Fixes for pandas 1.3.0 (scverse#1918)

* Fixes for pandas 1.3.0
yuzhenpeng · Jul 5, 2021 · c9b5913 · c9b5913
1 parent 87396a8
commit c9b5913
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diff --git a/docs/release-notes/1.8.1.rst b/docs/release-notes/1.8.1.rst
@@ -3,5 +3,6 @@
 
 .. rubric:: Bug fixes
 
+- Workarounds for some changes/ bugs in pandas 1.3 :pr:`1918` :smaller:`I Virshup`
 
 .. rubric:: Performance Enhancements
diff --git a/scanpy/plotting/_anndata.py b/scanpy/plotting/_anndata.py
@@ -1938,7 +1938,7 @@ def _prepare_dataframe(
         categorical.name = groupby[0]
     else:
         # join the groupby values  using "_" to make a new 'category'
-        categorical = obs_tidy[groupby].agg('_'.join, axis=1).astype('category')
+        categorical = obs_tidy[groupby].apply('_'.join, axis=1).astype('category')
         categorical.name = "_".join(groupby)
 
         # preserve category order

diff --git a/scanpy/preprocessing/_qc.py b/scanpy/preprocessing/_qc.py
@@ -106,7 +106,7 @@ def describe_obs(
         obs_metrics[f"log1p_n_{var_type}_by_{expr_type}"] = np.log1p(
             obs_metrics[f"n_{var_type}_by_{expr_type}"]
         )
-    obs_metrics[f"total_{expr_type}"] = X.sum(axis=1)
+    obs_metrics[f"total_{expr_type}"] = np.ravel(X.sum(axis=1))
     if log1p:
         obs_metrics[f"log1p_total_{expr_type}"] = np.log1p(
             obs_metrics[f"total_{expr_type}"]
@@ -119,8 +119,8 @@ def describe_obs(
                 proportions[:, i] * 100
             )
     for qc_var in qc_vars:
-        obs_metrics[f"total_{expr_type}_{qc_var}"] = X[:, adata.var[qc_var].values].sum(
-            axis=1
+        obs_metrics[f"total_{expr_type}_{qc_var}"] = np.ravel(
+            X[:, adata.var[qc_var].values].sum(axis=1)
         )
         if log1p:
             obs_metrics[f"log1p_total_{expr_type}_{qc_var}"] = np.log1p(
Original file line number	Diff line number	Diff line change
Expand Up		@@ -3,5 +3,6 @@

		.. rubric:: Bug fixes

		- Workarounds for some changes/ bugs in pandas 1.3 :pr:`1918` :smaller:`I Virshup`

		.. rubric:: Performance Enhancements