Try ruff (#346)

Fix most ruff errors: fix line length problems, prefer function definition over assigning to lambdas, unused variables and related issues, and add some new tests.

setup.py

@@ -12,7 +12,15 @@
 
 version = __version__
 
-authors = "Nicholas Landry, Leo Torres, Maxime Lucas, Iacopo Iacopini, Giovanni Petri, Alice Patania, and Alice Schwarze"
+authors = (
+    "Nicholas Landry, "
+    "Leo Torres, "
+    "Maxime Lucas, "
+    "Iacopo Iacopini, "
+    "Giovanni Petri, "
+    "Alice Patania, "
+    "and Alice Schwarze"
+)
 
 author_email = "[email protected]"
 

tests/algorithms/test_clustering.py

@@ -1,4 +1,3 @@
-import numpy as np
 import pytest
 
 import xgi

tests/algorithms/test_connected.py

@@ -7,8 +7,8 @@
 def test_is_connected(edgelist1, edgelist3):
     H1 = xgi.Hypergraph(edgelist1)
     H2 = xgi.Hypergraph(edgelist3)
-    assert xgi.is_connected(H1) == False
-    assert xgi.is_connected(H2) == True
+    assert xgi.is_connected(H1) is False
+    assert xgi.is_connected(H2) is True
 
 
 def test_connected_components(edgelist1, edgelist2, edgelist4):

tests/classes/test_function.py

@@ -21,7 +21,7 @@ def test_max_edge_order(edgelist1, edgelist4, edgelist5):
     H3 = xgi.Hypergraph(edgelist4)
     H4 = xgi.Hypergraph(edgelist5)
 
-    assert xgi.max_edge_order(H0) == None
+    assert xgi.max_edge_order(H0) is None
     assert xgi.max_edge_order(H1) == 0
     assert xgi.max_edge_order(H2) == 2
     assert xgi.max_edge_order(H3) == 3
@@ -31,11 +31,11 @@ def test_max_edge_order(edgelist1, edgelist4, edgelist5):
 def test_is_possible_order(edgelist1):
     H1 = xgi.Hypergraph(edgelist1)
 
-    assert xgi.is_possible_order(H1, -1) == False
-    assert xgi.is_possible_order(H1, 0) == True
-    assert xgi.is_possible_order(H1, 1) == True
-    assert xgi.is_possible_order(H1, 2) == True
-    assert xgi.is_possible_order(H1, 3) == False
+    assert xgi.is_possible_order(H1, -1) is False
+    assert xgi.is_possible_order(H1, 0) is True
+    assert xgi.is_possible_order(H1, 1) is True
+    assert xgi.is_possible_order(H1, 2) is True
+    assert xgi.is_possible_order(H1, 3) is False
 
 
 def test_is_uniform(edgelist1, edgelist6, edgelist7):
@@ -44,10 +44,10 @@ def test_is_uniform(edgelist1, edgelist6, edgelist7):
     H2 = xgi.Hypergraph(edgelist7)
     H3 = xgi.empty_hypergraph()
 
-    assert xgi.is_uniform(H0) == False
+    assert xgi.is_uniform(H0) is False
     assert xgi.is_uniform(H1) == 2
     assert xgi.is_uniform(H2) == 2
-    assert xgi.is_uniform(H3) == False
+    assert xgi.is_uniform(H3) is False
 
 
 def test_edge_neighborhood(edgelist3):
@@ -157,7 +157,7 @@ def test_create_empty_copy(edgelist1):
     assert E2["name"] == "test"
     assert E2["timestamp"] == "Nov. 20"
     with pytest.raises(XGIError):
-        author = E2["author"]
+        _ = E2["author"]
     for n in E2.nodes:
         assert E2.nodes[n]["name"] == attr_dict[n]["name"]
 
@@ -508,7 +508,9 @@ def test_density(edgelist1):
     with pytest.raises(ValueError):
         xgi.density(H, max_order=8)  # max_order cannot be larger than number of nodes
 
-    dens_ignore_sing = lambda m: xgi.density(H, max_order=m, ignore_singletons=True)
+    def dens_ignore_sing(m):
+        return xgi.density(H, max_order=m, ignore_singletons=True)
+
     assert abs(dens_ignore_sing(0) - 0.0) < tol
     assert abs(dens_ignore_sing(1) - 0.03571428571428571) < tol
     assert abs(dens_ignore_sing(2) - 0.03571428571428571) < tol
@@ -678,9 +680,9 @@ def test_incidence_density(edgelist1):
             H, max_order=8
         )  # max_order cannot be larger than number of nodes
 
-    dens_ignore_sing = lambda m: xgi.incidence_density(
-        H, max_order=m, ignore_singletons=True
-    )
+    def dens_ignore_sing(m):
+        return xgi.incidence_density(H, max_order=m, ignore_singletons=True)
+
     assert abs(dens_ignore_sing(0) - 0.0) < tol
     assert abs(dens_ignore_sing(1) - 0.25) < tol
     assert abs(dens_ignore_sing(2) - 1 / 3) < tol

tests/classes/test_simplicialcomplex.py

@@ -12,9 +12,9 @@ def test_constructor(edgelist5, dict5, incidence5, dataframe5):
     S_sc = xgi.SimplicialComplex(S_list)
 
     with pytest.raises(XGIError):
-        S_dict = xgi.SimplicialComplex(dict5)
+        _ = xgi.SimplicialComplex(dict5)
     with pytest.raises(XGIError):
-        S_mat = xgi.SimplicialComplex(incidence5)
+        _ = xgi.SimplicialComplex(incidence5)
 
     assert set(S_list.nodes) == set(S_df.nodes) == set(S_sc.nodes)
     assert set(S_list.edges) == set(S_df.edges) == set(S_sc.edges)

tests/drawing/test_layout.py

@@ -25,23 +25,30 @@ def test_random_layout():
     assert len(pos) == S.num_nodes
 
 
-def test_pairwise_spring_layout():
+def test_pairwise_spring_layout_hypergraph():
     H = xgi.random_hypergraph(10, [0.2], seed=1)
 
-    # seed
     pos1 = xgi.pairwise_spring_layout(H, seed=1)
     pos2 = xgi.pairwise_spring_layout(H, seed=2)
     pos3 = xgi.pairwise_spring_layout(H, seed=2)
-    assert pos1.keys() == pos2.keys()
-    assert pos2.keys() == pos3.keys()
+    assert pos1.keys() == pos2.keys() == pos3.keys()
     assert not np.allclose(list(pos1.values()), list(pos2.values()))
     assert np.allclose(list(pos2.values()), list(pos3.values()))
-
     assert len(pos1) == H.num_nodes
 
     # simplicial complex
+
+
+def test_pairwise_spring_layout_simplicial_complex():
     S = xgi.random_flag_complex_d2(10, 0.2, seed=1)
-    pos = xgi.pairwise_spring_layout(S, seed=1)
+
+    pos1 = xgi.pairwise_spring_layout(S, seed=1)
+    pos2 = xgi.pairwise_spring_layout(S, seed=2)
+    pos3 = xgi.pairwise_spring_layout(S, seed=2)
+    assert pos1.keys() == pos2.keys() == pos3.keys()
+    assert not np.allclose(list(pos1.values()), list(pos2.values()))
+    assert np.allclose(list(pos2.values()), list(pos3.values()))
+    assert len(pos1) == S.num_nodes
 
 
 def test_barycenter_spring_layout(hypergraph1):

tests/generators/test_classic.py

@@ -10,7 +10,7 @@ def test_empty_hypergraph():
     assert (H.num_nodes, H.num_edges) == (0, 0)
 
 
-def test_empty_hypergraph():
+def test_empty_simplicial_complex():
     SC = xgi.empty_simplicial_complex()
     assert (SC.num_nodes, SC.num_edges) == (0, 0)
 

tests/generators/test_nonuniform.py

@@ -20,9 +20,7 @@ def test_chung_lu_hypergraph():
     assert H2._edge == H3._edge
 
     with pytest.warns(Warning):
-        k1 = {1: 1, 2: 2}
-        k2 = {1: 2, 1: 2}
-        H = xgi.chung_lu_hypergraph(k1, k2)
+        _ = xgi.chung_lu_hypergraph({1: 1, 2: 2}, {1: 2, 2: 2})
 
 
 def test_dcsbm_hypergraph():

tests/stats/test_nodestats.py

@@ -75,15 +75,9 @@ def test_call_filterby(edgelist1, edgelist8):
     assert filtered.asdict() == {1: 3.5}
 
 
-def test_filterby_attr(hyperwithattrs, attr1, attr2, attr3, attr4, attr5):
+def test_filterby_attr(hyperwithattrs):
     H = hyperwithattrs
-    attrs = {
-        1: attr1,
-        2: attr2,
-        3: attr3,
-        4: attr4,
-        5: attr5,
-    }
+
     filtered = H.nodes.filterby_attr("age", 20, "eq")
     assert set(filtered) == {4}
 

xgi/algorithms/centrality.py

@@ -112,8 +112,8 @@ def h_eigenvector_centrality(H, max_iter=100, tol=1e-6):
 
     new_H = convert_labels_to_integers(H, "old-label")
 
-    f = lambda v, m: np.power(v, 1.0 / m)
-    g = lambda v, x: np.prod(v[list(x)])
+    f = lambda v, m: np.power(v, 1.0 / m)  # noqa: E731
+    g = lambda v, x: np.prod(v[list(x)])  # noqa: E731
 
     x = np.random.uniform(size=(new_H.num_nodes))
     x = x / norm(x, 1)
@@ -263,10 +263,11 @@ def line_vector_centrality(H):
 
     References
     ----------
-    Vector centrality in hypergraphs,
-    K. Kovalenko, M. Romance, E. Vasilyeva, D. Aleja, R. Criado, D. Musatov,
-    A.M. Raigorodskii, J. Flores, I. Samoylenko, K. Alfaro-Bittner, M. Perc, S. Boccaletti,
+    "Vector centrality in hypergraphs", K. Kovalenko, M. Romance, E. Vasilyeva,
+    D. Aleja, R. Criado, D. Musatov, A.M. Raigorodskii, J. Flores, I. Samoylenko,
+    K. Alfaro-Bittner, M. Perc, S. Boccaletti,
     https://doi.org/10.1016/j.chaos.2022.112397
+
     """
     from ..algorithms import is_connected
 

xgi/algorithms/clustering.py

@@ -103,8 +103,8 @@ def local_clustering_coefficient(H):
 
     References
     ----------
-    "Properties of metabolic graphs: biological organization or representation artifacts?"
-    by Wanding Zhou and Luay Nakhleh.
+    "Properties of metabolic graphs: biological organization or representation
+    artifacts?"  by Wanding Zhou and Luay Nakhleh.
     https://doi.org/10.1186/1471-2105-12-132
 
     "Hypergraphs for predicting essential genes using multiprotein complex data"
@@ -118,6 +118,7 @@ def local_clustering_coefficient(H):
     >>> cc = xgi.local_clustering_coefficient(H)
     >>> cc
     {0: 1.0, 1: 1.0, 2: 1.0}
+
     """
     result = {}
 
@@ -147,7 +148,7 @@ def local_clustering_coefficient(H):
                         # the neighbours of D1 and D2, respectively.
                         neighD1 = {i for d in D1 for i in H.nodes.neighbors(d)}
                         neighD2 = {i for d in D2 for i in H.nodes.neighbors(d)}
-                        # compute the extra overlap [len() is used for cardinality of edges]
+                        # compute extra overlap [len() is used for cardinality of edges]
                         eo = (
                             len(neighD1.intersection(D2))
                             + len(neighD2.intersection(D1))

xgi/classes/function.py

@@ -146,9 +146,9 @@ def is_uniform(H):
 def edge_neighborhood(H, n, include_self=False):
     """The edge neighborhood of the specified node.
 
-    The edge neighborhood of a node `n` in a hypergraph `H` is an edgelist of all the edges
-    containing `n` and its edges are all the edges in `H` that contain
-    `n`.  Usually, the edge neighborhood does not include `n` itself.  This can be controlled
+    The edge neighborhood of a node `n` in a hypergraph `H` is an edgelist of all the
+    edges containing `n` and its edges are all the edges in `H` that contain `n`.
+    Usually, the edge neighborhood does not include `n` itself.  This can be controlled
     with `include_self`.
 
     Parameters
@@ -573,7 +573,8 @@ def set_edge_attributes(H, values, name=None):
                     warn(f"Edge {e} does not exist!")
         except AttributeError:
             raise XGIError(
-                "name property has not been set and a dict-of-dicts has not been provided."
+                "name property has not been set and a "
+                "dict-of-dicts has not been provided."
             )
 
 
@@ -882,7 +883,8 @@ def subfaces(edges, order=None):
     max_order = len(max(edges, key=len)) - 1
     if order and order > max_order:
         raise XGIError(
-            f"order must be less or equal to the maximum order among the edges: {max_order}."
+            "order must be less or equal to the maximum "
+            f"order among the edges: {max_order}."
         )
 
     faces = []

xgi/classes/hypergraph.py

@@ -149,9 +149,15 @@ def __str__(self):
 
         """
         try:
-            return f"{type(self).__name__} named {self['name']} with {self.num_nodes} nodes and {self.num_edges} hyperedges"
+            return (
+                f"{type(self).__name__} named {self['name']} "
+                f"with {self.num_nodes} nodes and {self.num_edges} hyperedges"
+            )
         except XGIError:
-            return f"Unnamed {type(self).__name__} with {self.num_nodes} nodes and {self.num_edges} hyperedges"
+            return (
+                f"Unnamed {type(self).__name__} with "
+                f"{self.num_nodes} nodes and {self.num_edges} hyperedges"
+            )
 
     def __iter__(self):
         """Iterate over the nodes.
@@ -217,7 +223,8 @@ def __getattr__(self, attr):
         if stat is None:
             word = None
             raise AttributeError(
-                f"{attr} is not a method of Hypergraph or a recognized NodeStat or EdgeStat"
+                f"{attr} is not a method of Hypergraph or a "
+                "recognized NodeStat or EdgeStat"
             )
 
         def func(node=None, *args, **kwargs):
@@ -528,29 +535,29 @@ def add_edge(self, members, id=None, **attr):
             update_uid_counter(self, id)
 
     def add_edges_from(self, ebunch_to_add, **attr):
-        """Add multiple edges with optional attributes.
+        r"""Add multiple edges with optional attributes.
 
         Parameters
         ----------
         ebunch_to_add : Iterable
 
             An iterable of edges.  This may be an iterable of iterables (Format 1),
-            where each element contains the members of the edge specified as valid node IDs.
-            Alternatively, each element could also be a tuple in any of the following
-            formats:
+            where each element contains the members of the edge specified as valid node
+            IDs.  Alternatively, each element could also be a tuple in any of the
+            following formats:
 
             * Format 2: 2-tuple (members, edge_id), or
             * Format 3: 2-tuple (members, attr), or
             * Format 4: 3-tuple (members, edge_id, attr),
 
             where `members` is an iterable of node IDs, `edge_id` is a hashable to use
-            as edge ID, and `attr` is a dict of attributes. Finally, `ebunch_to_add`
-            may be a dict of the form `{edge_id: edge_members}` (Format 5).
+            as edge ID, and `attr` is a dict of attributes. Finally, `ebunch_to_add` may
+            be a dict of the form `{edge_id: edge_members}` (Format 5).
 
-            Formats 2 and 3 are unambiguous because `attr` dicts are not hashable, while `id`s must be.
-            In Formats 2-4, each element of `ebunch_to_add` must have the same length,
-            i.e. you cannot mix different formats.  The iterables containing edge
-            members cannot be strings.
+            Formats 2 and 3 are unambiguous because `attr` dicts are not hashable, while
+            `id`s must be.  In Formats 2-4, each element of `ebunch_to_add` must have
+            the same length, i.e. you cannot mix different formats.  The iterables
+            containing edge members cannot be strings.
 
         attr : \*\*kwargs, optional
             Additional attributes to be assigned to all edges. Attribues specified via
@@ -1172,7 +1179,8 @@ def merge_duplicate_edges(
 
         if merge_rule == "union":
             warn(
-                "You will not be able to color/draw by merged attributes with xgi.draw()!"
+                "You will not be able to color/draw by "
+                "merged attributes with xgi.draw()!"
             )
 
     def copy(self):
@@ -1235,15 +1243,18 @@ def cleanup(
         Parameters
         ----------
         isolates : bool, optional
-            Whether isolated nodes are allowed, by default False
+            Whether isolated nodes are allowed, by default False.
         singletons : bool, optional
-            Whether singleton edges are allowed, by default False
+            Whether singleton edges are allowed, by default False.
         multiedges : bool, optional
-            Whether multiedges are allowed, by default False
+            Whether multiedges are allowed, by default False.
         relabel : bool, optional
-            Whether to convert all node and edge labels to sequential integers, by default True
+            Whether to convert all node and edge labels to sequential integers, by
+            default True.
         in_place : bool, optional
-            Whether to modify the current hypergraph or output a new one, by default True
+            Whether to modify the current hypergraph or output a new one, by default
+            True.
+
         """
         if in_place:
             if not multiedges: