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enable future - calm down dependencies [WIP] #479

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enable future - calm down dependencies [WIP] #479

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63bfd37
pandas>2 groupby observed behavior in expected
sergpolly Jan 17, 2024
eaa7e3f
another groupby fix in is_track
sergpolly Jan 20, 2024
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4 changes: 2 additions & 2 deletions cooltools/api/expected.py
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Original file line number Diff line number Diff line change
Expand Up @@ -319,12 +319,12 @@ def make_diag_tables(clr, regions, regions2=None, clr_weight_name="weight"):
bins = clr.bins()[:]
if clr_weight_name is None:
# ignore bad bins
sizes = dict(bins.groupby("chrom").size())
sizes = dict(bins.groupby("chrom", observed=True).size())
bad_bin_dict = {
chrom: np.zeros(sizes[chrom], dtype=bool) for chrom in sizes.keys()
}
elif is_cooler_balanced(clr, clr_weight_name):
groups = dict(iter(bins.groupby("chrom")[clr_weight_name]))
groups = dict(iter(bins.groupby("chrom", observed=True)[clr_weight_name]))
bad_bin_dict = {
chrom: np.array(groups[chrom].isnull()) for chrom in groups.keys()
}
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2 changes: 1 addition & 1 deletion cooltools/lib/checks.py
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Expand Up @@ -547,7 +547,7 @@ def is_track(track, raise_errors=False):
else:
return False

for name, group in track.groupby(track.columns[0]):
for name, group in track.groupby(track.columns[0], observed=True):
if not _is_sorted_ascending(group[track.columns[1]].values):
if raise_errors:
raise ValueError(
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