Skip to content

Commit

Permalink
links + fixes
Browse files Browse the repository at this point in the history
  • Loading branch information
@orbeckst
orbeckst committed Nov 24, 2024
1 parent 61b7656 commit ce3462f
Showing 1 changed file with 32 additions and 15 deletions.
47 changes: 32 additions & 15 deletions _posts/2024-11-22-release-2.8.0.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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
Expand All @@ -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

0 comments on commit ce3462f

Please sign in to comment.