diff --git a/_posts/2024-01-04-release-2.7.0.md b/_posts/2024-01-04-release-2.7.0.md new file mode 100644 index 00000000..b78f6179 --- /dev/null +++ b/_posts/2024-01-04-release-2.7.0.md @@ -0,0 +1,125 @@ +--- +layout: post +title: Release 2.7.0 of MDAnalysis +--- + +We 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](https://www.gnu.org/licenses/gpl-3.0.en.html). +Additionally all contributions made from commit +[44733fc](https://github.com/MDAnalysis/mdanalysis/commit/44733fc214dcfdcc2b7cb3e3705258781bb491bd) +onwards are made under the +[LGPLv2.1+ license](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html). +More details about these license changes can be found in our [blog post][licensing update]. + +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: + - **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 2.7.0 + +To update with `conda` from the [conda-forge channel][] run + +```bash +conda update -c conda-forge mdanalysis +``` + +To update from [PyPi][] with `pip` run + +```bash +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 24 contributors, **5** of which are **new contributors**. + +Our **new contributors** are: +- @jennaswa +- @Sumit112192 +- @HeetVekariya +- @JoStoe +- @ljwoods2 + +## Acknowledgements + +MDAnalysis thanks [NumFOCUS][] for its continued support as our fiscal sponsor and +the [Chan Zuckerberg Initiative][] for supporting MDAnalysis under an EOSS4 award. + +— The MDAnalysis Team + +[x86-64]: https://en.wikipedia.org/wiki/X86-64 +[aarch64]: https://en.wikipedia.org/wiki/AArch64 +[ARM64]: https://en.wikipedia.org/wiki/Apple_M1 +[installation instructions in the User Guide]: https://userguide.mdanalysis.org/stable/installation.html +[conda-forge channel]: https://anaconda.org/conda-forge/mdanalysis +[PyPi]: https://pypi.org/project/MDAnalysis/ +[NumFOCUS]: https://www.numfocus.org +[CHANGELOG]: https://github.com/MDAnalysis/mdanalysis/blob/release-2.6.1/package/CHANGELOG +[Chan Zuckerberg Initiative]: https://chanzuckerberg.com/ +[licensing update]: {{ site.baseurl }}{% post_url 2023-09-22-licensing-update %}