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@dependabot dependabot bot commented on behalf of github Apr 14, 2025

⚠️ Dependabot is rebasing this PR ⚠️

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Bumps mdanalysis from 2.7.0 to 2.9.0.

Release notes

Sourced from mdanalysis's releases.

Release 2.9.0 of MDAnalysis

This is a minor release of MDAnalysis.

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 & changes

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

  • Support for Gromacs v2024.4 and v2025 TPR files.
  • A new "water" keyword for selecting water residues.
  • fasteners dependency has been switch to filelock.
  • Support for distopia 0.4.0 as an optional distance library backend.
  • Parallel analysis support for MDAnalysis.analysis.nucleicacids, MDAnalysis.analysis.contacts, and MDAnalysis.analysis.density.
  • XYZ writer can now write positions up to a user-supplied precision via the precision keyword argument.
  • MDAnalysis.analysis.hole2, MDAnalysis.analysis.psa, and MDAnalysis.analysis.waterdynamics, are now only available via optional dependencies (the mdahole2, pathsimanalysis, and waterdynamics mdakits). By default these will not be installed, you will need to install them separately if you wish to use them. Please note that in v3.0 theses modules will be removed completely from the MDAnalysis core library and you will need to use the mdakits directly.

New Contributors

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

... (truncated)

Commits

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Bumps [mdanalysis](https://github.com/mdanalysis/mdanalysis) from 2.7.0 to 2.9.0.
- [Release notes](https://github.com/mdanalysis/mdanalysis/releases)
- [Commits](MDAnalysis/mdanalysis@package-2.7.0...package-2.9.0)

---
updated-dependencies:
- dependency-name: mdanalysis
  dependency-version: 2.9.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update python code labels Apr 14, 2025
@github-actions github-actions bot merged commit eef0175 into main Apr 14, 2025
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@github-actions github-actions bot deleted the dependabot/pip/mdanalysis-2.9.0 branch April 14, 2025 07:30
@yaoyi92 yaoyi92 mentioned this pull request Apr 18, 2025
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