Release 2.6.0 and 2.6.1 of MDAnalysis

We are happy to release version 2.6.1 of MDAnalysis! (This blog post describes 2.6.1 and the initial release in the 2.6 series, 2.6.0.)

This is a minor update to the MDAnalysis library.

This release of MDAnalysis is packaged under a GPLv3+ license. Additionally all contributions made from commit 44733fc onwards are made under the LGPLv2.1+ license. More details about these license changes will be provided in an upcoming blog post.

In line with NEP 29, the minimum required NumPy version has been raised to 1.22.3.

Supported Python versions: 3.9, 3.10, 3.11

Supported Operating Systems:

• Linux (on x86-64, aarch64)
  • Note: aarch64 can only be installed via pip for now
• Windows (on x86-64)
• MacOS (on x86-64 and ARM64)

Upgrading to MDAnalysis version 2.6.1

To update with conda from the conda-forge channel run

conda update -c conda-forge mdanalysis

To update from PyPi with pip run

python -m pip install --upgrade MDAnalysis

For more help with installation see the installation instructions in the User Guide. Make sure you are using a Python version compatible with MDAnalysis before upgrading (Python >= 3.9).

Notable changes

For a full list of changes, bugfixes and deprecations see the CHANGELOG.

Fixes:

• Fix to element guessing code to more accurately interpret atom names split by numbers (i.e. N0A is now recognised as N rather than NA) [Issue #4167, PR #4168]
• The -ffast-math compiler flag is no longer used by default at build time, avoiding inconsistent (although still scientifically correct) results seen in Intel MacOS systems when calling AtomGroup.center_of_charge(..., unwrap=True). This also avoids potentially incorrect floating point results. (PR #4220)
• DATAWriter, CRD, PQR, and PDBQT files can now be correctly written to compressed files. Before this change, any attempt to write to a compressed format (gzip or bzip2) would lead to writing out an uncompressed file. (PR #4163)
• Prevent accidental merging of bond/angle/dihedral types when they are defined as LAMMPS style string integers instead of tuples. This was leading to an incorrect number of bond/angle/dihedral types being written to lammps data files. (PR #4003)

Enhancements:

• An exclude_same argument has been added to InterRDF allowing pairs of atoms that share the same residue, segment or chain to be excluded from the calculation. (PR #4161)
• LAMMPS reader now supports the continuous ChainReader option. (PR #4170)
• AtomGroup representation now returns atom indices in the same order as they are stored in the AtomGroup. (PR #4191)

Changes:

• As per NEP29, the minimum supported runtime version of NumPy has been increased to 1.22.3. (PR #4160)
• The GSD package is now an optional dependency. (PR #4174)
• The MDAnalysis package now only supports GSD versions 3.0.1 or above. (PR #4153)
• MDAnalysis no longer officially supports 32 bit installations, (they are no longer tested in our continuous integration pipelines). Note: no code changes have been made to disable 32 bit, although it is known that new versions of most MDAnalysis core dependencies no longer release 32 bit compatible versions. (PR #4176)
• The package license has been updated to GPLv3+ to better reflect the compatibility of GPLv2+ with Apache and GPLv3 licensed codes. Additionally all new contributions from commit 44733fc onwards are made under the LGPLv2.1+ license. (PR #4219)

Deprecations:

• The misspelt Boltzman_constant entry in MDAnalysis.units is now deprecated in favour the correctly spelt Boltzmann_constant. (PRs #4230 and #4214)
• MDAnalysis.analysis.hole2 is now deprecated in favour of a new HOLE2 MDAKit. (PR #4200)

Author statistics

This release was the work of 10 contributors, 4 of which are new contributors.

Our new contributors are:

@MohitKumar020291 @Shubx10 @ztimol @pillose

Acknowledgements

MDAnalysis thanks NumFOCUS for its continued support as our fiscal sponsor and the Chan Zuckerberg Initiative for supporting MDAnalysis under EOSS4 and EOSS5 awards.

— The MDAnalysis Team