MDAnalysis/mdanalysis package-2.8.0 on GitHub

Release 2.8.0 of MDAnalysis

This a minor release of MDAnalysis.

As of this release MDAnalysis is packaged under a LGPLv3+ license, and all code contributions are provided under the LGPLv2.1+ license.

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

Supported Python versions:

See the CHANGELOG and our release blog post for more details.

The MDAnalysis package license has changed from GPLv3+ to LGPLv3+ and all code contributions are now under LGPLv2.1+
MDAnalysis now has a brand new guesser API (PR #3753). See the DefaultGuesser class for more information. Please note that default guessing of types and masses will change in MDAnalysis v3.0.
DSSP analysis analysis.DSSP module for protein secondary structure assignment, based on pydssp was added.
An iterative average structure method was added to analysis.align based on DOI 10.1021/acs.jpcb.7b11988.
The TPR reader has been updated to support Gromacs 2024.
The AnalysisBase class was enhanced through the introduction of a parallelization API (Issue #4158, PR #4304). Various analyses now support parallel computation, including; RMSD, GNMAnalysis, BAT, dihdral calculations, DSSP, and HydrogenBondAnalysis.

MMTF support is now deprecated and will be removed in MDAnalysis v3.0. The fetch_mmtf method has been disabled as it no longer works.
MDAnalysis.analysis.hole2 has been moved to its own mdakit (mdahole2) and will be fully removed from the core library in MDAnalysis v3.0.
MDAnalysis.analysis.encore has been deprecated in favour of its own mdakit (mdaencore) and will be removed in MDAnalysis v3.0.
MDAnalysis.analysis.waterdynamics has been deprecated in favour of its own mdakit (waterdynamics) and will be removed in MDAnalysis v3.0.
MDAnalysis.analysis.psa has been deprecated in favour of its own mdakit (PathSimAnalysis) and will be removed in MDAnalysis v3.0.
The guess_bonds, vdwradii, fudge_factor, and lower_bound kwargs are deprecated for bond guessing during Universe creation.
Instead, pass ("bonds", "angles", "dihedrals") into to_guess or force_guess during Universe creation, and the associated vdwradii, fudge_factor, and lower_bound kwargs into Guesser creation. Alternatively, if vdwradii, fudge_factor, and lower_bound are passed into Universe.guess_TopologyAttrs, they will override the previous values of those kwargs.
MDAnalysis.topology.guessers and MDAnalysis.topology.tables are deprecated in favour of the new Guessers API and will be removed in MDAnalysis v3.0.
Unknown masses are set to 0.0 for current version, this will be depracated in MDAnalysis v3.0.0 and replaced by :class:Masses' no_value_label attribute (np.nan).