release 2.8.0 blog post (#411)

* release 2.8.0 blog post

* changelog 280

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

Co-authored-by: Irfan Alibay <[email protected]>

* added more recognition

* links + fixes

* finalized blog post

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

* untabified

* no cf package for py13

Co-authored-by: Irfan Alibay <[email protected]>

---------

Co-authored-by: Irfan Alibay <[email protected]>

Author: orbeckst

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

@@ -0,0 +1,290 @@
+---
+layout: post
+title: Release 2.8.0 of MDAnalysis
+---
+
+We are happy to release version 2.8.0 of MDAnalysis!
+
+This is a minor release of the MDAnalysis library, which means that it
+contains enhancements, bug fixes, deprecations, and other
+backwards-compatible changes.
+
+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](#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
+   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
+   [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
+   that is based on [MDAnalysis.analysis.base.AnalysisBase][] can
+   enable parallelization with a few lines of extra code---all the
+   hard work is done behind the scenes in the base class (in a way
+   that is fully backwards compatible!).
+
+   This new feature is the work of @marinegor who brought his
+   [GSoC 2023 project][] to completion, with great contributions by
+   @p-j-smith, @yuxuanzhuang and @RMeli [^parallelizationPR].
+   
+   Not all MDAnalysis analysis classes have parallelization enabled
+   yet but @talagayev has been working tirelessly on already updating
+   `GNMAnalysis`, `BAT`, `Dihedral`, `Ramachandran`, `Janin`, `DSSP`
+   (yes, MDAnalysis has _finally_ got DSSP, based on [pydssp][], also
+   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
+
+<a href="https://www.gnu.org/licenses/lgpl-3.0.en.html">
+<img src="https://www.gnu.org/graphics/lgplv3-with-text-154x68.png"
+title="LGPLv3" alt="LGPLv3 logo" style="float: right"/>
+</a>
+
+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 release (almost) concludes the process that we
+described in our [licensing update blog post][licensing update].
+
+
+* **All code** is now under [LGPLv2.1
+  license](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html)
+  or any higher version. 
+* The package is under the [LGPLv3
+  license](https://www.gnu.org/licenses/lgpl-3.0.html) or any higher
+  version. However, once we have removed dependencies that prevent
+  licensing under LGPLv2.1+ at the moment, we will also license the
+  package under the same **LGPLv2.1+** as the code itself.
+
+We would like to thank all our contributors who granted us permission to
+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][roles] was lead by @IAlibay and @orbeckst. 
+
+## Supported environments
+
+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
+dropped (following [SPEC 0][]).
+
+Please note that Python 3.13 is limited to [PyPi][] for now, the [conda-forge channel][] installs only provide support for Python 3.10 to 3.12.
+
+Supported Operating Systems:
+  - **Linux** (on [x86-64][])
+  - **Windows** (on [x86-64][])
+  - **MacOS** (on [x86-64][] and [ARM64][])
+
+
+## Upgrading to MDAnalysis version 2.8.0
+
+To update with `mamba` (or `conda`)  from the [conda-forge channel][] run
+
+```bash
+mamba update -c conda-forge mdanalysis
+```
+
+To update from [PyPi][] with `pip` run
+
+```bash
+python -m pip install --upgrade MDAnalysis
+```
+
+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 >= 3.10).
+
+
+## Notable changes
+
+For a full list of changes, bugfixes and deprecations see the [CHANGELOG][].
+
+#### Enhancements:
+
+* Added `guess_TopologyAttrs()` API to the Universe to handle attribute
+  guessing (PR #3753)
+* 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)
+* Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)
+* Improved performance of PDBWriter (Issue #2785, PR #4472)
+* Added parsing of arbitrary columns of the LAMMPS dump parser. (Issue #3504)
+* Implement average structures with iterative algorithm from
+  DOI 10.1021/acs.jpcb.7b11988. (Issue #2039, PR #4524)
+* Add support for TPR files produced by Gromacs 2024.1 (PR #4523)
+
+#### Fixes:
+
+ * Fix Bohrium (Bh) atomic mass in tables.py (PR #3753)
+ * Catch higher dimensional indexing in GroupBase & ComponentBase (Issue #4647)
+ * Do not raise an Error reading H5MD files with datasets like
+   `observables/<particle>/<property>` (part of Issue #4598, PR #4615)
+ * Fix failure in double-serialization of TextIOPicklable file reader.
+   (Issue #3723, PR #3722)
+ * Fix failure to preserve modification of coordinates after serialization,
+   e.g. with transformations
+   (Issue #4633, PR #3722)
+ * 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)
+ * Fix bug in PCA preventing use of `frames=...` syntax (PR #4423)
+ * Fix `analysis/diffusionmap.py` iteration through trajectory to iteration
+   over `self._sliced_trajectory`, hence supporting
+   `DistanceMatrix.run(frames=...)` (PR #4433)
+
+
+#### Changes:
+
+ * Relicense code contributions from GPLv2+ to LGPLv2.1+
+   and the package from GPLv3+ to LGPLv3+ (PR #4794)
+ * only use distopia < 0.3.0 due to API changes (Issue #4739)
+ * The `fetch_mmtf` method has been removed as the REST API service
+   for MMTF files has ceased to exist (Issue #4634)
+ * MDAnalysis now builds against numpy 2.0 rather than the
+   minimum supported numpy version (PR #4620)
+
+
+
+#### 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**.
+
+Our **new contributors** are:
+- @aditya292002
+- @pstaerk
+- @kainszs
+- @SampurnaM
+- @leonwehrhan
+- @PythonFZ
+- @kurtmckee
+- @laksh-krishna-sharma
+- @MattTDavies,
+- @talagayev
+
+## Acknowledgements
+
+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][roles]) on behalf of the [MDAnalysis Team][]
+
+
+----
+
+
+[^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).
+
+[^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
+
+[GSoC 2022 project]: {{ site.baseurl }}{% post_url 2022-12-9-Aya-gsoc-final-report %}
+[GSoC 2023 project]: {{ site.baseurl }}{% post_url 2024-01-18-gsoc2023_marinegor %}
+[parallel analysis]: https://docs.mdanalysis.org/stable/documentation_pages/analysis/parallelization.html
+[MDAnalysis.analysis.base.AnalysisBase]: https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase
+[PR #3753]: https://github.com/MDAnalysis/mdanalysis/pull/3753
+[PR #4162]: https://github.com/MDAnalysis/mdanalysis/pull/4162
+[pydssp]: https://github.com/ShintaroMinami/PyDSSP
+[MDAnalysis.analysis]: https://docs.mdanalysis.org/stable/documentation_pages/analysis_modules.html
+[PMDA]: https://github.com/mdanalysis/pmda
+[SPEC 0]: https://scientific-python.org/specs/spec-0000/
+[x86-64]: https://en.wikipedia.org/wiki/X86-64
+[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-2.8.0/package/CHANGELOG
+[Chan Zuckerberg Initiative]: https://chanzuckerberg.com/
+[licensing update]: {{ site.baseurl }}{% post_url 2023-09-22-licensing-update %}
+[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