finalized blog post

- all deprecations
- links to role list instead of role description
- MDAKits with links

_posts/2024-11-22-release-2.8.0.md

@@ -44,7 +44,7 @@ changes/additions:
 
    Not all MDAnalysis analysis classes have parallelization enabled
    yet but @talagayev has been working tirelessly on already updating
-   `GNMAnalysis`, `BAT`, `Dihdedral`, `Ramachandran`, `Janin`, `DSSP`
+   `GNMAnalysis`, `BAT`, `Dihedral`, `Ramachandran`, `Janin`, `DSSP`
    (yes, MDAnalysis has _finally_ got DSSP, based on [pydssp][], also
    thanks to @marinegor), `HydrogenBondAnalysis`, in addition to
    `RMSD`. 
@@ -64,7 +64,7 @@ title="LGPLv3" alt="LGPLv3 logo" style="float: right"/>
 
 This is the first release of MDAnalysis under the **Lesser General
 Public License**. We have been working towards this license change for
-the last 3 years; this (almost) concludes the process that we
+the last 3 years; this release (almost) concludes the process that we
 described in our [licensing update blog post][licensing update].
 
 
@@ -82,8 +82,8 @@ change the license. We would also like to thank a number of
 institutions who were especially supportive of our open source
 efforts, namely Arizona State University, Australian National
 University, Johns Hopkins University, and the Open Molecular Science
-Foundation. We are also grateful to NumFOCUS for legal
-support. The [relicensing team][] was lead by @IAlibay and @orbeckst. 
+Foundation. We are also grateful to [NumFOCUS][] for legal
+support. The [relicensing team][roles] was lead by @IAlibay and @orbeckst. 
 
 ## Supported environments
 
@@ -149,7 +149,7 @@ For a full list of changes, bugfixes and deprecations see the [CHANGELOG][].
  * Fix failure to preserve modification of coordinates after serialization,
    e.g. with transformations
    (Issue #4633, PR #3722)
- * Fix PSFParser error when encoutering string-like resids
+ * Fix PSFParser error when encountering string-like resids
    (Issue #2053, Issue #4189 PR #4582)
  * Convert openmm Quantity to raw value for KE and PE in OpenMMSimulationReader.
  * Atomname methods can handle empty groups (Issue #2879, PR #4529)
@@ -173,6 +173,47 @@ For a full list of changes, bugfixes and deprecations see the [CHANGELOG][].
 
 #### Deprecations:
 
+* Deprecations of old guessing functionality (in favor of the new
+  Guesser API)
+  * `MDAnalysis.topology.guessers` is deprecated in favour of the new
+	Guessers API and will be removed in version 3.0 (PR #4752)
+  * The `guess_bonds`, `vdwradii`, `fudge_factor`, and `lower_bound`
+    kwargs are deprecated for bond guessing during Universe
+    creation. Instead, pass `("bonds", "angles", "dihedrals")` into
+    `to_guess` or `force_guess` during Universe creation, and the
+    associated `vdwradii`, `fudge_factor`, and `lower_bound` kwargs
+    into `Guesser` creation. Alternatively, if `vdwradii`,
+    `fudge_factor`, and `lower_bound` are passed into
+    `Universe.guess_TopologyAttrs`, they will override the previous
+    values of those kwargs. (Issue #4756, PR #4757)
+  * `MDAnalysis.topology.tables` is deprecated in favour of
+	`MDAnalysis.guesser.tables` and will be removed in version 3.0 (PR #4752)
+  * Element guessing in the `ITPParser` is deprecated and will be removed in version 3.0
+	(Issue #4698)
+  * **Unknown masses are still set to 0.0 for current version**, this
+	will be changed **in version 3.0.0 and replaced by
+	`Masses` "no_value_label" attribute (`np.nan`)** (PR #3753)
+* A number of analysis modules have been moved into their own
+  [MDAKits][], following the [3.0 roadmap towards a trimmed down core
+  library][roadmap]. Until release 3.0, these modules are still
+  available through `MDAnalysis.analysis` (either as an import of the
+  MDAKit as an automatically installed dependency of the MDAnalysis
+  package or as the original code) but from 3.0 onwards, users must
+  install the MDAKit explicitly and then import it by themselves.
+
+  * The `MDAnalysis.analysis.encore` module has been deprecated in
+	favour of the [mdaencore]() MDAKit and will be removed in version
+	3.0.0 (PR #4737)
+  * The `MDAnalysis.analysis.waterdynamics` module has been deprecated in favour
+	of the [waterdynamics][] MDAKit and will be removed in version 3.0.0 (PR #4404)
+  * The `MDAnalysis.analysis.psa` module has been deprecated in favour of
+	the [PathSimAnalysis][] MDAKit and will be removed in version 3.0.0
+	(PR #4403)
+* The MMTF Reader is deprecated and will be removed in version 3.0 as
+  the MMTF format is no longer supported (Issue #4634).
+
+
+
 ## Author statistics
 
 This release was the work of 22 contributors, **10** of which are **new contributors**.
@@ -194,7 +235,10 @@ Our **new contributors** are:
 MDAnalysis thanks [NumFOCUS][] for its continued support as our fiscal sponsor and 
 the [Chan Zuckerberg Initiative][] for supporting MDAnalysis under EOSS4 and EOSS5 awards.
 
-— @IAlibay ([release manager][]) on behalf of the [MDAnalysis Team][]
+— @IAlibay ([release manager][roles]) on behalf of the [MDAnalysis Team][]
+
+
+----
 
 
 [^guesserPR]: The Guesser API was a _big_ undertaking: Her merged [PR
@@ -227,7 +271,6 @@ the [Chan Zuckerberg Initiative][] for supporting MDAnalysis under EOSS4 and EOS
 [PMDA]: https://github.com/mdanalysis/pmda
 [SPEC 0]: https://scientific-python.org/specs/spec-0000/
 [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
@@ -236,6 +279,10 @@ 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 }}/pages/team/#relicensing-coordinator
-[release manager]: {{ site.baseurl }}/pages/team/#releases-and-deployment
+[roles]: {{ site.baseurl }}/pages/team/#roles
 [MDAnalysis Team]: {{ site.baseurl }}/pages/team
+[MDAKits]: https://mdakits.mdanalysis.org/
+[roadmap]: {{ site.baseurl }}{% post_url 2023-10-25-towards_3.0 %}#a-trimmed-down-core-library
+[mdaencore]: https://mdakits.mdanalysis.org/mdaencore.html
+[waterdynamics]: https://mdakits.mdanalysis.org/waterdynamics.html
+[PathSimAnalysis]: https://mdakits.mdanalysis.org/PathSimAnalysis.html