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Fix: nodes at t #85

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BadPrograms wants to merge 3 commits into from
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Fix: nodes at t #85

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91c1bde
initial
BadPrograms Aug 5, 2025
f0653f5
fix for pr (no sets)
BadPrograms Aug 11, 2025
994a0f9
simplified logic
jules-vanaret Aug 26, 2025
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17 changes: 7 additions & 10 deletions src/lineagetree/_basics/_navigation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -360,23 +360,20 @@ def nodes_at_t(
list of int
list of ids of the nodes at time `t` spawned by `r`
"""
if not r and r != 0:
r = {root for root in lT.roots if lT.time[root] <= t}
if r is None:
return lT.time_nodes.get(t, [])
if isinstance(r, int):
r = [r]
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@leoguignard leoguignard Aug 11, 2025

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Also I guess one could do it that way at the beginning:

if r is None:
    ...

Instead of

if not r and r != 0:
    ...

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@leoguignard leoguignard Aug 11, 2025

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And yes, it would change the behavior since it would make the function return nothing in case the user gave [] for roots instead of returning the output of lT.roots which is I think a plus.
If the user specifically gave the empty list of nodes, it should not get any node in the return value.

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@BadPrograms BadPrograms Aug 11, 2025

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Since we have time_nodes again, I don't care about the behaviour, so I will do that.

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@BadPrograms BadPrograms Aug 11, 2025

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Actually since we have the time_nodes the function should change entirely.

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@BadPrograms BadPrograms Aug 11, 2025 •
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Also, I think we might want to return a set and not a list. There is no reason to index the result, and I like sets more. The only reason to use a list is that the rest of the LineageTree consists mostly of lists, so we can do so for the sake of consistency.

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@leoguignard leoguignard Aug 18, 2025

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Also I guess one could do it that way at the beginning:

if r is None:
...

Instead of

if not r and r != 0:
...

Dont you want to do that?

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@leoguignard leoguignard Aug 18, 2025

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Why should the function change? and what should it be instead?

About the list vs set, the list can have an advantadge since it is explicitly ordered and that currently the nodes are returned in a specific order (preorder)

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@BadPrograms BadPrograms Aug 18, 2025

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If we dont provide roots it should return lT.time_nodes[t]

if t is None:
t = lT.t_e
to_do = list(r)
final_nodes = []
while len(to_do) > 0:
while 0 < len(to_do):
curr = to_do.pop()
for _next in lT._successor[curr]:
if lT._time[_next] < t:
to_do.append(_next)
elif lT._time[_next] == t:
final_nodes.append(_next)
if not final_nodes:
return list(r)
if lT._time[curr] == t:
final_nodes.append(curr)
elif lT._time[curr] < t:
to_do.extend(lT.successor[curr])
return final_nodes


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