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haddocking / arctic3d

Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information
Apache License 2.0
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Bump mdanalysis from 2.6.1 to 2.7.0 #370

Closed dependabot[bot] closed 9 months ago

dependabot[bot] commented 9 months ago

Bumps mdanalysis from 2.6.1 to 2.7.0.

Release notes

Sourced from mdanalysis's releases.

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

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