Merge pull request #56 from petercorke/doc/vertex-details

docs: what a vertex holds (edge lists, with example and figure)

Author: petercorke

docs/source/edges_vertices.rst

@@ -15,6 +15,142 @@ For the directed case, each vertex maintains two edge lists: a list of outgoing
 The graph class provides methods for adding and removing vertices and edges (see :doc:`modification`)
 and for querying its structure (see :doc:`analysis`).
 
+What a vertex holds
+~~~~~~~~~~~~~~~~~~~~
+
+
+Each vertex has **two** private edge lists, plus a back-pointer to its graph.
+
+.. list-table::
+   :header-rows: 1
+   :widths: 15 55 30
+
+   * - Attribute
+     - For undirected graphs
+     - For directed graphs
+   * - ``_edgelist``
+     - the edges *incident on* it
+     - the edges *leaving* it
+   * - ``_inlist``
+     - empty
+     - the edges *entering* it
+   * - ``_graph``
+     - the graph it belongs to (``None`` if standalone)
+     - the graph it belongs to (``None`` if standalone)
+
+Every list entry is a reference to the same :class:`~pgraph.PGraph.Edge` class object, and
+there is exactly one edge object for each edge in the graph.
+
+* **Undirected:** one list does everything, since an undirected edge is both "out"
+  and "in".  That is also why a loop is stored twice, once for each end, and why it
+  counts 2 towards ``degree``.
+* **Directed:** the two lists are the out-list and the in-list.  A loop sits once in
+  each, so ``degree`` (in + out) is 2 there too.
+
+An example, as lists
+~~~~~~~~~~~~~~~~~~~~~~
+
+For these simple graphs
+
+.. plot::
+   :include-source: no
+   :alt: the example graph drawn as an undirected and as a directed graph: two parallel edges e1 and e2 from a to b, e3 from b to c and a loop e4 on c
+
+   import matplotlib.pyplot as plt
+   from matplotlib.patches import Circle, FancyArrowPatch
+
+   pos = {"a": (0.0, 0.0), "b": (2.0, 0.0), "c": (4.0, 0.0)}
+   # (name, from, to, curvature, label offset): e1 and e2 are parallel, drawn
+   # as two arcs curving to either side
+   edges = [("e1", "a", "b", 0.3, (0, 0.5)), ("e2", "a", "b", -0.3, (0, -0.5)),
+            ("e3", "b", "c", 0, (0, 0.18))]
+
+   fig, axs = plt.subplots(1, 2, figsize=(9, 2.3))
+   for ax, is_directed, title in zip(axs, (False, True), ("UGraph", "DGraph")):
+       style = "-|>" if is_directed else "-"
+       for name, p, q, rad, (dx, dy) in edges:
+           ax.add_patch(FancyArrowPatch(pos[p], pos[q], arrowstyle=style, mutation_scale=16,
+                                        connectionstyle=f"arc3,rad={rad}", shrinkA=15, shrinkB=15,
+                                        color="0.15", lw=1.6))
+           mx = (pos[p][0] + pos[q][0]) / 2 + dx
+           my = (pos[p][1] + pos[q][1]) / 2 + dy
+           ax.text(mx, my, name, ha="center", va="center", fontsize=10, color="0.15")
+       x, y = pos["c"]  # e4: a loop, an edge from c to itself
+       ax.add_patch(FancyArrowPatch((x - 0.15, y + 0.15), (x + 0.15, y + 0.15), arrowstyle=style,
+                                    mutation_scale=16, connectionstyle="arc3,rad=-1.8",
+                                    color="0.15", lw=1.6))
+       ax.text(x, y + 0.62, "e4", ha="center", va="center", fontsize=10, color="0.15")
+       for name, (x, y) in pos.items():
+           ax.add_patch(Circle((x, y), 0.2, fc="#1f77b4", ec="none", zorder=3))
+           ax.text(x, y, name, ha="center", va="center", color="white", fontsize=11, zorder=4)
+       ax.set_xlim(-0.6, 4.6)
+       ax.set_ylim(-0.8, 0.95)
+       ax.set_aspect("equal")
+       ax.axis("off")
+       ax.set_title(title, fontsize=11)
+   fig.tight_layout()
+
+The vertices ``a``, ``b`` and ``c`` and edges ``e1`` and ``e2`` are added in that order.
+The resulting vertex lists are
+
+.. list-table::
+   :header-rows: 1
+   :widths: 10 30 30 30
+
+   * - Vertex name
+     - ``UGraph`` ``_edgelist``
+     - ``DGraph`` ``_edgelist``
+     - ``DGraph`` ``_inlist``
+   * - ``a``
+     - ``[e1, e2]``
+     - ``[e1, e2]``
+     - ``[]``
+   * - ``b``
+     - ``[e1, e2, e3]``
+     - ``[e3]``
+     - ``[e1, e2]``
+   * - ``c``
+     - ``[e3, e4, e4]``
+     - ``[e4]``
+     - ``[e3, e4]``
+
+The graph also keeps **every edge once** in ``graph._edges`` (an insertion-ordered
+dict, so ``[e1, e2, e3, e4]``).
+
+The public view of those lists
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. list-table::
+   :header-rows: 1
+   :widths: 30 35 35
+
+   * - Method
+     - Returns for ``UGraph``
+     - Returns for ``DGraph``
+   * - ``edges()``, ``out_edges()``
+     - a copy of ``_edgelist``
+     - a copy of ``_edgelist`` 
+   * - ``in_edges()``
+     - a copy of ``_edgelist``
+     - a copy of ``_inlist`` 
+   * - ``degree``
+     - ``len(_edgelist)``
+     - ``len(_edgelist) + len(_inlist)``
+   * - ``in_degree``
+     - ``len(_edgelist)``
+     - ``len(_inlist)``
+   * - ``out_degree``
+     - ``len(_edgelist)``
+     - ``len(_edgelist)``
+   * - ``adjacent()``
+     - the far end of each edge in ``_edgelist``
+     - the far end of each edge in ``_edgelist``
+   * - ``incidences()``
+     - ``adjacent()`` paired with ``out_edges()``
+     - ``adjacent()`` paired with ``out_edges()``
+
+All are returned in the order the edges were connected.
+
 
 Working with vertices and edges directly
 -----------------------------------------