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| layout: post | ||
| title: Release 2.7.0 of MDAnalysis | ||
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| We are happy to release version 2.7.0 of MDAnalysis! | ||
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| This is a minor update to the MDAnalysis library. | ||
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| 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]. | ||
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| The minimum required NumPy version is 1.22.3. | ||
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| Supported Python versions: **3.9, 3.10, 3.11, 3.12**. Support for version | ||
| 3.12 has been added in this release. | ||
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| 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][]) | ||
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| ## Upgrading to MDAnalysis version 2.7.0 | ||
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| To update with `conda` from the [conda-forge channel][] run | ||
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| ```bash | ||
| conda update -c conda-forge mdanalysis | ||
| ``` | ||
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| To update from [PyPi][] with `pip` run | ||
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| ```bash | ||
| python -m pip install --upgrade MDAnalysis | ||
| ``` | ||
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| 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). | ||
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| ## Notable changes | ||
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| For a full list of changes, bugfixes and deprecations see the [CHANGELOG][]. | ||
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| #### 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). | ||
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| #### 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). | ||
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| #### 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). | ||
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| #### 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). | ||
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| ## Author statistics | ||
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| This release was the work of 24 contributors, **5** of which are **new contributors**. | ||
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| Our **new contributors** are: | ||
| - @jennaswa | ||
| - @Sumit112192 | ||
| - @HeetVekariya | ||
| - @JoStoe | ||
| - @ljwoods2 | ||
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| ## Acknowledgements | ||
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| MDAnalysis thanks [NumFOCUS][] for its continued support as our fiscal sponsor and | ||
| the [Chan Zuckerberg Initiative][] for supporting MDAnalysis under an EOSS4 award. | ||
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| — The MDAnalysis Team | ||
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| [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 %} |