Merge pull request #1652 from jamesmkrieger/v2.4.0_release_prep

release prep

PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: ProDy
-Version: 2.3.1
+Version: 2.4.0
 Summary: A Python Package for Protein Dynamics Analysis
 Home-page: http://www.csb.pitt.edu/ProDy
 Author: James Krieger, She Zhang, Hongchun Li, Cihan Kaya, Ahmet Bakan, and others

docs/release/v2.4_series.rst

@@ -0,0 +1,42 @@
+ProDy 2.4 Series
+===============================================================================
+
+.. contents::
+   :local:
+
+
+2.4.0 (Feb 2, 2023)
+------------------------------------------------------------------------------
+
+**New Features**:
+
+* New function alignBioPairwise to address Biopython deprecation
+* Added gromos rmsd clustering
+* New data_type option for refineEnsemble to use seqid instead of rmsd
+* New ignore_ids option for mergeMSA to use different ids for interacting proteins
+
+**Bug Fixes and Improvements**:
+
+* Fixed error during writeout PQR file
+* Proper handling of fragments when bonds are absent
+* Setting the atoms for ensemble even if the atoms is a subset
+* Allowing setFlags to take scalar values
+* Transpose princ axes matrix to get columns
+* New flag selpdbter to keep ter lines in selections
+* No sorting of strands in writing
+* Add cif datafiles to setup
+* Select app help fix
+* Fixes to mmcif parsing
+* Improvements to cutoffs in Dali filtering
+* Fix to protein definition
+* Set matrix interactive to false and fix to axes3d usage for matplotlib 3.6
+* Improved requirements
+* Fix to fetchPDB for files with two dots but not gz ending
+
+**New Contributors**:
+
+* @changephilip made their first contribution in https://github.com/prody/ProDy/pull/1618
+* @odcambc made their first contribution in https://github.com/prody/ProDy/pull/1634
+* @hrnciar made their first contribution in https://github.com/prody/ProDy/pull/1372
+
+**Full Changelog**: https://github.com/prody/ProDy/compare/v2.3.1...v2.4.0

prody/__init__.py

@@ -1,6 +1,6 @@
 """ProDy is a package for Protein Dynamics, Sequence, and Structure Analysis"""
 
-__version__ = '2.3.1'
+__version__ = '2.4.0'
 __release__ = __version__ # + '-dev' # comment out '-dev' before a release
 
 import sys