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replace append with set_columns #402

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Merged
petrelharp merged 1 commit into from
Oct 24, 2025
Merged

replace append with set_columns #402

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27 changes: 11 additions & 16 deletions pyslim/methods.py
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Original file line number Diff line number Diff line change
Expand Up @@ -714,21 +714,18 @@ def slim_time(ts, time, stage="late"):

def _shift_times(ts, dt):
"""
Add `dt` to the times ago of all nodes, and mutations.
Add `dt` to the times ago of all nodes and mutations.
(Note: migrations not currently supported by simplify,
so not used here.)
"""
tables = ts.dump_tables()
if dt != 0:
tables.nodes.clear()
tables.mutations.clear()
tables.migrations.clear()
for node in ts.nodes():
tables.nodes.append(node.replace(time=node.time + dt))
for mutation in ts.mutations():
tables.mutations.append(mutation.replace(time=mutation.time + dt))
# for mig in ts.migrations():
# tables.migrations.append(mig.replace(time=mig.time + dt))
d = tables.nodes.asdict()
d['time'] += dt
tables.nodes.set_columns(**d)
d = tables.mutations.asdict()
d['time'] += dt
tables.mutations.set_columns(**d)
return tables


Expand Down Expand Up @@ -777,12 +774,10 @@ def set_slim_state(ts, time=0, individuals=None):
md['SLiM']['cycle'] -= time
tables.metadata = md
if individuals is not None:
flags = tables.individuals.flags
flags &= ~INDIVIDUAL_ALIVE
flags[individuals] |= INDIVIDUAL_ALIVE
tables.individuals.clear()
for f, ind in zip(flags, ts.individuals()):
tables.individuals.append(ind.replace(flags=f))
d = tables.individuals.asdict()
d['flags'] &= ~INDIVIDUAL_ALIVE
d['flags'][individuals] |= INDIVIDUAL_ALIVE
tables.individuals.set_columns(**d)
return tables.tree_sequence()


Expand Down