Solved incorrect nodes positions and figure size in tree graph

[jules-vanaret]

This PR solves 2 problems:

• In plot_all_lineages, the figure grid is initialized with 2 lines by default, even if a single lineage is present. In that case, this leads to a figure with an incompressible white space below the lineage graph.
• The lineage graphs assigned incorrect depths (vertical positions) to the nodes. Mother and daughters nodes are at the same depth, and some leaf nodes are not reachable in the GUI even when the napari time slider is put to its maximum value.

Both problems can be seen using the following code:

from lineagetree import LineageTree
succs = {
    0: [1],
    1: [2],
    2: [3, 4],
    3: [5],
    5: [6],
    6: [],
    4: [7, 8],
    7: [9],
    9: [10],
    10: [],
    8: [11],
    11: [],
}
lt = LineageTree(successor=succs)
import matplotlib.pyplot as plt
lt.plot_all_lineages()
plt.show()

Results can be seen here:

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.43%. Comparing base (c431355) to head (b29f4f4).
⚠️ Report is 8 commits behind head on v3.x.

Additional details and impacted files

@@            Coverage Diff             @@
##             v3.x      #87      +/-   ##
==========================================
+ Coverage   86.40%   86.43%   +0.03%     
==========================================
  Files          20       20              
  Lines        1788     1792       +4     
==========================================
+ Hits         1545     1549       +4     
  Misses        243      243              

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