fixes bug when obs index is set

YosefLab · Apr 15, 2024 · 1470788 · 1470788
1 parent ee602c6
commit 1470788
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/src/mrvi/_model.py b/src/mrvi/_model.py
@@ -400,7 +400,7 @@ def per_sample_inference_fn(pair):
                     mean_zs_,
                     dims=["cell_name", "sample", "latent_dim"],
                     coords={
-                        "cell_name": self.adata.obs_names[indices],
+                        "cell_name": self.adata.obs_names[indices].values,
                         "sample": self.sample_order,
                     },
                     name="sample_representations",
@@ -419,7 +419,7 @@ def per_sample_inference_fn(pair):
                     sampled_zs_,
                     dims=["cell_name", "mc_sample", "sample", "latent_dim"],
                     coords={
-                        "cell_name": self.adata.obs_names[indices],
+                        "cell_name": self.adata.obs_names[indices].values,
                         "sample": self.sample_order,
                     },
                     name="sample_representations",
@@ -565,7 +565,7 @@ def _compute_distance(rep):
                 dists,
                 dims=["cell_name", "sample_x", "sample_y"],
                 coords={
-                    "cell_name": self.adata.obs_names[indices],
+                    "cell_name": self.adata.obs_names[indices].values,
                     "sample_x": self.sample_order,
                     "sample_y": self.sample_order,
                 },
@@ -578,7 +578,7 @@ def _compute_distance(rep):
                 dists,
                 dims=["cell_name", "mc_sample", "sample_x", "sample_y"],
                 coords={
-                    "cell_name": self.adata.obs_names[indices],
+                    "cell_name": self.adata.obs_names[indices].values,
                     "mc_sample": np.arange(reps.shape[1]),
                     "sample_x": self.sample_order,
                     "sample_y": self.sample_order,

diff --git a/tests/test_model.py b/tests/test_model.py
@@ -7,6 +7,7 @@
 @pytest.fixture
 def adata():
     adata = synthetic_iid()
+    adata.obs.index.name = "cell_id"
     adata.obs["sample"] = np.random.choice(15, size=adata.shape[0])
     meta1 = np.random.randint(0, 2, size=15)
     adata.obs["meta1"] = meta1[adata.obs["sample"].values]