Trac #29518: remove deprecated stuff from graphs

Goal: remove all the code of the graph module that has a deprecation
warning referring to a ticket closed for at least one year.
These tickets are:
- #26200 deprecate import of all_max_clique, max_clique and
clique_number in global namespace
- #27491 deprecate parameter copy in networkx_graph
- #19227 Graphs: DFS and broken distance-parameter
- #19517 Graphs: canonical_label() and several errors
- #25864 make LinearExtensions an iterator

Note that the current ticket completely deletes the file
`graphs/linearextensions.py`.

URL: https://trac.sagemath.org/29518
Reported by: gh-jfraymond
Ticket author(s): Jean-Florent Raymond
Reviewer(s): Frédéric Chapoton

Author: Release Manager

src/doc/en/reference/graphs/index.rst

@@ -75,7 +75,6 @@ Libraries of algorithms
    sage/graphs/matchpoly
    sage/graphs/genus
    sage/graphs/lovasz_theta
-   sage/graphs/linearextensions
    sage/graphs/schnyder
    sage/graphs/planarity
    sage/graphs/traversals

src/sage/combinat/posets/linear_extensions.py

@@ -417,7 +417,6 @@ class LinearExtensionsOfPoset(UniqueRepresentation, Parent):
     .. SEEALSO::
 
         - :meth:`sage.combinat.posets.posets.FinitePoset.linear_extensions`
-        - :class:`sage.graphs.linearextensions.LinearExtensions`
 
     EXAMPLES::
 

src/sage/graphs/all.py

@@ -14,9 +14,6 @@
 import sage.graphs.partial_cube
 from . import graph_list as graphs_list
 lazy_import("sage.graphs", "graph_coloring")
-lazy_import("sage.graphs.cliquer", ['all_max_clique', 'max_clique',
-                                    'clique_number'],
-            deprecation=26200)
 from .graph_database import graph_db_info
 lazy_import("sage.graphs.graph_editor", "graph_editor")
 
@@ -35,15 +32,15 @@
 sage.graphs.cliquer are deprecated from the global namespace (:trac:`26200`)::
 
     sage: all_max_clique(Graph())
-    doctest:...: DeprecationWarning: Importing all_max_clique from here is deprecated. If you need to use it, please import it directly from sage.graphs.cliquer
-    See https://trac.sagemath.org/26200 for details.
-    [[]]
+    Traceback (most recent call last):
+    ...
+    NameError: name 'all_max_clique' is not defined
     sage: max_clique(Graph())
-    doctest:...: DeprecationWarning: Importing max_clique from here is deprecated. If you need to use it, please import it directly from sage.graphs.cliquer
-    See https://trac.sagemath.org/26200 for details.
-    []
+    Traceback (most recent call last):
+    ...
+    NameError: name 'max_clique' is not defined
     sage: clique_number(Graph())
-    doctest:...: DeprecationWarning: Importing clique_number from here is deprecated. If you need to use it, please import it directly from sage.graphs.cliquer
-    See https://trac.sagemath.org/26200 for details.
-    0
+    Traceback (most recent call last):
+    ...
+    NameError: name 'clique_number' is not defined
 """

src/sage/graphs/generic_graph.py

@@ -1419,7 +1419,7 @@ def _scream_if_not_simple(self, allow_loops=False, allow_multiple_edges=False):
                    functions + ".")
             raise ValueError(msg)
 
-    def networkx_graph(self, copy=True, weight_function=None):
+    def networkx_graph(self, weight_function=None):
         """
         Return a new ``NetworkX`` graph from the Sage graph.
 
@@ -1447,8 +1447,6 @@ def networkx_graph(self, copy=True, weight_function=None):
             OutMultiEdgeDataView([(1, 2, {'weight': 1}), (1, 3, {'weight': 4}), (2, 3, {'weight': 3}), (3, 4, {'weight': 5}), (3, 4, {'weight': 4})])
 
         """
-        if copy is not True:
-            deprecation(27491, "parameter copy is removed")
         if weight_function is not None:
             self._check_weight_function(weight_function)
         import networkx
@@ -17677,7 +17675,7 @@ def breadth_first_search(self, start, ignore_direction=False,
                                 yield w
 
     def depth_first_search(self, start, ignore_direction=False,
-                           distance=None, neighbors=None, edges=False):
+                           neighbors=None, edges=False):
         """
         Return an iterator over the vertices in a depth-first ordering.
 
@@ -17690,8 +17688,6 @@ def depth_first_search(self, start, ignore_direction=False,
           directed graphs. If ``True``, searches across edges in either
           direction.
 
-        - ``distance`` -- Deprecated. Broken, do not use.
-
         - ``neighbors`` -- function (default: ``None``); a function that inputs
           a vertex and return a list of vertices. For an undirected graph,
           ``neighbors`` is by default the :meth:`.neighbors` function. For a
@@ -17786,11 +17782,8 @@ def depth_first_search(self, start, ignore_direction=False,
             [(1, 3), (3, 6), (6, 7), (7, 5), (5, 4), (1, 2)]
 
         """
-        if distance is not None:
-            deprecation(19227, "Parameter 'distance' is broken. Do not use.")
-
         # Preferably use the Cython implementation
-        if (neighbors is None and not isinstance(start, list) and distance is None
+        if (neighbors is None and not isinstance(start, list)
                 and hasattr(self._backend, "depth_first_search") and not edges):
             for v in self._backend.depth_first_search(start, ignore_direction=ignore_direction):
                 yield v
@@ -17813,10 +17806,9 @@ def depth_first_search(self, start, ignore_direction=False,
                     if v not in seen:
                         yield v
                         seen.add(v)
-                        if distance is None or d < distance:
-                            for w in neighbors(v):
-                                if w not in seen:
-                                    queue.append((w, d + 1))
+                        for w in neighbors(v):
+                            if w not in seen:
+                                queue.append((w, d + 1))
             else:
                 queue = [(None, v, d) for v, d in queue]
                 while queue:
@@ -17825,10 +17817,9 @@ def depth_first_search(self, start, ignore_direction=False,
                         if v is not None:
                             yield v, w                        
                         seen.add(w)
-                        if distance is None or d < distance:
-                            for x in neighbors(w):
-                                if x not in seen:
-                                    queue.append((w, x, d + 1))
+                        for x in neighbors(w):
+                            if x not in seen:
+                                queue.append((w, x, d + 1))
 
     ### Constructors
 
@@ -22864,7 +22855,7 @@ def is_isomorphic(self, other, certificate=False, verbosity=0, edge_labels=False
                     isom_trans[v] = other_vertices[isom[G_to[v]]]
             return True, isom_trans
 
-    def canonical_label(self, partition=None, certificate=False, verbosity=0,
+    def canonical_label(self, partition=None, certificate=False,
                         edge_labels=False, algorithm=None, return_graph=True):
         r"""
         Return the canonical graph.
@@ -22906,8 +22897,6 @@ class by some canonization function `c`. If `G` and `H` are graphs,
           instead of the canonical graph; only available when ``'bliss'``
           is explicitly set as algorithm.
 
-        - ``verbosity`` -- deprecated, does nothing
-
         EXAMPLES:
 
         Canonization changes isomorphism to equality::
@@ -23046,9 +23035,6 @@ class by some canonization function `c`. If `G` and `H` are graphs,
             ....:             assert gcan0 == gcan1, (edges, labels, part, pp)
             ....:             assert gcan0 == gcan2, (edges, labels, part, pp)
         """
-        # Deprecation
-        if verbosity != 0:
-            deprecation(19517, "Verbosity-parameter is removed.")
 
         # Check parameter combinations
         if algorithm not in [None, 'sage', 'bliss']: