Release 2.8.0 of MDAnalysis

We are happy to release version 2.8.0 of MDAnalysis!

This is a minor release of the MDAnalysis library, which means that it contains enhancements, bug fixes, deprecations, and other backwards-compatible changes.

However, in this case minor does not quite do justice to what is happening in this release, given that we have (at least) three big changes/additions:

  1. The license was changed to the GNU Lesser General Public License so that MDAnalysis can be used by packages under any license while keeping the source code itself free and protected.
  2. We introduce the Guesser API for guessing missing topology attributes such as element or mass in a context-dependent manner. Until release 3.0, you should not notice any differences but under the hood we are getting ready to make it easier to work with simulations in a different context (e.g., with the MARTINI force field or experimental PDB files). With consistent attributes, such as elements, it becomes a lot easier to interface with tools like the cheminformatics RDKit (via the converters).

    The guessers are the GSoC 2022 project of @aya9aladdin with help from @lilyminium, @IAlibay, and @jbarnoud.1

  3. We are introducing parallel analysis for tools in MDAnalysis.analysis following the simple split-apply-combine paradigm that we originally prototyped in PMDA 2. What’s really exciting is that any analysis code that is based on MDAnalysis.analysis.base.AnalysisBase can enable parallelization with a few lines of extra code—all the hard work is done behind the scenes in the base class (in a way that is fully backwards compatible!).

    This new feature is the work of @marinegor who brought his GSoC 2023 project to completion, with great contributions by @p-j-smith, @yuxuanzhuang and @RMeli 3.

    Not all MDAnalysis analysis classes have parallelization enabled yet but @talagayev has been working tirelessly on already updating GNMAnalysis, BAT, Dihedral, Ramachandran, Janin, DSSP (yes, MDAnalysis has finally got DSSP, based on pydssp, also thanks to @marinegor), HydrogenBondAnalysis, in addition to RMSD.

Read on for more details on the license change and the usual information on supported environments, upgrading your version of MDAnalysis, and a summary of the most important changes.

License change to LGPL

LGPLv3 logo

This is the first release of MDAnalysis under the Lesser General Public License. We have been working towards this license change for the last 3 years; this release (almost) concludes the process that we described in our licensing update blog post.

We would like to thank all our contributors who granted us permission to change the license. We would also like to thank a number of institutions who were especially supportive of our open source efforts, namely Arizona State University, Australian National University, Johns Hopkins University, and the Open Molecular Science Foundation. We are also grateful to NumFOCUS for legal support. The relicensing team was lead by @IAlibay and @orbeckst.

Supported environments

The minimum required NumPy version is 1.23.3; MDAnalysis now builds against NumPy 2.0.

Supported Python versions: 3.10, 3.11, 3.12, 3.13. Support for version 3.13 has been added in this release and support for 3.9 has been dropped (following SPEC 0).

Please note that Python 3.13 is limited to PyPi for now, the conda-forge channel installs only provide support for Python 3.10 to 3.12.

Supported Operating Systems:

Upgrading to MDAnalysis version 2.8.0

To update with mamba (or conda) from the conda-forge channel run

mamba update -c conda-forge mdanalysis

To update from PyPi with pip run

python -m pip install --upgrade MDAnalysis

For more help with installation see the installation instructions in the User Guide. Make sure you are using a Python version compatible with MDAnalysis before upgrading (Python >= 3.10).

Notable changes

For a full list of changes, bugfixes and deprecations see the CHANGELOG.

Enhancements:

Fixes:

Changes:

Deprecations:

Author statistics

This release was the work of 22 contributors, 10 of which are new contributors.

Our new contributors are:

Acknowledgements

MDAnalysis thanks NumFOCUS for its continued support as our fiscal sponsor and the Chan Zuckerberg Initiative for supporting MDAnalysis under EOSS4 and EOSS5 awards.

@IAlibay (release manager) on behalf of the MDAnalysis Team


  1. The Guesser API was a big undertaking: Her merged PR #3753 totalled 668 (!) comments. We look forward to the community providing Guessers for specific context. 

  2. Shujie Fan, Max Linke, Ioannis Paraskevakos, Richard J. Gowers, Michael Gecht, and Oliver Beckstein. PMDA - Parallel Molecular Dynamics Analysis. In Chris Calloway, David Lippa, Dillon Niederhut, and David Shupe, editors, Proceedings of the 18th Python in Science Conference, 134 – 142. Austin, TX, 2019. SciPy. doi:10.25080/Majora-7ddc1dd1-013

  3. Adding parallelization in a transparent manner was quite a difficult undertaking that touched many parts of the analysis code and required a lot of thought. Feedback is very welcome! See PR #4162 with 713 (!) comments.