biocutils 0.3.1.dev0__tar.gz → 0.3.2.dev1__tar.gz

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biocutils
-Version: 0.3.1.dev0
+Version: 0.3.2.dev1
 Summary: Utilities to use across the biocpy packages.
 Home-page: https://github.com/biocpy/biocutils
 Author: Aaron Lun

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/__init__.py

@@ -60,5 +60,3 @@ from .convert_to_dense import convert_to_dense
 
 from .get_height import get_height
 from .is_high_dimensional import is_high_dimensional
-
-from .bioc_object import BiocObject

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/_utils_combine.py

@@ -26,8 +26,6 @@ def _check_array_dimensions(x, active: int) -> bool:
                     + ")"
                 )
 
-    return True
-
 
 def _coerce_sparse_matrix(first, combined, module):
     if isinstance(first, module.csr_matrix):

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/assign.py

@@ -14,8 +14,7 @@ def assign(x: Any, indices: Sequence[int], replacement: Any) -> Any:
     :py:func:`~biocutils.assign_sequence.assign_sequence` instead.
 
     Args:
-        x:
-            Object to be assignted.
+        x: Object to be assignted.
 
     Returns:
         The object after assignment, typically the same type as ``x``.

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/assign_rows.py

@@ -31,15 +31,15 @@ def assign_rows(x: Any, indices: Sequence[int], replacement: Any) -> Any:
     tmp = [slice(None)] * len(x.shape)
     tmp[0] = indices
     output[(*tmp,)] = replacement
-
     return output
 
 
 @assign_rows.register
-def _assign_rows_numpy(x: numpy.ndarray, indices: Sequence[int], replacement: Any) -> numpy.ndarray:
+def _assign_rows_numpy(
+    x: numpy.ndarray, indices: Sequence[int], replacement: Any
+) -> numpy.ndarray:
     tmp = [slice(None)] * len(x.shape)
     tmp[0] = indices
     output = numpy.copy(x)
     output[(*tmp,)] = replacement
-
     return output

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/assign_sequence.py

@@ -41,14 +41,18 @@ def _assign_sequence_list(x: list, indices: Sequence[int], replacement: Any) ->
 
 
 @assign_sequence.register
-def _assign_sequence_numpy(x: numpy.ndarray, indices: Sequence[int], replacement: Any) -> numpy.ndarray:
+def _assign_sequence_numpy(
+    x: numpy.ndarray, indices: Sequence[int], replacement: Any
+) -> numpy.ndarray:
     output = numpy.copy(x)
     output[indices] = replacement
     return output
 
 
 @assign_sequence.register
-def _assign_sequence_range(x: range, indices: Sequence[int], replacement: Any) -> Union[range, list]:
+def _assign_sequence_range(
+    x: range, indices: Sequence[int], replacement: Any
+) -> Union[range, list]:
     if (
         isinstance(replacement, range)
         and isinstance(indices, range)

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/bioc_object.py

@@ -4,6 +4,11 @@ import copy
 from typing import Any, Dict, Optional, Union
 from warnings import warn
 
+try:
+    from typing import Self
+except ImportError:
+    Self = "BiocObject"
+
 from .named_list import NamedList
 
 __author__ = "Jayaram Kancherla"
@@ -35,22 +40,22 @@ class BiocObject:
     Provides a standardized `metadata` slot and copy-on-write semantics.
     """
 
-    def __init__(self, metadata: Optional[Union[Dict[str, Any], NamedList]] = None, _validate: bool = True) -> None:
+    def __init__(self, metadata: Optional[Union[Dict[str, Any], NamedList]] = None, validate: bool = True) -> None:
         """Initialize the BiocObject.
 
         Args:
             metadata:
                 Additional metadata. Defaults to an empty NamedList.
 
-            _validate:
+            validate:
                 Whether to validate the input. Defaults to True.
         """
-        if _validate and metadata is not None:
+        if validate and metadata is not None:
             _validate_metadata(metadata)
 
         self._metadata = sanitize_metadata(metadata)
 
-    def _define_output(self, in_place: bool = False) -> BiocObject:
+    def _define_output(self, in_place: bool = False) -> Self:
         """Internal utility to handle in-place vs copy-on-modify."""
         if in_place:
             return self
@@ -88,7 +93,7 @@ class BiocObject:
         """Alias for :py:attr:`~metadata` getter."""
         return self.metadata
 
-    def set_metadata(self, metadata: Optional[Union[Dict[str, Any], NamedList]], in_place: bool = False) -> BiocObject:
+    def set_metadata(self, metadata: Optional[Union[Dict[str, Any], NamedList]], in_place: bool = False) -> Self:
         """Set new metadata.
 
         Args:

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/boolean_list.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from typing import Any, Iterable, Optional, Sequence, Union
 
 from .named_list import NamedList
@@ -18,8 +16,7 @@ class _SubscriptCoercer:
         """Initialize the coercer.
 
         Args:
-            data:
-                Sequence of values to coerce.
+            data: Sequence of values to coerce.
         """
         self._data = data
 
@@ -27,8 +24,7 @@ class _SubscriptCoercer:
         """Get an item and coerce it to boolean.
 
         Args:
-            index:
-                Index of the item.
+            index: Index of the item.
 
         Returns:
             Coerced boolean value.
@@ -46,7 +42,7 @@ class BooleanList(NamedList):
 
     def __init__(
         self,
-        data: Optional[Sequence] = None,
+        data: Optional[Iterable] = None,
         names: Optional[Names] = None,
         _validate: bool = True,
     ):
@@ -64,34 +60,41 @@ class BooleanList(NamedList):
             _validate:
                 Internal use only.
         """
-        if data is not None:
-            if isinstance(data, BooleanList):
-                data = data._data
-            else:
-                if isinstance(data, NamedList):
+        if _validate:
+            if data is not None:
+                if isinstance(data, BooleanList):
                     data = data._data
-
-                original = data
-                data = list(_coerce_to_bool(item) for item in original)
-
+                else:
+                    if isinstance(data, NamedList):
+                        data = data._data
+                    original = data
+                    data = list(_coerce_to_bool(item) for item in original)
         super().__init__(data, names, _validate=_validate)
 
-    def set_value(self, index: Union[int, str], value: Any, in_place: bool = False) -> BooleanList:
+    def set_value(
+        self, index: Union[int, str], value: Any, in_place: bool = False
+    ) -> "BooleanList":
         """Calls :py:meth:`~biocutils.NamedList.NamedList.set_value` after coercing ``value`` to a boolean."""
         return super().set_value(index, _coerce_to_bool(value), in_place=in_place)
 
-    def set_slice(self, index: SubscriptTypes, value: Sequence, in_place: bool = False) -> BooleanList:
+    def set_slice(
+        self, index: SubscriptTypes, value: Sequence, in_place: bool = False
+    ) -> "BooleanList":
         """Calls :py:meth:`~biocutils.NamedList.NamedList.set_slice` after coercing ``value`` to booleans."""
         return super().set_slice(index, _SubscriptCoercer(value), in_place=in_place)
 
-    def safe_insert(self, index: Union[int, str], value: Any, in_place: bool = False) -> BooleanList:
+    def safe_insert(
+        self, index: Union[int, str], value: Any, in_place: bool = False
+    ) -> "BooleanList":
         """Calls :py:meth:`~biocutils.NamedList.NamedList.safe_insert` after coercing ``value`` to a boolean."""
         return super().safe_insert(index, _coerce_to_bool(value), in_place=in_place)
 
-    def safe_append(self, value: Any, in_place: bool = False) -> BooleanList:
+    def safe_append(self, value: Any, in_place: bool = False) -> "BooleanList":
         """Calls :py:meth:`~biocutils.NamedList.NamedList.safe_append` after coercing ``value`` to a boolean."""
         return super().safe_append(_coerce_to_bool(value), in_place=in_place)
 
-    def safe_extend(self, other: Iterable, in_place: bool = False) -> BooleanList:
+    def safe_extend(self, other: Iterable, in_place: bool = True) -> "BooleanList":
         """Calls :py:meth:`~biocutils.NamedList.NamedList.safe_extend` after coercing elements of ``other`` to booleans."""
-        return super().safe_extend((_coerce_to_bool(y) for y in other), in_place=in_place)
+        return super().safe_extend(
+            (_coerce_to_bool(y) for y in other), in_place=in_place
+        )

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/combine.py

@@ -5,7 +5,7 @@ from .combine_sequences import combine_sequences
 from .is_high_dimensional import is_high_dimensional
 
 
-def combine(*x: Any) -> Any:
+def combine(*x: Any):
     """
     Generic combine that checks if the objects are n-dimensional for n > 1
     (i.e. has a ``shape`` property of length greater than 1); if so, it calls
@@ -14,8 +14,7 @@ def combine(*x: Any) -> Any:
     :py:func:`~biocutils.combine_sequences.combine_sequences` instead.
 
     Args:
-        x:
-            Objects to combine.
+        x: Objects to combine.
 
     Returns:
         A combined object, typically the same type as the first element in ``x``.
@@ -29,8 +28,9 @@ def combine(*x: Any) -> Any:
             has_1d = True
 
     if has_nd and has_1d:
-        raise ValueError("cannot mix 1-dimensional and higher-dimensional objects in `combine`")
-
+        raise ValueError(
+            "cannot mix 1-dimensional and higher-dimensional objects in `combine`"
+        )
     if has_nd:
         return combine_rows(*x)
     else:

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/combine_columns.py

@@ -19,7 +19,7 @@ __license__ = "MIT"
 
 
 @singledispatch
-def combine_columns(*x: Any) -> Any:
+def combine_columns(*x: Any):
     """Combine n-dimensional objects along the second dimension.
 
     If all elements are :py:class:`~numpy.ndarray`,
@@ -40,7 +40,11 @@ def combine_columns(*x: Any) -> Any:
     Returns:
         Combined object, typically the same type as the first entry of ``x``
     """
-    raise NotImplementedError("no `combine_columns` method implemented for '" + type(x[0]).__name__ + "' objects")
+    raise NotImplementedError(
+        "no `combine_columns` method implemented for '"
+        + type(x[0]).__name__
+        + "' objects"
+    )
 
 
 @combine_columns.register
@@ -53,7 +57,7 @@ def _combine_columns_dense_arrays(*x: numpy.ndarray):
     return numpy.concatenate(x, axis=1)
 
 
-if is_package_installed("scipy"):
+if is_package_installed("scipy") is True:
     import scipy.sparse as sp
 
     def _combine_columns_sparse_matrices(*x):
@@ -81,13 +85,8 @@ if is_package_installed("scipy"):
         x = [convert_to_dense(y) for y in x]
         return numpy.concatenate(x, axis=1)
 
-    try:
-        combine_columns.register(sp.sparray, _combine_columns_sparse_arrays)
-    except Exception:
-        pass
-
 
-if is_package_installed("pandas"):
+if is_package_installed("pandas") is True:
     from pandas import DataFrame, concat
 
     @combine_columns.register(DataFrame)

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/combine_rows.py

@@ -19,7 +19,7 @@ __license__ = "MIT"
 
 
 @singledispatch
-def combine_rows(*x: Any) -> Any:
+def combine_rows(*x: Any):
     """Combine n-dimensional objects along their first dimension.
 
     If all elements are :py:class:`~numpy.ndarray`, we combine them using
@@ -40,7 +40,9 @@ def combine_rows(*x: Any) -> Any:
     Returns:
         Combined object, typically the same type as the first entry of ``x``.
     """
-    raise NotImplementedError("no `combine_rows` method implemented for '" + type(x[0]).__name__ + "' objects")
+    raise NotImplementedError(
+        "no `combine_rows` method implemented for '" + type(x[0]).__name__ + "' objects"
+    )
 
 
 @combine_rows.register(numpy.ndarray)
@@ -67,7 +69,7 @@ if is_package_installed("scipy"):
         return numpy.concatenate(x)
 
     try:
-        combine_rows.register(sp.spmatrix, _combine_rows_sparse_matrices)
+        combine_rows.register(sp.sparray, _combine_rows_sparse_arrays)
     except Exception:
         pass
 
@@ -82,7 +84,7 @@ if is_package_installed("scipy"):
         return numpy.concatenate(x)
 
     try:
-        combine_rows.register(sp.sparray, _combine_rows_sparse_arrays)
+        combine_rows.register(sp.spmatrix, _combine_rows_sparse_matrices)
     except Exception:
         pass
 

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/combine_sequences.py

@@ -13,7 +13,7 @@ __license__ = "MIT"
 
 
 @singledispatch
-def combine_sequences(*x: Any) -> Any:
+def combine_sequences(*x: Any):
     """Combine vector-like objects (1-dimensional arrays).
 
     If all elements are :py:class:`~numpy.ndarray`,
@@ -34,7 +34,11 @@ def combine_sequences(*x: Any) -> Any:
     Returns:
         A combined object, ideally of the same type as the first element in ``x``.
     """
-    raise NotImplementedError("no `combine_sequences` method implemented for '" + type(x[0]).__name__ + "' objects")
+    raise NotImplementedError(
+        "no `combine_sequences` method implemented for '"
+        + type(x[0]).__name__
+        + "' objects"
+    )
 
 
 @combine_sequences.register(list)
@@ -47,7 +51,6 @@ def _combine_sequences_dense_arrays(*x: numpy.ndarray):
     for y in x:
         if numpy.ma.is_masked(y):
             return numpy.ma.concatenate(x, axis=None)
-
     return numpy.concatenate(x, axis=None)
 
 
@@ -82,7 +85,6 @@ def _combine_sequences_ranges(*x: range):
 
     if not failed:
         return range(start, stop, step)
-
     return list(chain(*x))
 
 
@@ -99,5 +101,4 @@ if is_package_installed("pandas") is True:
                 else:
                     elems.append(elem)
             x = elems
-
         return concat(x)

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/convert_to_dense.py

@@ -15,8 +15,7 @@ def convert_to_dense(x: Any) -> numpy.ndarray:
     ``numpy.concatenate`` doesn't understand.
 
     Args:
-        x:
-            Some array-like object to be stored as a NumPy array.
+        x: Some array-like object to be stored as a NumPy array.
 
     Returns:
         A NumPy array.

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/extract_column_names.py

@@ -11,12 +11,11 @@ __license__ = "MIT"
 
 
 @singledispatch
-def extract_column_names(x: Any) -> Any:
+def extract_column_names(x: Any) -> numpy.ndarray:
     """Access column names from 2-dimensional representations.
 
     Args:
-        x:
-            Any object with column names.
+        x: Any object with column names.
 
     Returns:
         Array of strings containing column names.
@@ -28,5 +27,5 @@ if is_package_installed("pandas") is True:
     from pandas import DataFrame
 
     @extract_column_names.register(DataFrame)
-    def _colnames_dataframe(x):
+    def _colnames_dataframe(x: DataFrame) -> list:
         return numpy.array(x.columns, dtype=str)

{biocutils-0.3.1.dev0 → biocutils-0.3.2.dev1}/src/biocutils/extract_row_names.py

@@ -11,7 +11,7 @@ __license__ = "MIT"
 
 
 @singledispatch
-def extract_row_names(x: Any) -> Any:
+def extract_row_names(x: Any) -> numpy.ndarray:
     """Access row names from 2-dimensional representations.
 
     Args:
@@ -27,5 +27,5 @@ if is_package_installed("pandas") is True:
     from pandas import DataFrame
 
     @extract_row_names.register(DataFrame)
-    def _rownames_dataframe(x):
+    def _rownames_dataframe(x: DataFrame) -> list:
         return numpy.array(x.index, dtype=str)