vdata 0.3.1__tar.gz → 0.3.2__tar.gz

{vdata-0.3.1 → vdata-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vdata
-Version: 0.3.1
+Version: 0.3.2
 Summary: Annotated multivariate observation of timestamped data
 Author: Matteo Bouvier
 Author-email: Matteo Bouvier <matteo.bouvier@hotmail.fr>
@@ -11,7 +11,7 @@ Requires-Dist: anndata>=0.10.4
 Requires-Dist: scipy>=1.12.0
 Requires-Dist: numpy-indexed>=0.3.7
 Requires-Dist: ch5mpy>=0.5.1
-Requires-Dist: ezarr>=1.1.0
+Requires-Dist: ezarr>=1.1.1
 Requires-Dist: h5dataframe>=0.2.3 ; extra == 'update'
 Requires-Python: >=3.12
 Provides-Extra: update

{vdata-0.3.1 → vdata-0.3.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "vdata"
-version = "0.3.1"
+version = "0.3.2"
 description = "Annotated multivariate observation of timestamped data"
 authors = [{ name = "Matteo Bouvier", email="matteo.bouvier@hotmail.fr"}]
 license = "CECILL-B"
@@ -14,7 +14,7 @@ dependencies = [
     "scipy>=1.12.0",
     "numpy-indexed>=0.3.7",
     "ch5mpy>=0.5.1",
-    "ezarr>=1.1.0",
+    "ezarr>=1.1.1",
 ]
 
 [dependency-groups]

{vdata-0.3.1 → vdata-0.3.2}/vdata/__init__.py

@@ -1,5 +1,7 @@
 """Annotated, temporal and multivariate observation data."""
 
+from importlib.metadata import metadata
+
 from vdata.data import VData, VDataView, concatenate, convert_anndata_to_vdata
 from vdata.IO import (
     IncoherenceError,
@@ -9,13 +11,15 @@ from vdata.IO import (
 )
 from vdata.tdf import RepeatingIndex, TemporalDataFrame, TemporalDataFrameView
 from vdata.timepoint import TimePoint
-from vdata.update import CURRENT_VERSION, update_vdata
 
 read = VData.read
 read_from_csv = VData.read_from_csv
 read_from_anndata = VData.read_from_anndata
 read_from_pickle = VData.read_from_pickle
 
+__version__ = metadata("vdata").get("version")
+
+
 __all__ = [
     "VData",
     "TemporalDataFrame",
@@ -29,6 +33,4 @@ __all__ = [
     "VLockError",
     "TimePoint",
     "RepeatingIndex",
-    "CURRENT_VERSION",
-    "update_vdata",
 ]

{vdata-0.3.1 → vdata-0.3.2}/vdata/_typing.py

@@ -1,8 +1,7 @@
-from collections.abc import Collection, MutableMapping
+from collections.abc import Collection
 from types import EllipsisType
 from typing import SupportsIndex, TypedDict
 
-import ezarr as ez
 import numpy as np
 import numpy.typing as npt
 import zarr
@@ -23,7 +22,6 @@ type NDArrayLike_IFS = npt.NDArray[np_IFS] | zarr.Array
 type AnyNDArrayLike_IFS = npt.NDArray[np_IFS] | NDArrayView[np_IFS] | zarr.Array
 
 type Collection_IFS = Collection[IFS]
-type DictLike[T: ez.SupportsEZReadWrite] = MutableMapping[str, T] | ez.EZDict[T]
 
 type Slicer = IFS | tp.TimePoint | Collection[IFS | tp.TimePoint] | range | slice | EllipsisType
 type MultiSlicer = Collection[IFS | tp.TimePoint] | range | slice | EllipsisType

{vdata-0.3.1 → vdata-0.3.2}/vdata/anndata_proxy/anndata.py

@@ -1,15 +1,16 @@
 from __future__ import annotations
 
-from collections.abc import Sequence
-from pathlib import Path
-from typing import TYPE_CHECKING, Any, Literal, override
+from collections.abc import MutableMapping, Sequence
+from os import PathLike
+from typing import TYPE_CHECKING, Any, Literal, final, override
 
 import numpy.typing as npt
 import pandas as pd
 from anndata import AnnData
+from ezarr.dataframe import EZDataFrame
 from scipy import sparse
 
-from vdata._typing import AnyNDArrayLike, DictLike
+from vdata._typing import AnyNDArrayLike
 from vdata.anndata_proxy.containers import ArrayStack2DProxy, EZDataFrameContainerProxy, TemporalDataFrameContainerProxy
 from vdata.anndata_proxy.dataframe import DataFrameProxy_TDF
 
@@ -19,25 +20,26 @@ if TYPE_CHECKING:
 
 def skip_time_axis(slicer: Any) -> tuple[Any, ...]:
     if isinstance(slicer, tuple):
-        return (slice(None),) + slicer
+        return (slice(None),) + slicer  # pyright: ignore[reportUnknownVariableType]
 
     return (slice(None), slicer)
 
 
-class AnnDataProxy(AnnData):  # type: ignore[misc]
+@final
+class AnnDataProxy(AnnData):
     """
     Class faking to be an anndata.AnnData object but actually wrapping a VData.
     """
 
     __slots__: tuple[str, ...] = "_vdata", "_X", "_layers", "_obs", "_obsm", "_obsp", "_var", "_varm", "_varp", "_uns"
 
-    def __init__(self, vdata: VData | VDataView, X: str | None = None) -> None:
+    def __init__(self, vdata: VData | VDataView, X: str | None = None) -> None:  # pyright: ignore[reportMissingSuperCall]
         """
         Args:
             vdata: a VData object to wrap.
             X: an optional layer name to use as X.
         """
-        self._X = None if X is None else str(X)
+        self._X: str | None = None if X is None else str(X)  # pyright: ignore[reportConstantRedefinition]
 
         if self._X is not None and self._X not in vdata.layers:
             raise ValueError(f"Could not find layer '{self._X}' in the given VData.")
@@ -55,32 +57,40 @@ class AnnDataProxy(AnnData):  # type: ignore[misc]
         self._varp = EZDataFrameContainerProxy(vdata.varp, name="Varp", index=vdata.var.index, columns=vdata.var.index)
         self._uns = vdata.uns
 
+    @override
     def __repr__(self) -> str:
         return f"AnnDataProxy from {self._vdata}"
 
-    def __sizeof__(self, show_stratified: bool | None = None, with_disk: bool = False) -> int:
+    @override
+    def __sizeof__(self, *, show_stratified: bool | None = None, with_disk: bool = False) -> int:
         del show_stratified, with_disk
         raise NotImplementedError
 
+    @override
     def __delitem__(self, index: Any) -> None:
         raise NotImplementedError
 
+    @override
     def __getitem__(self, index: Any) -> AnnDataProxy:
         """Returns a sliced view of the object."""
         return AnnDataProxy(self._vdata[skip_time_axis(index)], X=self._X)
 
+    @override
     def __setitem__(self, index: Any, val: int | float | npt.NDArray[Any] | sparse.spmatrix) -> None:
         raise NotImplementedError
 
     @property
-    def _n_obs(self) -> int:
+    @override
+    def n_obs(self) -> int:
         return self._vdata.n_obs_total
 
     @property
-    def _n_vars(self) -> int:
+    @override
+    def n_vars(self) -> int:
         return self._vdata.n_var
 
     @property
+    @override
     def X(self) -> AnyNDArrayLike[Any] | None:
         if self._X is None:
             return None
@@ -91,15 +101,16 @@ class AnnDataProxy(AnnData):  # type: ignore[misc]
         if isinstance(value, ArrayStack2DProxy):
             if value.layer_name is None:
                 self._layers["X"] = value.stack()
-                self._X = "X"
+                self._X = "X"  # pyright: ignore[reportConstantRedefinition]
 
         raise NotImplementedError
 
     @X.deleter
     def X(self) -> None:
-        self._X = None
+        self._X = None  # pyright: ignore[reportConstantRedefinition]
 
     @property
+    @override
     def layers(self) -> TemporalDataFrameContainerProxy:
         return self._layers
 
@@ -113,11 +124,12 @@ class AnnDataProxy(AnnData):  # type: ignore[misc]
         raise NotImplementedError
 
     @property
-    def raw(self) -> None:
+    @override
+    def raw(self) -> None:  # pyright: ignore[reportIncompatibleMethodOverride]
         raise NotImplementedError
 
     @raw.setter
-    def raw(self, value: AnnData) -> None:
+    def raw(self, value: AnnData) -> None:  # pyright: ignore[reportPropertyTypeMismatch]
         raise NotImplementedError
 
     @raw.deleter
@@ -125,11 +137,12 @@ class AnnDataProxy(AnnData):  # type: ignore[misc]
         raise NotImplementedError
 
     @property
-    def obs(self) -> DataFrameProxy_TDF:
+    @override
+    def obs(self) -> DataFrameProxy_TDF:  # pyright: ignore[reportIncompatibleMethodOverride]
         return self._obs
 
     @obs.setter
-    def obs(self, value: pd.DataFrame) -> None:
+    def obs(self, value: pd.DataFrame) -> None:  # pyright: ignore[reportPropertyTypeMismatch]
         raise NotImplementedError
 
     @obs.deleter
@@ -137,21 +150,23 @@ class AnnDataProxy(AnnData):  # type: ignore[misc]
         raise NotImplementedError
 
     @property
+    @override
     def obs_names(self) -> pd.Index:
         """Names of observations (alias for `.obs.index`)."""
         return self.obs.index
 
     @obs_names.setter
-    def obs_names(self, names: Sequence[str]) -> None:
+    def obs_names(self, names: Sequence[str]) -> None:  # pyright: ignore[reportPropertyTypeMismatch]
         raise NotImplementedError
 
     @property
+    @override
     def var(self) -> EZDataFrame:
         """One-dimensional annotation of variables/ features (`pd.DataFrame`)."""
         return self._var
 
     @var.setter
-    def var(self, value: pd.DataFrame) -> None:
+    def var(self, value: pd.DataFrame) -> None:  # pyright: ignore[reportPropertyTypeMismatch]
         raise NotImplementedError
 
     @var.deleter
@@ -159,21 +174,23 @@ class AnnDataProxy(AnnData):  # type: ignore[misc]
         raise NotImplementedError
 
     @property
+    @override
     def var_names(self) -> pd.Index:
         """Names of variables (alias for `.var.index`)."""
         return self.var.index
 
     @var_names.setter
-    def var_names(self, names: Sequence[str]) -> None:
+    def var_names(self, names: Sequence[str]) -> None:  # pyright: ignore[reportPropertyTypeMismatch]
         raise NotImplementedError
 
     @property
-    def uns(self) -> DictLike[Any]:
+    @override
+    def uns(self) -> MutableMapping[str, Any]:
         """Unstructured annotation (ordered dictionary)."""
         return self._uns
 
     @uns.setter
-    def uns(self, value: DictLike[Any]) -> None:
+    def uns(self, value: MutableMapping[str, Any]) -> None:
         raise NotImplementedError
 
     @uns.deleter
@@ -181,6 +198,7 @@ class AnnDataProxy(AnnData):  # type: ignore[misc]
         raise NotImplementedError
 
     @property
+    @override
     def obsm(self) -> TemporalDataFrameContainerProxy:
         return self._obsm
 
@@ -193,6 +211,7 @@ class AnnDataProxy(AnnData):  # type: ignore[misc]
         raise NotImplementedError
 
     @property
+    @override
     def varm(self) -> EZDataFrameContainerProxy:
         return self._varm
 
@@ -205,6 +224,7 @@ class AnnDataProxy(AnnData):  # type: ignore[misc]
         raise NotImplementedError
 
     @property
+    @override
     def obsp(self) -> EZDataFrameContainerProxy:
         return self._obsp
 
@@ -217,6 +237,7 @@ class AnnDataProxy(AnnData):  # type: ignore[misc]
         raise NotImplementedError
 
     @property
+    @override
     def varp(self) -> EZDataFrameContainerProxy:
         return self._varp
 
@@ -265,15 +286,19 @@ class AnnDataProxy(AnnData):  # type: ignore[misc]
         self._init_from_vdata(self._vdata[skip_time_axis(index)])
 
     @override
-    def copy(self, filename: Path | None = None) -> None:
+    def copy(self, filename: PathLike[str] | str | None = None) -> AnnData:
         """Full copy, optionally on disk."""
+        AnnData.copy
         raise NotImplementedError
 
+    @override
     def write_h5ad(
         self,
-        filename: Path | None = None,
+        filename: PathLike[str] | str | None = None,
+        *,
+        convert_strings_to_categoricals: bool = True,
         compression: Literal["gzip", "lzf"] | None = None,
-        compression_opts: Any = None,
+        compression_opts: int | Any = None,
         as_dense: Sequence[str] = (),
     ) -> None:
         raise NotImplementedError

{vdata-0.3.1 → vdata-0.3.2}/vdata/anndata_proxy/containers.py

@@ -1,29 +1,33 @@
 from __future__ import annotations
 
 import operator as op
-from functools import partialmethod
-from typing import (
-    Any,
-    Callable,
-    ClassVar,
+from collections.abc import (
     Collection,
     ItemsView,
     KeysView,
     MutableMapping,
-    Union,
     ValuesView,
+)
+from functools import partialmethod
+from typing import (
+    Any,
+    Callable,
+    ClassVar,
     cast,
+    final,
     override,
 )
 
 import numpy as np
 import numpy.typing as npt
+import pandas as pd
 import scipy.sparse as ss
+from ezarr.dataframe import EZDataFrame
 
-# from h5dataframe import EZDataFrame
 import vdata
-from vdata._typing import IFS, AnyNDArrayLike, AnyNDArrayLike_IFS
+from vdata._typing import IFS, AnyNDArrayLike
 from vdata.tdf import TemporalDataFrame, TemporalDataFrameBase
+from vdata.tdf.index import RepeatingIndex
 
 type _NP_IF = np.integer | np.floating
 
@@ -77,7 +81,7 @@ class ArrayStack2DProxy:
     ) -> None:
         self._array_numeric: AnyNDArrayLike[_NP_IF] | None = array_numeric if array_numeric.size else None
         self._array_string: AnyNDArrayLike[_NP_IF] | None = array_string if array_string.size else None
-        self.layer_name: str = layer_name
+        self.layer_name: str | None = layer_name
 
     @override
     def __repr__(self) -> str:
@@ -176,6 +180,7 @@ class ArrayStack2DProxy:
         )
 
 
+@final
 class EZDataFrameContainerProxy:
     __slots__: tuple[str, ...] = "_h5dfs", "_index", "_columns", "_name", "_sparse_matrices"
 
@@ -183,8 +188,8 @@ class EZDataFrameContainerProxy:
         self,
         h5dfs: MutableMapping[str, EZDataFrame],
         name: str,
-        index: AnyNDArrayLike_IFS,
-        columns: AnyNDArrayLike_IFS | None = None,
+        index: RepeatingIndex | pd.Index,
+        columns: RepeatingIndex | pd.Index | None = None,
     ) -> None:
         self._h5dfs = h5dfs
         self._index = index

{vdata-0.3.1 → vdata-0.3.2}/vdata/array_view.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from collections.abc import Iterable, Iterator, Sequence
+from collections.abc import Collection, Iterable, Iterator
 from typing import TYPE_CHECKING, Any, SupportsIndex, cast, overload, override
 
 import ch5mpy.indexing as ci
@@ -25,7 +25,7 @@ _RESERVED_ATTRIBUTES = frozenset(
 )
 
 
-class NDArrayView[T: np.generic | TimePoint](Sequence[T]):
+class NDArrayView[T: np.generic | TimePoint](Collection[T]):
     """View on a numpy ndarray that can be subsetted infinitely without copying."""
 
     __slots__: tuple[str, ...] = "_array", "_index", "_exposed_attr"

{vdata-0.3.1 → vdata-0.3.2}/vdata/data/__init__.py

@@ -1,11 +1,13 @@
 from vdata.data.concatenate import concatenate
 from vdata.data.convert import convert_anndata_to_vdata
+from vdata.data.name import WRITE_PROTOCOL_VERSION
 from vdata.data.vdata import VData
 from vdata.data.view import VDataView
 
 __all__ = [
-    'VData', 
-    'VDataView',
-    'concatenate',
-    'convert_anndata_to_vdata'
+    "VData",
+    "VDataView",
+    "concatenate",
+    "convert_anndata_to_vdata",
+    "WRITE_PROTOCOL_VERSION",
 ]

{vdata-0.3.1 → vdata-0.3.2}/vdata/data/_indexing.py

@@ -53,7 +53,7 @@ def slicer_to_array(
         return np.array(reference_index)[np.where(slicer.flatten())]
 
     if isinstance(slicer, tp.TimePointNArray):
-        return slicer[np.where(np.in1d(slicer, reference_index))]
+        return slicer[np.where(np.isin(slicer, reference_index))]
 
     if not isCollection(slicer):
         return np.array([slicer]) if slicer in reference_index else np.array([])
@@ -63,7 +63,7 @@ def slicer_to_array(
     if slicer.dtype == bool:
         return reference_index[slicer]
 
-    return slicer[np.where(np.in1d(slicer, reference_index))]
+    return slicer[np.where(np.isin(slicer, reference_index))]
 
 
 def _gets_whole_axis(slicer: PreSlicer) -> bool:

{vdata-0.3.1 → vdata-0.3.2}/vdata/data/_parse/time.py

@@ -44,7 +44,7 @@ def parse_timepoints_list(
 def parse_timepoints(timepoints: pd.DataFrame | EZDataFrame | None) -> EZDataFrame:
     if timepoints is None:
         generalLogger.debug("  'time points' DataFrame was not given.")
-        return EZDataFrame(pd.DataFrame(columns=np.array(["value"])))
+        return EZDataFrame(pd.DataFrame(columns=np.array(["value"]), dtype=float))
 
     if not isinstance(timepoints, (pd.DataFrame, EZDataFrame)):  # pyright: ignore[reportUnnecessaryIsInstance]
         raise TypeError(f"'time points' must be a DataFrame, got '{type(timepoints).__name__}'.")  # pyright: ignore[reportUnreachable]
@@ -55,7 +55,7 @@ def parse_timepoints(timepoints: pd.DataFrame | EZDataFrame | None) -> EZDataFra
     timepoints_col = tp.as_timepointarray(timepoints["value"])
     timepoints_col.sort()
     timepoints = EZDataFrame(timepoints.drop("value", axis=1))
-    timepoints.insert(0, "value", timepoints_col)
+    timepoints.insert(0, "value", timepoints_col)  # pyright: ignore[reportArgumentType]
     log_timepoints(timepoints)
 
     return timepoints
@@ -81,11 +81,11 @@ def check_time_match(data: ParsingDataIn) -> None:
 
     # check that timepoints and _time_list and _time_col_name match
     if data.timepoints_list is not None and not np.all(
-        np.in1d(data.timepoints_list, tp.as_timepointarray(data.timepoints.value))
+        np.isin(data.timepoints_list, tp.as_timepointarray(data.timepoints.value))
     ):
         raise ValueError("There are values in 'timepoints_list' unknown in 'timepoints'.")
 
     elif data.time_col_name is not None and not np.all(
-        np.in1d(tp.as_timepointarray(data.obs.timepoints), tp.as_timepointarray(data.timepoints.value))
+        np.isin(tp.as_timepointarray(data.obs.timepoints), tp.as_timepointarray(data.timepoints.value))
     ):
         raise ValueError(f"There are values in obs['{data.time_col_name}'] unknown in 'timepoints'.")

{vdata-0.3.1 → vdata-0.3.2}/vdata/data/arrays/base.py

@@ -10,21 +10,17 @@ import pandas as pd
 from ezarr.dataframe import EZDataFrame
 
 import vdata
-from vdata._typing import IFS, DictLike
-
-# from vdata.data.arrays.lazy import LazyLoc
+from vdata._typing import IFS
+from vdata.data.arrays.lazy import LazyLoc
 from vdata.IO import generalLogger
 from vdata.tdf import RepeatingIndex, TemporalDataFrame, TemporalDataFrameView
 from vdata.tdf.base import TemporalDataFrameBase
 from vdata.utils import first_in
 
-# D = TypeVar("D", Union[TemporalDataFrame, TemporalDataFrameView], TemporalDataFrameView, EZDataFrame, LazyLoc)
-# D_copy = TypeVar("D_copy", TemporalDataFrame, pd.DataFrame)
-
 
 # Base Containers -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
 class ArrayContainerMixin[
-    D: TemporalDataFrameBase | EZDataFrame,
+    D: TemporalDataFrameBase | EZDataFrame | LazyLoc,
     D_copy: TemporalDataFrame | pd.DataFrame,
 ](MutableMapping[str, D], ABC):
     @property
@@ -119,7 +115,7 @@ class VBaseArrayContainer[
 
     __slots__: tuple[str, ...] = "_vdata", "_data"
 
-    def __init__(self, *, data: DictLike[D], vdata: vdata.VData):
+    def __init__(self, *, data: MutableMapping[str, D], vdata: vdata.VData):
         """
         Args:
             vdata: the parent VData object this ArrayContainer is linked to.
@@ -129,10 +125,10 @@ class VBaseArrayContainer[
         generalLogger.debug(f"== Creating {type(self).__name__}. ==========================")
 
         self._vdata: vdata.VData = vdata
-        self._data: DictLike[D] = self._check_init_data(data)
+        self._data: MutableMapping[str, D] = self._check_init_data(data)
 
     @abstractmethod
-    def _check_init_data(self, data: DictLike[D]) -> DictLike[D]:
+    def _check_init_data(self, data: MutableMapping[str, D]) -> MutableMapping[str, D]:
         """
         Function for checking, at ArrayContainer creation, that the supplied data has the correct format.
 
@@ -230,7 +226,7 @@ class VBaseArrayContainer[
         pass
 
     @property
-    def data(self) -> DictLike[D]:
+    def data(self) -> MutableMapping[str, D]:
         """
         Data of this ArrayContainer.
 
@@ -277,7 +273,7 @@ class VTDFArrayContainer(VBaseArrayContainer[TemporalDataFrame | TemporalDataFra
     It is based on VBaseArrayContainer and defines some functions shared by obsm and layers.
     """
 
-    def __init__(self, *, data: dict[str, TemporalDataFrame | TemporalDataFrameView], vdata: vdata.VData):
+    def __init__(self, *, data: MutableMapping[str, TemporalDataFrame | TemporalDataFrameView], vdata: vdata.VData):
         """
         Args:
             parent: the parent VData object this ArrayContainer is linked to.

{vdata-0.3.1 → vdata-0.3.2}/vdata/data/arrays/layers.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from collections.abc import MutableMapping
 from typing import override
 
 import ezarr as ez
@@ -21,8 +22,8 @@ class VLayersArrayContainer(VTDFArrayContainer):
 
     @override
     def _check_init_data(
-        self, data: dict[str, TemporalDataFrame | TemporalDataFrameView]
-    ) -> dict[str, TemporalDataFrame | TemporalDataFrameView]:
+        self, data: MutableMapping[str, TemporalDataFrame | TemporalDataFrameView]
+    ) -> MutableMapping[str, TemporalDataFrame | TemporalDataFrameView]:
         """
         Function for checking, at VLayerArrayContainer creation, that the supplied data has the correct format :
             - the shape of the TemporalDataFrames in 'data' match the parent VData object's shape.
@@ -44,7 +45,9 @@ class VLayersArrayContainer(VTDFArrayContainer):
         generalLogger.debug("  Data was found.")
 
         _shape = (self._vdata.timepoints.shape[0], self._vdata.obs.shape[1], self._vdata.var.shape[0])
-        _data: dict[str, TemporalDataFrame | TemporalDataFrameView] = {} if not isinstance(data, ez.EZDict) else data
+        _data: MutableMapping[str, TemporalDataFrame | TemporalDataFrameView] = (
+            {} if not isinstance(data, ez.EZDict) else data
+        )
 
         generalLogger.debug(f"  Reference shape is {_shape}.")
 

{vdata-0.3.1 → vdata-0.3.2}/vdata/data/arrays/obs.py

@@ -83,8 +83,7 @@ class VObsmArrayContainer(VTDFArrayContainer):
                     f"Time points of TemporalDataFrame '{TDF_index}' ({tdf.timepoints}) do not match time_point's index. ({self._vdata.timepoints.value.values})"
                 )
 
-            if tdf.data is None or ch.H5Mode.has_write_intent(tdf.data.mode):
-                tdf.lock_indices()
+            tdf.lock_indices()
 
             if isinstance(data, dict):
                 _data[str(TDF_index)] = tdf

{vdata-0.3.1 → vdata-0.3.2}/vdata/data/arrays/var.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from collections.abc import Collection
+from collections.abc import Collection, MutableMapping
 from typing import cast, override
 
 import ezarr as ez
@@ -8,7 +8,7 @@ import numpy.typing as npt
 import pandas as pd
 from ezarr.dataframe import EZDataFrame
 
-from vdata._typing import IFS, DictLike, np_IFS
+from vdata._typing import IFS, np_IFS
 from vdata.data.arrays.base import VBaseArrayContainer
 from vdata.data.arrays.lazy import LazyLoc
 from vdata.data.arrays.view import VBaseArrayContainerView
@@ -21,7 +21,7 @@ from vdata.IO import (
 from vdata.utils import first_in
 
 
-class VVarmArrayContainer(VBaseArrayContainer[pd.DataFrame | EZDataFrame]):
+class VVarmArrayContainer(VBaseArrayContainer[EZDataFrame, pd.DataFrame]):
     """
     Class for varm.
     This object contains any number of DataFrames, with shape (n_var, any).
@@ -30,7 +30,7 @@ class VVarmArrayContainer(VBaseArrayContainer[pd.DataFrame | EZDataFrame]):
     """
 
     @override
-    def _check_init_data(self, data: DictLike[EZDataFrame]) -> DictLike[EZDataFrame]:
+    def _check_init_data(self, data: MutableMapping[str, EZDataFrame]) -> MutableMapping[str, EZDataFrame]:
         """
         Function for checking, at VVarmArrayContainer creation, that the supplied data has the correct format :
             - the index of the DataFrames in 'data' match the index of the parent VData's var DataFrame.
@@ -42,7 +42,7 @@ class VVarmArrayContainer(VBaseArrayContainer[pd.DataFrame | EZDataFrame]):
         generalLogger.debug("  Data was found.")
 
         _index = self._vdata.var.index
-        _data: DictLike[EZDataFrame] = {} if not isinstance(data, ez.EZDict) else data
+        _data: MutableMapping[str, EZDataFrame] = {} if not isinstance(data, ez.EZDict) else data
 
         for DF_index, DF in data.items():
             if not _index.equals(DF.index):
@@ -97,7 +97,7 @@ class VVarmArrayContainer(VBaseArrayContainer[pd.DataFrame | EZDataFrame]):
             arr.index = pd.Index(values)
 
 
-class VVarmArrayContainerView(VBaseArrayContainerView[LazyLoc, pd.DataFrame | EZDataFrame]):
+class VVarmArrayContainerView(VBaseArrayContainerView[LazyLoc | EZDataFrame, pd.DataFrame]):
     # region magic methods
     def __init__(self, array_container: VVarmArrayContainer, var_slicer: npt.NDArray[np_IFS]):
         super().__init__(
@@ -164,7 +164,7 @@ class VVarmArrayContainerView(VBaseArrayContainerView[LazyLoc, pd.DataFrame | EZ
             arr.index = pd.Index(values)
 
 
-class VVarpArrayContainer(VBaseArrayContainer[pd.DataFrame]):  # EZDataFrame,
+class VVarpArrayContainer(VBaseArrayContainer[EZDataFrame, pd.DataFrame]):
     """
     Class for varp.
     This object contains any number of DataFrames, with shape (n_var, n_var).
@@ -173,7 +173,7 @@ class VVarpArrayContainer(VBaseArrayContainer[pd.DataFrame]):  # EZDataFrame,
     """
 
     @override
-    def _check_init_data(self, data: DictLike[EZDataFrame]) -> DictLike[EZDataFrame]:
+    def _check_init_data(self, data: MutableMapping[str, EZDataFrame]) -> MutableMapping[str, EZDataFrame]:
         """
         Function for checking, at ArrayContainer creation, that the supplied data has the correct format :
             - the index and column names of the DataFrames in 'data' match the index of the parent VData's var
@@ -186,7 +186,7 @@ class VVarpArrayContainer(VBaseArrayContainer[pd.DataFrame]):  # EZDataFrame,
         generalLogger.debug("  Data was found.")
 
         _index = self._vdata.var.index
-        _data: DictLike[EZDataFrame] = {} if not isinstance(data, ez.EZDict) else data
+        _data: MutableMapping[str, EZDataFrame] = {} if not isinstance(data, ez.EZDict) else data
 
         for DF_index, DF in data.items():
             if not _index.equals(DF.index):