lamindb 0.64.0__py3-none-any.whl → 0.64.2__py3-none-any.whl

lamindb/dev/datasets/_core.py

@@ -8,7 +8,7 @@ import pandas as pd
 from lnschema_core import ids
 from upath import UPath
 
-from .._settings import settings
+from lamindb.dev._settings import settings
 
 
 def file_fcs() -> Path:
@@ -26,7 +26,7 @@ def file_fcs_alpert19(populate_registries: bool = False) -> Path:  # pragma: no
         populate_registries: pre-populate metadata records to simulate existing registries  # noqa
     """
     filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/Alpert19-070314-Mike-Study+15-2013-plate+1-15-004-1-13_cells_found.fcs",  # noqa
+        "https://lamindb-test.s3.amazonaws.com/Alpert19-070314-Mike-Study+15-2013-plate+1-15-004-1-13_cells_found.fcs",
         "Alpert19.fcs",
     )
     if populate_registries:
@@ -56,7 +56,7 @@ def file_jpg_paradisi05() -> Path:
     """Return jpg file example.
 
     Originally from: https://upload.wikimedia.org/wikipedia/commons/2/28/Laminopathic_nuclei.jpg
-    """  # noqa
+    """
     filepath, _ = urlretrieve(
         "https://lamindb-test.s3.amazonaws.com/Laminopathic_nuclei.jpg",
         "paradisi05_laminopathic_nuclei.jpg",
@@ -94,7 +94,7 @@ def file_tsv_rnaseq_nfcore_salmon_merged_gene_counts(
 
 def file_fastq(in_storage_root=False) -> Path:
     """Mini mock fastq artifact."""
-    basedir = Path(".") if not in_storage_root else settings.storage
+    basedir = Path() if not in_storage_root else settings.storage
     filepath = basedir / "input.fastq.gz"
     with open(filepath, "w") as f:
         f.write("Mock fastq artifact.")
@@ -103,7 +103,7 @@ def file_fastq(in_storage_root=False) -> Path:
 
 def file_bam(in_storage_root=False) -> Path:  # pragma: no cover
     """Mini mock bam artifact."""
-    basedir = Path(".") if not in_storage_root else settings.storage
+    basedir = Path() if not in_storage_root else settings.storage
     filepath = basedir / "output.bam"
     with open(filepath, "w") as f:
         f.write("Mock bam artifact.")
@@ -112,7 +112,7 @@ def file_bam(in_storage_root=False) -> Path:  # pragma: no cover
 
 def file_mini_csv(in_storage_root=False) -> Path:
     """Mini csv artifact."""
-    basedir = Path(".") if not in_storage_root else settings.storage
+    basedir = Path() if not in_storage_root else settings.storage
     filepath = basedir / "mini.csv"
     df = pd.DataFrame([1, 2, 3], columns=["test"])
     df.to_csv(filepath, index=False)
@@ -168,7 +168,7 @@ def anndata_mouse_sc_lymph_node(
         .str.replace("developmental stage", "developmental_stage")
         .str.replace("cell type", "cell_type")
         # the last one could be interesting, too
-        # .str.replace("Factor Value:Ontology Term[inferred cell_type - authors labels", "cell_type_authors")  # noqa
+        # .str.replace("Factor Value:Ontology Term[inferred cell_type - authors labels", "cell_type_authors")
     )
     # subset columns to only the ones with names
     columns = [
@@ -396,7 +396,7 @@ def mudata_papalexi21_subset():  # pragma: no cover
     import mudata as md
 
     filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/papalexi21_subset_200x300_lamindb_demo_2023-07-25.h5mu",  # noqa
+        "https://lamindb-test.s3.amazonaws.com/papalexi21_subset_200x300_lamindb_demo_2023-07-25.h5mu",
         "papalexi21_subset.h5mu",
     )
 

lamindb/dev/fields.py

@@ -9,4 +9,4 @@ The field accessor of a :class:`~lamindb.dev.Registry`:
 
 """
 
-from lnschema_core.types import FieldAttr  # noqa
+from lnschema_core.types import FieldAttr

lamindb/dev/storage/_backed_access.py

@@ -399,7 +399,7 @@ class _AnnDataAttrsMixin:
         indices = getattr(self, "indices", None)
         if indices is not None:
             indices = (indices[0], slice(None))
-            obj = registry.safer_read_partial(self.storage["obs"], indices=indices)  # type: ignore # noqa
+            obj = registry.safer_read_partial(self.storage["obs"], indices=indices)  # type: ignore
             return _records_to_df(obj)
         else:
             return registry.read_dataframe(self.storage["obs"])  # type: ignore
@@ -411,7 +411,7 @@ class _AnnDataAttrsMixin:
         indices = getattr(self, "indices", None)
         if indices is not None:
             indices = (indices[1], slice(None))
-            obj = registry.safer_read_partial(self.storage["var"], indices=indices)  # type: ignore # noqa
+            obj = registry.safer_read_partial(self.storage["var"], indices=indices)  # type: ignore
             return _records_to_df(obj)
         else:
             return registry.read_dataframe(self.storage["var"])  # type: ignore
@@ -588,9 +588,9 @@ class AnnDataRawAccessor(AnnDataAccessorSubset):
             else:
                 # for some reason list(var_raw.keys()) is very slow for zarr
                 # maybe also directly get keys from the underlying mapper
-                attrs_keys["var"] = [key for key in var_raw]
+                attrs_keys["var"] = list(var_raw)
             if "varm" in storage_raw:
-                varm_keys_raw = [key for key in storage_raw["varm"]]
+                varm_keys_raw = list(storage_raw["varm"])
                 if len(varm_keys_raw) > 0:
                     attrs_keys["varm"] = varm_keys_raw
 
@@ -684,7 +684,7 @@ class BackedAccessor:
 
 
 def backed_access(
-    artifact_or_filepath: Union[Artifact, Path]
+    artifact_or_filepath: Union[Artifact, Path],
 ) -> Union[AnnDataAccessor, BackedAccessor]:
     if isinstance(artifact_or_filepath, Artifact):
         filepath = filepath_from_artifact(artifact_or_filepath)

lamindb/dev/storage/file.py

@@ -134,7 +134,7 @@ def read_fcs(*args, **kwargs):
     try:
         import readfcs
     except ImportError:  # pragma: no cover
-        raise ImportError("Please install readfcs: pip install readfcs")
+        raise ImportError("Please install readfcs: pip install readfcs") from None
     return readfcs.read(*args, **kwargs)
 
 

lamindb/dev/types.py

@@ -9,7 +9,7 @@
    ListLike
    TransformType
 """
-from lnschema_core.types import (  # noqa
+from lnschema_core.types import (
     DataLike,
     ListLike,
     PathLike,

lamindb/dev/versioning.py

@@ -12,7 +12,7 @@ def set_version(version: Optional[str] = None, previous_version: Optional[str] =
 
     Args:
         version: Version string.
-        stored_version: Mock stored version for testing purposes.
+        previous_version: Previous version string.
     """
     if version == previous_version:
         raise ValueError(f"Please increment the previous version: '{previous_version}'")
@@ -23,7 +23,7 @@ def set_version(version: Optional[str] = None, previous_version: Optional[str] =
             raise ValueError(
                 "Cannot auto-increment non-integer castable version, please provide"
                 " manually"
-            )
+            ) from None
     return version
 
 
@@ -59,7 +59,7 @@ def get_ids_from_old_version(
     version: Optional[str],
     n_full_id: int = 20,
 ) -> Tuple[str, int, str]:
-    """{}"""
+    """{}."""
     msg = ""
     if is_new_version_of.version is None:
         previous_version = "1"

lamindb/setup/__init__.py

@@ -1,5 +1,5 @@
 import lamindb_setup as _lamindb_setup
-from lamindb_setup import *
+from lamindb_setup import *  # noqa: F403
 from lamindb_setup import settings
 
 from . import dev

{lamindb-0.64.0.dist-info → lamindb-0.64.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.64.0
+Version: 0.64.2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,7 +9,7 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Requires-Dist: lnschema_core==0.58.1
-Requires-Dist: lamindb_setup==0.61.3
+Requires-Dist: lamindb_setup==0.61.4
 Requires-Dist: lamin_utils==0.12.0
 Requires-Dist: lamin_cli==0.3.0
 Requires-Dist: rapidfuzz

lamindb-0.64.2.dist-info/RECORD

@@ -0,0 +1,48 @@
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+lamindb/_delete.py,sha256=jO6kcIoxY6EFgqiVF2vlbXaCaqlI25AvBo7nre3JXkQ,1968
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lamindb-0.64.0.dist-info/RECORD

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