Updating dependencies to work with python3.12

Author: skfegan

CodeEntropy/GeometricFunctions.py

@@ -33,11 +33,6 @@ def get_beads(data_container, level):
             atom_group = "index " + str(atom.index) + " or (name H* and bonded index " + str(atom.index) +")"
             list_of_beads.append(data_container.select_atoms(atom_group))
 
-    #TODO temporary print
-    print("list of beads")
-    print(level)
-    print(list_of_beads)
-
     return list_of_beads
 #END
 
@@ -125,7 +120,6 @@ def get_avg_pos(atom_set, center):
     Input
     -----
     atoms : MDAnalysis atom group
-    arg_frame : frame index (integer)
     center : position for center of rotation
 
     Output

setup.py

@@ -63,11 +63,11 @@
 	zip_safe = False,
 
     install_requires=[
-        'numpy==1.22.4', #updated from 1.22.3 for the MDAnalysis update
+        'numpy==1.26.4', # updated on 17 Oct 2024 to work with python3.12
         'bitarray==2.5.0',
-        'mdanalysis==2.6.1', #updated from MDAnalysis 2.1.0 
-        'pandas==2.1.0', #updated from 1.4.2 for the MDAnalysis update
-        'psutil==5.9.5', #with update
+        'mdanalysis==2.7.0', # updated on 17 Oct 2024
+        'pandas==2.2.3', # updated on 17 Oct 2024 to work with python3.12
+        'psutil==5.9.5', 
         'dill==0.3.5.1',
         'pathos==0.2.9',
     ],

versioneer.py

@@ -339,9 +339,9 @@ def get_config_from_root(root):
     # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
     # the top of versioneer.py for instructions on writing your setup.cfg .
     setup_cfg = os.path.join(root, "setup.cfg")
-    parser = configparser.SafeConfigParser()
+    parser = configparser.ConfigParser()
     with open(setup_cfg, "r") as f:
-        parser.readfp(f)
+        parser.read_file(f)
     VCS = parser.get("versioneer", "VCS")  # mandatory
 
     def get(parser, name):