we are getting somewhere now...

src/summarizedexperiment/RangedSummarizedExperiment.py

@@ -129,7 +129,7 @@ def __init__(
             metadata (Dict, optional): Additional experimental metadata describing the
                 methods. Defaults to None.
         """
-        super().__init__(assays, row_data, col_data, metadata)
+        super().__init__(assays, rows=row_data, cols=col_data, metadata=metadata)
 
         if row_ranges is None:
             row_ranges = GenomicRangesList.empty(n=self._shape[0])

src/summarizedexperiment/SummarizedExperiment.py

@@ -2,9 +2,10 @@
 from warnings import warn
 
 from genomicranges import GenomicRanges
+from biocframe import BiocFrame
 
 from .BaseSE import BaseSE
-from .types import BiocOrPandasFrame, MatrixTypes, SlicerArgTypes
+from .types import MatrixTypes, SlicerArgTypes
 
 __author__ = "jkanche"
 __copyright__ = "jkanche"
@@ -29,11 +30,11 @@ class SummarizedExperiment(BaseSE):
             All matrices in assays must be 2-dimensional and have the same shape
             (number of rows, number of columns).
 
-        row_data (BiocOrPandasFrame, optional): Features, which must be of the same length as the rows of
+        row_data (BiocFrame, optional): Features, which must be of the same length as the rows of
             the matrices in assays. Features can be either a :py:class:`~pandas.DataFrame` or
             :py:class:`~biocframe.BiocFrame.BiocFrame`. Defaults to None.
 
-        col_data (BiocOrPandasFrame, optional): Sample data, which must be of the same length as the
+        col_data (BiocFrame, optional): Sample data, which must be of the same length as the
             columns of the matrices in assays. Sample Information can be either a :py:class:`~pandas.DataFrame`
             or :py:class:`~biocframe.BiocFrame.BiocFrame`. Defaults to None.
 
@@ -43,8 +44,8 @@ class SummarizedExperiment(BaseSE):
     def __init__(
         self,
         assays: Dict[str, MatrixTypes],
-        row_data: Optional[BiocOrPandasFrame] = None,
-        col_data: Optional[BiocOrPandasFrame] = None,
+        row_data: Optional[BiocFrame] = None,
+        col_data: Optional[BiocFrame] = None,
         metadata: Optional[Dict] = None,
     ) -> None:
         """Initialize a Summarized Experiment (SE).
@@ -60,11 +61,11 @@ def __init__(
                 All matrices in assays must be 2-dimensional and have the same shape
                 (number of rows, number of columns).
 
-            row_data (BiocOrPandasFrame, optional): Features, which must be of the same length as the rows of
+            row_data (BiocFrame, optional): Features, which must be of the same length as the rows of
                 the matrices in assays. Features can be either a :py:class:`~pandas.DataFrame` or
                 :py:class:`~biocframe.BiocFrame.BiocFrame`. Defaults to None.
 
-            col_data (BiocOrPandasFrame, optional): Sample data, which must be of the same length as the
+            col_data (BiocFrame, optional): Sample data, which must be of the same length as the
                 columns of the matrices in assays. Sample Information can be either a :py:class:`~pandas.DataFrame`
                 or :py:class:`~biocframe.BiocFrame.BiocFrame`. Defaults to None.
 
@@ -76,7 +77,7 @@ def __init__(
                 "`row_data` is `GenomicRanges`, consider using `RangeSummarizedExperiment`."
             )
 
-        super().__init__(assays, row_data, col_data, metadata)
+        super().__init__(assays, rows=row_data, cols=col_data, metadata=metadata)
 
     def __getitem__(
         self,

src/summarizedexperiment/__init__.py

@@ -16,4 +16,4 @@
     del version, PackageNotFoundError
 
 from .SummarizedExperiment import SummarizedExperiment
-from .RangedSummarizedExperiment import RangedSummarizedExperiment
+# from .RangedSummarizedExperiment import RangedSummarizedExperiment

src/summarizedexperiment/_frameutils.py

@@ -1,6 +1,6 @@
-from biocframe import BiocFrame, from_pandas
+from typing import Any
 
-from .type_checks import is_pandas
+from biocframe import BiocFrame, from_pandas
 
 __author__ = "jkanche"
 __copyright__ = "jkanche"
@@ -14,3 +14,19 @@ def _sanitize_frame(frame, num_rows: int):
         frame = from_pandas(frame)
 
     return frame
+
+
+def is_pandas(x: Any) -> bool:
+    """Check if ``x`` is a :py:class:`~pandas.DataFrame`.
+
+    Args:
+        x:
+            Any object.
+
+    Returns:
+        True if ``x`` is a :py:class:`~pandas.DataFrame`.
+    """
+    if hasattr(x, "dtypes"):
+        return True
+
+    return False

src/summarizedexperiment/type_checks.py

@@ -74,19 +74,3 @@ def is_list_of_type(x: Any, target_type: Callable) -> bool:
     return (isinstance(x, list) or isinstance(x, tuple)) and all(
         isinstance(item, target_type) for item in x
     )
-
-
-def is_pandas(x: Any) -> bool:
-    """Check if ``x`` is a :py:class:`~pandas.DataFrame`.
-
-    Args:
-        x:
-            Any object.
-
-    Returns:
-        True if ``x`` is a :py:class:`~pandas.DataFrame`.
-    """
-    if hasattr(x, "dtypes"):
-        return True
-
-    return False

src/summarizedexperiment/types.py

@@ -13,6 +13,7 @@
 MatrixSlicerTypes = Union[List[int], List[bool], slice]
 SlicerTypes = Union[List[int], List[bool], List[str], slice]
 SlicerArgTypes = Union[Tuple[SlicerTypes], List[SlicerTypes], slice]
-SlicerResult = namedtuple(
-    "SlicerResult", ["row_data", "col_data", "assays", "row_indices", "col_indices"]
-)
+
+SliceResult = namedtuple(
+    "SlicerResult", ["rows", "columns", "assays", "row_indices", "col_indices"]
+)