Bump mdanalysis from 2.7.0 to 2.8.0

[dependabot]

Bumps mdanalysis from 2.7.0 to 2.8.0.

Release notes

Sourced from mdanalysis's releases.

Release 2.8.0 of MDAnalysis

This a minor release of MDAnalysis.

As of this release MDAnalysis is packaged under a LGPLv3+ license, and all code contributions are provided under the LGPLv2.1+ license.

This release supports NumPy 2.0+ and offers backwards compatibility through to NumPy 1.23.2

Supported Python versions:

• 3.10, 3.11, 3.12, 3.13

Major features

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

• The MDAnalysis package license has changed from GPLv3+ to LGPLv3+ and all code contributions are now under LGPLv2.1+
• MDAnalysis now has a brand new guesser API (PR #3753). See the DefaultGuesser class for more information. Please note that default guessing of types and masses will change in MDAnalysis v3.0.
• DSSP analysis analysis.DSSP module for protein secondary structure assignment, based on pydssp was added.
• An iterative average structure method was added to analysis.align based on DOI 10.1021/acs.jpcb.7b11988.
• The TPR reader has been updated to support Gromacs 2024.
• The AnalysisBase class was enhanced through the introduction of a parallelization API (Issue #4158, PR #4304). Various analyses now support parallel computation, including; RMSD, GNMAnalysis, BAT, dihdral calculations, DSSP, and HydrogenBondAnalysis.

Notable changes / upcoming deprecations

• MMTF support is now deprecated and will be removed in MDAnalysis v3.0. The fetch_mmtf method has been disabled as it no longer works.
• MDAnalysis.analysis.hole2 has been moved to its own mdakit (mdahole2) and will be fully removed from the core library in MDAnalysis v3.0.
• MDAnalysis.analysis.encore has been deprecated in favour of its own mdakit (mdaencore) and will be removed in MDAnalysis v3.0.
• MDAnalysis.analysis.waterdynamics has been deprecated in favour of its own mdakit (waterdynamics) and will be removed in MDAnalysis v3.0.
• MDAnalysis.analysis.psa has been deprecated in favour of its own mdakit (PathSimAnalysis) and will be removed in MDAnalysis v3.0.
• The guess_bonds, vdwradii, fudge_factor, and lower_bound kwargs are deprecated for bond guessing during Universe creation. Instead, pass ("bonds", "angles", "dihedrals") into to_guess or force_guess during Universe creation, and the associated vdwradii, fudge_factor, and lower_bound kwargs into Guesser creation. Alternatively, if vdwradii, fudge_factor, and lower_bound are passed into Universe.guess_TopologyAttrs, they will override the previous values of those kwargs.
• MDAnalysis.topology.guessers and MDAnalysis.topology.tables are deprecated in favour of the new Guessers API and will be removed in MDAnalysis v3.0.
• Unknown masses are set to 0.0 for current version, this will be depracated in MDAnalysis v3.0.0 and replaced by :class:Masses' no_value_label attribute (np.nan).

Commits

• 1cfe404 Add Cython 3.0.11 generated files (#4798)
• c48962e Fix deployment workflow (#4795)
• 0a91d2c change license to LGPL switch (#4794)
• 4e42f7a Addition of isInstance test of BackendSerial (#4773)
• b254921 revert to artifact upload/download to v3 for 2.8.0 release (#4784)
• 5eeedd6 Finalize v2.8.0 release (#4780)
• e6bc096 Allow bonds etc to be additively guessed when present (#4761)
• c9a3778 Bump the github-actions group with 2 updates (#4776)
• e776f12 Expose MDAnalysis.topology.guessers and MDAnalysis.guesser.tables under `...
• 800b4b2 Fix bond deletion (#4763)
• Additional commits viewable in compare view

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