Release 2.7.0 of MDAnalysis
04 Jan 2024We are happy to release version 2.7.0 of MDAnalysis!
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 can be found in our blog post.
The minimum required NumPy version is 1.22.3.
Supported Python versions: 3.9, 3.10, 3.11, 3.12. Support for version 3.12 has been added in this release.
Supported Operating Systems:
Upgrading to MDAnalysis version 2.7.0
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:
- NoJump now properly handles jumps that occur on the second frame of NPT trajectories (PR #4258).
- Fixed 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 Autodock PDBQT files (PR #4284), GROMACS TPR topologies (PR #4281) and amber prmtop topologies (PR #4007).
- 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).
Author statistics
This release was the work of 13 contributors, 5 of which are new contributors.
Our new contributors are:
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