cap-anndata 0.3.0__py3-none-any.whl → 0.4.0__py3-none-any.whl

cap_anndata/__init__.py

@@ -1,10 +1,10 @@
-from .backed_df import CapAnnDataDF
-from .backed_dict import CapAnnDataDict
-from .cap_anndata import CapAnnData
-from .reader import (
-    read_directly,
-    read_h5ad,
-)
-
-
-__all__ = ["CapAnnData"]
+from .backed_df import CapAnnDataDF
+from .backed_dict import CapAnnDataDict
+from .cap_anndata import CapAnnData
+from .reader import (
+    read_directly,
+    read_h5ad,
+)
+
+
+__all__ = ["CapAnnData"]

cap_anndata/backed_df.py

@@ -1,69 +1,81 @@
-import pandas as pd
-import numpy as np
-from typing import List, Any, Union
-import logging
-
-from pandas._typing import Self
-from pandas.core.generic import bool_t
-
-logger = logging.getLogger(__name__)
-
-
-class CapAnnDataDF(pd.DataFrame):
-    """
-    The class to expand the pandas DataFrame behaviour to support partial
-    reading and writing of AnnData obs and var (raw.var) fields.
-    The main feature of the class is handling <column-order> attribute
-    which must be a copy of h5py.Group attribute
-    """
-
-    _metadata = ["column_order"]
-
-    def rename_column(self, old_name: str, new_name: str) -> None:
-        i = np.where(self.column_order == old_name)[0]
-        self.column_order[i] = new_name
-        self.rename(columns={old_name: new_name}, inplace=True)
-
-    def remove_column(self, col_name: str) -> None:
-        i = np.where(self.column_order == col_name)[0]
-        self.column_order = np.delete(self.column_order, i)
-        self.drop(columns=[col_name], inplace=True)
-
-    def __setitem__(self, key, value) -> None:
-        if key not in self.column_order:
-            self.column_order = np.append(self.column_order, key)
-        return super().__setitem__(key, value)
-
-    @classmethod
-    def from_df(cls, df: pd.DataFrame, column_order: List[str] = None) -> Self:
-        if column_order is None:
-            column_order = df.columns.to_numpy()
-
-        new_inst = cls(df)
-        new_inst.column_order = column_order
-        return new_inst
-
-    def join(self, other: Any, **kwargs) -> Self:
-        result = super().join(other=other, **kwargs)
-        if isinstance(other, CapAnnDataDF):
-            new_columns = [
-                col for col in other.column_order if col not in self.column_order
-            ]
-        else:
-            new_columns = [col for col in other.columns if col not in self.column_order]
-        column_order = np.append(self.column_order, new_columns)
-        return self.from_df(result, column_order=column_order)
-
-    def merge(self, right, **kwargs) -> Self:
-        result = super().merge(right=right, **kwargs)
-        if isinstance(right, CapAnnDataDF):
-            new_columns = [
-                col for col in right.column_order if col not in self.column_order
-            ]
-        else:
-            new_columns = [col for col in right.columns if col not in self.column_order]
-        column_order = np.append(self.column_order, new_columns)
-        return self.from_df(result, column_order=column_order)
-
-    def copy(self, deep: Union[bool_t, None] = True) -> Self:
-        return self.from_df(super().copy(deep=deep), column_order=self.column_order)
+import pandas as pd
+import numpy as np
+from typing import List, Any, Union
+
+from pandas._typing import Self
+from pandas.core.generic import bool_t
+
+
+class CapAnnDataDF(pd.DataFrame):
+    """
+    The class to expand the pandas DataFrame behaviour to support partial
+    reading and writing of AnnData obs and var (raw.var) fields.
+    The main feature of the class is handling <column-order> attribute
+    which must be a copy of h5py.Group attribute
+    """
+
+    _metadata = ["column_order"]
+
+    def column_order_array(self) -> np.array:
+        order = self.column_order
+        if order is not None and isinstance(order, List):
+            # Convert it to numpy array of str elements
+            return np.array(order, dtype=object)
+        else:
+            return order
+
+    def rename_column(self, old_name: str, new_name: str) -> None:
+        i = np.where(self.column_order_array() == old_name)[0]
+        tmp_array = self.column_order_array().copy()
+        tmp_array[i] = new_name
+        self.column_order = tmp_array.copy()
+        self.rename(columns={old_name: new_name}, inplace=True)
+
+    def remove_column(self, col_name: str) -> None:
+        i = np.where(self.column_order_array() == col_name)[0]
+        self.column_order = np.delete(self.column_order_array(), i)
+        self.drop(columns=[col_name], inplace=True)
+
+    def __setitem__(self, key, value) -> None:
+        if key not in self.column_order_array():
+            self.column_order = np.append(self.column_order_array(), key)
+        return super().__setitem__(key, value)
+
+    @classmethod
+    def from_df(cls, df: pd.DataFrame, column_order: Union[np.array, List[str], None] = None) -> Self:
+        if column_order is None:
+            column_order = df.columns.to_numpy()
+        elif isinstance(column_order, List):
+            column_order = np.array(column_order)
+        new_inst = cls(df)
+        new_inst.column_order = column_order
+        return new_inst
+
+    def join(self, other: Any, **kwargs) -> Self:
+        result = super().join(other=other, **kwargs)
+        if isinstance(other, CapAnnDataDF):
+            new_columns = [
+                col for col in other.column_order_array() if col not in self.column_order_array()
+            ]
+        else:
+            new_columns = [col for col in other.columns if col not in self.column_order_array()]
+        column_order = np.append(self.column_order_array(), new_columns)
+        df = self.from_df(result, column_order=column_order)
+        return df
+
+    def merge(self, right, **kwargs) -> Self:
+        result = super().merge(right=right, **kwargs)
+        if isinstance(right, CapAnnDataDF):
+            new_columns = [
+                col for col in right.column_order_array() if col not in self.column_order_array()
+            ]
+        else:
+            new_columns = [col for col in right.columns if col not in self.column_order_array()]
+        column_order = np.append(self.column_order_array(), new_columns)
+        df = self.from_df(result, column_order=column_order)
+        return df
+
+    def copy(self, deep: Union[bool_t, None] = True) -> Self:
+        column_order = self.column_order_array()
+        df = self.from_df(super().copy(deep=deep), column_order=column_order)
+        return df

cap_anndata/backed_dict.py

@@ -1,34 +1,34 @@
-from typing import Set, Any
-
-
-class CapAnnDataDict(dict):
-    __keys_to_remove: Set[str] = None
-
-    def __delitem__(self, __key: Any) -> None:
-        self.keys_to_remove.add(__key)
-        return super().__delitem__(__key)
-
-    def __setitem__(self, __key: Any, __value: Any) -> None:
-        if __value is not None:
-            if __key in self.keys_to_remove:
-                self.keys_to_remove.remove(__key)
-        else:
-            self.keys_to_remove.add(__key)
-        return super().__setitem__(__key, __value)
-
-    @property
-    def keys_to_remove(self) -> Set[str]:
-        if self.__keys_to_remove is None:
-            self.__keys_to_remove = set()
-        return self.__keys_to_remove
-
-    def pop(self, __key: Any, __default: Any = None) -> Any:
-        if __key in self:
-            self.keys_to_remove.add(__key)
-        return super().pop(__key, __default)
-
-    def popitem(self) -> Any:
-        item = super().popitem()
-        key = item[0]
-        self.keys_to_remove.add(key)
-        return item
+from typing import Set, Any
+
+
+class CapAnnDataDict(dict):
+    __keys_to_remove: Set[str] = None
+
+    def __delitem__(self, __key: Any) -> None:
+        self.keys_to_remove.add(__key)
+        return super().__delitem__(__key)
+
+    def __setitem__(self, __key: Any, __value: Any) -> None:
+        if __value is not None:
+            if __key in self.keys_to_remove:
+                self.keys_to_remove.remove(__key)
+        else:
+            self.keys_to_remove.add(__key)
+        return super().__setitem__(__key, __value)
+
+    @property
+    def keys_to_remove(self) -> Set[str]:
+        if self.__keys_to_remove is None:
+            self.__keys_to_remove = set()
+        return self.__keys_to_remove
+
+    def pop(self, __key: Any, __default: Any = None) -> Any:
+        if __key in self:
+            self.keys_to_remove.add(__key)
+        return super().pop(__key, __default)
+
+    def popitem(self) -> Any:
+        item = super().popitem()
+        key = item[0]
+        self.keys_to_remove.add(key)
+        return item