fix bugs with row/col name setters

src/summarizedexperiment/BaseSE.py

@@ -6,6 +6,7 @@
 import biocframe
 import biocutils as ut
 
+from ._assayutils import check_assays_are_equal, merge_assays
 from ._frameutils import _sanitize_frame
 from .type_checks import is_matrix_like
 from .types import SliceResult
@@ -275,8 +276,8 @@ def __repr__(self) -> str:
         pattern = (
             f"Class {type(self).__name__} with {self.shape[0]} features and {self.shape[1]} samples \n"
             f"  assays: {', '.join(list(self.assays.keys()))} \n"
-            f"  row_data: {self._rows.names if self._rows is not None else None} \n"
-            f"  column_data: {self._cols.names if self._cols is not None else None}"
+            f"  row_data: {self._rows.row_names if self._rows is not None else None} \n"
+            f"  column_data: {self._cols.column_names if self._cols is not None else None}"
         )
         return pattern
 
@@ -591,7 +592,7 @@ def get_columnnames(self) -> Optional[ut.Names]:
         Returns:
             List of column names, or None if no column names are available.
         """
-        return self._cols.get_rownames()
+        return self._column_names
 
     def set_columnnames(
         self, names: Optional[List[str]], in_place: bool = False
@@ -614,7 +615,7 @@ def set_columnnames(
         if names is not None and not isinstance(names, ut.Names):
             names = ut.Names(names)
 
-        _validate_rows(self._cols, names, self.shape)
+        _validate_cols(self._cols, names, self.shape)
 
         output = self._define_output(in_place)
         output._column_names = names
@@ -640,7 +641,7 @@ def columnnames(self, names: Optional[List[str]]):
     @property
     def colnames(self) -> Optional[ut.Names]:
         """Alias for :py:attr:`~get_columnnames`, provided for back-compatibility."""
-        return self.get_colnames()
+        return self.get_columnnames()
 
     @colnames.setter
     def colnames(self, names: Optional[List[str]]):
@@ -657,7 +658,7 @@ def colnames(self, names: Optional[List[str]]):
     @property
     def col_names(self) -> Optional[ut.Names]:
         """Alias for :py:attr:`~get_columnnames`, provided for back-compatibility."""
-        return self.get_colnames()
+        return self.get_columnnames()
 
     @col_names.setter
     def col_names(self, names: Optional[List[str]]):
@@ -1044,40 +1045,44 @@ def to_anndata(self):
     ######>> combine ops <<#####
     ############################
 
-    # def combine_rows(self, *experiments: "BaseSE"):
-    #     _all_objects = [self] + experiments
+    def combine_rows(self, *experiments: "BaseSE"):
+        _all_objects = [self] + experiments
 
-    #     _new_assays = merge_assays([x.assays for x in _all_objects])
+        _all_assays = [x.assays for x in _all_objects]
+        check_assays_are_equal(_all_assays)
+        _new_assays = merge_assays(_all_assays, by="row")
 
-    #     _all_rows = [x._rows for x in _all_objects]
-    #     _new_rows = ut.combine_rows(_all_rows)
+        _all_rows = [x._rows for x in _all_objects]
+        _new_rows = ut.combine_rows(_all_rows)
 
-    #     _all_cols = [x._cols for x in _all_objects]
-    #     _new_cols = ut.combine_columns(_all_cols)
+        _all_cols = [x._cols for x in _all_objects]
+        _new_cols = ut.combine_columns(_all_cols)
 
-    #     current_class_const = type(self)
-    #     return current_class_const(
-    #         assays=_new_assays,
-    #         row_data=_new_rows,
-    #         column_data=_new_cols,
-    #         metadata=self._metadata,
-    #     )
+        current_class_const = type(self)
+        return current_class_const(
+            assays=_new_assays,
+            row_data=_new_rows,
+            column_data=_new_cols,
+            metadata=self._metadata,
+        )
 
-    # def combine_cols(self, *experiments: "BaseSE"):
-    #     _all_objects = [self] + experiments
+    def combine_cols(self, *experiments: "BaseSE"):
+        _all_objects = [self] + experiments
 
-    #     _new_assays = merge_assays([x.assays for x in _all_objects])
+        _all_assays = [x.assays for x in _all_objects]
+        check_assays_are_equal(_all_assays)
+        _new_assays = merge_assays(_all_assays, by="column")
 
-    #     _all_rows = [x._rows for x in _all_objects]
-    #     _new_rows = ut.combine_columns(_all_rows)
+        _all_rows = [x._rows for x in _all_objects]
+        _new_rows = ut.combine_columns(_all_rows)
 
-    #     _all_cols = [x._cols for x in _all_objects]
-    #     _new_cols = ut.combine_rows(_all_cols)
+        _all_cols = [x._cols for x in _all_objects]
+        _new_cols = ut.combine_rows(_all_cols)
 
-    #     current_class_const = type(self)
-    #     return current_class_const(
-    #         assays=_new_assays,
-    #         row_data=_new_rows,
-    #         column_data=_new_cols,
-    #         metadata=self._metadata,
-    #     )
+        current_class_const = type(self)
+        return current_class_const(
+            assays=_new_assays,
+            row_data=_new_rows,
+            column_data=_new_cols,
+            metadata=self._metadata,
+        )

src/summarizedexperiment/_assayutils.py

@@ -1,24 +1,35 @@
 import itertools
 
+import biocutils as ut
+
 __author__ = "jkanche"
 __copyright__ = "jkanche"
 __license__ = "MIT"
 
 
-def merge_assays(assays):
-    _all_keys = [list(x.keys() for x in assays)]
+def merge_assays(assays, by):
+    if by not in ["row", "column"]:
+        raise ValueError("'by' must be either 'row' or 'column'.")
+
+    _all_keys = [list(x.keys()) for x in assays]
+    _all_keys = list(set(itertools.chain.from_iterable(_all_keys)))
+
+    _all_assays = {}
+    for k in _all_keys:
+        _all_mats = [x[k] for x in assays]
+
+        if by == "row":
+            _all_assays[k] = ut.combine_rows(*_all_mats)
+        else:
+            _all_assays[k] = ut.combine_columns(*_all_mats)
 
-    _set = set()
-    for k_idx in range(len(_all_keys)):
-        kx = _all_keys[k_idx]
-        for ky in kx:
-            if ky in _set:
-                ky = f"{ky}_{k_idx}"
+    return _all_assays
 
-            _set.add(ky)
 
-    _new_all_keys = list(_set)
+def check_assays_are_equal(assays):
+    _first = assays[0]
+    _first_keys = set(list(_first.keys()))
 
-    _all_assays = [list(x.values()) for x in assays]
-    _all_assays = list(itertools.chain.from_iterable(_all_assays))
-    return dict(zip(_new_all_keys, _all_assays))
+    for x in assays[1:]:
+        if len(list(_first_keys - set(x.keys()))) != 0:
+            raise ValueError("Not all experiments contain the same assays.")

tests/test_RSE_methods.py

@@ -73,7 +73,7 @@ def test_RSE_props():
     assert tse.width is not None
 
     assert tse.rownames is None
-    assert tse.colnames is not None
+    assert tse.colnames is None
 
 
 def test_RSE_subset():

tests/test_SE.py

@@ -83,7 +83,7 @@ def test_SE_no_row_or_col_data():
     assert tse.col_data is not None
     assert isinstance(tse.col_data, BiocFrame)
 
-    tse.row_data = tse.row_data.set_row_names([f"row_{i}" for i in range(200)])
+    tse.row_names = [f"row_{i}" for i in range(200)]
     assert tse.rownames is not None
     assert len(tse.rownames) == 200
     assert tse.row_data.shape[0] == 200
@@ -92,7 +92,7 @@ def test_SE_no_row_or_col_data():
     assert tse.col_data is not None
     assert isinstance(tse.col_data, BiocFrame)
 
-    tse.col_data = tse.coldata.set_row_names([f"col_{i}" for i in range(6)])
+    tse.col_names = [f"col_{i}" for i in range(6)]
     assert tse.colnames is not None
     assert len(tse.colnames) == 6
     assert tse.col_data.shape[0] == 6