feat: directed vertices record incoming edges; degree is in plus out; validate(); BaseGraph

[petercorke]

Summary

Directed vertices now record the edges that end at them as well as the ones that leave them, and the rest of the in-edge / degree / hygiene work that follows from it. Six commits, each verified green on exactly its own contents:

1. BaseGraph is the public name of the common base class (_BaseGraph was never released, so no alias); BaseGraph and BaseVertex are exported with an __all__.
2. In-edges and degree. predecessors(), successors() (= adjacent()), in_edges(), out_edges(), in_degree, out_degree. remove_vertex finds a vertex's edges from its own lists (O(degree), was O(E)); iscyclic uses in-degrees (O(V), was O(E)).
3. graph.validate() returns a list of the ways the graph's records disagree (empty when consistent). It does not change the graph, costs O(V+E) and never raises on corruption.
4. Hygiene. Vertex.label is read-only; assigning Vertex.name updates the graph's name table, refuses a duplicate or None; exporters use only the public API.
5. add_vertex names. A duplicate name raises ValueError and changes nothing; the default #N name is the first free one (it could collide after a removal); a vertex that already belongs to a graph is refused.

Breaking change for DGraph (1.0)

degree is now the graph-theory degree, in plus out, so a self-loop counts 2 and the degrees of a graph sum to twice its edges. It counted only the edges leaving the vertex.

Changed	Old value
vertex.degree	vertex.out_degree
graph.degree()	np.diag([v.out_degree for v in g])
graph.connectivity()	[v.out_degree for v in g]
graph.average_degree() is 2E/N	g.ne / g.n

Laplacian() is unchanged (it is D_out - A, and now takes the out-degree explicitly). For an undirected graph every quantity is as before. Each is documented with a versionchanged note. A survey of RTB, MVTB and RVC3 found no caller of any of them on a DGraph.

Tests

New: test_in_edges, test_validate (27 deliberate corruptions each detected and named; random edit sequences stay valid), test_attribute_hygiene, test_add_vertex_names.

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[codacy-production]

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

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🟢 Metrics 166 complexity · 2 duplication

Metric	Results
Complexity	166
Duplication	2

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[codecov]

Codecov Report

❌ Patch coverage is 99.41520% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 94.60%. Comparing base (9ac0001) to head (8cab999).
⚠️ Report is 8 commits behind head on main.

Files with missing lines	Patch %	Lines
src/pgraph/PGraph.py	99.37%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #40      +/-   ##
==========================================
+ Coverage   93.86%   94.60%   +0.73%     
==========================================
  Files           3        3              
  Lines        1076     1205     +129     
==========================================
+ Hits         1010     1140     +130     
+ Misses         66       65       -1     

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