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Attempt to fix pandas errors in testing #4

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Merged
kretep merged 4 commits into from
Jan 22, 2026
Merged

Attempt to fix pandas errors in testing #4

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9ad878f
Attempt to fix pandas errors in testing
kretep Jan 22, 2026
45901ff
Constrain dependency versions more
kretep Jan 22, 2026
bec5dfe
Using unique site_ids to avoid singular matrix issues
kretep Jan 22, 2026
0721181
Revert "Constrain dependency versions more"
kretep Jan 22, 2026
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6 changes: 5 additions & 1 deletion cvasl/vendor/open_nested_combat/nest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -125,7 +125,11 @@ def OPNestedComBat(
for item in order:
f.write("%s\n" % item)

output_df = pd.DataFrame.from_records(n_dat.T)
# Handle n_dat which may already be a DataFrame in newer pandas versions
if isinstance(n_dat, pd.DataFrame):
output_df = n_dat.T
else:
output_df = pd.DataFrame.from_records(n_dat.T)
output_df.columns = dat.index
if return_estimates:
return output_df, final_estimate
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -41,7 +41,7 @@ dependencies = [
"nipy",
"numpy<2",
"opencv-python",
"pandas>=1.2.0",
"pandas>=1.2.0,<3",
"patsy",
"pingouin",
"grad-cam",
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5 changes: 3 additions & 2 deletions tests/test_basics.py
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Expand Up @@ -20,8 +20,9 @@ def load_datasets(shared_datadir):
os.path.realpath(shared_datadir / "TestingData_Site2_fake.csv"),
os.path.realpath(shared_datadir / "TrainingData_Site1_fake.csv")
]
# Using duplicate site_id (1, 2, 1) to test that harmonizers handle multiple datasets from the same site correctly
input_sites = [1, 2, 1]
# Using unique site_ids to avoid singular matrix issues in neuroharmonize
# (the third file is also from site 1 but we assign it site 3 to ensure uniqueness)
input_sites = [1, 2, 3]

mri_datasets = [
MRIdataset(input_path, input_site, "participant_id", features_to_drop=[])
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