Finalize v2.9.0 release (#4955)

* Finalize v2.9.0 release

Author: IAlibay

package/CHANGELOG

@@ -14,29 +14,32 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
-??/??/?? IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy,
+03/11/25 IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy,
          marinegor, hmacdope, jauy123, al42and
 
  * 2.9.0
 
 Fixes
  * Add support for TPR files produced by GROMACS 2024.4 and GROMACS 2025.0
- * Fixes invalid default unit from Angstrom to Angstrom^{-3} for convert_density() function. (Issue #4829)
- * Fixes deprecation warning Array to scalar convertion. Replaced atan2() with np.arctan2() (Issue #4339)
+ * Fixes invalid default unit from Angstrom to Angstrom^{-3} for
+   convert_density() function. (Issue #4829)
+ * Fixes deprecation warning Array to scalar convertion. Replaced atan2()
+   with np.arctan2() (Issue #4339)
  * Replaced mutable defaults with None and initialized them within
    the function to prevent shared state. (Issue #4655)
 
 Enhancements
  * Improve distopia backend support in line with new functionality available 
    in distopia >= 0.3.1 (PR #4734)
  * Addition of 'water' token for water selection (Issue #4839)
- * Enables parallelization for analysis.density.DensityAnalysis (Issue #4677, PR #4729)
+ * Enables parallelization for analysis.density.DensityAnalysis
+   (Issue #4677, PR #4729)
  * Enables parallelization for analysis.contacts.Contacts (Issue #4660)
  * Enable parallelization for analysis.nucleicacids.NucPairDist (Issue #4670)
- * Add check and warning for empty (all zero) coordinates in RDKit converter (PR #4824)
+ * Add check and warning for empty (all zero) coordinates in RDKit converter
+   (PR #4824)
  * Added `precision` for XYZWriter (Issue #4775, PR #4771) 
 
-
 Changes
  * MDAnalysis.analysis.psa, MDAnalysis.analysis.waterdynamics and
    MDAnalysis.analysis.hole2 are now no longer available by default in
@@ -46,8 +49,6 @@ Changes
  * Changed `fasteners` dependency to  `filelock` (Issue #4797, PR #4800)
  * Codebase is now formatted with black (version `24`) (PR #4886)
 
-Deprecations
-
 
 11/11/24 IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,

package/MDAnalysis/version.py

@@ -67,4 +67,4 @@
 # e.g. with lib.log
 
 #: Release of MDAnalysis as a string, using `semantic versioning`_.
-__version__ = "2.9.0-dev0"  # NOTE: keep in sync with RELEASE in setup.py
+__version__ = "2.9.0"  # NOTE: keep in sync with RELEASE in setup.py

package/setup.py

@@ -58,7 +58,7 @@
 from subprocess import getoutput
 
 # NOTE: keep in sync with MDAnalysis.__version__ in version.py
-RELEASE = "2.9.0-dev0"
+RELEASE = "2.9.0"
 
 is_release = "dev" not in RELEASE
 

testsuite/MDAnalysisTests/__init__.py

@@ -97,7 +97,7 @@
 logger = logging.getLogger("MDAnalysisTests.__init__")
 
 # keep in sync with RELEASE in setup.py
-__version__ = "2.9.0-dev0"
+__version__ = "2.9.0"
 
 
 # Do NOT import MDAnalysis at this level. Tests should do it themselves.

testsuite/setup.py

@@ -75,7 +75,7 @@ def run(self):
 
 if __name__ == "__main__":
     # this must be in-sync with MDAnalysis
-    RELEASE = "2.9.0-dev0"
+    RELEASE = "2.9.0"
 
     setup(
         version=RELEASE,