Upgrade grandiso to use generator API (#102)

* Upgrade grandiso dependency

* Use generator API from grandiso

* Update changelog

Author: j6k4m8

CHANGELOG.md

@@ -1,5 +1,8 @@
 # Changelog
 
+-   **0.9.1**
+    -   Features:
+        -   `GrandIsoExecutor`: Adds support for the `grandiso.find_motifs_iter` generator API in grandiso v1.2.0; this reduces the runtime of queries with nonzero `limit` #102
 -   **0.9.0** (March 23 2021)
     -   Features:
         -   `Neo4jExecutor#create_index`. This function call adds an index to the database on the node attribute specified, in order to improve query performance (#95)

dotmotif/executors/GrandIsoExecutor.py

@@ -15,7 +15,7 @@
 """
 
 import networkx as nx
-from grandiso import find_motifs
+from grandiso import find_motifs_iter
 
 from .NetworkXExecutor import NetworkXExecutor
 
@@ -52,7 +52,7 @@ def find(self, motif, limit: int = None):
         # should be smart enough to know what you want while avoiding adding
         # complexity. Anyway, soapbox over.) To that end, this confirmation
         # that the motif is directed is kinda... Unimportant.
-        graph_matcher = find_motifs
+        graph_matcher = find_motifs_iter
 
         if motif.ignore_direction or not self.graph.is_directed:
             graph_constructor = nx.Graph
@@ -67,33 +67,18 @@ def find(self, motif, limit: int = None):
             elif attrs["exists"] is False:
                 # Collect a list of neg-edges to check for again in a moment
                 must_not_exist_edges.append((u, v))
-        graph_matches = graph_matcher(only_positive_edges_motif, self.graph)
 
         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]):
                     return False
             return True
 
-        # Another note. In the NetworkX executor, results are returned in what
-        # I perceive to be silly order. Why would you tell me "what nodes are
-        # the result of the mapping to B from A" rather that just "here's the
-        # mapping from A to B"...? I digress. Anyhow, in the NX executor we
-        # have to flip the results. Here, we don't. That's why there's a code
-        # block dict-comprehension missing from this function. Neato.
-
-        # Now, filter out those that have edges they should not:
-        results = [
-            mapping
-            for mapping in graph_matches
-            if _doesnt_have_any_of_motifs_negative_edges(mapping)
-        ]
-
-        # Now, filter on attributes:
-        res = [
-            r
-            for r in results
-            if (
+        graph_matches = graph_matcher(only_positive_edges_motif, self.graph)
+
+        results = []
+        for r in graph_matches:
+            if _doesnt_have_any_of_motifs_negative_edges(r) and (
                 self._validate_edge_constraints(
                     r, self.graph, motif.list_edge_constraints()
                 )
@@ -111,6 +96,9 @@ def _doesnt_have_any_of_motifs_negative_edges(mapping):
                     (not motif.exclude_automorphisms)
                     or all(r[a] <= r[b] for (a, b) in motif.list_automorphisms())
                 )
-            )
-        ]
-        return res
+            ):
+                results.append(r)
+                if limit and len(results) >= limit:
+                    return results
+
+        return results

requirements.txt

@@ -7,4 +7,4 @@ py2neo
 dask[dataframe]
 tamarind>=0.2.0
 neuprint-python
-grandiso>=1.1.0
+grandiso>=1.2.0

setup.py

@@ -11,7 +11,7 @@
 twine upload dist/*
 """
 
-VERSION = "0.9.0"
+VERSION = "0.9.1"
 
 here = os.path.abspath(os.path.dirname(__file__))
 with io.open(os.path.join(here, "README.md"), encoding="utf-8") as f:
@@ -25,7 +25,7 @@
     description=("Find graph motifs using simple, intuitive notation"),
     long_description=long_description,
     long_description_content_type="text/markdown",
-    license="ISC",
+    license="Apache 2.0",
     keywords=["graph", "motif"],
     url="https://github.com/aplbrain/dotmotif/tarball/" + VERSION,
     packages=find_packages(exclude=["tests", "*.tests", "*.tests.*", "tests.*"]),
@@ -40,7 +40,7 @@
         "dask[dataframe]",
         "tamarind>=0.1.5",
         "neuprint-python",
-        "grandiso",
+        "grandiso>=1.2.0",
     ],
     include_package_data=True,
 )