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Merged
canergen merged 2 commits into from
May 8, 2025
Merged

Python 3.11 changes. #88

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dcfd4d1
Python 3.11 changes.
canergen May 8, 2025
d4fbdbe
Merge branch 'main' into release_hub
canergen May 8, 2025
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2 changes: 1 addition & 1 deletion popv/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
if sys.version_info[:2] != (3, 10):
warnings.warn(
"Pretrained models on huggingface are trained with Python 3.11. "
f"Detected Python {sys.version.split()[0]} will not load these models.",
"Detected Python {sys.version.split()[:2]} will not load these models.",
UserWarning,
stacklevel=3,
)
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4 changes: 2 additions & 2 deletions popv/algorithms/_svm.py
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Expand Up @@ -76,14 +76,14 @@ def predict(self, adata):
if adata.uns["_prediction_mode"] == "retrain":
train_idx = adata.obs["_ref_subsample"]
train_x = adata[train_idx].layers[self.layer_key] if self.layer_key else adata[train_idx].X
train_x = np.array(train_x.todense())
train_y = adata.obs.loc[train_idx, self.labels_key].cat.codes.to_numpy()
if settings.cuml:
from cuml.svm import LinearSVC
from sklearn.multiclass import OneVsRestClassifier

self.classifier_dict["probability"] = self.return_probabilities
clf = OneVsRestClassifier(LinearSVC(**self.classifier_dict))
train_x = train_x.todense()
clf.fit(train_x, train_y)
joblib.dump(
clf,
Expand Down Expand Up @@ -131,7 +131,7 @@ def predict(self, adata):
for i in range(0, adata.n_obs, shard_size):
tmp_x = test_x[i : i + shard_size]
names_x = adata.obs_names[i : i + shard_size]
tmp_x = tmp_x.todense()
tmp_x = np.array(tmp_x.todense())
result_df.loc[names_x, self.result_key] = adata.uns["label_categories"][clf.predict(tmp_x).astype(int)]
if self.return_probabilities:
result_df.loc[names_x, f"{self.result_key}_probabilities"] = np.max(
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2 changes: 2 additions & 0 deletions popv/hub/_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import json
import os
import sys
from dataclasses import asdict, dataclass, field

from anndata import AnnData
Expand Down Expand Up @@ -194,6 +195,7 @@ def _to_model_card(self) -> ModelCard:
"genomics",
"single-cell",
f"anndata_version:{self.anndata_version}",
f"python_version:{'.'.join([str(i) for i in sys.version_info[:3]])}",
"popV",
]
for t in self.tissues:
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