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Assert the computed D-E weight in the Fig. 2a test - #47
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Fig. 2a of the edgeHOG paper shows weight 2 for D-E in the propagated graph of species 3 (A Y C D1 E1 D2 E2), and 3 at the root. Each of the three extant adjacencies D1-E1, E1-D2 and D2-E2 supports D-E, so the computed weights of 3 and 4 are correct and the figure simplifies this. Turn the xfail test into a regular test of the computed weights. Fixes DessimozLab#39
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Fixes #39 (part of #43).
In the example of Fig. 2a of the edgeHOG paper, species 3 has the gene order A Y C D1 E1 D2 E2. The figure shows weight 2 for D–E in the propagated graph of species 3, and 3 at the root.
Each of the three extant adjacencies D1–E1, E1–D2 and D2–E2 supports the ancestral adjacency D–E, so the weights computed by edgeHOG (3 in species 3, 4 at the root) are correct, and the figure simplifies this. The weights only matter for linearization, and the linearized result of the example is the same either way.
This PR turns the
xfailtesttest_paper_figure2.py::test_fig2a_tandem_duplicate_weights, which encoded the figure's values, into a regular test of the computed weights. No code change.