Classes extend BiocObject (#10)

Author: jkanche

.github/workflows/run-tests.yml

@@ -28,7 +28,7 @@ jobs:
   test:
     strategy:
       matrix:
-        python: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python: ["3.10", "3.11", "3.12", "3.13", "3.14"]
         platform:
           - ubuntu-latest
           - macos-latest

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## Version 0.4.0
+
+- Classes extend `BiocObject` from biocutils. `metadata` is a named list.
+- Update actions to run from 3.10-3.14
+
 ## Version 0.3.0
 
 - Renamed `CompressedBiocFrameList` to `CompressedSplitBiocFrameList` since the current implementation can only handle dataframes with the same number and names of columns.

setup.cfg

@@ -49,9 +49,9 @@ python_requires = >=3.9
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    biocutils
+    biocutils>=0.3.1
     numpy
-    biocframe
+    biocframe>=0.7.1
 
 
 [options.packages.find]

src/compressed_lists/base.py

@@ -1,4 +1,6 @@
-from typing import Any, Callable, Iterator, List, Optional, Sequence, Union
+from __future__ import annotations
+
+from typing import Any, Callable, Dict, Iterator, List, Optional, Sequence, Union
 from warnings import warn
 
 import biocutils as ut
@@ -19,7 +21,7 @@ def _validate_data_and_partitions(unlist_data, partition):
         )
 
 
-class CompressedList:
+class CompressedList(ut.BiocObject):
     """Base class for compressed list objects.
 
     `CompressedList` stores list elements concatenated in a single vector-like object
@@ -32,8 +34,8 @@ def __init__(
         partitioning: Partitioning,
         element_type: Any = None,
         element_metadata: Optional[dict] = None,
-        metadata: Optional[dict] = None,
-        validate: bool = True,
+        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+        _validate: bool = True,
     ):
         """Initialize a CompressedList.
 
@@ -53,24 +55,20 @@ class for the type of elements.
             metadata:
                 Optional general metadata.
 
-            validate:
+            _validate:
                 Internal use only.
         """
+
+        super().__init__(metadata=metadata, _validate=_validate)
+
         self._unlist_data = unlist_data
         self._partitioning = partitioning
         self._element_type = element_type
         self._element_metadata = element_metadata or {}
-        self._metadata = metadata or {}
 
-        if validate:
+        if _validate:
             _validate_data_and_partitions(self._unlist_data, self._partitioning)
 
-    def _define_output(self, in_place: bool = False) -> "CompressedList":
-        if in_place is True:
-            return self
-        else:
-            return self.__copy__()
-
     #########################
     ######>> Copying <<######
     #########################
@@ -219,7 +217,7 @@ def get_names(self) -> Optional[ut.Names]:
         """Get the names of list elements."""
         return self._partitioning.get_names()
 
-    def set_names(self, names: Sequence[str], in_place: bool = False) -> "CompressedList":
+    def set_names(self, names: Sequence[str], in_place: bool = False) -> CompressedList:
         """Set the names of list elements.
 
         names:
@@ -263,7 +261,7 @@ def get_unlist_data(self) -> Any:
         """Get all elements."""
         return self._unlist_data
 
-    def set_unlist_data(self, unlist_data: Any, in_place: bool = False) -> "CompressedList":
+    def set_unlist_data(self, unlist_data: Any, in_place: bool = False) -> CompressedList:
         """Set new list elements.
 
         Args:
@@ -312,7 +310,7 @@ def get_element_metadata(self) -> dict:
         """
         return self._element_metadata
 
-    def set_element_metadata(self, element_metadata: dict, in_place: bool = False) -> "CompressedList":
+    def set_element_metadata(self, element_metadata: dict, in_place: bool = False) -> CompressedList:
         """Set new element metadata.
 
         Args:
@@ -349,54 +347,6 @@ def element_metadata(self, element_metadata: dict):
         )
         self.set_element_metadata(element_metadata, in_place=True)
 
-    ###########################
-    ######>> metadata <<#######
-    ###########################
-
-    def get_metadata(self) -> dict:
-        """
-        Returns:
-            Dictionary of metadata for this object.
-        """
-        return self._metadata
-
-    def set_metadata(self, metadata: dict, in_place: bool = False) -> "CompressedList":
-        """Set additional metadata.
-
-        Args:
-            metadata:
-                New metadata for this object.
-
-            in_place:
-                Whether to modify the ``CompressedList`` in place.
-
-        Returns:
-            A modified ``CompressedList`` 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:
-        """Alias for :py:attr:`~get_metadata`."""
-        return self.get_metadata()
-
-    @metadata.setter
-    def metadata(self, metadata: dict):
-        """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)
-
     ##########################
     ######>> accessors <<#####
     ##########################
@@ -472,8 +422,11 @@ def extract_range(self, start: int, end: int) -> Any:
 
     @classmethod
     def from_list(
-        cls, lst: Any, names: Optional[Union[ut.Names, Sequence[str]]] = None, metadata: Optional[dict] = None
-    ) -> "CompressedList":
+        cls,
+        lst: Any,
+        names: Optional[Union[ut.Names, Sequence[str]]] = None,
+        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+    ) -> CompressedList:
         """Create a CompressedList from a regular list.
 
         This method must be implemented by subclasses to handle
@@ -544,7 +497,7 @@ def unlist(self, use_names: bool = False) -> Any:
             else self._unlist_data.set_names(self.get_partitioning().get_names(), in_place=False)
         )
 
-    def relist(self, unlist_data: Any) -> "CompressedList":
+    def relist(self, unlist_data: Any) -> CompressedList:
         """Create a new `CompressedList` with the same partitioning but different data.
 
         Args:
@@ -565,7 +518,7 @@ def relist(self, unlist_data: Any) -> "CompressedList":
             metadata=self._metadata.copy(),
         )
 
-    def extract_subset(self, indices: Sequence[int]) -> "CompressedList":
+    def extract_subset(self, indices: Sequence[int]) -> CompressedList:
         """Extract a subset of elements by indices.
 
         Args:
@@ -608,7 +561,7 @@ def extract_subset(self, indices: Sequence[int]) -> "CompressedList":
             metadata=self._metadata.copy(),
         )
 
-    def lapply(self, func: Callable) -> "CompressedList":
+    def lapply(self, func: Callable) -> CompressedList:
         """Apply a function to each element.
 
         Args:

src/compressed_lists/biocframe_list.py

@@ -1,4 +1,6 @@
-from typing import List, Optional, Sequence, Union
+from __future__ import annotations
+
+from typing import Any, Dict, List, Optional, Sequence, Union
 
 import biocutils as ut
 from biocframe import BiocFrame
@@ -22,7 +24,7 @@ def __init__(
         unlist_data: BiocFrame,
         partitioning: Partitioning,
         element_metadata: Optional[dict] = None,
-        metadata: Optional[dict] = None,
+        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
         **kwargs,
     ):
         """Initialize a CompressedSplitBiocFrameList.
@@ -56,7 +58,7 @@ def from_list(
         lst: List[BiocFrame],
         names: Optional[Union[ut.Names, Sequence[str]]] = None,
         metadata: Optional[dict] = None,
-    ) -> "CompressedSplitBiocFrameList":
+    ) -> CompressedSplitBiocFrameList:
         """Create a `CompressedSplitBiocFrameList` from a regular list.
 
         This concatenates the list of `BiocFrame` objects.

src/compressed_lists/bool_list.py

@@ -1,4 +1,4 @@
-from typing import Optional, Sequence, Union
+from typing import Any, Dict, Optional, Sequence, Union
 from warnings import warn
 
 import biocutils as ut
@@ -20,7 +20,7 @@ def __init__(
         unlist_data: ut.BooleanList,
         partitioning: Partitioning,
         element_metadata: Optional[dict] = None,
-        metadata: Optional[dict] = None,
+        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
         **kwargs,
     ):
         """Initialize a CompressedBooleanList.

src/compressed_lists/float_list.py

@@ -1,4 +1,4 @@
-from typing import Optional, Sequence, Union
+from typing import Any, Dict, Optional, Sequence, Union
 from warnings import warn
 
 import biocutils as ut
@@ -20,7 +20,7 @@ def __init__(
         unlist_data: ut.FloatList,
         partitioning: Partitioning,
         element_metadata: Optional[dict] = None,
-        metadata: Optional[dict] = None,
+        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
         **kwargs,
     ):
         """Initialize a CompressedFloatList.

src/compressed_lists/integer_list.py

@@ -1,4 +1,4 @@
-from typing import Optional, Sequence, Union
+from typing import Any, Dict, Optional, Sequence, Union
 from warnings import warn
 
 import biocutils as ut
@@ -20,7 +20,7 @@ def __init__(
         unlist_data: ut.IntegerList,
         partitioning: Partitioning,
         element_metadata: Optional[dict] = None,
-        metadata: Optional[dict] = None,
+        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
         **kwargs,
     ):
         """Initialize a CompressedIntegerList.

src/compressed_lists/numpy_list.py

@@ -1,4 +1,6 @@
-from typing import List, Optional, Sequence, Union
+from __future__ import annotations
+
+from typing import Any, Dict, List, Optional, Sequence, Union
 from warnings import warn
 
 import biocutils as ut
@@ -21,7 +23,7 @@ def __init__(
         unlist_data: np.ndarray,
         partitioning: Partitioning,
         element_metadata: Optional[dict] = None,
-        metadata: Optional[dict] = None,
+        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
         **kwargs,
     ):
         """Initialize a CompressedNumpyList.
@@ -63,7 +65,7 @@ def from_list(
         lst: List[np.ndarray],
         names: Optional[Union[ut.Names, Sequence[str]]] = None,
         metadata: Optional[dict] = None,
-    ) -> "CompressedNumpyList":
+    ) -> CompressedNumpyList:
         """
         Create a `CompressedNumpyList` from a list of NumPy vectors.
 

src/compressed_lists/partition.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from typing import List, Optional, Sequence, Union
 from warnings import warn
 
@@ -56,7 +58,7 @@ def __init__(
     @classmethod
     def from_lengths(
         cls, lengths: Sequence[int], names: Optional[Union[ut.Names, Sequence[str]]] = None
-    ) -> "Partitioning":
+    ) -> Partitioning:
         """Create a Partitioning from a sequence of lengths.
 
         Args:
@@ -73,7 +75,7 @@ def from_lengths(
         return cls(ends, names)
 
     @classmethod
-    def from_list(cls, lst: List, names: Optional[Union[ut.Names, Sequence[str]]] = None) -> "Partitioning":
+    def from_list(cls, lst: List, names: Optional[Union[ut.Names, Sequence[str]]] = None) -> Partitioning:
         """Create a Partitioning from a list by using the lengths of each element.
 
         Args:
@@ -89,7 +91,7 @@ def from_list(cls, lst: List, names: Optional[Union[ut.Names, Sequence[str]]] =
         lengths = [len(item) if hasattr(item, "__len__") else 1 for item in lst]
         return cls.from_lengths(lengths, names)
 
-    def _define_output(self, in_place: bool = False) -> "Partitioning":
+    def _define_output(self, in_place: bool = False) -> Partitioning:
         if in_place is True:
             return self
         else:
@@ -220,7 +222,7 @@ def get_names(self) -> Optional[ut.Names]:
         """Return the names of each partition."""
         return self._names
 
-    def set_names(self, names: Optional[Union[ut.Names, Sequence[str]]], in_place: bool = False) -> "Partitioning":
+    def set_names(self, names: Optional[Union[ut.Names, Sequence[str]]], in_place: bool = False) -> Partitioning:
         """Set the names of list elements.
 
         Args: