fix column setter, add row get/set

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## Version 0.6.0 - 0.6.4
+## Version 0.6.0 - 0.6.5
 
 - Classes now extend `BiocObject` from biocutils, which provides a metadata field.
 - `valdiate` is renamed to `_validate` for consistency with other classes and packages.

src/summarizedexperiment/base.py

@@ -1198,9 +1198,9 @@ def to_anndata(self):
 
         return obj
 
-    ######################################
-    ######>> col_data accessors <<########
-    ######################################
+    ##########################################
+    ######>> col/row data accessors <<########
+    ##########################################
 
     def get_column_data_column(self, column: str) -> Any:
         """Access a column from the ``column_data``.
@@ -1232,5 +1232,38 @@ def set_column_data_column(self, column: str, value: Any, in_place: bool = False
             or as a reference to the (in-place-modified) original.
         """
         output = self._define_output(in_place)
-        output._cols = output._cols.set_column(column, value, in_place=False)
+        output._cols = output._cols.set_column(column, value, in_place=in_place)
+        return output
+
+    def get_row_data_column(self, column: str) -> Any:
+        """Access a column from the ``row_data``.
+
+        Args:
+            column:
+                Name of the column to retrieve.
+
+        Returns:
+            The content of the column.
+        """
+        return self._rows.get_column(column)
+
+    def set_row_data_column(self, column: str, value: Any, in_place: bool = False) -> BaseSE:
+        """Set or replace a column in ``row_data``.
+
+        Args:
+            column:
+                Name of the column to set.
+
+            value:
+                Values for the column. Must match the number of features (rows).
+
+            in_place:
+                Whether to modify the ``BaseSE`` in place.
+
+        Returns:
+            A modified ``BaseSE`` object, either as a copy of the original
+            or as a reference to the (in-place-modified) original.
+        """
+        output = self._define_output(in_place)
+        output._rows = output._rows.set_column(column, value, in_place=in_place)
         return output

tests/test_SE_methods.py

@@ -187,3 +187,19 @@ def test_SE_coldata_accessors():
 
     tse.set_column_data_column("stuff", [1, 2, 3, 4, 5, 6], in_place=True)
     assert "stuff" in tse.col_data.column_names
+
+def test_SE_rowdata_accessors():
+    tse = SummarizedExperiment(
+        assays={"counts": counts}, row_data=row_data, column_data=col_data
+    )
+
+    assert tse.get_row_data_column("strand") is not None
+    assert len(tse.get_row_data_column("strand")) == 200
+
+    new_tse = tse.set_row_data_column("new_scores", np.arange(200) * 2)
+    assert new_tse.shape == tse.shape
+    assert "new_scores" in new_tse.row_data.column_names
+    assert "new_scores" not in tse.row_data.column_names
+
+    tse.set_row_data_column("new_scores", np.arange(200) * 3, in_place=True)
+    assert "new_scores" in tse.row_data.column_names