MDAnalysis/mdanalysis release-1.0.1

MDAnalysis 1.0.1

on GitHub

First bugfix release for 1.0.x

Python support is kept the same as 1.0.0, with python 3.9 not supported.
Supported python versions:

• 2.7, 3.5, 3.6, 3.7, 3.8

Major changes:

Bug fixes

• Temporary disabling of the default nsgrid backend (in favour of PDKTree) to the capped_distance code due to a bug affecting accuracy (#2930)
• Fixes issues with importing matplotlib versions > 3.3 (#2938)
• TRZ reader and writer now checks and writes n_atoms (#2817)
• The density keyword for rdf.InterRDF_s is now documented and has been fixed to give correct results (#2811)
• Fixed reading of masses and charges from hoomdxml files (#2888)
• The DMSParser now handles the creation of multiple segids sharing residues with identical resids (#1387)

Deprecations:

• waterdynamics.HydrogenBondLifetimes will be replaced with hydrogenbonds.HydrogenBondAnalysis.lifetime in 2.0.0 (#2547)
• analysis.helanal will be removed in 2.0.0 and will be replaced with analysis.helix_analysis (#2622)
• lib.util.echo and core.universe.as_Universe will be removed in 2.0.0.
• analysis.leaflets.LeafletFinder will no longer accept non-Universe inputs as of version 2.0.0.

Performance improvements:

• Fixes a performance regression seen in 1.0.0 when doing string selections with select_atoms (#2751)
• Performance improvements to the TPR parser and ParmEd converter (#2804 and #3028)

See the CHANGELOG for more changes and details.

Known issues:

• PyPI and conda-forge releases of 1.0.1 are not compatible with Windows OS due to issues with our setup.py. We aim to fix this for the upcoming 1.0.2 release (#3129)

As detailed in the 1.0.0 release, the 1.x releases only include bug fix changes. New features are being developed for MDAnalysis 2.x.