers. Only a clean up
of the new Cython / DCD handling code and updated documentation is required. You
can check our progress here.