MDAnalysis/mdanalysis package-2.1.0

MDAnalysis 2.1.0

on GitHub

Release 2.1.0 of MDAnalysis

In line with ongoing attempts to align with NEP29, this version of MDAnalysis drops support for Python 3.6 and raises the minimum NumPy version to 1.18.0.

Please note that at time of release whilst all the MDAnalysis core functionality supports Python 3.10, some optional modules do not due to a lack of support by dependencies which they require. We hope that this support will gradually be added as more of these dependencies release new versions compatible with Python 3.10.

Supported python versions:

• 3.7, 3.8, 3.9, 3.10

Major changes:

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

Enhancements:

• Addition of a new dielectric analysis module (PR #2118)
• The TPR parser now supports reading files from GROMACS 2022 (PR #3514)
• The H5MDReader can now load trajectories without a topology (PR #3466)
• Custom compiler flags can be used when building MDAnalysis from source (PR #3429)
• The RDKit reader now supports parsing R/S chirality (PR #3445)
• A new method to apply the minimum image convention to a collection of vectors, minimize_vectors, has been introduced (PR #3472)

Fixes:

• Fixed various integer overflow issues in the distance calculation backend of MDAnalysis which would prevent calculations on large systems (Issues #3183, #3512).
• Fixed issues with the creation of VMD surfaces in HOLE2 when using a non-contiguous start/stop/step.
• Fixes reading of charges with the ITPParser (Issue #3419).
• Fixed issue with the creation of a Universe from a custom object which only provides a topology (Issue #3443).
• Fixed issue with accessing newly created values added via add_Segment or add_Residue (Issue #3437).

Changes:

• packaging is now a core dependency of MDAnalysis.
• Indexing a Group (AtomGroup, ResidueGroup, SegmentGroup) with None now raises a TypeError. Prior to this indexing by None would incorrectly return the whole Group but claim to have a length of 1 atom (Issue #3092).
• The TRZReader now defaults to a dt value of 1.0 ps instead of the previous 0.0 ps (Issue #3257).

Deprecations:

• The pbc keyword argument for various Group methods has been deprecated in favor of wrap. The deprecated keyword will be removed in version 3.0.0 (Issue #1760).

Known test failures:

• pytest-xdist and more than 4 workers
  • Under these conditions a test related to logging for HydrogenBondAnalysis can fail. This is not thought to impact the validity of MDAnalysis. See here for more details: #3543
• Windows builds
  • In some cases users may get permission errors with tests involving symlinks. This should not impact the behaviour of MDAnalysis but may impact the creation of temporary files when using HOLE2 (see: #3556).