Release 2.9.0 of MDAnalysis

We are happy to release version 2.9.0 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.

Supported environments

This release supports NumPy 2.0+ and offers backwards compatibility through to NumPy 1.23.2.

Supported Python versions: 3.10, 3.11, 3.12, 3.13.

Supported Operating Systems:

• Linux (on x86-64)
• Windows (on x86-64)
• MacOS (on x86-64 and ARM64)

Upgrading to MDAnalysis version 2.9.0

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, bug fixes and deprecations see the CHANGELOG.

Enhancements:

• Support for Gromacs v2024.4 and v2025 TPR files.
• A new “water” keyword for selecting water residues.

• Support for distopia 0.4.0 as an optional distance library backend that now supports many more distance functions for all box types (including general triclinic unit cells).

  On supported x86-64 platforms, install distopia with

  mamba install -c conda-forge distopia
  

  You can then enable distopia as a backend to make use of the optimized distopia code for compute-intensive distance calculations, such as distance_array():

  protein = u.select_atoms("protein and not name H*")
  lipids = u.select_atoms("resname POPC CHOL and not name H*")
  d = MDAnalysis.lib.distances.distance_array(protein, lipids,
                                              box=u.dimensions, 
                                              backend="distopia")
  

  If you want to see if distopia is available as a backend in a running program, check that the variable MDAnalysis.lib.distances.HAS_DISTOPIA is True.

• Parallel analysis support for MDAnalysis.analysis.nucleicacids, MDAnalysis.analysis.contacts, and MDAnalysis.analysis.density.
• XYZ writer can now write positions up to a user-supplied precision via the precision keyword argument.

Changes:

• MDAnalysis.analysis.hole2, MDAnalysis.analysis.psa, and MDAnalysis.analysis.waterdynamics, are now only available via optional dependencies (the mdahole2, pathsimanalysis, and waterdynamics MDAKits). By default these will not be installed, you will need to install them separately if you wish to use them from within MDAnalysis.analysis. Please note that in v3.0 theses modules will be removed completely from the MDAnalysis core library and you will need to use the MDAKits directly.
• fasteners dependency has been switched to filelock.
• Codebase is now formatted with black (version 24)

Author statistics

This release was the work of 10 contributors, 3 of which are new contributors.

Our new contributors are:

• @ChiahsinChu
• @tanishy7777
• @jauy123

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 and @p-j-smith (release managers) on behalf of the MDAnalysis Team