Fixed tests.

popv/visualization.py

@@ -186,11 +186,11 @@ def celltype_ratio_bar_plot(
         prop.loc[x, "query"] = np.sum(labels[is_query] == x)
         prop.loc[x, "ref"] = np.sum(labels[~is_query] == x)
     if normalize:
-        prop = prop.div(prop.sum(axis=1))
+        prop = prop.div(prop.sum(axis=0), axis=1)
 
-    ax = prop.loc[cell_types].plot(kind="bar", figsize=(len(cell_types) * 0.5, 4), logy=True)
+    ax = prop.loc[cell_types].plot(kind="bar", figsize=(len(cell_types) * 0.5, 4), logy=(not normalize))
     ax.set_ylabel("Celltype")
-    ax.set_ylabel("log Celltype Abundance")
+    ax.set_ylabel("Celltype Abundance")
     if save_folder is not None:
         save_path = os.path.join(save_folder, "celltype_prop_barplot.pdf")
         ax.get_figure().savefig(save_path, bbox_inches="tight", dpi=300)

pyproject.toml

@@ -10,7 +10,7 @@ exclude = ["resources/*", "tests/*", "dataset/*"]
 
 [project]
 name = "PopV"
-version = "0.4.1"
+version = "0.4.2"
 description = "Consensus prediction of cell type labels with popV"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -33,8 +33,6 @@ dependencies = [
     "gdown>4.6.0",
     "h5py>3.7.0",
     "huggingface-hub>=0.11.1",
-    "jax<0.4.24", # Remove with scvi-tools 1.1
-    "jaxlib<0.4.24",
     "onclass>=1.3",
     "scanorama>1.7.2",
     "scanpy>1.9.0",

tests/core/test_models.py

@@ -177,7 +177,9 @@ def test_celltypist():
 def test_annotation():
     """Test Annotation and Plotting pipeline."""
     adata = _get_test_anndata().adata
-    popv.annotation.annotate_data(adata, methods=["svm", "rf"], save_path="tests/tmp_testing/popv_test_results/")
+    popv.annotation.annotate_data(
+        adata, methods=["svm", "rf"],
+        save_path="tests/tmp_testing/popv_test_results/")
     popv.visualization.agreement_score_bar_plot(adata)
     popv.visualization.prediction_score_bar_plot(adata)
     popv.visualization.make_agreement_plots(adata, prediction_keys=adata.uns["prediction_keys"])
@@ -190,11 +192,14 @@ def test_annotation():
 def test_annotation_no_ontology():
     """Test Annotation and Plotting pipeline without ontology."""
     adata = _get_test_anndata(cl_obo_folder=False).adata
-    popv.annotation.annotate_data(adata, methods=["svm", "rf"], save_path="tests/tmp_testing/popv_test_results/")
+    popv.annotation.annotate_data(
+        adata, methods=["svm", "rf"],
+        save_path="tests/tmp_testing/popv_test_results/")
     popv.visualization.agreement_score_bar_plot(adata)
     popv.visualization.prediction_score_bar_plot(adata)
     popv.visualization.make_agreement_plots(adata, prediction_keys=adata.uns["prediction_keys"])
-    popv.visualization.celltype_ratio_bar_plot(adata)
+    popv.visualization.celltype_ratio_bar_plot(adata, save_folder="tests/tmp_testing/popv_test_results/")
+    popv.visualization.celltype_ratio_bar_plot(adata, normalize=False)
 
     assert "popv_majority_vote_prediction" in adata.obs.columns
     assert not adata.obs["popv_majority_vote_prediction"].isnull().any()