Merge remote-tracking branch 'upstream/main' into develop

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
     submodules: false
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.2.0
+  rev: v4.3.0
   hooks:
     - id: check-yaml
     - id: end-of-file-fixer

docs/conf.py

@@ -23,8 +23,8 @@
 author = "Matt Thompson, Alex Yang, Ray Matsumoto, Parashara Shamaprasad, Umesh Timalsina, Co Quach, Ryan S. DeFever, Justin Gilmer"
 
 # The full version, including alpha/beta/rc tags
-version = "0.8.0"
-release = "0.8.0"
+version = "0.8.1"
+release = "0.8.1"
 
 
 # -- General configuration ---------------------------------------------------

gmso/__init__.py

@@ -16,4 +16,4 @@
 from .core.subtopology import SubTopology
 from .core.topology import Topology
 
-__version__ = "0.8.0"
+__version__ = "0.8.1"

gmso/core/angle.py

@@ -61,32 +61,6 @@ def equivalent_members(self):
             [self.connection_members, tuple(reversed(self.connection_members))]
         )
 
-    def _equivalent_members_hash(self):
-        """Return a unique hash representing the connection.
-
-        Returns
-        -------
-        int
-            A unique hash to represent the connection members
-
-        Notes
-        -----
-        For an angle:
-            i, j, k == k, j, i
-        where i, j, and k are the connection members.
-        Here, j is fixed and i and k are replaceable.
-        """
-        return hash(
-            tuple(
-                [
-                    self.connection_members[1],
-                    frozenset(
-                        [self.connection_members[0], self.connection_members[2]]
-                    ),
-                ]
-            )
-        )
-
     def __setattr__(self, key, value):
         """Set the attributes of the angle."""
         if key == "connection_type":

gmso/core/bond.py

@@ -62,24 +62,6 @@ def equivalent_members(self):
             [self.connection_members, tuple(reversed(self.connection_members))]
         )
 
-    def _equivalent_members_hash(self):
-        """Return a unique hash representing the connection.
-
-        Returns
-        -------
-        int
-            A unique hash to represent the connection members
-        Notes
-        -----
-        For a bond:
-            i, j == j, i
-        where i and j are the connection members.
-        Here, i and j are interchangeable.
-        """
-        return hash(
-            frozenset([self.connection_members[0], self.connection_members[1]])
-        )
-
     def __setattr__(self, key, value):
         """Handle attribute assignment."""
         if key == "connection_type":

gmso/core/dihedral.py

@@ -64,38 +64,6 @@ def equivalent_members(self):
             [self.connection_members, tuple(reversed(self.connection_members))]
         )
 
-    def _equivalent_members_hash(self):
-        """Returns a unique hash representing the connection
-        Returns
-        _______
-        int
-            A unique hash to represent the connection members
-        Notes
-        _____
-        For a dihedral:
-            i, j, k, l == l, k, j, i
-        where i, j, k, and l are the connection members.
-        Here i and j are interchangeable, j and k are interchangeable,
-        and k and l are interchangeble, as long as each are adjacent to
-        one another.
-        """
-
-        return hash(
-            frozenset(
-                [
-                    frozenset(
-                        [self.connection_members[0], self.connection_members[1]]
-                    ),
-                    frozenset(
-                        [self.connection_members[1], self.connection_members[2]]
-                    ),
-                    frozenset(
-                        [self.connection_members[2], self.connection_members[3]]
-                    ),
-                ]
-            )
-        )
-
     def __setattr__(self, key, value):
         if key == "connection_type":
             super(Dihedral, self).__setattr__("dihedral_type", value)

gmso/core/improper.py

@@ -79,33 +79,6 @@ def equivalent_members(self):
 
         return frozenset([self.connection_members, tuple(equiv_members)])
 
-    def _equivalent_members_hash(self):
-        """Return a unique hash representing the connection.
-
-        Returns
-        -------
-        int
-            A unique hash to represent the connection members
-
-        Notes
-        -----
-        For an improper:
-            i, j, k, l == i, k, j, l
-        where i, j, k, and l are the connection members.
-        Here j and k are interchangeable and i and l are fixed.
-        """
-        return hash(
-            tuple(
-                [
-                    self.connection_members[0],
-                    self.connection_members[3],
-                    frozenset(
-                        [self.connection_members[1], self.connection_members[2]]
-                    ),
-                ]
-            )
-        )
-
     def __setattr__(self, key, value):
         """Set attribute override to support connection_type key."""
         if key == "connection_type":

gmso/core/topology.py

@@ -714,7 +714,7 @@ def add_connection(self, connection, update_types=False):
             is in the topology
         """
         # Check if an equivalent connection is in the topology
-        equivalent_members = connection._equivalent_members_hash()
+        equivalent_members = connection.equivalent_members()
         if equivalent_members in self._unique_connections:
             warnings.warn(
                 "An equivalent connection already exists. "

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.8.0
+current_version = 0.8.1
 commit = True
 tag = True
 message = Bump to version {new_version}

setup.py

@@ -3,7 +3,7 @@
 from setuptools import find_packages, setup
 
 #####################################
-VERSION = "0.8.0"
+VERSION = "0.8.1"
 ISRELEASED = False
 if ISRELEASED:
     __version__ = VERSION