lamindb 0.69.7__py3-none-any.whl → 0.69.9__py3-none-any.whl

lamindb/_parents.py

@@ -1,5 +1,7 @@
+from __future__ import annotations
+
 import builtins
-from typing import List, Optional, Set, Union
+from typing import TYPE_CHECKING
 
 import lamindb_setup as ln_setup
 from lamin_utils import logger
@@ -8,7 +10,10 @@ from lnschema_core.models import HasParents, format_field_value
 
 from lamindb._utils import attach_func_to_class_method
 
-from ._registry import StrField, get_default_str_field
+from ._registry import get_default_str_field
+
+if TYPE_CHECKING:
+    from lnschema_core.types import StrField
 
 LAMIN_GREEN_LIGHTER = "#10b981"
 LAMIN_GREEN_DARKER = "#065f46"
@@ -47,7 +52,7 @@ def _view(u):
 
 def view_parents(
     self,
-    field: Optional[StrField] = None,
+    field: StrField | None = None,
     with_children: bool = False,
     distance: int = 5,
 ):
@@ -61,7 +66,7 @@ def view_parents(
     )
 
 
-def view_lineage(data: Union[Artifact, Collection], with_children: bool = True) -> None:
+def view_lineage(data: Artifact | Collection, with_children: bool = True) -> None:
     """Graph of data flow.
 
     Notes:
@@ -81,7 +86,7 @@ def view_lineage(data: Union[Artifact, Collection], with_children: bool = True)
     data_label = _record_label(data)
 
     def add_node(
-        record: Union[Run, Artifact, Collection],
+        record: Run | Artifact | Collection,
         node_id: str,
         node_label: str,
         u: graphviz.Digraph,
@@ -256,7 +261,7 @@ def _df_edges_from_parents(
     return df_edges
 
 
-def _record_label(record: Registry, field: Optional[str] = None):
+def _record_label(record: Registry, field: str | None = None):
     if isinstance(record, Artifact):
         if record.description is None:
             name = record.key
@@ -310,7 +315,7 @@ def _add_emoji(record: Registry, label: str):
     return f"{emoji} {label}"
 
 
-def _get_all_parent_runs(data: Union[Artifact, Collection]) -> List:
+def _get_all_parent_runs(data: Artifact | Collection) -> list:
     """Get all input file/collection runs recursively."""
     name = data._meta.model_name
     run_inputs_outputs = []
@@ -346,10 +351,10 @@ def _get_all_parent_runs(data: Union[Artifact, Collection]) -> List:
     return run_inputs_outputs
 
 
-def _get_all_child_runs(data: Union[Artifact, Collection]) -> List:
+def _get_all_child_runs(data: Artifact | Collection) -> list:
     """Get all output file/collection runs recursively."""
     name = data._meta.model_name
-    all_runs: Set[Run] = set()
+    all_runs: set[Run] = set()
     run_inputs_outputs = []
 
     if data.run is not None:
@@ -367,7 +372,7 @@ def _get_all_child_runs(data: Union[Artifact, Collection]) -> List:
         )
     while runs.difference(all_runs):
         all_runs.update(runs)
-        child_runs: Set[Run] = set()
+        child_runs: set[Run] = set()
         for r in runs:
             inputs_run = (
                 r.__getattribute__(f"input_{name}s")
@@ -409,7 +414,7 @@ def _get_all_child_runs(data: Union[Artifact, Collection]) -> List:
     return run_inputs_outputs
 
 
-def _df_edges_from_runs(df_values: List):
+def _df_edges_from_runs(df_values: list):
     import pandas as pd
 
     df = pd.DataFrame(df_values, columns=["source_record", "target_record"])

lamindb/_query_manager.py

@@ -1,13 +1,17 @@
-from typing import NamedTuple, Optional
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, NamedTuple
 
 from django.db import models
 from lamin_utils import logger
 from lamindb_setup.core._docs import doc_args
 from lnschema_core.models import Registry
-from lnschema_core.types import StrField
 
 from .core._feature_manager import get_feature_set_by_slot
 
+if TYPE_CHECKING:
+    from lnschema_core.types import StrField
+
 
 class QueryManager(models.Manager):
     """Manage queries through fields.
@@ -41,7 +45,7 @@ class QueryManager(models.Manager):
                     logger.warning(WARNING_RUN_TRANSFORM)
                 _track_run_input(self.instance)
 
-    def list(self, field: Optional[str] = None):
+    def list(self, field: str | None = None):
         """Populate a list with the results.
 
         Examples:
@@ -83,7 +87,7 @@ class QueryManager(models.Manager):
         return _search(cls=self.all(), string=string, **kwargs)
 
     @doc_args(Registry.lookup.__doc__)
-    def lookup(self, field: Optional[StrField] = None, **kwargs) -> NamedTuple:
+    def lookup(self, field: StrField | None = None, **kwargs) -> NamedTuple:
         """{}."""
         from ._registry import _lookup
 

lamindb/_query_set.py

@@ -1,5 +1,7 @@
+from __future__ import annotations
+
 from collections import UserList
-from typing import Dict, Iterable, List, NamedTuple, Optional, Union
+from typing import TYPE_CHECKING, Iterable, NamedTuple
 
 import pandas as pd
 from django.db import models
@@ -15,7 +17,9 @@ from lnschema_core.models import (
     Run,
     Transform,
 )
-from lnschema_core.types import ListLike, StrField
+
+if TYPE_CHECKING:
+    from lnschema_core.types import ListLike, StrField
 
 
 class NoResultFound(Exception):
@@ -32,7 +36,7 @@ class MultipleResultsFound(Exception):
 #     return (series + timedelta).dt.strftime("%Y-%m-%d %H:%M:%S %Z")
 
 
-def get_keys_from_df(data: List, registry: Registry) -> List[str]:
+def get_keys_from_df(data: list, registry: Registry) -> list[str]:
     if len(data) > 0:
         if isinstance(data[0], dict):
             keys = list(data[0].keys())
@@ -94,7 +98,7 @@ class QuerySet(models.QuerySet, CanValidate, IsTree):
     """
 
     @doc_args(Registry.df.__doc__)
-    def df(self, include: Optional[Union[str, List[str]]] = None) -> pd.DataFrame:
+    def df(self, include: str | list[str] | None = None) -> pd.DataFrame:
         """{}."""
         data = self.values()
         keys = get_keys_from_df(data, self.model)
@@ -173,7 +177,7 @@ class QuerySet(models.QuerySet, CanValidate, IsTree):
         else:
             self._delete_base_class(*args, **kwargs)
 
-    def list(self, field: Optional[str] = None) -> List[Registry]:
+    def list(self, field: str | None = None) -> list[Registry]:
         """Populate a list with the results.
 
         Examples:
@@ -185,7 +189,7 @@ class QuerySet(models.QuerySet, CanValidate, IsTree):
         else:
             return list(self.values_list(field, flat=True))
 
-    def first(self) -> Optional[Registry]:
+    def first(self) -> Registry | None:
         """If non-empty, the first result in the query set, otherwise ``None``.
 
         Examples:
@@ -203,7 +207,7 @@ class QuerySet(models.QuerySet, CanValidate, IsTree):
         """
         return one_helper(self)
 
-    def one_or_none(self) -> Optional[Registry]:
+    def one_or_none(self) -> Registry | None:
         """At most one result. Returns it if there is one, otherwise returns ``None``.
 
         Examples:
@@ -232,25 +236,21 @@ class QuerySet(models.QuerySet, CanValidate, IsTree):
         return _search(cls=self, string=string, **kwargs)
 
     @doc_args(Registry.lookup.__doc__)
-    def lookup(self, field: Optional[StrField] = None, **kwargs) -> NamedTuple:
+    def lookup(self, field: StrField | None = None, **kwargs) -> NamedTuple:
         """{}."""
         from ._registry import _lookup
 
         return _lookup(cls=self, field=field, **kwargs)
 
     @doc_args(CanValidate.validate.__doc__)
-    def validate(
-        self, values: ListLike, field: Optional[Union[str, StrField]] = None, **kwargs
-    ):
+    def validate(self, values: ListLike, field: str | StrField | None = None, **kwargs):
         """{}."""
         from ._can_validate import _validate
 
         return _validate(cls=self, values=values, field=field, **kwargs)
 
     @doc_args(CanValidate.inspect.__doc__)
-    def inspect(
-        self, values: ListLike, field: Optional[Union[str, StrField]] = None, **kwargs
-    ):
+    def inspect(self, values: ListLike, field: str | StrField | None = None, **kwargs):
         """{}."""
         from ._can_validate import _inspect
 
@@ -258,7 +258,7 @@ class QuerySet(models.QuerySet, CanValidate, IsTree):
 
     @doc_args(CanValidate.standardize.__doc__)
     def standardize(
-        self, values: Iterable, field: Optional[Union[str, StrField]] = None, **kwargs
+        self, values: Iterable, field: str | StrField | None = None, **kwargs
     ):
         """{}."""
         from ._can_validate import _standardize

lamindb/_registry.py

@@ -1,5 +1,7 @@
+from __future__ import annotations
+
 import builtins
-from typing import Iterable, List, NamedTuple, Optional, Union
+from typing import TYPE_CHECKING, Iterable, List, NamedTuple
 from uuid import UUID
 
 import dj_database_url
@@ -17,13 +19,15 @@ from lamindb_setup.core._docs import doc_args
 from lamindb_setup.core._hub_core import connect_instance
 from lamindb_setup.core._settings_storage import StorageSettings
 from lnschema_core import Registry
-from lnschema_core.types import ListLike, StrField
 
 from lamindb._utils import attach_func_to_class_method
 from lamindb.core._settings import settings
 
 from ._from_values import get_or_create_records
 
+if TYPE_CHECKING:
+    from lnschema_core.types import ListLike, StrField
+
 IPYTHON = getattr(builtins, "__IPYTHON__", False)
 
 
@@ -53,7 +57,7 @@ def validate_required_fields(orm: Registry, kwargs):
         raise TypeError(f"{missing_fields} are required.")
 
 
-def suggest_objects_with_same_name(orm: Registry, kwargs) -> Optional[str]:
+def suggest_objects_with_same_name(orm: Registry, kwargs) -> str | None:
     if kwargs.get("name") is None:
         return None
     else:
@@ -125,8 +129,8 @@ def __init__(orm: Registry, *args, **kwargs):
 @classmethod  # type:ignore
 @doc_args(Registry.from_values.__doc__)
 def from_values(
-    cls, values: ListLike, field: Optional[StrField] = None, **kwargs
-) -> List["Registry"]:
+    cls, values: ListLike, field: StrField | None = None, **kwargs
+) -> list[Registry]:
     """{}."""
     from_public = True if cls.__module__.startswith("lnschema_bionty.") else False
     field_str = get_default_str_field(cls, field=field)
@@ -150,21 +154,21 @@ def _search(
     cls,
     string: str,
     *,
-    field: Optional[Union[StrField, List[StrField]]] = None,
-    limit: Optional[int] = 10,
+    field: StrField | list[StrField] | None = None,
+    limit: int | None = 10,
     return_queryset: bool = False,
     case_sensitive: bool = False,
-    synonyms_field: Optional[StrField] = "synonyms",
-    using_key: Optional[str] = None,
-) -> Union["pd.DataFrame", "QuerySet"]:
+    synonyms_field: StrField | None = "synonyms",
+    using_key: str | None = None,
+) -> pd.DataFrame | QuerySet:
     queryset = _queryset(cls, using_key=using_key)
     orm = queryset.model
 
     def _search_single_field(
         string: str,
-        field: Optional[StrField],
-        synonyms_field: Optional[StrField] = "synonyms",
-    ) -> "pd.DataFrame":
+        field: StrField | None,
+        synonyms_field: StrField | None = "synonyms",
+    ) -> pd.DataFrame:
         field = get_default_str_field(orm=orm, field=field)
 
         try:
@@ -233,12 +237,12 @@ def search(
     cls,
     string: str,
     *,
-    field: Optional[StrField] = None,
-    limit: Optional[int] = 20,
+    field: StrField | None = None,
+    limit: int | None = 20,
     return_queryset: bool = False,
     case_sensitive: bool = False,
-    synonyms_field: Optional[StrField] = "synonyms",
-) -> Union["pd.DataFrame", "QuerySet"]:
+    synonyms_field: StrField | None = "synonyms",
+) -> pd.DataFrame | QuerySet:
     """{}."""
     return _search(
         cls=cls,
@@ -253,9 +257,9 @@ def search(
 
 def _lookup(
     cls,
-    field: Optional[StrField] = None,
-    return_field: Optional[StrField] = None,
-    using_key: Optional[str] = None,
+    field: StrField | None = None,
+    return_field: StrField | None = None,
+    using_key: str | None = None,
 ) -> NamedTuple:
     """{}."""
     queryset = _queryset(cls, using_key=using_key)
@@ -279,17 +283,17 @@ def _lookup(
 @doc_args(Registry.lookup.__doc__)
 def lookup(
     cls,
-    field: Optional[StrField] = None,
-    return_field: Optional[StrField] = None,
+    field: StrField | None = None,
+    return_field: StrField | None = None,
 ) -> NamedTuple:
     """{}."""
     return _lookup(cls=cls, field=field, return_field=return_field)
 
 
 def get_default_str_field(
-    orm: Union[Registry, QuerySet, Manager],
+    orm: Registry | QuerySet | Manager,
     *,
-    field: Optional[Union[str, StrField]] = None,
+    field: str | StrField | None = None,
 ) -> str:
     """Get the 1st char or text field from the orm."""
     if isinstance(orm, (QuerySet, Manager)):
@@ -332,7 +336,7 @@ def get_default_str_field(
     return field
 
 
-def _queryset(cls: Union[Registry, QuerySet, Manager], using_key: str) -> QuerySet:
+def _queryset(cls: Registry | QuerySet | Manager, using_key: str) -> QuerySet:
     queryset = (
         cls.all() if isinstance(cls, QuerySet) else cls.objects.using(using_key).all()
     )
@@ -354,7 +358,7 @@ def add_db_connection(db: str, using: str):
 def using(
     cls,
     instance: str,
-) -> "QuerySet":
+) -> QuerySet:
     """{}."""
     from lamindb_setup._connect_instance import (
         load_instance_settings,
@@ -388,9 +392,9 @@ REGISTRY_UNIQUE_FIELD = {
 
 
 def update_fk_to_default_db(
-    records: Union[Registry, List[Registry], QuerySet],
+    records: Registry | list[Registry] | QuerySet,
     fk: str,
-    using_key: Optional[str],
+    using_key: str | None,
 ):
     record = records[0] if isinstance(records, (List, QuerySet)) else records
     if hasattr(record, f"{fk}_id") and getattr(record, f"{fk}_id") is not None:
@@ -424,20 +428,18 @@ FKBULK = [
 ]
 
 
-def transfer_fk_to_default_db_bulk(
-    records: Union[List, QuerySet], using_key: Optional[str]
-):
+def transfer_fk_to_default_db_bulk(records: list | QuerySet, using_key: str | None):
     for fk in FKBULK:
         update_fk_to_default_db(records, fk, using_key)
 
 
 def transfer_to_default_db(
     record: Registry,
-    using_key: Optional[str],
+    using_key: str | None,
     save: bool = False,
     mute: bool = False,
     transfer_fk: bool = True,
-) -> Optional[Registry]:
+) -> Registry | None:
     db = record._state.db
     if db is not None and db != "default" and using_key is None:
         registry = record.__class__
@@ -495,7 +497,7 @@ def save(self, *args, **kwargs) -> None:
         using_key = kwargs["using"]
     db = self._state.db
     pk_on_db = self.pk
-    artifacts: List = []
+    artifacts: list = []
     if self.__class__.__name__ == "Collection" and self.id is not None:
         # when creating a new collection without being able to access artifacts
         artifacts = self.artifacts.list()

lamindb/_run.py

@@ -1,4 +1,4 @@
-from typing import Optional
+from __future__ import annotations
 
 from lnschema_core.models import Run, Transform
 
@@ -13,10 +13,8 @@ def __init__(run: Run, *args, **kwargs):
     transform: Transform = None
     if "transform" in kwargs or len(args) == 1:
         transform = kwargs.pop("transform") if len(args) == 0 else args[0]
-    reference: Optional[str] = (
-        kwargs.pop("reference") if "reference" in kwargs else None
-    )
-    reference_type: Optional[str] = (
+    reference: str | None = kwargs.pop("reference") if "reference" in kwargs else None
+    reference_type: str | None = (
         kwargs.pop("reference_type") if "reference_type" in kwargs else None
     )
     if transform is None:

lamindb/_save.py

@@ -1,10 +1,12 @@
+from __future__ import annotations
+
 import os
 import shutil
 import traceback
 from collections import defaultdict
 from datetime import datetime
 from functools import partial
-from typing import Iterable, List, Optional, Tuple, Union, overload
+from typing import Iterable, overload
 
 import lamindb_setup
 from django.db import transaction
@@ -30,7 +32,7 @@ except ImportError:
 
 
 def save(
-    records: Iterable[Registry], ignore_conflicts: Optional[bool] = False, **kwargs
+    records: Iterable[Registry], ignore_conflicts: bool | None = False, **kwargs
 ) -> None:
     """Bulk save to registries & storage.
 
@@ -123,7 +125,7 @@ def save(
     return None
 
 
-def bulk_create(records: Iterable[Registry], ignore_conflicts: Optional[bool] = False):
+def bulk_create(records: Iterable[Registry], ignore_conflicts: bool | None = False):
     records_by_orm = defaultdict(list)
     for record in records:
         records_by_orm[record.__class__].append(record)
@@ -134,9 +136,9 @@ def bulk_create(records: Iterable[Registry], ignore_conflicts: Optional[bool] =
 # This is also used within Artifact.save()
 def check_and_attempt_upload(
     artifact: Artifact,
-    using_key: Optional[str] = None,
-    access_token: Optional[str] = None,
-) -> Optional[Exception]:
+    using_key: str | None = None,
+    access_token: str | None = None,
+) -> Exception | None:
     # if Artifact object is either newly instantiated or replace() was called on
     # a local env it will have a _local_filepath and needs to be uploaded
     if hasattr(artifact, "_local_filepath"):
@@ -199,8 +201,8 @@ def copy_or_move_to_cache(artifact: Artifact, storage_path: UPath):
 
 # This is also used within Artifact.save()
 def check_and_attempt_clearing(
-    artifact: Artifact, using_key: Optional[str] = None
-) -> Optional[Exception]:
+    artifact: Artifact, using_key: str | None = None
+) -> Exception | None:
     # this is a clean-up operation after replace() was called
     # this will only evaluate to True if replace() was called
     if hasattr(artifact, "_clear_storagekey"):
@@ -220,13 +222,13 @@ def check_and_attempt_clearing(
 
 
 def store_artifacts(
-    artifacts: Iterable[Artifact], using_key: Optional[str] = None
+    artifacts: Iterable[Artifact], using_key: str | None = None
 ) -> None:
     """Upload artifacts in a list of database-committed artifacts to storage.
 
     If any upload fails, subsequent artifacts are cleaned up from the DB.
     """
-    exception: Optional[Exception] = None
+    exception: Exception | None = None
     # because uploads might fail, we need to maintain a new list
     # of the succeeded uploads
     stored_artifacts = []
@@ -274,7 +276,7 @@ def prepare_error_message(records, stored_artifacts, exception) -> str:
 
 
 def upload_artifact(
-    artifact, using_key: Optional[str] = None, access_token: Optional[str] = None
+    artifact, using_key: str | None = None, access_token: str | None = None
 ) -> UPath:
     """Store and add file and its linked entries."""
     # can't currently use  filepath_from_artifact here because it resolves to ._local_filepath

lamindb/_transform.py

@@ -1,4 +1,4 @@
-from typing import Optional
+from __future__ import annotations
 
 from lnschema_core.models import Artifact, Run, Transform
 from lnschema_core.types import TransformType
@@ -11,24 +11,22 @@ def __init__(transform: Transform, *args, **kwargs):
     if len(args) == len(transform._meta.concrete_fields):
         super(Transform, transform).__init__(*args, **kwargs)
         return None
-    name: Optional[str] = kwargs.pop("name") if "name" in kwargs else None
-    key: Optional[str] = kwargs.pop("key") if "key" in kwargs else None
-    is_new_version_of: Optional[Transform] = (
+    name: str | None = kwargs.pop("name") if "name" in kwargs else None
+    key: str | None = kwargs.pop("key") if "key" in kwargs else None
+    is_new_version_of: Transform | None = (
         kwargs.pop("is_new_version_of") if "is_new_version_of" in kwargs else None
     )
     (kwargs.pop("initial_version_id") if "initial_version_id" in kwargs else None)
-    version: Optional[str] = kwargs.pop("version") if "version" in kwargs else None
-    type: Optional[TransformType] = (
+    version: str | None = kwargs.pop("version") if "version" in kwargs else None
+    type: TransformType | None = (
         kwargs.pop("type") if "type" in kwargs else TransformType.pipeline
     )
-    reference: Optional[str] = (
-        kwargs.pop("reference") if "reference" in kwargs else None
-    )
-    reference_type: Optional[str] = (
+    reference: str | None = kwargs.pop("reference") if "reference" in kwargs else None
+    reference_type: str | None = (
         kwargs.pop("reference_type") if "reference_type" in kwargs else None
     )
     # below is internal use that we'll hopefully be able to eliminate
-    uid: Optional[str] = kwargs.pop("uid") if "uid" in kwargs else None
+    uid: str | None = kwargs.pop("uid") if "uid" in kwargs else None
     if not len(kwargs) == 0:
         raise ValueError(
             "Only name, key, version, type, is_new_version_of, reference, "

lamindb/_ulabel.py

@@ -1,14 +1,18 @@
-from typing import List, Optional
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
 
 import lamindb_setup as ln_setup
 from lamindb_setup.core._docs import doc_args
 from lnschema_core import ULabel
-from lnschema_core.types import ListLike
 
 from lamindb._utils import attach_func_to_class_method
 
 from ._from_values import get_or_create_records
 
+if TYPE_CHECKING:
+    from lnschema_core.types import ListLike
+
 
 def __init__(self, *args, **kwargs):
     if len(args) == len(self._meta.concrete_fields):
@@ -17,14 +21,12 @@ def __init__(self, *args, **kwargs):
     # now we proceed with the user-facing constructor
     if len(args) > 0:
         raise ValueError("Only one non-keyword arg allowed")
-    name: Optional[str] = kwargs.pop("name") if "name" in kwargs else None
-    description: Optional[str] = (
+    name: str | None = kwargs.pop("name") if "name" in kwargs else None
+    description: str | None = (
         kwargs.pop("description") if "description" in kwargs else None
     )
-    reference: Optional[str] = (
-        kwargs.pop("reference") if "reference" in kwargs else None
-    )
-    reference_type: Optional[str] = (
+    reference: str | None = kwargs.pop("reference") if "reference" in kwargs else None
+    reference_type: str | None = (
         kwargs.pop("reference_type") if "reference_type" in kwargs else None
     )
     if len(kwargs) > 0:
@@ -41,7 +43,7 @@ def __init__(self, *args, **kwargs):
 
 @classmethod  # type:ignore
 @doc_args(ULabel.from_values.__doc__)
-def from_values(cls, values: ListLike, **kwargs) -> List["ULabel"]:
+def from_values(cls, values: ListLike, **kwargs) -> list[ULabel]:
     """{}."""
     records = get_or_create_records(
         iterable=values,

lamindb/_view.py

@@ -1,6 +1,7 @@
+from __future__ import annotations
+
 import importlib
 import inspect
-from typing import List, Optional
 
 from IPython.display import display
 from lamin_utils import colors, logger
@@ -10,7 +11,7 @@ from lnschema_core import Registry
 
 
 def view(
-    n: int = 7, schema: Optional[str] = None, registries: Optional[List[str]] = None
+    n: int = 7, schema: str | None = None, registries: list[str] | None = None
 ) -> None:
     """View latest metadata state.