Add tests for no-attr-in-host (#31)

* Add tests for no-attr-in-host

* Add broken-motif tests

* Fix counting bug (thanks test-coverage obsession!)

* Update changelog

* Update to version 2.1.1 in notation

* Add Python 3.9, 3.10 to CI

* Fix Python 3.10 notation in CI

Author: j6k4m8

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9, '3.10']
 
     steps:
     - uses: actions/checkout@v2

CHANGELOG.md

@@ -1,5 +1,12 @@
 # CHANGELOG
 
+## [v2.1.1 (December 21 2021)](https://pypi.org/project/grandiso/2.1.0/)
+
+-   Fixes
+    -   Fixed a minor bug in which counts were one-off when using `count_only=False` and `limit=int`.
+    -   Achieved 100% test coverage, woo!
+    -   Added support for Python 3.6 (thanks @aleclearmind!), and added 3.9 and 3.10 to CI.
+
 ## [v2.1.0 (December 16 2021)](https://pypi.org/project/grandiso/2.1.0/)
 
 -   Features

grandiso/__init__.py

@@ -25,7 +25,7 @@
 import networkx as nx
 from .queues import SimpleQueue
 
-__version__ = "2.1.0"
+__version__ = "2.1.1"
 
 
 @lru_cache()
@@ -157,8 +157,9 @@ def get_next_backbone_candidates(
     # interesting node to start with:
     if next_node is None and len(backbone) == 0:
         # This is the starting-case, where we have NO backbone nodes set yet.
-        next_node = max(interestingness.keys(),
-                        key=lambda node: interestingness.get(node, 0.0))
+        next_node = max(
+            interestingness.keys(), key=lambda node: interestingness.get(node, 0.0)
+        )
         # Let's return ALL possible node choices for this next_node. To do this
         # without being an insane person, let's filter on max degree in host:
         return [
@@ -201,8 +202,10 @@ def get_next_backbone_candidates(
                 _nodes_with_greatest_backbone_count.append(motif_node_id)
         # Now we have _node_with_greatest_backbone_count as the best candidate
         # for `next_node`.
-        next_node = max(_nodes_with_greatest_backbone_count,
-                        key=lambda node: interestingness.get(node, 0.0))
+        next_node = max(
+            _nodes_with_greatest_backbone_count,
+            key=lambda node: interestingness.get(node, 0.0),
+        )
 
     # Now we have a node `next_node` which we know is connected to the current
     # backbone. Get all edges between `next_node` and nodes in the backbone,
@@ -480,7 +483,10 @@ def find_motifs(
             if count_only:
                 return results_count
             else:
-                if limit and results_count >= limit:
+                # Subtract 1 from results_count because we have not yet
+                # added the new result to the results list, but we HAVE
+                # already added +1 to the count.
+                if limit and (results_count - 1) >= limit:
                     return results
         if not count_only:
             results.append(result)

grandiso/test_grandiso.py

@@ -437,7 +437,7 @@ def test_limit_one(self):
     def test_limit_eq_answer(self):
         host = nx.complete_graph(8)
         motif = nx.complete_graph(3)
-        assert find_motifs(motif, host, count_only=True, limit=336) == 336
+        assert len(find_motifs(motif, host, limit=300)) == 300
 
     def test_limit_gt_answer(self):
         host = nx.complete_graph(8)
@@ -507,3 +507,50 @@ def test_node_and_edge_attributes(self):
         motif.add_node("c", flavor="lint")
 
         assert find_motifs(motif, host) == []
+
+    def test_attr_not_in_node(self):
+        host = nx.DiGraph()
+        nx.add_path(host, ["A", "B", "C", "A"])
+        host.add_edge("A", "B")
+        host.add_edge("B", "C")
+        host.add_edge("C", "A")
+        host.add_node("A")
+        host.add_node("B")
+        host.add_node("C")
+
+        motif = nx.DiGraph()
+        motif.add_edge("a", "b")
+        motif.add_node("a", flavor="coffee")
+
+        assert find_motifs(motif, host) == []
+
+    def test_attr_not_in_edge(self):
+        host = nx.DiGraph()
+        nx.add_path(host, ["A", "B", "C", "A"])
+        host.add_edge("A", "B")
+        host.add_edge("B", "C")
+        host.add_edge("C", "A")
+        host.add_node("A")
+        host.add_node("B")
+        host.add_node("C")
+
+        motif = nx.DiGraph()
+        motif.add_edge("a", "b", type="delicious")
+
+        assert find_motifs(motif, host) == []
+
+
+class TestBrokenMotifFailures:
+    def test_disconnected_motif(self):
+        host = nx.complete_graph(8, nx.DiGraph())
+        motif = nx.DiGraph()
+        motif.add_node("a")
+        motif.add_node("b")
+        with pytest.raises(ValueError):
+            find_motifs(motif, host)
+
+    def test_empty_motif(self):
+        host = nx.complete_graph(8, nx.DiGraph())
+        motif = nx.DiGraph()
+        with pytest.raises(ValueError):
+            find_motifs(motif, host)

requirements.txt

@@ -1 +1 @@
-networkx==2.5.1
+networkx>=2.5.1

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="grandiso",
-    version="2.1.0",
+    version="2.1.1",
     author="Jordan Matelsky",
     author_email="opensource@matelsky.com",
     description="Performant subgraph isomorphism",