release 2.9.0 blog post

_posts/2025-03-11-release-2.9.0.md

@@ -0,0 +1,135 @@
+---
+layout: post
+title: Release 2.9.0 of MDAnalysis
+---
+
+We are happy to release version 2.9.0 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.
+
+
+## Supported environments
+
+This release supports NumPy 2.0+ and offers backwards compatibility
+through to NumPy 1.23.2.
+
+Supported Python versions: **3.10, 3.11, 3.12, 3.13**.
+
+Supported Operating Systems:
+  - **Linux** (on [x86-64][])
+  - **Windows** (on [x86-64][])
+  - **MacOS** (on [x86-64][] and [ARM64][])
+
+
+## Upgrading to MDAnalysis version 2.9.0
+
+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, bug fixes and deprecations see the [CHANGELOG][].
+
+#### Enhancements:
+
+* Support for Gromacs v2024.4 and v2025 TPR files.
+* A new "water" keyword for selecting water residues.
+* Support for **[distopia][] 0.4.0** as an optional distance library
+  backend that now supports [many more distance
+  functions](https://docs.mdanalysis.org/stable/documentation_pages/lib/distances.html#id2)
+  for *all box types* (including general triclinic unit cells).
+
+  On supported [x86-64][] platforms, install *distopia* with
+  ```bash
+  mamba install -c conda-forge distopia
+  ```
+
+  You can then [enable *distopia* as a
+  backend](https://docs.mdanalysis.org/stable/documentation_pages/lib/distances.html#use-of-the-distopia-library)
+  to make use of the optimized *distopia* code for 
+  compute-intensive distance calculations, such as
+  [`distance_array()`](https://docs.mdanalysis.org/stable/documentation_pages/lib/distances.html#MDAnalysis.lib.distances.distance_array):
+
+  ```python
+  protein = u.select_atoms("protein and not name H*")
+  lipids = u.select_atoms("resname POPC CHOL and not name H*")
+  d = MDAnalysis.lib.distances.distance_array(protein, lipids,
+                                              box=u.dimensions, 
+                                              backend="distopia")
+  ```
+
+  If you want to see if *distopia* is available as a backend in a running
+  program, check that the variable `MDAnalysis.lib.distances.HAS_DISTOPIA` is
+  `True`.
+
+* Parallel analysis support for `MDAnalysis.analysis.nucleicacids`, `MDAnalysis.analysis.contacts`, and `MDAnalysis.analysis.density`.
+* XYZ writer can now write positions up to a user-supplied precision via the `precision` keyword argument.
+
+
+#### Changes:
+
+* `MDAnalysis.analysis.hole2`, `MDAnalysis.analysis.psa`, and
+  `MDAnalysis.analysis.waterdynamics`, are now only available via
+  optional dependencies (the mdahole2, pathsimanalysis, and
+  waterdynamics [MDAKits][]). By default these will not be installed, you
+  will need to install them separately if you wish to use them from
+  within `MDAnalysis.analysis`. Please
+  note that *in v3.0* theses modules will be *removed completely from the
+  MDAnalysis core library* and you will need to use the MDAKits
+  directly.
+* `fasteners` dependency has been switched to `filelock`.
+* Codebase is now formatted with black (version 24)
+
+
+
+## Author statistics
+
+This release was the work of 10 contributors, **3** of which are **new contributors**.
+
+Our **new contributors** are:
+
+* @ChiahsinChu
+* @tanishy7777
+* @jauy123
+
+
+## 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 and @p-j-smith ([release managers][roles]) on behalf of the [MDAnalysis Team][]
+
+
+----
+
+
+[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-2.9.0/package/CHANGELOG
+[Chan Zuckerberg Initiative]: https://chanzuckerberg.com/
+[roles]: {{ site.baseurl }}/pages/team/#roles
+[MDAnalysis Team]: {{ site.baseurl }}/pages/team
+[MDAKits]: https://mdakits.mdanalysis.org/
+[distopia]: https://github.com/MDAnalysis/distopia