Release 2.7.0 of MDAnalysis

Release 2.7.0 of MDAnalysis

This a minor release of MDAnalysis.

This release of MDAnalysis is packaged under a GPLv3+ license, additionally all contributions made from commit 44733fc214dcfdcc2b7cb3e3705258781bb491bd onwards are made under the LGPLv2.1+ license.

The minimum supported NumPy version is 1.22.3.

Supported Python versions:

• 3.9, 3.10, 3.11, 3.12

Major changes:

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

Fixes:

• NoJump now properly handles jumps that occur on the second frame of NPT trajectories, PR #4258
• Fix charge reading from PDBQT files. PR #4283
• Fixed a case where qcprot.CalcRMSDRotationalMatrix would return a RMSD of None. PR #4273

Enhancements:

• Support was added for reading chainID from prmtop AMBER topologies (PR #4007)
• Added support for Python 3.12 (PR #4309, #4300, #4301, #4319, #4325, #4327, #4329)
• Added support for reading chainID from PDBQT files (PR #4284)
• TPR reader now sets chainID from molblock (PR #4281)
• Various improvements to the organization and performance of Major and Minor Pair analyses (PR #3735)
• C distance backend is now exposed via libmdanalysis.pxd (PR #4342)
• Added a GROMOS11 Reader (PR #4294)

Changes:

• Added mda_xdrlib as a core dependency to replace the now deprecated Python xdrlib code (PR #4271)
• ConverterBase has been moved to MDAnalysis.converters.base (PR #4253)
• networkx is now an optional dependency of MDAnalysis (PR #4331)
• BioPython is now an optional dependency of MDAnalysis (PR #4332)
• Results for WatsonCrickDist nucleic acids analysis are now stored in analysis.nucleicacids.WatsonCrickDist.results.distances (PR #3735)

Deprecations:

• Importing ConverterBase from MDAnalysis.coordinates.base will not be possible after MDAnalysis 3.0 (PR #4253)
• Deprecation with intent of removal in MDAnalysis v3.0 of the X3DNA legacy code (PR #4333)
• Deprecation with intent of removal in MDAnalysis v3.0 of the TRZ reader and writer (PR #4335)
• Deprecation with intent of removal in MDAnalysis v3.0 of the MDAnalysis.lib.util.which method (PR #4340)
• The asel argument of the timeseries attribute of Readers is now deprecated in favour of the atomgroup argument (PR #4343)
• In nucleicacids.WatsonCrickDist, accepting lists of Residue objects was deprecated in favor of using ResidueGroup: using List[Residue] will be removed in release 3.0.0; instead use a ResidueGroup (PR #3735)
• In nucleicacids.WatsonCrickDist the result results.pair_distances was deprecated and will be removed in 3.0.0; use results.distances instead (PR #3735)

New Contributors

• @jennaswa made their first contribution in #4289
• @Sumit112192 made their first contribution in #4346
• @HeetVekariya made their first contribution in #4359
• @JoStoe made their first contribution in #4292
• @ljwoods2 made their first contribution in #4366