lamindb 0.76.8__py3-none-any.whl → 0.76.10__py3-none-any.whl

lamindb/_storage.py

@@ -1,14 +1,14 @@
-from lamindb_setup.core._docs import doc_args
-from lamindb_setup.core.upath import UPath, create_path
-from lnschema_core import Storage
-
-
-@property  # type: ignore
-@doc_args(Storage.path.__doc__)
-def path(self) -> UPath:
-    """{}"""  # noqa: D415
-    access_token = self._access_token if hasattr(self, "_access_token") else None
-    return create_path(self.root, access_token=access_token)
-
-
-Storage.path = path
+from lamindb_setup.core._docs import doc_args
+from lamindb_setup.core.upath import UPath, create_path
+from lnschema_core import Storage
+
+
+@property  # type: ignore
+@doc_args(Storage.path.__doc__)
+def path(self) -> UPath:
+    """{}"""  # noqa: D415
+    access_token = self._access_token if hasattr(self, "_access_token") else None
+    return create_path(self.root, access_token=access_token)
+
+
+Storage.path = path

lamindb/_transform.py

@@ -1,127 +1,130 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING
-
-from lamin_utils import logger
-from lamindb_setup.core._docs import doc_args
-from lnschema_core.models import Run, Transform
-
-from ._parents import _view_parents
-from ._run import delete_run_artifacts
-from .core.versioning import message_update_key_in_version_family, process_revises
-
-if TYPE_CHECKING:
-    from lnschema_core.types import TransformType
-
-
-def __init__(transform: Transform, *args, **kwargs):
-    if len(args) == len(transform._meta.concrete_fields):
-        super(Transform, transform).__init__(*args, **kwargs)
-        return None
-    name: str | None = kwargs.pop("name") if "name" in kwargs else None
-    key: str | None = kwargs.pop("key") if "key" in kwargs else None
-    revises: Transform | None = kwargs.pop("revises") if "revises" in kwargs else None
-    version: str | None = kwargs.pop("version") if "version" in kwargs else None
-    type: TransformType | None = kwargs.pop("type") if "type" in kwargs else "pipeline"
-    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 "is_new_version_of" in kwargs:
-        logger.warning("`is_new_version_of` will be removed soon, please use `revises`")
-        revises = kwargs.pop("is_new_version_of")
-    # below is internal use that we'll hopefully be able to eliminate
-    uid: str | None = kwargs.pop("uid") if "uid" in kwargs else None
-    if not len(kwargs) == 0:
-        raise ValueError(
-            "Only name, key, version, type, revises, reference, "
-            f"reference_type can be passed, but you passed: {kwargs}"
-        )
-    if revises is None:
-        if key is not None:
-            revises = (
-                Transform.filter(key=key, is_latest=True)
-                .order_by("-created_at")
-                .first()
-            )
-        elif uid is not None:
-            revises = (
-                Transform.filter(uid__startswith=uid[:-4], is_latest=True)
-                .order_by("-created_at")
-                .first()
-            )
-    if revises is not None and uid is not None and uid == revises.uid:
-        from ._record import init_self_from_db, update_attributes
-
-        init_self_from_db(transform, revises)
-        update_attributes(transform, {"name": name})
-        return None
-    if revises is not None and key is not None and revises.key != key:
-        note = message_update_key_in_version_family(
-            suid=revises.stem_uid,
-            existing_key=revises.key,
-            new_key=key,
-            registry="Artifact",
-        )
-        raise ValueError(
-            f"`key` is {key}, but `revises.key` is '{revises.key}'\n\n Either do *not* pass `key`.\n\n{note}"
-        )
-    new_uid, version, name, revises = process_revises(revises, version, name, Transform)
-    # this is only because the user-facing constructor allows passing a uid
-    # most others don't
-    if uid is None:
-        has_consciously_provided_uid = False
-        uid = new_uid
-    else:
-        has_consciously_provided_uid = True
-    super(Transform, transform).__init__(
-        uid=uid,
-        name=name,
-        key=key,
-        type=type,
-        version=version,
-        reference=reference,
-        reference_type=reference_type,
-        _has_consciously_provided_uid=has_consciously_provided_uid,
-        revises=revises,
-    )
-
-
-def delete(self) -> None:
-    _source_code_artifact = None
-    if self._source_code_artifact is not None:
-        _source_code_artifact = self._source_code_artifact
-        self._source_code_artifact = None
-        self.save()
-    if _source_code_artifact is not None:
-        _source_code_artifact.delete(permanent=True)
-    # query all runs and delete their artifacts
-    runs = Run.filter(transform=self)
-    for run in runs:
-        delete_run_artifacts(run)
-    # at this point, all artifacts have been taken care of
-    # we can now leverage CASCADE delete
-    super(Transform, self).delete()
-
-
-@property  # type: ignore
-@doc_args(Transform.latest_run.__doc__)
-def latest_run(self) -> Run:
-    """{}"""  # noqa: D415
-    return self.runs.order_by("-started_at").first()
-
-
-def view_lineage(self, with_successors: bool = False, distance: int = 5):
-    return _view_parents(
-        record=self,
-        field="name",
-        with_children=with_successors,
-        distance=distance,
-        attr_name="predecessors",
-    )
-
-
-Transform.__init__ = __init__
-Transform.delete = delete
-Transform.latest_run = latest_run
-Transform.view_lineage = view_lineage
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from lamin_utils import logger
+from lamindb_setup.core._docs import doc_args
+from lnschema_core.models import Run, Transform
+
+from lamindb.core.exceptions import InconsistentKey
+
+from ._parents import _view_parents
+from ._run import delete_run_artifacts
+from .core.versioning import message_update_key_in_version_family, process_revises
+
+if TYPE_CHECKING:
+    from lnschema_core.types import TransformType
+
+
+def __init__(transform: Transform, *args, **kwargs):
+    if len(args) == len(transform._meta.concrete_fields):
+        super(Transform, transform).__init__(*args, **kwargs)
+        return None
+    name: str | None = kwargs.pop("name") if "name" in kwargs else None
+    key: str | None = kwargs.pop("key") if "key" in kwargs else None
+    revises: Transform | None = kwargs.pop("revises") if "revises" in kwargs else None
+    version: str | None = kwargs.pop("version") if "version" in kwargs else None
+    type: TransformType | None = kwargs.pop("type") if "type" in kwargs else "pipeline"
+    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 "is_new_version_of" in kwargs:
+        logger.warning("`is_new_version_of` will be removed soon, please use `revises`")
+        revises = kwargs.pop("is_new_version_of")
+    # below is internal use that we'll hopefully be able to eliminate
+    uid: str | None = kwargs.pop("uid") if "uid" in kwargs else None
+    if not len(kwargs) == 0:
+        raise ValueError(
+            "Only name, key, version, type, revises, reference, "
+            f"reference_type can be passed, but you passed: {kwargs}"
+        )
+    if revises is None:
+        # need to check uid before checking key
+        if uid is not None:
+            revises = (
+                Transform.filter(uid__startswith=uid[:-4], is_latest=True)
+                .order_by("-created_at")
+                .first()
+            )
+        elif key is not None:
+            revises = (
+                Transform.filter(key=key, is_latest=True)
+                .order_by("-created_at")
+                .first()
+            )
+    if revises is not None and uid is not None and uid == revises.uid:
+        from ._record import init_self_from_db, update_attributes
+
+        init_self_from_db(transform, revises)
+        update_attributes(transform, {"name": name})
+        return None
+    if revises is not None and key is not None and revises.key != key:
+        note = message_update_key_in_version_family(
+            suid=revises.stem_uid,
+            existing_key=revises.key,
+            new_key=key,
+            registry="Artifact",
+        )
+        raise InconsistentKey(
+            f"`key` is {key}, but `revises.key` is '{revises.key}'\n\nEither do *not* pass `key`.\n\n{note}"
+        )
+    new_uid, version, name, revises = process_revises(revises, version, name, Transform)
+    # this is only because the user-facing constructor allows passing a uid
+    # most others don't
+    if uid is None:
+        has_consciously_provided_uid = False
+        uid = new_uid
+    else:
+        has_consciously_provided_uid = True
+    super(Transform, transform).__init__(
+        uid=uid,
+        name=name,
+        key=key,
+        type=type,
+        version=version,
+        reference=reference,
+        reference_type=reference_type,
+        _has_consciously_provided_uid=has_consciously_provided_uid,
+        revises=revises,
+    )
+
+
+def delete(self) -> None:
+    _source_code_artifact = None
+    if self._source_code_artifact is not None:
+        _source_code_artifact = self._source_code_artifact
+        self._source_code_artifact = None
+        self.save()
+    if _source_code_artifact is not None:
+        _source_code_artifact.delete(permanent=True)
+    # query all runs and delete their artifacts
+    runs = Run.filter(transform=self)
+    for run in runs:
+        delete_run_artifacts(run)
+    # at this point, all artifacts have been taken care of
+    # we can now leverage CASCADE delete
+    super(Transform, self).delete()
+
+
+@property  # type: ignore
+@doc_args(Transform.latest_run.__doc__)
+def latest_run(self) -> Run:
+    """{}"""  # noqa: D415
+    return self.runs.order_by("-started_at").first()
+
+
+def view_lineage(self, with_successors: bool = False, distance: int = 5):
+    return _view_parents(
+        record=self,
+        field="name",
+        with_children=with_successors,
+        distance=distance,
+        attr_name="predecessors",
+    )
+
+
+Transform.__init__ = __init__
+Transform.delete = delete
+Transform.latest_run = latest_run
+Transform.view_lineage = view_lineage

lamindb/_ulabel.py

@@ -1,56 +1,56 @@
-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 lamindb._utils import attach_func_to_class_method
-
-if TYPE_CHECKING:
-    from lnschema_core.types import ListLike
-
-
-def __init__(self, *args, **kwargs):
-    if len(args) == len(self._meta.concrete_fields):
-        super(ULabel, self).__init__(*args, **kwargs)
-        return None
-    # now we proceed with the user-facing constructor
-    if len(args) > 0:
-        raise ValueError("Only one non-keyword arg allowed")
-    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: 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:
-        raise ValueError(
-            "Only name, description, reference, reference_type are valid keyword arguments"
-        )
-    super(ULabel, self).__init__(
-        name=name,
-        description=description,
-        reference=reference,
-        reference_type=reference_type,
-    )
-
-
-METHOD_NAMES = [
-    "__init__",
-]
-
-if ln_setup._TESTING:
-    from inspect import signature
-
-    SIGS = {
-        name: signature(getattr(ULabel, name))
-        for name in METHOD_NAMES
-        if name != "__init__"
-    }
-
-for name in METHOD_NAMES:
-    attach_func_to_class_method(name, ULabel, globals())
+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 lamindb._utils import attach_func_to_class_method
+
+if TYPE_CHECKING:
+    from lnschema_core.types import ListLike
+
+
+def __init__(self, *args, **kwargs):
+    if len(args) == len(self._meta.concrete_fields):
+        super(ULabel, self).__init__(*args, **kwargs)
+        return None
+    # now we proceed with the user-facing constructor
+    if len(args) > 0:
+        raise ValueError("Only one non-keyword arg allowed")
+    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: 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:
+        raise ValueError(
+            "Only name, description, reference, reference_type are valid keyword arguments"
+        )
+    super(ULabel, self).__init__(
+        name=name,
+        description=description,
+        reference=reference,
+        reference_type=reference_type,
+    )
+
+
+METHOD_NAMES = [
+    "__init__",
+]
+
+if ln_setup._TESTING:
+    from inspect import signature
+
+    SIGS = {
+        name: signature(getattr(ULabel, name))
+        for name in METHOD_NAMES
+        if name != "__init__"
+    }
+
+for name in METHOD_NAMES:
+    attach_func_to_class_method(name, ULabel, globals())

lamindb/_utils.py

@@ -1,9 +1,9 @@
-def attach_func_to_class_method(func_name, cls, globals):
-    implementation = globals[func_name]
-    target = getattr(cls, func_name)
-    # assigning the original class definition docstring
-    # to the implementation only has an effect for regular methods
-    # not for class methods
-    # this is why we need @doc_args for class methods
-    implementation.__doc__ = target.__doc__
-    setattr(cls, func_name, implementation)
+def attach_func_to_class_method(func_name, cls, globals):
+    implementation = globals[func_name]
+    target = getattr(cls, func_name)
+    # assigning the original class definition docstring
+    # to the implementation only has an effect for regular methods
+    # not for class methods
+    # this is why we need @doc_args for class methods
+    implementation.__doc__ = target.__doc__
+    setattr(cls, func_name, implementation)

lamindb/_view.py

@@ -1,72 +1,72 @@
-from __future__ import annotations
-
-import builtins
-import importlib
-import inspect
-
-from lamin_utils import colors, logger
-from lamindb_setup import settings
-from lamindb_setup._init_instance import get_schema_module_name
-from lnschema_core import Record
-
-is_run_from_ipython = getattr(builtins, "__IPYTHON__", False)
-
-
-def view(
-    n: int = 7, schema: str | None = None, registries: list[str] | None = None
-) -> None:
-    """View latest metadata state.
-
-    Args:
-        n: Display the last `n` rows of a registry.
-        schema: Schema module to view. Default's to
-            `None` and displays all schema modules.
-        registries: List of Record names. Defaults to
-            `None` and lists all registries.
-
-    Examples:
-        >>> ln.view()
-    """
-    if is_run_from_ipython:
-        from IPython.display import display as show
-    else:
-        show = logger.print
-
-    if schema is not None:
-        schema_names = [schema]
-    else:
-        schema_names = ["core"] + list(settings.instance.schema)
-
-    for schema_name in schema_names:
-        schema_module = importlib.import_module(get_schema_module_name(schema_name))
-
-        all_registries = {
-            registry
-            for registry in schema_module.__dict__.values()
-            if inspect.isclass(registry)
-            and issubclass(registry, Record)
-            and registry is not Record
-        }
-        if registries is not None:
-            filtered_registries = {
-                registry
-                for registry in all_registries
-                if registry.__name__ in registries
-            }
-        else:
-            filtered_registries = all_registries
-        if len(schema_names) > 1:
-            section = f"* module: {colors.green(colors.bold(schema_name))} *"
-            section_no_color = f"* module: {schema_name} *"
-            logger.print("*" * len(section_no_color))
-            logger.print(section)
-            logger.print("*" * len(section_no_color))
-        for registry in sorted(filtered_registries, key=lambda x: x.__name__):
-            if hasattr(registry, "updated_at"):
-                df = registry.filter().order_by("-updated_at")[:n].df()
-            else:
-                # need to adjust in the future
-                df = registry.df().iloc[-n:]
-            if df.shape[0] > 0:
-                logger.print(colors.blue(colors.bold(registry.__name__)))
-                show(df)
+from __future__ import annotations
+
+import builtins
+import importlib
+import inspect
+
+from lamin_utils import colors, logger
+from lamindb_setup import settings
+from lamindb_setup._init_instance import get_schema_module_name
+from lnschema_core import Record
+
+is_run_from_ipython = getattr(builtins, "__IPYTHON__", False)
+
+
+def view(
+    n: int = 7, schema: str | None = None, registries: list[str] | None = None
+) -> None:
+    """View latest metadata state.
+
+    Args:
+        n: Display the last `n` rows of a registry.
+        schema: Schema module to view. Default's to
+            `None` and displays all schema modules.
+        registries: List of Record names. Defaults to
+            `None` and lists all registries.
+
+    Examples:
+        >>> ln.view()
+    """
+    if is_run_from_ipython:
+        from IPython.display import display as show
+    else:
+        show = logger.print
+
+    if schema is not None:
+        schema_names = [schema]
+    else:
+        schema_names = ["core"] + list(settings.instance.schema)
+
+    for schema_name in schema_names:
+        schema_module = importlib.import_module(get_schema_module_name(schema_name))
+
+        all_registries = {
+            registry
+            for registry in schema_module.__dict__.values()
+            if inspect.isclass(registry)
+            and issubclass(registry, Record)
+            and registry is not Record
+        }
+        if registries is not None:
+            filtered_registries = {
+                registry
+                for registry in all_registries
+                if registry.__name__ in registries
+            }
+        else:
+            filtered_registries = all_registries
+        if len(schema_names) > 1:
+            section = f"* module: {colors.green(colors.bold(schema_name))} *"
+            section_no_color = f"* module: {schema_name} *"
+            logger.print("*" * len(section_no_color))
+            logger.print(section)
+            logger.print("*" * len(section_no_color))
+        for registry in sorted(filtered_registries, key=lambda x: x.__name__):
+            if hasattr(registry, "updated_at"):
+                df = registry.filter().order_by("-updated_at")[:n].df()
+            else:
+                # need to adjust in the future
+                df = registry.df().iloc[-n:]
+            if df.shape[0] > 0:
+                logger.print(colors.blue(colors.bold(registry.__name__)))
+                show(df)