fix flake8

discovered a few real errors in the tests doing this!

Also setup isort to play nice with black

ipycytoscape/__init__.py

@@ -7,7 +7,14 @@
 # The full license is in the file LICENSE, distributed with this software.
 
 from ._version import __version__, version_info
-from .cytoscape import *
+from .cytoscape import (
+    MONITORED_USER_INTERACTIONS,
+    MONITORED_USER_TYPES,
+    CytoscapeWidget,
+    Edge,
+    Graph,
+    Node,
+)
 from .nbextension import _jupyter_nbextension_paths
 
 npm_pkg_name = "jupyter-cytoscape"

ipycytoscape/cytoscape.py

@@ -75,17 +75,17 @@
     "vmousedown",  # alias for 'tapstart'
     "tapdrag",  # normalised move event (either touchmove or mousemove)
     "vmousemove",  # alias for 'tapdrag'
-    "tapdragover",  # normalised over element event (either touchmove or mousemove/mouseover)
-    "tapdragout",  # normalised off of element event (either touchmove or mousemove/mouseout)
+    "tapdragover",  # normalised over element event (either touchmove or mousemove/mouseover) # noqa
+    "tapdragout",  # normalised off of element event (either touchmove or mousemove/mouseout) # noqa
     "tapend",  # normalised tap end event (either mouseup or touchend)
     "vmouseup",  # alias for 'tapend'
-    "tap",  # normalised tap event (either click, or touchstart followed by touchend without touchmove)
+    "tap",  # normalised tap event (either click, or touchstart followed by touchend without touchmove) # noqa
     "vclick",  # alias for 'tap'
     "taphold",  # normalised tap hold event
     "cxttapstart",  # normalised right-click mousedown or two-finger tapstart
     "cxttapend",  # normalised right-click mouseup or two-finger tapend
     "cxttap",  # normalised right-click or two-finger tap
-    "cxtdrag",  # normalised mousemove or two-finger drag after cxttapstart but before cxttapend
+    "cxtdrag",  # normalised mousemove or two-finger drag after cxttapstart but before cxttapend # noqa
     "cxtdragover",  # when going over a node via cxtdrag
     "cxtdragout",  # when going off a node via cxtdrag
     "boxstart",  # when starting box selection
@@ -335,8 +335,9 @@ def add_edge(self, edge, directed=False, multiple_edges=False):
 
     def add_edges(self, edges, directed=False, multiple_edges=False):
         """
-        Appends edges from the end of the list. If either the source or target Node of an
-        Edge is not already in the graph it will be created and added to he Nodes list.
+        Appends edges from the end of the list. If either the source or target Node
+        of an Edge is not already in the graph it will be created and added to
+        the Nodes list.
 
         Parameters
         ----------
@@ -354,13 +355,16 @@ def add_edges(self, edges, directed=False, multiple_edges=False):
             if multiple_edges and "multiple_edges" not in edge.classes:
                 edge.classes += " multiple_edges "
 
-            # If multiple edges are allowed, it's okay to add more edges between the source and target
+            # If multiple edges are allowed, it's okay to add more
+            # edges between the source and target
             if multiple_edges:
                 new_edge = True
-            # Check to see if the edge source -> target exists in the graph (don't add it again)
+            # Check to see if the edge source -> target exists in the graph
+            # If it does then don't add it again
             elif source in self._adj and target in self._adj[source]:
                 new_edge = False
-            # Check to see if the edge target-> source exists in an undirected graph (don't add it again)
+            # Check to see if the edge target-> source exists in an
+            # undirected graph (don't add it again)
             elif not directed and target in self._adj and source in self._adj[target]:
                 new_edge = False
             # If the edge doesn't exist already
@@ -419,7 +423,8 @@ def remove_edge(self, edge):
                     self._adj[target][source] -= 1
         except ValueError:
             raise ValueError(
-                f"Edge from {edge.data['source']} to {edge.data['target']} is not present in the graph."
+                f"Edge from {edge.data['source']} to {edge.data['target']} "
+                "is not present in the graph."
             )
 
     def remove_edge_by_id(self, source_id, target_id):
@@ -717,7 +722,7 @@ def create_tooltip(node_attributes, node_labels):
             node_attributes = convert_types_to_string(node_attributes)
 
             # create tooltip text string
-            if not "tooltip" in node_attributes:
+            if "tooltip" not in node_attributes:
                 tooltip_text = create_tooltip(node_attributes, node.labels)
                 node_attributes["tooltip"] = tooltip_text
 
@@ -750,7 +755,7 @@ def create_tooltip(node_attributes, node_labels):
             rel_attributes = convert_types_to_string(rel_attributes)
 
             # assign name of the relationship
-            if not "name" in rel_attributes:
+            if "name" not in rel_attributes:
                 rel_attributes["name"] = rel.__class__.__name__
 
             # assign unique node ids

ipycytoscape/tests/_util.py

@@ -0,0 +1,19 @@
+from typing import List
+
+from ipycytoscape.cytoscape import Edge, Node
+
+
+def compare_nodes(expected_nodes: List[Node], actual_nodes: List[Node]):
+    # if one list is empty
+    assert bool(expected_nodes) == bool(actual_nodes)
+    for expected, actual in zip(expected_nodes, actual_nodes):
+        assert expected.data == actual.data
+        assert expected.classes == actual.classes
+        assert expected.position == actual.position
+
+
+def compare_edges(expected_edges: List[Edge], actual_edges: List[Edge]):
+    assert bool(expected_edges) == bool(actual_edges)
+    for expected, actual in zip(expected_edges, actual_edges):
+        assert expected.data == actual.data
+        assert expected.classes == actual.classes

ipycytoscape/tests/test_graph_creation.py

@@ -11,18 +11,7 @@
 
 from ipycytoscape.cytoscape import Edge, Graph, Node
 
-
-def compare_nodes(expected_nodes, actual_nodes):
-    for expected, actual in zip(expected_nodes, actual_nodes):
-        assert expected.data == actual.data
-        assert expected.classes == actual.classes
-        assert expected.position == actual.position
-
-
-def compare_edges(expected_edges, actual_edges):
-    for expected, actual in zip(expected_edges, actual_edges):
-        assert expected.data == actual.data
-        assert expected.classes == actual.classes
+from ._util import compare_edges, compare_nodes
 
 
 class TestNetworkx:

ipycytoscape/tests/test_graph_deletion.py

@@ -11,6 +11,8 @@
 
 from ipycytoscape.cytoscape import Graph, Node
 
+from ._util import compare_nodes
+
 
 class TestNetworkx:
     def test_lonely_nodes(self):
@@ -34,6 +36,7 @@ def test_lonely_nodes(self):
             Node(data={"id": "unconnected_node"}, position={}),
         ]
 
+        compare_nodes(expected_nodes, graph.nodes)
         # remove individual node using node as input
         graph.remove_node(graph.nodes[0])
 
@@ -44,6 +47,7 @@ def test_lonely_nodes(self):
             Node(data={"id": "4"}, position={}),
             Node(data={"id": "unconnected_node"}, position={}),
         ]
+        compare_nodes(expected_nodes, graph.nodes)
 
         # remove individual node using index node as input
         graph.remove_node_by_id("3")
@@ -54,6 +58,8 @@ def test_lonely_nodes(self):
             Node(data={"id": "4"}, position={}),
             Node(data={"id": "unconnected_node"}, position={}),
         ]
+        compare_nodes(expected_nodes, graph.nodes)
 
         # remove all nodes of the graph
         graph.clear()
+        compare_nodes([], graph.nodes)

ipycytoscape/tests/test_graph_methods.py

@@ -11,21 +11,7 @@
 
 from ipycytoscape.cytoscape import Edge, Graph, Node
 
-
-def compare_nodes(expected_nodes, actual_nodes):
-    # if one list is empty
-    assert bool(expected_nodes) == bool(actual_nodes)
-    for expected, actual in zip(expected_nodes, actual_nodes):
-        assert expected.data == actual.data
-        assert expected.classes == actual.classes
-        assert expected.position == actual.position
-
-
-def compare_edges(expected_edges, actual_edges):
-    assert bool(expected_edges) == bool(actual_edges)
-    for expected, actual in zip(expected_edges, actual_edges):
-        assert expected.data == actual.data
-        assert expected.classes == actual.classes
+from ._util import compare_edges, compare_nodes
 
 
 @pytest.fixture(name="edges", scope="function")
@@ -264,7 +250,8 @@ def test_add_node(self):
 
     def test_add_edges(self, edges):
         """
-        Test to ensure that edges with the corresponding nodes will be added to the graph
+        Test to ensure that edges with the corresponding nodes will be
+        added to the graph.
         """
 
         expected_nodes = [
@@ -336,7 +323,8 @@ def test_add_edges_multiple_edges(self, edges):
 
     def test_add_edges_2(self):
         """
-        Test to ensure that an edge with the corresponding nodes will be added to the graph
+        Test to ensure that an edge with the corresponding nodes will be
+        added to the graph.
         """
         edge = Edge(data={"source": "0", "target": "1"})
         edge_inv = Edge(data={"source": "1", "target": "0"})

pyproject.toml

@@ -1,3 +1,9 @@
 [build-system]
 requires = ["jupyter_packaging~=0.7.0", "jupyterlab>=3.0.0rc4,==3.*", "setuptools>=40.8.0", "wheel"]
 build-backend = "setuptools.build_meta"
+
+
+[tool.isort]
+profile = "black"
+src_paths = "ipycytoscape"
+multi_line_output = 3

setup.cfg

@@ -5,12 +5,12 @@ universal=1
 license_file = LICENSE
 
 [flake8]
-exclude = docs, _version.py, .eggs, example
+exclude = docs/*, _version.py, .eggs, example/*
 max-line-length = 88
 docstring-convention = "numpy"
 extend-ignore =
     # See https://github.com/PyCQA/pycodestyle/issues/373
-    E203,
+    E203, E302, E303
 per-file-ignores =
     ipycytoscape/__init__.py:F401
     ipycytoscape/nbextension/__init__.py:F401