v0.14.0 (#131)

CHANGELOG.md

@@ -1,5 +1,8 @@
 # Changelog
 
+-   **0.14.0** (May 16 2023)
+    -   Housekeeping:
+        -   Upgraded the package manager to Poetry, with version-pinning now handled by the `pyproject.toml` file.
 -   **0.13.0** (October 11 2022)
     -   Features:
         -   Introduced propagation of constraints when nodes are explicitly marked as automorphic to one another.

dotmotif/__init__.py

@@ -15,7 +15,7 @@
 limitations under the License.
 """
 
-from typing import Union, IO
+from typing import List, Optional, Union, IO
 import copy
 import pickle
 import warnings
@@ -25,12 +25,12 @@
 from networkx.algorithms import isomorphism
 
 from .parsers.v2 import ParserV2
-from .validators import DisagreeingEdgesValidator
+from .validators import DisagreeingEdgesValidator, Validator
 
 from .executors.NetworkXExecutor import NetworkXExecutor
 from .executors.GrandIsoExecutor import GrandIsoExecutor
 
-__version__ = "0.13.0"
+__version__ = "0.14.0"
 
 DEFAULT_MOTIF_PARSER = ParserV2
 
@@ -46,7 +46,7 @@ class Motif:
     See __init__ documentation for more details.
     """
 
-    def __init__(self, input_motif: str = None, **kwargs):
+    def __init__(self, input_motif: Optional[str] = None, **kwargs):
         """
         Create a new dotmotif object.
 
@@ -74,7 +74,9 @@ def __init__(self, input_motif: str = None, **kwargs):
         self.pretty_print = kwargs.get("pretty_print", True)
         self.parser = kwargs.get("parser", DEFAULT_MOTIF_PARSER)
         self.exclude_automorphisms = kwargs.get("exclude_automorphisms", False)
-        self.validators = kwargs.get("validators", [DisagreeingEdgesValidator()])
+        self.validators: List[Validator] = kwargs.get(
+            "validators", [DisagreeingEdgesValidator()]
+        )
         self._g = nx.MultiDiGraph()
 
         self._edge_constraints = {}
@@ -186,7 +188,7 @@ def _propagate_automorphic_constraints(self):
         # Note to future self: We DON'T loop over implicit automorphisms because
         # there is no guarantee that the user intends for structural symmetries
         # to also be symmetries in the constraint space.
-        for (u, v) in self._automorphisms:
+        for u, v in self._automorphisms:
             # Add a superset of constraints on the two nodes.
             # First add attributes on the nodes themselves:
             constraints = _deep_merge_constraint_dicts(

dotmotif/executors/GrandIsoExecutor.py

@@ -14,6 +14,7 @@
 limitations under the License.`
 """
 from functools import lru_cache
+from typing import Optional
 import networkx as nx
 from grandiso import find_motifs_iter
 
@@ -31,7 +32,7 @@ class GrandIsoExecutor(NetworkXExecutor):
 
     """
 
-    def find(self, motif, limit: int = None):
+    def find(self, motif, limit: Optional[int] = None):
         """
         Find a motif in a larger graph.
 
@@ -46,7 +47,7 @@ def find(self, motif, limit: int = None):
         # We need to first remove "negative" nodes from the motif, and then
         # filter them out later on.
 
-        if motif.ignore_direction or not self.graph.is_directed:
+        if motif.ignore_direction or not self.graph.is_directed:  # type: ignore
             graph_constructor = nx.Graph
         else:
             graph_constructor = nx.DiGraph
@@ -62,7 +63,7 @@ def find(self, motif, limit: int = None):
 
         def _doesnt_have_any_of_motifs_negative_edges(mapping):
             for u, v in must_not_exist_edges:
-                if self.graph.has_edge(mapping[u], mapping[v]):
+                if self.graph.has_edge(mapping[u], mapping[v]):  # type: ignore
                     return False
             return True
 

dotmotif/executors/NetworkXExecutor.py

@@ -14,14 +14,14 @@
 limitations under the License.`
 """
 
-from typing import TYPE_CHECKING, List, Tuple
+from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple
 import copy
 import networkx as nx
 
 from .Executor import Executor
 
 if TYPE_CHECKING:
-    from .. import dotmotif
+    from .. import dotmotif  # type: ignore
 
 _OPERATORS = {
     "=": lambda x, y: x == y,
@@ -124,7 +124,7 @@ def __init__(self, **kwargs) -> None:
 
         """
         if "graph" in kwargs:
-            self.graph = kwargs.get("graph")
+            self.graph: nx.Graph = kwargs["graph"]
         else:
             raise ValueError(
                 "You must pass a graph to the NetworkXExecutor constructor."
@@ -143,7 +143,7 @@ def __init__(self, **kwargs) -> None:
             ), "_multigraph_edge_match must be one of 'all' or 'any'."
 
     def _validate_node_constraints(
-        self, node_isomorphism_map: dict, graph: nx.DiGraph, constraints: dict
+        self, node_isomorphism_map: dict, graph: nx.Graph, constraints: dict
     ) -> bool:
         """
         Validate nodes against their isomorphism's constraints in the motif.
@@ -162,7 +162,7 @@ def _validate_node_constraints(
         return True
 
     def _validate_dynamic_node_constraints(
-        self, node_isomorphism_map: dict, graph: nx.DiGraph, constraints: dict
+        self, node_isomorphism_map: dict, graph: nx.Graph, constraints: dict
     ) -> bool:
         """
         Validate a graph against its dynamic node constraints.
@@ -183,7 +183,7 @@ def _validate_dynamic_node_constraints(
             this_node = node_isomorphism_map[motif_U]
             for this_key, operators in constraint_list.items():
                 for operator, that_node_list in operators.items():
-                    for (that_node_V, that_key) in that_node_list:
+                    for that_node_V, that_key in that_node_list:
                         that_node = node_isomorphism_map[that_node_V]
                         if this_key not in graph.nodes[this_node]:
                             return False
@@ -197,7 +197,7 @@ def _validate_dynamic_node_constraints(
         return True
 
     def _validate_edge_constraints(
-        self, node_isomorphism_map: dict, graph: nx.DiGraph, constraints: dict
+        self, node_isomorphism_map: dict, graph: nx.Graph, constraints: dict
     ):
         """
         Validate all edge constraints on a subgraph.
@@ -234,15 +234,15 @@ def _validate_edge_constraints(
             graph_v = node_isomorphism_map[motif_V]
 
             # Check edge in graph for constraints
-            edge_attrs = graph.get_edge_data(graph_u, graph_v)
+            edge_attrs: Dict[Any, Any] = graph.get_edge_data(graph_u, graph_v)  # type: ignore
 
             if not _edge_satisfies_constraints(edge_attrs, constraint_list):
                 # Fail fast
                 return False
         return True
 
     def _validate_dynamic_edge_constraints(
-        self, node_isomorphism_map: dict, graph: nx.DiGraph, constraints: dict
+        self, node_isomorphism_map: dict, graph: nx.Graph, constraints: dict
     ):
         """
         Validate all edge constraints on a subgraph.
@@ -264,7 +264,7 @@ def _validate_dynamic_edge_constraints(
 
         """
         for (motif_U, motif_V), constraint_list in constraints.items():
-            for (this_attr, ops) in constraint_list.items():
+            for this_attr, ops in constraint_list.items():
                 for op, (that_u, that_v, that_attr) in ops.items():
                     this_graph_u = node_isomorphism_map[motif_U]
                     this_graph_v = node_isomorphism_map[motif_V]
@@ -281,7 +281,7 @@ def _validate_dynamic_edge_constraints(
         return True
 
     def _validate_multigraph_all_edge_constraints(
-        self, node_isomorphism_map: dict, graph: nx.DiGraph, constraints: dict
+        self, node_isomorphism_map: dict, graph: nx.Graph, constraints: dict
     ):
         """
         Reuses logic from the simple _validate_edge_constraints case.
@@ -304,7 +304,7 @@ def _validate_multigraph_all_edge_constraints(
         return True
 
     def _validate_multigraph_any_edge_constraints(
-        self, node_isomorphism_map: dict, graph: nx.DiGraph, constraints: dict
+        self, node_isomorphism_map: dict, graph: nx.Graph, constraints: dict
     ):
         """
         Reuses logic from the simple _validate_edge_constraints case.
@@ -351,15 +351,15 @@ def _validate_multigraph_any_edge_constraints(
 
         return True
 
-    def count(self, motif: "dotmotif.Motif", limit: int = None):
+    def count(self, motif: "dotmotif.Motif", limit: Optional[int] = None):
         """
         Count the occurrences of a motif in a graph.
 
         See NetworkXExecutor#find for more documentation.
         """
         return len(self.find(motif, limit))
 
-    def find(self, motif: "dotmotif.Motif", limit: int = None):
+    def find(self, motif: "dotmotif.Motif", limit: Optional[int] = None):
         """
         Find a motif in a larger graph.