BiocFrame extends BiocObject, metadata is now a named list. (#134)

Author: jkanche

CHANGELOG.md

@@ -1,15 +1,17 @@
 # Changelog
 
-## Version 0.7.0
+## Version 0.7.0 - 0.7.1
 
 - Major update to type hints throughout the module for better type safety and consistency.
 - Fixed bug in slice operations where column indices might be incorrectly initialized.
 - Added missing index validation in `get_row()` for integer row indices. Similar index validation in `remove_columns()` and `remove_rows()` for out-of-range indices.
 - Accept a list of column values and column names to initialize a biocframe object.
 - Implement empty, contains, head, tail,
 - Coercions to list and `NamedList` from bioctuls.
+- `BiocFrame` now extends `BiocObject`, with metadata attribute now a `NamedList` from the biocutils package.
 
 ## Version 0.6.3
+
 - Implement `remove_rows()`.
 - Implement `has_row()`.
 - Add support for slice objects in `remove_columns()` and enforce homogeneous types.
@@ -47,6 +49,7 @@
 - Internal refactoring to use generics from the BiocUtils package.
 
 ## Version 0.3
+
 This release migrates the package to a more palatable Google's Python style guide. A major modification to the package is with casing, all `camelCase` methods, functions and parameters are now `snake_case`.
 
 In addition, docstrings and documentation has been updated to use sphinx's features of linking objects to their types. Sphinx now also documents private and special dunder methods (e.g. `__getitem__`, `__copy__` etc). Intersphinx has been updated to link to references from dependent packages.
@@ -56,6 +59,7 @@ configuration for flake8, ruff and black has been added to pyproject.toml and se
 In addition, pyscaffold has been updated to use "myst-parser" as the markdown compiler instead of recommonmark. As part of the pyscaffold setup, one may use pre-commits to run some of the routine tasks of linting and formatting before every commit. While this is sometimes annoying and can be ignored with `--no-verify`, it brings some consistency to the code base.
 
 ## Version 0.2
+
 - refactor DataFrame as BiocFrame
 - implementing slicing methods, tests
 

src/biocframe/frame.py

@@ -104,7 +104,7 @@ def __next__(self) -> Tuple[Optional[Union[ut.Names, str]], Dict[str, Any]]:
 ############################
 
 
-class BiocFrame:
+class BiocFrame(ut.BiocObject):
     """`BiocFrame` is an alternative to :class:`~pandas.DataFrame`, with support for nested and flexible column types.
     Inspired by the ``DFrame`` class from Bioconductor's **S4Vectors** package. Any object may be used as a column,
     provided it has:
@@ -168,6 +168,12 @@ def __init__(
             _validate:
                 Internal use only.
         """
+
+        super().__init__(
+            metadata=metadata,
+            _validate=_validate,
+        )
+
         if data is None:
             data = {}
 
@@ -176,7 +182,7 @@ def __init__(
             # making sure all column values are lists
             for k, v in data.items():
                 if not isinstance(v, list):
-                    # if its a scalar, make a list else corce to list
+                    # if its a scalar, make a list else coerce to list
                     data[k] = list(v) if isinstance(v, abc.Sequence) else [v]
         elif isinstance(data, Sequence) and not isinstance(data, (str, dict)):
             if column_names is None:
@@ -206,19 +212,12 @@ def __init__(
         else:
             self._column_names = column_names if isinstance(column_names, ut.Names) else ut.Names(column_names)
 
-        self._metadata = {} if metadata is None else metadata
         self._column_data = column_data
 
         if _validate:
             _validate_rows(self._number_of_rows, self._data, self._row_names)
             _validate_columns(self._column_names, self._data, self._column_data)
 
-    def _define_output(self, in_place: bool = False) -> BiocFrame:
-        if in_place is True:
-            return self
-        else:
-            return self.__copy__()
-
     def __eq__(self, other: Any) -> bool:
         """Check if the current object is equal to another.
 
@@ -668,51 +667,6 @@ def column_data(self, column_data: Optional[BiocFrame]) -> None:
         )
         self.set_column_data(column_data, in_place=True)
 
-    def get_metadata(self) -> dict:
-        """Get the metadata.
-
-        Returns:
-            Dictionary of metadata for this object.
-        """
-        return self._metadata
-
-    def set_metadata(self, metadata: Dict[str, Any], in_place: bool = False) -> BiocFrame:
-        """Set new metadata.
-
-        Args:
-            metadata:
-                New metadata for this object.
-
-            in_place:
-                Whether to modify the ``BiocFrame`` object in place.
-
-        Returns:
-            A modified ``BiocFrame`` object, either as a copy of the original
-            or as a reference to the (in-place-modified) original.
-        """
-        if not isinstance(metadata, dict):
-            raise TypeError(f"`metadata` must be a dictionary, provided {type(metadata)}.")
-        output = self._define_output(in_place)
-        output._metadata = metadata
-        return output
-
-    @property
-    def metadata(self) -> Dict[str, Any]:
-        """Alias for :py:attr:`~get_metadata`."""
-        return self.get_metadata()
-
-    @metadata.setter
-    def metadata(self, metadata: Dict[str, Any]) -> None:
-        """Alias for :py:attr:`~set_metadata` with ``in_place = True``.
-
-        As this mutates the original object, a warning is raised.
-        """
-        warn(
-            "Setting property 'metadata' is an in-place operation, use 'set_metadata' instead",
-            UserWarning,
-        )
-        self.set_metadata(metadata, in_place=True)
-
     ################################
     ######>> Single getters <<######
     ################################

tests/test_methods.py

@@ -59,7 +59,7 @@ def test_bframe_basic_ops():
     assert len(bframe.column_names) == 3
 
     assert bframe.get_column_data() is None
-    assert bframe.metadata == {}
+    assert bframe.metadata == ut.NamedList()
 
     assert len(bframe.dims) == 2
     assert bframe.dims == (3, 3)
@@ -104,7 +104,7 @@ def test_bframe_setters():
     assert bframe.column_names is not None
     assert len(bframe.column_names) == 3
 
-    assert bframe.metadata == {}
+    assert bframe.metadata == ut.NamedList()
 
     bframe.metadata = {"a": "b"}
     assert bframe.metadata is not None