gh-35647: sage.graphs: More # optional and other modularization fixes

<!-- Please provide a concise, informative and self-explanatory title.
-->
<!-- Don't put issue numbers in the title. Put it in the Description
below. -->
<!-- For example, instead of "Fixes #12345", use "Add a new method to
multiply two integers" -->

### 📚 Description

<!-- Describe your changes here in detail. -->
<!-- Why is this change required? What problem does it solve? -->
<!-- If this PR resolves an open issue, please link to it here. For
example "Fixes #12345". -->
<!-- If your change requires a documentation PR, please link it
appropriately. -->
Part of:
- #29705

### 📝 Checklist

<!-- Put an `x` in all the boxes that apply. It should be `[x]` not `[x
]`. -->

- [x] The title is concise, informative, and self-explanatory.
- [ ] The description explains in detail what this PR is about.
- [x] I have linked a relevant issue or discussion.
- [ ] I have created tests covering the changes.
- [ ] I have updated the documentation accordingly.

### ⌛ Dependencies

<!-- List all open PRs that this PR logically depends on
- #12345: short description why this is a dependency
- #34567: ...
-->

<!-- If you're unsure about any of these, don't hesitate to ask. We're
here to help! -->

URL: #35647
Reported by: Matthias Köppe
Reviewer(s): David Coudert

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=e55fd192510499ab59847906bf0abc0e1776aecb
-md5=7adfc7ea92837b419c9cf91085b4c0c2
-cksum=2479564476
+sha1=1ef3ccb4e221787756f5d865edd4883d6e8a2aab
+md5=f7ca42afb156ba5aa99de96f825948b7
+cksum=3849472062

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-8455792fc708dc9b848e9d084e96a6a890bca822
+111d02b0cbc6552b1650930728c7084a72f88a73

src/sage/graphs/base/c_graph.pyx

@@ -4548,7 +4548,7 @@ cdef class CGraphBackend(GenericGraphBackend):
         At first, the following graph is acyclic::
 
             sage: D = DiGraph({ 0:[1,2,3], 4:[2,5], 1:[8], 2:[7], 3:[7], 5:[6,7], 7:[8], 6:[9], 8:[10], 9:[10] })
-            sage: D.plot(layout='circular').show()
+            sage: D.plot(layout='circular').show()                                      # optional - sage.plot
             sage: D.is_directed_acyclic()
             True
 

src/sage/graphs/bipartite_graph.py

@@ -158,7 +158,7 @@ class BipartiteGraph(Graph):
         sage: B = BipartiteGraph(P, partition, check=False)
         sage: B.left
         {0, 1, 2, 3, 4}
-        sage: B.show()
+        sage: B.show()                                                                  # optional - sage.plot
 
        ::
 
@@ -304,14 +304,14 @@ class BipartiteGraph(Graph):
          sage: B = BipartiteGraph('F?^T_\n', partition=[[0, 1, 2], [3, 4, 5, 6]], check=False)
          sage: B.left
          {0, 1, 2}
-         sage: B.show()
+         sage: B.show()                                                                 # optional - sage.plot
 
     #. From a NetworkX bipartite graph::
 
-        sage: import networkx                                                                       # optional - networkx
-        sage: G = graphs.OctahedralGraph()                                                          # optional - networkx
-        sage: N = networkx.make_clique_bipartite(G.networkx_graph())                                # optional - networkx
-        sage: B = BipartiteGraph(N)                                                                 # optional - networkx
+        sage: import networkx                                                           # optional - networkx
+        sage: G = graphs.OctahedralGraph()                                              # optional - networkx
+        sage: N = networkx.make_clique_bipartite(G.networkx_graph())                    # optional - networkx
+        sage: B = BipartiteGraph(N)                                                     # optional - networkx
 
     TESTS:
 
@@ -1464,7 +1464,7 @@ def plot(self, *args, **kwds):
         EXAMPLES::
 
             sage: B = BipartiteGraph(graphs.CycleGraph(20))
-            sage: B.plot()
+            sage: B.plot()                                                              # optional - sage.plot
             Graphics object consisting of 41 graphics primitives
         """
         if "pos" not in kwds:

src/sage/graphs/cliquer.pyx

@@ -115,7 +115,7 @@ def all_max_clique(graph):
          [2, 6], [2, 8], [3, 4], [3, 7], [3, 9], [4, 5], [4, 8], [5, 10],
          [5, 11], [6, 10], [6, 11], [7, 8], [7, 11], [8, 10], [9, 10], [9, 11]]
         sage: G = Graph({0:[1,2,3], 1:[2], 3:[0,1]})
-        sage: G.show(figsize=[2,2])
+        sage: G.show(figsize=[2,2])                                                     # optional - sage.plot
         sage: G.cliques_maximum()
         [[0, 1, 2], [0, 1, 3]]
         sage: C = graphs.PetersenGraph()
@@ -302,7 +302,7 @@ def clique_number(graph):
         sage: C.clique_number()
         4
         sage: G = Graph({0:[1,2,3], 1:[2], 3:[0,1]})
-        sage: G.show(figsize=[2,2])
+        sage: G.show(figsize=[2,2])                                                     # optional - sage.plot
         sage: G.clique_number()
         3
 

src/sage/graphs/comparability.pyx

@@ -642,7 +642,7 @@ def is_permutation(g, algorithm="greedy", certificate=False, check=True,
         sage: p1 = Permutation([nn+1 for nn in perm[0]])
         sage: p2 = Permutation([nn+1 for nn in perm[1]])
         sage: p = p2 * p1.inverse()
-        sage: p.show(representation = "braid")
+        sage: p.show(representation="braid")                                            # optional - sage.plot
 
     TESTS:
 

src/sage/graphs/connectivity.pyx

@@ -215,12 +215,12 @@ def connected_components_subgraphs(G):
         sage: from sage.graphs.connectivity import connected_components_subgraphs
         sage: G = Graph({0: [1, 3], 1: [2], 2: [3], 4: [5, 6], 5: [6]})
         sage: L = connected_components_subgraphs(G)
-        sage: graphs_list.show_graphs(L)
+        sage: graphs_list.show_graphs(L)                                                # optional - sage.plot
         sage: D = DiGraph({0: [1, 3], 1: [2], 2: [3], 4: [5, 6], 5: [6]})
         sage: L = connected_components_subgraphs(D)
-        sage: graphs_list.show_graphs(L)
+        sage: graphs_list.show_graphs(L)                                                # optional - sage.plot
         sage: L = D.connected_components_subgraphs()
-        sage: graphs_list.show_graphs(L)
+        sage: graphs_list.show_graphs(L)                                                # optional - sage.plot
 
     TESTS:
 

src/sage/graphs/digraph.py

@@ -951,7 +951,7 @@ def is_directed_acyclic(self, certificate=False):
         At first, the following graph is acyclic::
 
             sage: D = DiGraph({0:[1, 2, 3], 4:[2, 5], 1:[8], 2:[7], 3:[7], 5:[6,7], 7:[8], 6:[9], 8:[10], 9:[10]})
-            sage: D.plot(layout='circular').show()
+            sage: D.plot(layout='circular').show()                                      # optional - sage.plot
             sage: D.is_directed_acyclic()
             True
 
@@ -3140,7 +3140,7 @@ def topological_sort(self, implementation="default"):
 
             sage: D = DiGraph({0: [1, 2, 3], 4: [2, 5], 1: [8], 2: [7], 3: [7],
             ....:   5: [6, 7], 7: [8], 6: [9], 8: [10], 9: [10]})
-            sage: D.plot(layout='circular').show()
+            sage: D.plot(layout='circular').show()                                      # optional - sage.plot
             sage: D.topological_sort()
             [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10]
 
@@ -3220,7 +3220,7 @@ def topological_sort_generator(self):
         EXAMPLES::
 
             sage: D = DiGraph({0: [1, 2], 1: [3], 2: [3, 4]})
-            sage: D.plot(layout='circular').show()
+            sage: D.plot(layout='circular').show()                                      # optional - sage.plot
             sage: list(D.topological_sort_generator())
             [[0, 1, 2, 3, 4], [0, 2, 1, 3, 4], [0, 2, 1, 4, 3], [0, 2, 4, 1, 3], [0, 1, 2, 4, 3]]