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colinvwood wants to merge 4 commits into from
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LANG: 2025.10 update & pin templating #385

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8d73777
np.inf
colinvwood Aug 19, 2025
066f972
n_iter -> max_iter
colinvwood Aug 19, 2025
2b4f74f
np.NaN -> np.nan and slice objects hashable pandas bug
colinvwood Aug 19, 2025
b97a98f
nj parameter rename
colinvwood Aug 19, 2025
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4 changes: 2 additions & 2 deletions q2_diversity/_alpha/_visualizer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -292,7 +292,7 @@ def _compute_rarefaction_data(feature_table, min_depth, max_depth, steps,
cols = pd.MultiIndex.from_product(
[list(depth_range), list(iter_range)],
names=['_alpha_rarefaction_depth_column_', 'iter'])
data = {k: pd.DataFrame(np.NaN, index=rows, columns=cols)
data = {k: pd.DataFrame(np.nan, index=rows, columns=cols)
for k in metrics}

ctx = qiime2.sdk.Context()
Expand Down Expand Up @@ -377,7 +377,7 @@ def alpha_rarefaction(output_dir: str, table: biom.Table, max_depth: int,
raise ValueError("All metadata filtered after dropping columns "
"that contained non-categorical data.")
metadata_df.columns = pd.MultiIndex.from_tuples(
[(c, '') for c in metadata_df.columns],
[(c, '_') for c in metadata_df.columns],
names=('_alpha_rarefaction_depth_column_', 'iter'))
columns = metadata_df.columns.get_level_values(0)
data = _compute_rarefaction_data(table, min_depth, max_depth,
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2 changes: 1 addition & 1 deletion q2_diversity/_beta/_beta_rarefaction.py
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Expand Up @@ -160,7 +160,7 @@ def _upgma(dm):
def _nj(dm):
# Negative branch lengths are strange, BUT we are clustering, not modeling
# evolution, so it's not necessarily a problem
nj = skbio.tree.nj(dm, disallow_negative_branch_length=False)
nj = skbio.tree.nj(dm, neg_as_zero=False)
return nj.root_at_midpoint()


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2 changes: 1 addition & 1 deletion q2_diversity/_ordination.py
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Expand Up @@ -53,7 +53,7 @@ def tsne(distance_matrix: skbio.DistanceMatrix,

tsne = TSNE(number_of_dimensions, perplexity=perplexity,
learning_rate=learning_rate,
n_iter=n_iter,
max_iter=n_iter,
early_exaggeration=early_exaggeration,
random_state=random_state).fit_transform(data)

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2 changes: 1 addition & 1 deletion q2_diversity/tests/test_adonis.py
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Expand Up @@ -39,7 +39,7 @@ def test_execute_and_validate_output(self):
exp = pd.DataFrame(
[[1.0, 0.322916667, 0.322916667, 0.0, 0.534482759, 1.0],
[1.0, 0.281250000, 0.281250000, 0.0, 0.465517241, 1.0],
[0.0, -1.403048e-18, -np.Infinity, np.nan, -2.322286e-18, np.nan],
[0.0, -1.403048e-18, -np.inf, np.nan, -2.322286e-18, np.nan],
[2.0, 0.604166667, np.nan, np.nan, 1.0, np.nan]],
columns=['Df', 'SumsOfSqs', 'MeanSqs', 'F.Model', 'R2', 'Pr(>F)'],
index=['letter', 'number', 'Residuals', 'Total'])
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