Release 2.4.0 of MDAnalysis
This a minor release of MDAnalysis, as per our once-every-three-months schedule.
The minimum NumPy and Python versions remain largely unchanged, however the minimum version of biopython has been raised to 1.80. This is also the first release to officially support Python 3.11.
Supported Python versions:
- 3.8, 3.9, 3.10, 3.11
Major changes:
See the CHANGELOG and our release blog post for more details.
Fixes:
Enchancements:
- As part of their outreachy project @umak has started adding type annotations throughout the MDAnalysis codebase
- As part of their GSoC project @BFedder has added an auxialliary reader for EDR files (PR #3749)
- As part of their GSoC project @aya9aladdin has fixed various issues with guessing and and attribute reading. This will be followed by the introduction of a new guesser system in a future release.
- A reader for TNG files has been added by @hmacdope, follow up on his previous GSoC 2020 work on creating a python library for reading TNG files (PR 3765)
- Addition of a new isolayer selection method (PR #3846)
- Various enchancements and fixes to the LAMMPS DUMP Parser (allowing box translation on reading, allowing coordinates to be unwrapped based on dump image flags, and importing of forces and velocities) (PR #3844)
- All readers now have a timeseries attribute (PR #3890)
- ReaderBase file formats now accept pathlib inputs (PR #3935)
- Added ability for hbond analysis to use types when resnames are not present (PR #3848)
Changes:
- The deprecated setup.py
extra_requiresAMBERentry has been removed in favor ofextra_formats(PR #3810) - Various issues with the auxilliary reader, this should not be much more robust (PR #3749)
- The Cython headers have been moved to MDAnalysis.lib.libmdanalysis (PR #3913)
- The
MDAnalysis.analysis.align.sequence_alignmentnow uses Bio.Align.PairwiseAligner instead of the deprecated Bio.pairwise2 (PR #3951)
Deprecations:
- The MemoryReader's timeseries inclusive indexing will be changed to exclusive in version 3.0.0 (PR #3894)
- The
sequence_aligment()method has been deprecated and will be removed in version 3.0.0 (PR #3951) - MDAnalysis.analysis.nucleicacids' direct indexing of selection indices to obtain pair distances results has been deprecated in favor of accessing
results.pair_distances(PR #3958)
New Contributors
- @jaclark5 made their first contribution in #3846
- @pgbarletta made their first contribution in #3876
- @jfennick made their first contribution in #3832
- @Hakarishirenai made their first contribution in #3956