gh-36967: fixing some details in graphs/ (pep E275; ruff UP024, etc)
    
just fixing a few very minor details in the graphs folder

### 📝 Checklist

- [x] The title is concise, informative, and self-explanatory.
- [x] The description explains in detail what this PR is about.
    
URL: #36967
Reported by: Frédéric Chapoton
Reviewer(s): David Coudert

Author: Release Manager

src/sage/combinat/cluster_algebra_quiver/quiver.py

@@ -2175,7 +2175,7 @@ def d_vector_fan(self):
             ...
             ValueError: only makes sense for quivers of finite type
         """
-        if not(self.is_finite()):
+        if not self.is_finite():
             raise ValueError('only makes sense for quivers of finite type')
 
         from .cluster_seed import ClusterSeed

src/sage/graphs/bipartite_graph.py

@@ -979,7 +979,7 @@ def _flip_vertices(self, vertices):
                 self.right.remove(vertex)
                 self.left.add(vertex)
             else:
-                raise RuntimeError("vertex ({0}) is neither in left nor in right".format(vertex))
+                raise RuntimeError(f"vertex ({vertex}) is neither in left nor in right")
 
     def add_edge(self, u, v=None, label=None):
         r"""
@@ -1749,7 +1749,7 @@ def load_afile(self, fname):
         # open the file
         try:
             fi = open(fname, "r")
-        except IOError:
+        except OSError:
             print("unable to open file <<" + fname + ">>")
             return None
 
@@ -1849,7 +1849,7 @@ def save_afile(self, fname):
         # open the file
         try:
             fi = open(fname, "w")
-        except IOError:
+        except OSError:
             print("Unable to open file <<" + fname + ">>.")
             return
 

src/sage/graphs/digraph.py

@@ -3000,7 +3000,7 @@ def cycle_iter(v):
             try:
                 cycle = next(vi)
                 cycles.append((len(cycle), cycle))
-            except(StopIteration):
+            except StopIteration:
                 pass
         # Since we always extract a shortest path, using a heap
         # can speed up the algorithm
@@ -3015,7 +3015,7 @@ def cycle_iter(v):
             try:
                 cycle = next(vertex_iterators[shortest_cycle[0]])
                 heappush(cycles, (len(cycle), cycle))
-            except(StopIteration):
+            except StopIteration:
                 pass
 
     def all_simple_cycles(self, starting_vertices=None, rooted=False,

src/sage/graphs/generators/smallgraphs.py

@@ -4803,7 +4803,7 @@ def JankoKharaghaniGraph(v):
     # The notations of [JK02] are rather tricky, and so this code attempts to
     # stick as much as possible to the paper's variable names.
 
-    assert(v in [1800, 936])
+    assert v in [1800, 936]
 
     J = matrix.ones
     I = matrix.identity
@@ -4842,7 +4842,7 @@ def JankoKharaghaniGraph(v):
     U = matrix.circulant([int(i == 1) for i in range(2 * n)])
     N = matrix.diagonal([1 if i else -1 for i in range(2 * n)])
     Omega = (U * N)**6
-    assert(Omega**12 == I(36))
+    assert Omega**12 == I(36)
 
     # The value w_{ij} is understood in the paper as matrix generated by Omega
     # acting on the left of a matrix L, which we now define.

src/sage/graphs/generic_graph.py

@@ -6276,7 +6276,7 @@ def genus(self, set_embedding=True, on_embedding=None, minimal=True, maximal=Fal
                 raise ValueError("on_embedding is not a valid option when circular is defined")
             boundary = circular
             if hasattr(G, '_embedding'):
-                del(G._embedding)
+                del G._embedding
 
             extra = G.add_vertex()
             G.add_edges((vertex, extra) for vertex in boundary)

src/sage/graphs/graph_decompositions/modular_decomposition.py

@@ -1245,7 +1245,7 @@ def test_gamma_modules(trials, vertices, prob, verbose=False):
             m_list = list(module)
             for v in g:
                 if v not in module:
-                    assert(either_connected_or_not_connected(v, m_list, g))
+                    assert either_connected_or_not_connected(v, m_list, g)
         if verbose:
             print("Passes!")
 
@@ -1275,10 +1275,10 @@ def permute_decomposition(trials, algorithm, vertices, prob, verbose=False):
             print(random_perm)
         t1 = algorithm(g1)
         t2 = algorithm(g2)
-        assert(test_modular_decomposition(t1, g1))
-        assert(test_modular_decomposition(t2, g2))
+        assert test_modular_decomposition(t1, g1)
+        assert test_modular_decomposition(t2, g2)
         t1p = relabel_tree(t1, random_perm)
-        assert(equivalent_trees(t1p, t2))
+        assert equivalent_trees(t1p, t2)
         if verbose:
             print("Passes!")
 
@@ -1422,6 +1422,6 @@ def recreate_decomposition(trials, algorithm, max_depth, max_fan_out,
         reconstruction = algorithm(graph)
         if verbose:
             print_md_tree(reconstruction)
-        assert(equivalent_trees(rand_tree, reconstruction))
+        assert equivalent_trees(rand_tree, reconstruction)
         if verbose:
             print("Passes!")

src/sage/graphs/graph_generators.py

@@ -1529,10 +1529,10 @@ def _read_planar_code(self, code_input):
                     has_loops = True
             G = graph.Graph(edges_g, loops=has_loops)
 
-            if not(G.has_multiple_edges() or has_loops):
+            if not (G.has_multiple_edges() or has_loops):
                 embed_g = {i + 1: di for i, di in enumerate(g)}
                 G.set_embedding(embed_g)
-            yield(G)
+            yield G
 
     def fullerenes(self, order, ipr=False):
         r"""
@@ -1710,7 +1710,7 @@ def fusenes(self, hexagon_count, benzenoids=False):
             g = {1: [6, 2], 2: [1, 3], 3: [2, 4], 4: [3, 5], 5: [4, 6], 6: [5, 1]}
             G = graph.Graph(g)
             G.set_embedding(g)
-            yield(G)
+            yield G
             return
 
         from sage.features.graph_generators import Benzene
@@ -1728,7 +1728,7 @@ def fusenes(self, hexagon_count, benzenoids=False):
         sp.stdout.reconfigure(newline='')
 
         for G in graphs._read_planar_code(sp.stdout):
-            yield(G)
+            yield G
 
     def plantri_gen(self, options=""):
         r"""
@@ -2144,7 +2144,7 @@ def planar_graphs(self, order, minimum_degree=None,
             if minimum_degree == 0:
                 G = graph.Graph(1)
                 G.set_embedding({0: []})
-                yield(G)
+                yield G
             return
 
         cmd = '-p{}m{}c{}{}{} {} {} {}'

src/sage/graphs/graph_latex.py

@@ -589,10 +589,9 @@ def __eq__(self, other):
             sage: opts1 == opts2
             False
         """
-        if not(isinstance(other, GraphLatex)):
+        if not isinstance(other, GraphLatex):
             return False
-        else:
-            return self._options == other._options
+        return self._options == other._options
 
     def _repr_(self):
         r"""
@@ -1128,9 +1127,9 @@ def set_option(self, option_name, option_value=None):
                 raise ValueError('%s option must be one of: tkz_graph, dot2tex not %s' % (name, value))
             elif name == 'units' and value not in unit_names:
                 raise ValueError('%s option must be one of: in, mm, cm, pt, em, ex, not %s' % (name, value))
-            elif name == 'graphic_size' and not(isinstance(value, tuple) and (len(value) == 2)):
+            elif name == 'graphic_size' and not (isinstance(value, tuple) and (len(value) == 2)):
                 raise ValueError('%s option must be an ordered pair, not %s' % (name, value))
-            elif name == 'margins' and not((isinstance(value, tuple)) and (len(value) == 4)):
+            elif name == 'margins' and not ((isinstance(value, tuple)) and (len(value) == 4)):
                 raise ValueError('%s option must be 4-tuple, not %s' % (name, value))
             elif name in color_options:
                 try:
@@ -1204,14 +1203,14 @@ def set_option(self, option_name, option_value=None):
                     raise TypeError('%s option must be a dictionary, not %s' % (name, value))
                 else:
                     for key, p in value.items():
-                        if not(type(p) in [float, RealLiteral] and (0 <= p) and (p <= 1)) and not(p in label_places):
+                        if not (type(p) in [float, RealLiteral] and (0 <= p) and (p <= 1)) and (p not in label_places):
                             raise ValueError('%s option for %s needs to be a number between 0.0 and 1.0 or a place (like "above"), not %s' % (name, key, p))
             elif name == 'loop_placements':
                 if not isinstance(value, dict):
                     raise TypeError('%s option must be a dictionary, not %s' % (name, value))
                 else:
                     for key, p in value.items():
-                        if not((isinstance(p, tuple)) and (len(p) == 2) and (p[0] >= 0) and (p[1] in compass_points)):
+                        if not ((isinstance(p, tuple)) and (len(p) == 2) and (p[0] >= 0) and (p[1] in compass_points)):
                             raise ValueError('%s option for %s needs to be a positive number and a compass point (like "EA"), not %s' % (name, key, p))
             # These have been verified as tuples before going into this next check
             elif name in positive_tuples:

src/sage/graphs/isgci.py

@@ -806,7 +806,7 @@ def _download_db(self):
             try:
                 z.extract(_XML_FILE, GRAPHS_DATA_DIR)
                 z.extract(_SMALLGRAPHS_FILE, GRAPHS_DATA_DIR)
-            except IOError:
+            except OSError:
                 pass
 
     def _parse_db(self, directory):
@@ -915,7 +915,7 @@ def _get_ISGCI(self):
             else:
                 directory = os.path.join(GRAPHS_DATA_DIR, _XML_FILE)
 
-        except IOError:
+        except OSError:
             directory = os.path.join(GRAPHS_DATA_DIR, _XML_FILE)
 
         self._parse_db(directory)

src/sage/graphs/schnyder.py

@@ -804,7 +804,7 @@ def minimal_schnyder_wood(graph, root_edge=None, minimal=True, check=True):
             raise ValueError('not a planar graph')
         if not all(len(u) == 3 for u in graph.faces()):
             raise ValueError('not a triangulation')
-        if not(a in graph.neighbors(b)):
+        if a not in graph.neighbors(b):
             raise ValueError('not a valid root edge')
 
     new_g = DiGraph()