diff --git a/_posts/2024-11-22-release-2.8.0.md b/_posts/2024-11-22-release-2.8.0.md index 036ca02b..d3576a74 100644 --- a/_posts/2024-11-22-release-2.8.0.md +++ b/_posts/2024-11-22-release-2.8.0.md @@ -13,22 +13,23 @@ However, in this case *minor* does not quite do justice to what is happening in this release, given that we have (at least) three big changes/additions: -1. The license was changed to the **Lesser General Public License** so - that MDAnalysis can be used by packages under *any* license while - keeping the source code itself free and protected. -2. We introduce the [Guesser][guesser modules docs] API for +1. The [license was changed](#license-change-to-lgpl) to the **GNU + Lesser General Public License** so that MDAnalysis can be used by + packages under *any* license while keeping the source code itself + free and protected. +2. We introduce the **[Guesser][guesser modules docs] API** for guessing missing topology attributes such as element or mass in a *context-dependent* manner. Until release 3.0, you should not notice any differences but under the hood we are getting ready to make it easier to work with simulations in a different *context* - (e.g., with the MARTINI force field) or experimental PDB + (e.g., with the MARTINI force field or experimental PDB files). With consistent attributes, such as elements, it becomes a lot easier to interface with tools like the cheminformatics RDKit (via the [converters][converter modules docs]). The guessers are the [GSoC 2022 project][] of @aya9aladdin with help from @lilyminium, @IAlibay, and @jbarnoud.[^guesserPR] -3. We are introducing [parallel analysis][] for tools in +3. We are introducing **[parallel analysis][]** for tools in [MDAnalysis.analysis][] following the simple *split-apply-combine* paradigm that we originally prototyped in [PMDA][] [^PMDApaper]. What's really exciting is that *any* analysis code @@ -48,6 +49,11 @@ changes/additions: thanks to @marinegor), `HydrogenBondAnalysis`, in addition to `RMSD`. +Read on for more details on the license change and the usual +information on [supported environments](#supported-environments), +[upgrading](#upgrading-to-mdanalysis-version-280) your version of MDAnalysis, and a +[summary of the most important changes](#notable-changes). + ## License change to LGPL @@ -81,7 +87,8 @@ support. The [relicensing team][] was lead by @IAlibay and @orbeckst. ## Supported environments -The minimum required NumPy version is 1.23.3. +The minimum required NumPy version is 1.23.3; MDAnalysis now builds +against NumPy 2.0. Supported Python versions: **3.10, 3.11, 3.12, 3.13**. Support for version 3.13 has been added in this release and support for 3.9 has been @@ -118,9 +125,9 @@ For a full list of changes, bugfixes and deprecations see the [CHANGELOG][]. #### Enhancements: -* Added guess_TopologyAttrs() API to the Universe to handle attribute +* Added `guess_TopologyAttrs()` API to the Universe to handle attribute guessing (PR #3753) -* Added the DefaultGuesser class, which is a general-purpose guesser with +* Added the `DefaultGuesser` class, which is a general-purpose guesser with the same functionalities as the existing guesser.py methods (PR #3753) * Introduce parallelization API to `AnalysisBase` and to `analysis.rms.RMSD` class (Issue #4158, PR #4304) @@ -190,11 +197,21 @@ the [Chan Zuckerberg Initiative][] for supporting MDAnalysis under EOSS4 and EOS — @IAlibay ([release manager][]) on behalf of the [MDAnalysis Team][] -[^guesserPR]: Her [PR #3753][] totalled 668 (!) comments. +[^guesserPR]: The Guesser API was a _big_ undertaking: Her merged [PR + #3753][] totalled 668 (!) comments. We look forward to the + community providing Guessers for specific context. -[^PMDApaper]: Shujie Fan, Max Linke, Ioannis Paraskevakos, Richard J. Gowers, Michael Gecht, and Oliver Beckstein. *PMDA - Parallel Molecular Dynamics Analysis.* In Chris Calloway, David Lippa, Dillon Niederhut, and David Shupe, editors, *Proceedings of the 18th Python in Science Conference*, 134 – 142. Austin, TX, 2019. SciPy. doi:[10.25080/Majora-7ddc1dd1-013](https://doi.org/10.25080/Majora-7ddc1dd1-013). +[^PMDApaper]: Shujie Fan, Max Linke, Ioannis Paraskevakos, Richard + J. Gowers, Michael Gecht, and Oliver Beckstein. *PMDA - Parallel + Molecular Dynamics Analysis.* In Chris Calloway, David Lippa, + Dillon Niederhut, and David Shupe, editors, *Proceedings of the + 18th Python in Science Conference*, 134 – 142. Austin, + TX, 2019. SciPy. doi:[10.25080/Majora-7ddc1dd1-013](https://doi.org/10.25080/Majora-7ddc1dd1-013). -[^parallelizationPR]: See [PR #4162][] with 713 (!) comments. +[^parallelizationPR]: Adding parallelization in a transparent manner + was quite a difficult undertaking that touched many parts of the + analysis code and required a lot of thought. Feedback is very + welcome! See [PR #4162][] with 713 (!) comments. [guesser modules docs]: https://docs.mdanalysis.org/stable/documentation_pages/guesser_modules.html [converter modules docs]: https://docs.mdanalysis.org/stable/documentation_pages/converters.html @@ -219,6 +236,6 @@ the [Chan Zuckerberg Initiative][] for supporting MDAnalysis under EOSS4 and EOS [CHANGELOG]: https://github.com/MDAnalysis/mdanalysis/blob/release-2.8.0/package/CHANGELOG [Chan Zuckerberg Initiative]: https://chanzuckerberg.com/ [licensing update]: {{ site.baseurl }}{% post_url 2023-09-22-licensing-update %} -[relicensing team]: {{ site.baseurl }}team/#relicensing-coordinator -[release manager]: {{ site.baseurl }}team/#releases-and-deployment -[MDAnalysis Team]: {{ site.baseurl }}team +[relicensing team]: {{ site.baseurl }}/team/#relicensing-coordinator +[release manager]: {{ site.baseurl }}/team/#releases-and-deployment +[MDAnalysis Team]: {{ site.baseurl }}/team