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Fix a few minor issues #621

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Merged
jeromekelleher merged 2 commits into from
Jul 21, 2026
Merged

Fix a few minor issues #621

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1e3c192
Remove np._str from retro group log messages
jeromekelleher Jul 21, 2026
416e018
Detect gid prefix collisions.
jeromekelleher Jul 21, 2026
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9 changes: 9 additions & 0 deletions sc2ts/debug.py
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Original file line number Diff line number Diff line change
Expand Up @@ -458,6 +458,7 @@ def _preprocess_nodes(self, show_progress):
total=ts.num_nodes,
disable=not show_progress,
)
group_id_prefix_map = {}
for node in iterator:
md = node.metadata
self.nodes_metadata[node.id] = md
Expand All @@ -468,6 +469,14 @@ def _preprocess_nodes(self, show_progress):
if group_id is not None:
# Shorten key for readability.
gid = group_id[: self.sample_group_id_prefix_len]
if gid not in group_id_prefix_map:
group_id_prefix_map[gid] = group_id
if group_id != group_id_prefix_map[gid]:
raise ValueError(
"Sample group ID prefix collision. "
"Increase sample_group_id_prefix_len "
"(default=10)"
)
self.sample_group_nodes[gid].append(node.id)
if node.is_sample():
self.nodes_date[node.id] = md["date"]
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6 changes: 3 additions & 3 deletions sc2ts/inference.py
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Expand Up @@ -932,15 +932,15 @@ def __post_init__(self):

@property
def strains(self):
return [s.strain for s in self.samples]
return [str(s.strain) for s in self.samples]

@property
def date_count(self):
return collections.Counter([s.date for s in self.samples])
return collections.Counter([str(s.date) for s in self.samples])

@property
def pango_count(self):
return collections.Counter([s.pango for s in self.samples])
return collections.Counter([str(s.pango) for s in self.samples])

def __len__(self):
return len(self.samples)
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