refactor: Graph and Vertex are the names of the common base classes

README.md

@@ -96,7 +96,7 @@ Graphs belong to the class `UGraph` or `DGraph` for undirected or directed graph
 - `g.incidence()` incidence matrix
 
 ### Properties and methods of a vertex
-Vertices belong to the class `UVertex` (for undirected graphs) or `DVertex` (for directed graphs), which are each subclasses of `BaseVertex`.
+Vertices belong to the class `UVertex` (for undirected graphs) or `DVertex` (for directed graphs), which are each subclasses of `Vertex`.
 
 - `v.coord` the coordinate vector for embedded graph (optional)
 - `v.name` the name of the vertex (optional)

docs/source/analysis.rst

@@ -13,55 +13,55 @@ Graph
 .. autosummary::
    :nosignatures:
 
-   ~pgraph.PGraph.BaseGraph.n
-   ~pgraph.PGraph.BaseGraph.ne
-   ~pgraph.PGraph.BaseGraph.nc
-   ~pgraph.PGraph.BaseGraph.edges
-   ~pgraph.PGraph.BaseGraph.average_degree
-   ~pgraph.PGraph.BaseGraph.iscyclic
-   ~pgraph.PGraph.BaseGraph.connectivity
-   ~pgraph.PGraph.BaseGraph.component
-   ~pgraph.PGraph.BaseGraph.samecomponent
-   ~pgraph.PGraph.BaseGraph.closest
+   ~pgraph.PGraph.Graph.n
+   ~pgraph.PGraph.Graph.ne
+   ~pgraph.PGraph.Graph.nc
+   ~pgraph.PGraph.Graph.edges
+   ~pgraph.PGraph.Graph.average_degree
+   ~pgraph.PGraph.Graph.iscyclic
+   ~pgraph.PGraph.Graph.connectivity
+   ~pgraph.PGraph.Graph.component
+   ~pgraph.PGraph.Graph.samecomponent
+   ~pgraph.PGraph.Graph.closest
 
 Vertex
 ------
 
 .. autosummary::
    :nosignatures:
 
-   ~pgraph.PGraph.BaseVertex.edges
-   ~pgraph.PGraph.BaseVertex.adjacent
-   ~pgraph.PGraph.BaseVertex.isadjacent
-   ~pgraph.PGraph.BaseVertex.incidences
-   ~pgraph.PGraph.BaseVertex.degree
-   ~pgraph.PGraph.BaseVertex.heuristic_distance
-   ~pgraph.PGraph.BaseVertex.distance
-   ~pgraph.PGraph.BaseVertex.x
-   ~pgraph.PGraph.BaseVertex.y
-   ~pgraph.PGraph.BaseVertex.z
+   ~pgraph.PGraph.Vertex.edges
+   ~pgraph.PGraph.Vertex.adjacent
+   ~pgraph.PGraph.Vertex.isadjacent
+   ~pgraph.PGraph.Vertex.incidences
+   ~pgraph.PGraph.Vertex.degree
+   ~pgraph.PGraph.Vertex.heuristic_distance
+   ~pgraph.PGraph.Vertex.distance
+   ~pgraph.PGraph.Vertex.x
+   ~pgraph.PGraph.Vertex.y
+   ~pgraph.PGraph.Vertex.z
 
 Details
 -------
 
-.. autoproperty:: pgraph.PGraph.BaseGraph.n
-.. autoproperty:: pgraph.PGraph.BaseGraph.ne
-.. autoproperty:: pgraph.PGraph.BaseGraph.nc
-.. automethod:: pgraph.PGraph.BaseGraph.edges
-.. automethod:: pgraph.PGraph.BaseGraph.average_degree
-.. automethod:: pgraph.PGraph.BaseGraph.iscyclic
-.. automethod:: pgraph.PGraph.BaseGraph.connectivity
-.. automethod:: pgraph.PGraph.BaseGraph.component
-.. automethod:: pgraph.PGraph.BaseGraph.samecomponent
-.. automethod:: pgraph.PGraph.BaseGraph.closest
+.. autoproperty:: pgraph.PGraph.Graph.n
+.. autoproperty:: pgraph.PGraph.Graph.ne
+.. autoproperty:: pgraph.PGraph.Graph.nc
+.. automethod:: pgraph.PGraph.Graph.edges
+.. automethod:: pgraph.PGraph.Graph.average_degree
+.. automethod:: pgraph.PGraph.Graph.iscyclic
+.. automethod:: pgraph.PGraph.Graph.connectivity
+.. automethod:: pgraph.PGraph.Graph.component
+.. automethod:: pgraph.PGraph.Graph.samecomponent
+.. automethod:: pgraph.PGraph.Graph.closest
 
-.. automethod:: pgraph.PGraph.BaseVertex.edges
-.. automethod:: pgraph.PGraph.BaseVertex.adjacent
-.. automethod:: pgraph.PGraph.BaseVertex.isadjacent
-.. automethod:: pgraph.PGraph.BaseVertex.incidences
-.. autoproperty:: pgraph.PGraph.BaseVertex.degree
-.. automethod:: pgraph.PGraph.BaseVertex.heuristic_distance
-.. automethod:: pgraph.PGraph.BaseVertex.distance
-.. autoproperty:: pgraph.PGraph.BaseVertex.x
-.. autoproperty:: pgraph.PGraph.BaseVertex.y
-.. autoproperty:: pgraph.PGraph.BaseVertex.z
+.. automethod:: pgraph.PGraph.Vertex.edges
+.. automethod:: pgraph.PGraph.Vertex.adjacent
+.. automethod:: pgraph.PGraph.Vertex.isadjacent
+.. automethod:: pgraph.PGraph.Vertex.incidences
+.. autoproperty:: pgraph.PGraph.Vertex.degree
+.. automethod:: pgraph.PGraph.Vertex.heuristic_distance
+.. automethod:: pgraph.PGraph.Vertex.distance
+.. autoproperty:: pgraph.PGraph.Vertex.x
+.. autoproperty:: pgraph.PGraph.Vertex.y
+.. autoproperty:: pgraph.PGraph.Vertex.z

docs/source/common.rst

@@ -4,12 +4,12 @@ Common methods
 The package supports both directed (prefix ``D``) and undirected graphs (prefix ``U``), and the classes for these
 share a common interface. 
 
-The graph classes represent a single graph, either directed or undirected, and they share :class:`BaseGraph`:
+The graph classes represent a single graph, either directed or undirected, and they share :class:`Graph`:
 
 .. inheritance-diagram:: pgraph.PGraph.UGraph pgraph.PGraph.DGraph
    :parts: 1
    :private-bases:
-   :top-classes: pgraph.PGraph.BaseGraph
+   :top-classes: pgraph.PGraph.Graph
 
 The vertices in a directed graph (``DGraph``) inherit from :class:`DVertex` and the
 vertices in an undirected graph (``UGraph``) inherit from :class:`UVertex`. 
@@ -19,7 +19,7 @@ vertices in an undirected graph (``UGraph``) inherit from :class:`UVertex`.
 
 The vertex classes share
 almost their entire interface, defined once on their common base classes
-(:class:`BaseGraph`, :class:`BaseVertex`). This section documents that
+(:class:`Graph`, :class:`Vertex`). This section documents that
 shared interface by task rather than by class; see :doc:`construction` for
 the :class:`DGraph` and :class:`UGraph` classes and :doc:`edges_vertices` for
 what's specific to directed vs. undirected vertices.

docs/source/construction.rst

@@ -12,8 +12,8 @@ standalone, independent of a graph.
 
    ~pgraph.PGraph.DGraph
    ~pgraph.PGraph.UGraph
-   ~pgraph.PGraph.BaseGraph.Dict
-   ~pgraph.PGraph.BaseGraph.Adjacency
+   ~pgraph.PGraph.Graph.Dict
+   ~pgraph.PGraph.Graph.Adjacency
 
 
 .. autoclass:: pgraph.PGraph.DGraph
@@ -22,17 +22,17 @@ standalone, independent of a graph.
 .. autoclass:: pgraph.PGraph.UGraph
    :show-inheritance:
 
-.. autoclass:: pgraph.PGraph.BaseGraph.Adjacency
+.. autoclass:: pgraph.PGraph.Graph.Adjacency
    :show-inheritance:
 
-.. autoclass:: pgraph.PGraph.BaseGraph.Dict
+.. autoclass:: pgraph.PGraph.Graph.Dict
    :show-inheritance:
 
 
 Inherited methods for all graph types
 --------------------------------------
 
-.. autoclass:: pgraph.PGraph.BaseGraph
+.. autoclass:: pgraph.PGraph.Graph
    :members: copy, vertex_copy, metric, heuristic, show, vertex_class, edge_class
    :special-members: __init__, __str__, __repr__, __getitem__, __iter__, __contains__
 

docs/source/export.rst

@@ -13,11 +13,11 @@ it.
 .. autosummary::
    :nosignatures:
 
-   ~pgraph.PGraph.BaseGraph.export
-   ~pgraph.PGraph.BaseGraph.dotfile
+   ~pgraph.PGraph.Graph.export
+   ~pgraph.PGraph.Graph.dotfile
 
 Details
 -------
 
-.. automethod:: pgraph.PGraph.BaseGraph.export
-.. automethod:: pgraph.PGraph.BaseGraph.dotfile
+.. automethod:: pgraph.PGraph.Graph.export
+.. automethod:: pgraph.PGraph.Graph.dotfile

docs/source/modification.rst

@@ -13,30 +13,30 @@ Graph
 .. autosummary::
    :nosignatures:
 
-   ~pgraph.PGraph.BaseGraph.add_vertex
-   ~pgraph.PGraph.BaseGraph.add_edge
-   ~pgraph.PGraph.BaseGraph.remove_edge
-   ~pgraph.PGraph.BaseGraph.remove_vertex
+   ~pgraph.PGraph.Graph.add_vertex
+   ~pgraph.PGraph.Graph.add_edge
+   ~pgraph.PGraph.Graph.remove_edge
+   ~pgraph.PGraph.Graph.remove_vertex
 
 Vertex
 ------
 
 .. autosummary::
    :nosignatures:
 
-   ~pgraph.PGraph.BaseVertex.connect
-   ~pgraph.PGraph.BaseVertex.edgeto
-   ~pgraph.PGraph.BaseVertex.remove
+   ~pgraph.PGraph.Vertex.connect
+   ~pgraph.PGraph.Vertex.edgeto
+   ~pgraph.PGraph.Vertex.remove
 
 Details
 -------
 
-.. automethod:: pgraph.PGraph.BaseGraph.add_vertex
-.. automethod:: pgraph.PGraph.BaseGraph.add_edge
-.. automethod:: pgraph.PGraph.BaseGraph.remove_edge
-.. automethod:: pgraph.PGraph.BaseGraph.remove_vertex
-.. automethod:: pgraph.PGraph.BaseGraph.remove
+.. automethod:: pgraph.PGraph.Graph.add_vertex
+.. automethod:: pgraph.PGraph.Graph.add_edge
+.. automethod:: pgraph.PGraph.Graph.remove_edge
+.. automethod:: pgraph.PGraph.Graph.remove_vertex
+.. automethod:: pgraph.PGraph.Graph.remove
 
-.. automethod:: pgraph.PGraph.BaseVertex.connect
-.. automethod:: pgraph.PGraph.BaseVertex.edgeto
-.. automethod:: pgraph.PGraph.BaseVertex.remove
+.. automethod:: pgraph.PGraph.Vertex.connect
+.. automethod:: pgraph.PGraph.Vertex.edgeto
+.. automethod:: pgraph.PGraph.Vertex.remove

docs/source/planning.rst

@@ -6,13 +6,13 @@ These methods find optimal paths from a start vertex to a goal vertex.
 .. autosummary::
    :nosignatures:
 
-   ~pgraph.PGraph.BaseGraph.path_BFS
-   ~pgraph.PGraph.BaseGraph.path_UCS
-   ~pgraph.PGraph.BaseGraph.path_Astar
+   ~pgraph.PGraph.Graph.path_BFS
+   ~pgraph.PGraph.Graph.path_UCS
+   ~pgraph.PGraph.Graph.path_Astar
 
 Details
 -------
 
-.. automethod:: pgraph.PGraph.BaseGraph.path_BFS
-.. automethod:: pgraph.PGraph.BaseGraph.path_UCS
-.. automethod:: pgraph.PGraph.BaseGraph.path_Astar
+.. automethod:: pgraph.PGraph.Graph.path_BFS
+.. automethod:: pgraph.PGraph.Graph.path_UCS
+.. automethod:: pgraph.PGraph.Graph.path_Astar

docs/source/policy.rst

@@ -1,7 +1,7 @@
 Object lifecycle and graph-membership policy
 =============================================
 
-``BaseVertex``, ``UVertex``, ``DVertex`` and ``Edge`` can all be constructed
+``Vertex``, ``UVertex``, ``DVertex`` and ``Edge`` can all be constructed
 directly, independent of any graph. This is deliberate -- it is not an
 oversight and not a "factory-only" design -- but it means the rules for what
 those objects can and can't do *before* they belong to a graph need to be
@@ -26,7 +26,7 @@ Adding a vertex to a graph
 :meth:`UGraph.add_vertex` and :meth:`DGraph.add_vertex` each only accept
 their own matching vertex subclass -- a ``UVertex`` (or coordinate data, from
 which one is built) for :class:`UGraph`, a ``DVertex`` for :class:`DGraph`.
-Passing the wrong kind of vertex -- a plain ``BaseVertex``, or the other
+Passing the wrong kind of vertex -- a plain ``Vertex``, or the other
 graph's subclass -- raises ``TypeError`` rather than being silently accepted
 or converted.
 
@@ -79,7 +79,7 @@ Summary
    * - Operation
      - Requires graph membership?
      - Failure mode
-   * - ``UVertex()`` / ``DVertex()`` / ``BaseVertex()``
+   * - ``UVertex()`` / ``DVertex()`` / ``Vertex()``
      - No
      - --
    * - ``Edge(v1, v2)``

docs/source/representations.rst

@@ -7,19 +7,19 @@ These methods convert the graph to a number of different matrix representations.
 .. autosummary::
    :nosignatures:
 
-   ~pgraph.PGraph.BaseGraph.distance
-   ~pgraph.PGraph.BaseGraph.adjacency
-   ~pgraph.PGraph.BaseGraph.degree
-   ~pgraph.PGraph.BaseGraph.incidence
-   ~pgraph.PGraph.BaseGraph.laplacian
+   ~pgraph.PGraph.Graph.distance
+   ~pgraph.PGraph.Graph.adjacency
+   ~pgraph.PGraph.Graph.degree
+   ~pgraph.PGraph.Graph.incidence
+   ~pgraph.PGraph.Graph.laplacian
 
 Details
 -------
 
-.. automethod:: pgraph.PGraph.BaseGraph.distance
-.. automethod:: pgraph.PGraph.BaseGraph.adjacency
-.. automethod:: pgraph.PGraph.BaseGraph.degree
-.. automethod:: pgraph.PGraph.BaseGraph.incidence
-.. automethod:: pgraph.PGraph.BaseGraph.laplacian
+.. automethod:: pgraph.PGraph.Graph.distance
+.. automethod:: pgraph.PGraph.Graph.adjacency
+.. automethod:: pgraph.PGraph.Graph.degree
+.. automethod:: pgraph.PGraph.Graph.incidence
+.. automethod:: pgraph.PGraph.Graph.laplacian
 
 

docs/source/visualization.rst

@@ -8,17 +8,17 @@ file) rather than displaying it.
 .. autosummary::
    :nosignatures:
 
-   ~pgraph.PGraph.BaseGraph.plot
-   ~pgraph.PGraph.BaseGraph.showgraph
-   ~pgraph.PGraph.BaseGraph.highlight_path
-   ~pgraph.PGraph.BaseGraph.highlight_edge
-   ~pgraph.PGraph.BaseGraph.highlight_vertex
+   ~pgraph.PGraph.Graph.plot
+   ~pgraph.PGraph.Graph.showgraph
+   ~pgraph.PGraph.Graph.highlight_path
+   ~pgraph.PGraph.Graph.highlight_edge
+   ~pgraph.PGraph.Graph.highlight_vertex
 
 Details
 -------
 
-.. automethod:: pgraph.PGraph.BaseGraph.plot
-.. automethod:: pgraph.PGraph.BaseGraph.showgraph
-.. automethod:: pgraph.PGraph.BaseGraph.highlight_path
-.. automethod:: pgraph.PGraph.BaseGraph.highlight_edge
-.. automethod:: pgraph.PGraph.BaseGraph.highlight_vertex
+.. automethod:: pgraph.PGraph.Graph.plot
+.. automethod:: pgraph.PGraph.Graph.showgraph
+.. automethod:: pgraph.PGraph.Graph.highlight_path
+.. automethod:: pgraph.PGraph.Graph.highlight_edge
+.. automethod:: pgraph.PGraph.Graph.highlight_vertex