links + fixes

Author: orbeckst

_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