Release 0.16.1

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.


You can upgrade with pip install --upgrade MDAnalysis . If you use the conda package manager run conda update -c conda-forge mdanalysis

Google Summer of Code Student 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 Bansal

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.

NumFOCUS small grant for Python 3 support

NumFOCUS Foundation

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.