trac #15553: Broken links in the doc of graph/ and numerical/

Author: nathanncohen

src/sage/graphs/distances_all_pairs.pyx

@@ -483,8 +483,8 @@ def is_distance_regular(G, parameters = False):
 
     .. SEEALSO::
 
-        * :meth:`Graph.is_regular`
-        * :meth:`Graph.is_strongly_regular`
+        * :meth:`~sage.graphs.generic_graph.GenericGraph.is_regular`
+        * :meth:`~Graph.is_strongly_regular`
 
     EXAMPLES::
 

src/sage/graphs/generic_graph.py

@@ -1224,10 +1224,11 @@ def distance_matrix(self):
         .. WARNING::
 
             The ordering of vertices in the matrix has no reason to correspond
-            to the order of vertices in :meth:`~Graph.vertices`. In particular,
-            if two integers `i,j` are vertices of a graph `G` with distance
-            matrix ``M``, then ``M[i][i]`` is not necessarily the distance
-            between vertices `i` and `j`.
+            to the order of vertices in
+            :meth:`~sage.graphs.generic_graph.GenericGraph.vertices`. In
+            particular, if two integers `i,j` are vertices of a graph `G` with
+            distance matrix ``M``, then ``M[i][i]`` is not necessarily the
+            distance between vertices `i` and `j`.
 
         EXAMPLES::
 
@@ -1250,8 +1251,8 @@ def distance_matrix(self):
 
         .. SEEALSO::
 
-            * :meth:`~sage.graphs.generic_graph.distance_all_pairs` -- computes
-              the distance between any two vertices.
+            * :meth:`~sage.graphs.generic_graph.GenericGraph.distance_all_pairs`
+              -- computes the distance between any two vertices.
         """
 
         from sage.matrix.constructor import matrix
@@ -10828,9 +10829,10 @@ def is_circulant(self, certificate = False):
         lists_of_parameters)`` each element of ``lists_of_parameters`` can be
         used to define the graph as a circulant graph.
 
-        See the documentation of :meth:`graphs.CirculantGraph` and
-        :meth:`digraphs.CirculantGraph` for more information, and the examples
-        below.
+        See the documentation of
+        :func:`~sage.graphs.graph_generators.GraphGenerators.CirculantGraph` and
+        :meth:`~sage.graphs.digraph_generators.DiGraphGenerators.Circulant` for
+        more information, and the examples below.
 
         .. SEEALSO::
 
@@ -11562,7 +11564,7 @@ def distance_all_pairs(self, algorithm = "auto"):
 
         .. SEEALSO::
 
-            * :meth:`~sage.graphs.generic_graph.distance_matrix`
+            * :meth:`~sage.graphs.generic_graph.GenericGraph.distance_matrix`
         """
         if algorithm == "auto":
             if self.order() <= 20:
@@ -14731,7 +14733,7 @@ def plot(self, **options):
               be set through the :class:`~sage.misc.decorators.options`
               mechanism. For more information on this different way to set
               default parameters, see the help of the :class:`options decorator
-              <~sage.misc.decorators.options>`.
+              <sage.misc.decorators.options>`.
 
             - See also the :mod:`sage.graphs.graph_latex` module for ways to use
               LaTeX to produce an image of a graph.
@@ -14932,8 +14934,8 @@ def show(self, **kwds):
         INPUT:
 
         This method accepts any option understood by
-        :meth:`~sage.graphs.generic_graph.plot` (graph-specific) or by
-        :meth:`sage.plot.graphics.Graphics.show`.
+        :meth:`~sage.graphs.generic_graph.GenericGraph.plot` (graph-specific) or
+        by :meth:`sage.plot.graphics.Graphics.show`.
 
         .. NOTE::
 
@@ -15094,7 +15096,6 @@ def plot3d(self, bgcolor=(1,1,1),
 
             - :meth:`plot`
             - :meth:`graphviz_string`
-            - :meth:`_color_by_label`
         """
         import graph_plot
         layout_options = dict( (key,kwds[key]) for key in kwds.keys() if key     in graph_plot.layout_options )
@@ -15935,7 +15936,7 @@ def eigenspaces(self, laplacian=False):
 
         For some graphs, some of the the eigenspaces are described
         exactly by vector spaces over a
-        :class:`~sage.rings.number_field.number_field.NumberField`.
+        :func:`~sage.rings.number_field.number_field.NumberField`.
         For numerical eigenvectors use :meth:`eigenvectors`.
 
         EXAMPLES::

src/sage/graphs/graph.py

@@ -2821,7 +2821,7 @@ def is_semi_symmetric(self):
 
           - :meth:`~Graph.is_edge_transitive`
           - :meth:`~Graph.is_arc_transitive`
-          - :meth:`~Graph.is_half-transitive`
+          - :meth:`~Graph.is_half_transitive`
 
         EXAMPLES:
 
@@ -4918,7 +4918,7 @@ def clique_maximum(self,  algorithm="Cliquer"):
            - If ``algorithm = "MILP"``, the problem is solved through a Mixed
              Integer Linear Program.
 
-             (see :class:`MixedIntegerLinearProgram <sage.numerical.mip>`)
+             (see :class:`~sage.numerical.mip.MixedIntegerLinearProgram`)
 
         .. NOTE::
 
@@ -4984,7 +4984,7 @@ def clique_number(self, algorithm="Cliquer", cliques=None):
            - If ``algorithm = "MILP"``, the problem is solved through a Mixed
              Integer Linear Program.
 
-             (see :class:`MixedIntegerLinearProgram <sage.numerical.mip>`)
+             (see :class:`~sage.numerical.mip.MixedIntegerLinearProgram`)
 
         - ``cliques`` - an optional list of cliques that can be input if
           already computed. Ignored unless ``algorithm=="networkx"``.
@@ -5164,7 +5164,7 @@ def independent_set(self, algorithm = "Cliquer", value_only = False, reduction_r
             * If ``algorithm = "MILP"``, the problem is solved through a Mixed
               Integer Linear Program.
 
-              (see :class:`MixedIntegerLinearProgram <sage.numerical.mip>`)
+              (see :class:`~sage.numerical.mip.MixedIntegerLinearProgram`)
 
         - ``value_only`` -- boolean (default: ``False``). If set to ``True``,
           only the size of a maximum independent set is returned. Otherwise,
@@ -5179,9 +5179,9 @@ def independent_set(self, algorithm = "Cliquer", value_only = False, reduction_r
           solver to be used. If set to ``None``, the default one is used. For
           more information on LP solvers and which default solver is used, see
           the method
-          :meth:`solve <sage.numerical.mip.MixedIntegerLinearProgram.solve>`
+          :meth:`~sage.numerical.mip.MixedIntegerLinearProgram.solve`
           of the class
-          :class:`MixedIntegerLinearProgram <sage.numerical.mip.MixedIntegerLinearProgram>`.
+          :class:`~sage.numerical.mip.MixedIntegerLinearProgram`.
 
         - ``verbosity`` -- non-negative integer (default: ``0``). Set the level
           of verbosity you want from the linear program solver. Since the

src/sage/graphs/graph_plot.py

@@ -26,8 +26,8 @@
 
 **Plot options**
 
-Here is the list of options accepted by :meth:`GenericGraph.plot
-<sage.graphs.generic_graph.GenericGraph.plot>` and the constructor of
+Here is the list of options accepted by
+:meth:`~sage.graphs.generic_graph.GenericGraph.plot` and the constructor of
 :class:`GraphPlot`.
 
 .. csv-table::
@@ -94,16 +94,17 @@
 **Default options**
 
 This module defines two dictionaries containing default options for the
-:meth:`GenericGraph.plot` and :meth:`GenericGraph.show` methods. These two
-dictionaries are ``sage.graphs.graph_plot.DEFAULT_PLOT_OPTIONS`` and
+:meth:`~sage.graphs.generic_graph.GenericGraph.plot` and
+:meth:`~sage.graphs.generic_graph.GenericGraph.show` methods. These two dictionaries are
+``sage.graphs.graph_plot.DEFAULT_PLOT_OPTIONS`` and
 ``sage.graphs.graph_plot.DEFAULT_SHOW_OPTIONS``, respectively.
 
 
 Obviously, these values are overruled when arguments are given explicitly.
 
 Here is how to define the default size of a graph drawing to be ``[6,6]``. The
-first two calls to :meth:`~sage.graphs.generic_graph.show` use this option,
-while the third does not (a value for ``figsize`` is explicitly given)::
+first two calls to :meth:`~sage.graphs.generic_graph.GenericGraph.show` use this
+option, while the third does not (a value for ``figsize`` is explicitly given)::
 
     sage: sage.graphs.graph_plot.DEFAULT_SHOW_OPTIONS['figsize'] = [6,6]
     sage: graphs.PetersenGraph().show() # long time
@@ -696,7 +697,7 @@ def show(self, **kwds):
               information on default values of this method.
 
             - Any options not used by plot will be passed on to the
-              :meth:`~sage.plot.plot.Graphics.show` method.
+              :meth:`~sage.plot.graphics.Graphics.show` method.
 
         EXAMPLE::
 
@@ -719,7 +720,7 @@ def plot(self, **kwds):
 
         The options accepted by this method are to be found in the documentation
         of the :mod:`sage.graphs.graph_plot` module, and the
-        :meth:`~sage.plot.plot.Graphics.show` method.
+        :meth:`~sage.plot.graphics.Graphics.show` method.
 
         .. NOTE::
 

src/sage/graphs/isgci.py

@@ -111,7 +111,7 @@
    * - BinaryTrees
 
      - :meth:`~sage.graphs.graph_generators.GraphGenerators.BalancedTree`,
-       :meth:`~sage.graphs.generic_graph.GenericGraph.is_tree`
+       :meth:`~Graph.is_tree`
 
    * - Bipartite
 
@@ -172,7 +172,7 @@
    * - Tree
 
      - :meth:`~sage.graphs.graph_generators.GraphGenerators.trees`,
-       :meth:`~sage.graphs.generic_graph.GenericGraph.is_tree`
+       :meth:`~Graph.is_tree`
 
    * - UnitDisk
      - :meth:`~sage.graphs.graph_generators.GraphGenerators.IntervalGraph`,

src/sage/graphs/line_graph.py

@@ -161,10 +161,11 @@ def is_line_graph(g, certificate = False):
 
         This method sequentially tests each of the forbidden subgraphs in order
         to know whether the graph is a line graph, which is a very slow
-        method. It could eventually be replaced by :meth:`root_graph` when this
-        method will not require an exponential time to run on general graphs
-        anymore (see its documentation for more information on this problem)...
-        and if it can be improved to return negative certificates !
+        method. It could eventually be replaced by
+        :func:`~sage.graphs.line_graph.root_graph` when this method will not
+        require an exponential time to run on general graphs anymore (see its
+        documentation for more information on this problem)...  and if it can be
+        improved to return negative certificates !
 
     .. NOTE::
 

src/sage/numerical/backends/generic_backend.pyx

@@ -848,7 +848,7 @@ cdef class GenericBackend:
         .. NOTE::
 
            The list of available parameters is available at
-           :meth:`sage.numerical.mip.MixedIntegerlinearProgram.solver_parameter`
+           :meth:`~sage.numerical.mip.MixedIntegerLinearProgram.solver_parameter`.
 
         EXAMPLE::
 

src/sage/numerical/mip.pyx

@@ -358,7 +358,7 @@ cdef class MixedIntegerLinearProgram(SageObject):
         """
         Return the parent for all linear constraints
 
-        See :mod:`~sage.numerical.linear_constraints` for more
+        See :mod:`~sage.numerical.linear_functions` for more
         details.
 
         EXAMPLES::
@@ -739,11 +739,11 @@ cdef class MixedIntegerLinearProgram(SageObject):
         INPUT:
 
         All arguments given to this method are forwarded to the constructor of
-        the :class:`Polyhedron` class.
+        the :func:`Polyhedron` class.
 
         OUTPUT:
 
-        A :class:`Polyhedron` object whose `i`-th variable represents the `i`-th
+        A :func:`Polyhedron` object whose `i`-th variable represents the `i`-th
         variable of ``self``.
 
         .. warning::
@@ -1994,13 +1994,13 @@ cdef class MixedIntegerLinearProgram(SageObject):
     cpdef sum(self, L):
         r"""
         Efficiently computes the sum of a sequence of
-        :class:`~sage.numerical.linear_function.LinearFunction` elements
+        :class:`~sage.numerical.linear_functions.LinearFunction` elements
 
         INPUT:
 
         - ``mip`` -- the :class:`MixedIntegerLinearProgram` parent.
 
-        - ``L`` -- list of :class:`~sage.numerical.linear_function.LinearFunction` instances.
+        - ``L`` -- list of :class:`~sage.numerical.linear_functions.LinearFunction` instances.
 
         .. NOTE::