MDAnalysis/mdanalysis package-2.3.0

MDAnalysis 2.3.0

on GitHub

Release 2.3.0 of MDAnalysis

This a minor release of MDAnalysis, as per our once-every-three-months schedule.

The minimum NumPy version has been raised to 1.20.0 (1.21 for macosx-arm64) in line with NEP29.

Supported python versions:

• 3.8, 3.9, 3.10

Major changes:

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

Fixes:

• Fixed reading error when dealing with corrupt PDB CONECT records, and an issue where MDAnalysis would write out unusable CONECT records with index>100000 (Issue #988).

Enhancements:

• Formal charges are now read from PDB files and stored in a formalcharge attribute (PR #3755).
• A new normalizing norm parameter for the InterRDF and InterRDF_s analysis methods (Issue #3687).
• Improved Universe serialization performance (Issue #3721, PR #3710).

Changes:

• To install optional packages for different file formats supported by MDAnalysis, use pip install ./package[extra_formats] (Issue #3701, PR #3711).

Deprecations:

• The extra_requires target AMBER for pip install ./package[AMBER] will be removed in 2.4.0. Use extra_formats (Issue #3701, PR #3711).

CZI EOSS Performance Improvements:

A series of performance improvements to the MDAnalysis library's backend have been made as per planned work under MDAnalysis' CZI EOSS4 grant. Further details about these will be provided in a future blog post.

• MDAnalysis.lib.distances now accepts AtomGroups as well as NumPy arrays (PR #3730).
• Timestep has been converted to a Cython Extension type (PR #3683).