lamindb 0.76.6__py3-none-any.whl → 0.76.8__py3-none-any.whl

lamindb/core/storage/_anndata_sizes.py

@@ -1,41 +1,41 @@
-from __future__ import annotations
-
-import warnings
-
-import scipy.sparse as sparse
-from pandas import DataFrame
-
-
-def _size_val(val):
-    with warnings.catch_warnings():
-        warnings.filterwarnings("ignore", category=FutureWarning)
-
-        if sparse.issparse(val):
-            val_csr = sparse.csr_matrix(val)
-            return val_csr.data.nbytes + val_csr.indptr.nbytes + val_csr.indices.nbytes
-        else:
-            return val.__sizeof__()
-
-
-def _size_elem(elem):
-    if hasattr(elem, "keys") and not isinstance(elem, DataFrame):
-        return sum([_size_val(elem[k]) for k in elem.keys()])
-    else:
-        return _size_val(elem)
-
-
-def _size_raw(raw):
-    return _size_val(raw.X) + _size_val(raw.var) + _size_elem(raw.varm)
-
-
-def size_adata(adata):
-    with warnings.catch_warnings():
-        warnings.filterwarnings("ignore", category=FutureWarning)
-
-        total_size = adata.__sizeof__()
-
-        raw = adata.raw
-        if raw is not None:
-            total_size += _size_raw(raw)
-
-        return total_size
+from __future__ import annotations
+
+import warnings
+
+import scipy.sparse as sparse
+from pandas import DataFrame
+
+
+def _size_val(val):
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", category=FutureWarning)
+
+        if sparse.issparse(val):
+            val_csr = sparse.csr_matrix(val)
+            return val_csr.data.nbytes + val_csr.indptr.nbytes + val_csr.indices.nbytes
+        else:
+            return val.__sizeof__()
+
+
+def _size_elem(elem):
+    if hasattr(elem, "keys") and not isinstance(elem, DataFrame):
+        return sum([_size_val(elem[k]) for k in elem.keys()])
+    else:
+        return _size_val(elem)
+
+
+def _size_raw(raw):
+    return _size_val(raw.X) + _size_val(raw.var) + _size_elem(raw.varm)
+
+
+def size_adata(adata):
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", category=FutureWarning)
+
+        total_size = adata.__sizeof__()
+
+        raw = adata.raw
+        if raw is not None:
+            total_size += _size_raw(raw)
+
+        return total_size

lamindb/core/storage/_backed_access.py

@@ -1,98 +1,98 @@
-from __future__ import annotations
-
-from dataclasses import dataclass
-from typing import TYPE_CHECKING, Any, Callable
-
-from anndata._io.specs.registry import get_spec
-from lnschema_core import Artifact
-
-from ._anndata_accessor import AnnDataAccessor, StorageType, registry
-from ._tiledbsoma import _open_tiledbsoma
-from .paths import filepath_from_artifact
-
-if TYPE_CHECKING:
-    from fsspec.core import OpenFile
-    from tiledbsoma import Collection as SOMACollection
-    from tiledbsoma import Experiment as SOMAExperiment
-    from upath import UPath
-
-
-# this dynamically creates a subclass of a context manager class
-# and reassigns it to an instance of the superclass
-# so that the instance calls finalize on close or exit
-def _track_writes_factory(obj: Any, finalize: Callable):
-    closed: bool = False
-
-    tracked_class = obj.__class__
-    type_dict = {"__doc__": tracked_class.__doc__}
-    if hasattr(tracked_class, "__slots__"):
-        type_dict["__slots__"] = ()
-    if hasattr(tracked_class, "__exit__"):
-
-        def __exit__(self, exc_type, exc_val, exc_tb):
-            nonlocal closed
-            tracked_class.__exit__(self, exc_type, exc_val, exc_tb)
-            if not closed:
-                finalize()
-                closed = True
-
-        type_dict["__exit__"] = __exit__
-    if hasattr(tracked_class, "close"):
-
-        def close(self, *args, **kwargs):
-            nonlocal closed
-            tracked_class.close(self, *args, **kwargs)
-            if not closed:
-                finalize()
-                closed = True
-
-        type_dict["close"] = close
-
-    Track = type(tracked_class.__name__ + "Track", (tracked_class,), type_dict)
-    obj.__class__ = Track
-    return obj
-
-
-@dataclass
-class BackedAccessor:
-    """h5py.File or zarr.Group accessor."""
-
-    connection: OpenFile
-    """The connection."""
-    storage: StorageType
-    """The storage access."""
-
-
-def backed_access(
-    artifact_or_filepath: Artifact | UPath,
-    mode: str = "r",
-    using_key: str | None = None,
-) -> AnnDataAccessor | BackedAccessor | SOMACollection | SOMAExperiment:
-    if isinstance(artifact_or_filepath, Artifact):
-        filepath = filepath_from_artifact(artifact_or_filepath, using_key=using_key)
-    else:
-        filepath = artifact_or_filepath
-    name = filepath.name
-    suffix = filepath.suffix
-
-    if name == "soma" or suffix == ".tiledbsoma":
-        if mode not in {"r", "w"}:
-            raise ValueError("`mode` should be either 'r' or 'w' for tiledbsoma.")
-        return _open_tiledbsoma(filepath, mode=mode)  # type: ignore
-    elif suffix in {".h5", ".hdf5", ".h5ad"}:
-        conn, storage = registry.open("h5py", filepath, mode=mode)
-    elif suffix == ".zarr":
-        conn, storage = registry.open("zarr", filepath, mode=mode)
-    else:
-        raise ValueError(
-            "object should have .h5, .hdf5, .h5ad, .zarr, .tiledbsoma suffix, not"
-            f" {suffix}."
-        )
-
-    is_anndata = suffix == ".h5ad" or get_spec(storage).encoding_type == "anndata"
-    if is_anndata:
-        if mode != "r":
-            raise ValueError("Can only access `AnnData` with mode='r'.")
-        return AnnDataAccessor(conn, storage, name)
-    else:
-        return BackedAccessor(conn, storage)
+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import TYPE_CHECKING, Any, Callable
+
+from anndata._io.specs.registry import get_spec
+from lnschema_core import Artifact
+
+from ._anndata_accessor import AnnDataAccessor, StorageType, registry
+from ._tiledbsoma import _open_tiledbsoma
+from .paths import filepath_from_artifact
+
+if TYPE_CHECKING:
+    from fsspec.core import OpenFile
+    from tiledbsoma import Collection as SOMACollection
+    from tiledbsoma import Experiment as SOMAExperiment
+    from upath import UPath
+
+
+# this dynamically creates a subclass of a context manager class
+# and reassigns it to an instance of the superclass
+# so that the instance calls finalize on close or exit
+def _track_writes_factory(obj: Any, finalize: Callable):
+    closed: bool = False
+
+    tracked_class = obj.__class__
+    type_dict = {"__doc__": tracked_class.__doc__}
+    if hasattr(tracked_class, "__slots__"):
+        type_dict["__slots__"] = ()
+    if hasattr(tracked_class, "__exit__"):
+
+        def __exit__(self, exc_type, exc_val, exc_tb):
+            nonlocal closed
+            tracked_class.__exit__(self, exc_type, exc_val, exc_tb)
+            if not closed:
+                finalize()
+                closed = True
+
+        type_dict["__exit__"] = __exit__
+    if hasattr(tracked_class, "close"):
+
+        def close(self, *args, **kwargs):
+            nonlocal closed
+            tracked_class.close(self, *args, **kwargs)
+            if not closed:
+                finalize()
+                closed = True
+
+        type_dict["close"] = close
+
+    Track = type(tracked_class.__name__ + "Track", (tracked_class,), type_dict)
+    obj.__class__ = Track
+    return obj
+
+
+@dataclass
+class BackedAccessor:
+    """h5py.File or zarr.Group accessor."""
+
+    connection: OpenFile
+    """The connection."""
+    storage: StorageType
+    """The storage access."""
+
+
+def backed_access(
+    artifact_or_filepath: Artifact | UPath,
+    mode: str = "r",
+    using_key: str | None = None,
+) -> AnnDataAccessor | BackedAccessor | SOMACollection | SOMAExperiment:
+    if isinstance(artifact_or_filepath, Artifact):
+        filepath, _ = filepath_from_artifact(artifact_or_filepath, using_key=using_key)
+    else:
+        filepath = artifact_or_filepath
+    name = filepath.name
+    suffix = filepath.suffix
+
+    if name == "soma" or suffix == ".tiledbsoma":
+        if mode not in {"r", "w"}:
+            raise ValueError("`mode` should be either 'r' or 'w' for tiledbsoma.")
+        return _open_tiledbsoma(filepath, mode=mode)  # type: ignore
+    elif suffix in {".h5", ".hdf5", ".h5ad"}:
+        conn, storage = registry.open("h5py", filepath, mode=mode)
+    elif suffix == ".zarr":
+        conn, storage = registry.open("zarr", filepath, mode=mode)
+    else:
+        raise ValueError(
+            "object should have .h5, .hdf5, .h5ad, .zarr, .tiledbsoma suffix, not"
+            f" {suffix}."
+        )
+
+    is_anndata = suffix == ".h5ad" or get_spec(storage).encoding_type == "anndata"
+    if is_anndata:
+        if mode != "r":
+            raise ValueError("Can only access `AnnData` with mode='r'.")
+        return AnnDataAccessor(conn, storage, name)
+    else:
+        return BackedAccessor(conn, storage)