Fix all-NaN extra obs after PseudobulkSpace with groups_col

pertpy/tools/_perturbation_space/_simple.py

@@ -147,14 +147,18 @@ def compute(
             ps_adata.X = ps_adata.layers[mode]
 
         missing_cols = [col for col in original_obs.columns if col not in ps_adata.obs.columns]
-        new_cols_data = {}
 
-        for col in missing_cols:
-            grouped_values = original_obs.groupby(grouping_cols, observed=False)[col].first()
-            new_cols_data[col] = grouped_values.reindex(ps_adata.obs.index).values
-
-        if new_cols_data:
-            ps_adata.obs = pd.concat([ps_adata.obs, pd.DataFrame(new_cols_data, index=ps_adata.obs.index)], axis=1)
+        if missing_cols:
+            grouped = original_obs.groupby(grouping_cols, observed=False)[missing_cols].first()
+            # `ps_adata.obs` is indexed by joined group keys (e.g. "patient_cluster"),
+            # so reindex by the grouping columns themselves rather than the joined index.
+            if len(grouping_cols) == 1:
+                lookup = pd.Index(ps_adata.obs[grouping_cols[0]])
+            else:
+                lookup = pd.MultiIndex.from_frame(ps_adata.obs[grouping_cols])
+            aligned = grouped.reindex(lookup)
+            aligned.index = ps_adata.obs.index
+            ps_adata.obs = pd.concat([ps_adata.obs, aligned], axis=1)
 
         ps_adata.obs[target_col] = ps_adata.obs[target_col].astype("category")
 

tests/tools/_perturbation_space/test_simple_perturbation_space.py

@@ -93,6 +93,39 @@ def test_pseudobulk_response(adata_simple):
         )
 
 
+def test_pseudobulk_preserves_extra_obs_with_groups_col(rng):
+    """Regression test for https://github.com/scverse/pertpy/issues/1003.
+
+    When `groups_col` is provided, the pseudobulk output's obs index is joined (e.g. "P0_C0"),
+    so reindexing extra obs columns must use the grouping columns as keys, not the joined index.
+    Otherwise every extra column ends up all-NaN and downstream tools (e.g. PyDESeq2) fail.
+    """
+    patients = [f"P{i}" for i in range(4)]
+    clusters = [f"C{i}" for i in range(2)]
+    efficacy_per_patient = {"P0": "SD", "P1": "PR", "P2": "PD", "P3": "SD"}
+    n_cells = 200
+    patient_choice = rng.choice(patients, size=n_cells)
+    cluster_choice = rng.choice(clusters, size=n_cells)
+    obs = pd.DataFrame(
+        {
+            "Patient": pd.Categorical(patient_choice, categories=patients),
+            "Cluster": pd.Categorical(cluster_choice, categories=clusters),
+            "Efficacy": pd.Categorical(
+                [efficacy_per_patient[p] for p in patient_choice], categories=["SD", "PR", "PD"]
+            ),
+        }
+    )
+    X = rng.poisson(5, size=(n_cells, 10)).astype(float)
+    adata = AnnData(X=X, obs=obs)
+
+    ps = pt.tl.PseudobulkSpace()
+    pdata = ps.compute(adata, target_col="Patient", groups_col="Cluster", mode="sum")
+
+    assert pdata.obs["Efficacy"].isna().sum() == 0
+    for row in pdata.obs.itertuples():
+        assert row.Efficacy == efficacy_per_patient[row.Patient]
+
+
 def test_centroid_umap_response():
     X = np.zeros((10, 5))