lamindb 0.66.1__py3-none-any.whl → 0.67.1__py3-none-any.whl

lamindb/__init__.py

@@ -54,7 +54,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.66.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.67.1"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 
@@ -102,20 +102,20 @@ if _INSTANCE_SETUP:
         User,
     )
 
-    File = Artifact  # backward compat
-    from . import _artifact  # noqa
-    from . import _collection
-    from . import _feature
-    from . import _feature_set
-    from . import _parents
-    from . import _registry
-    from . import _run
-    from . import _storage
-    from . import _transform
-    from . import _ulabel
-    from . import _validate
-    from . import dev
-    from ._delete import delete
+    from . import (
+        _artifact,
+        _collection,
+        _feature,
+        _feature_set,
+        _parents,
+        _registry,
+        _run,
+        _storage,
+        _transform,
+        _ulabel,
+        _validate,
+        dev,
+    )
     from ._save import save
     from ._view import view
     from .dev._run_context import run_context

lamindb/_artifact.py

@@ -911,13 +911,13 @@ def delete(
     self, permanent: Optional[bool] = None, storage: Optional[bool] = None
 ) -> None:
     # by default, we only move artifacts into the trash
-    if self.visibility > VisibilityChoice.trash.value and permanent is not True:
+    if self.visibility > -1 and permanent is not True:
         if storage is not None:
             logger.warning("moving artifact to trash, storage arg is ignored")
         # move to trash
-        self.visibility = VisibilityChoice.trash.value
+        self.visibility = -1
         self.save()
-        logger.warning("moved artifact to trash")
+        logger.warning("moved artifact to trash (visibility = -1)")
         return
 
     # if the artifact is already in the trash
@@ -929,6 +929,7 @@ def delete(
         )
         delete_record = response == "y"
     else:
+        # this second option doesn't feel very intuitive
         delete_record = permanent
 
     if delete_record:

lamindb/_collection.py

@@ -424,8 +424,12 @@ def save(self, *args, **kwargs) -> None:
         self.artifact.save()
     # we don't need to save feature sets again
     save_feature_sets(self)
+    state_was_adding = self._state.adding
     super(Collection, self).save()
-    if hasattr(self, "_artifacts"):
+    # we don't allow updating the collection of artifacts
+    # if users want to update the set of artifacts, they
+    # have to create a new collection
+    if state_was_adding and hasattr(self, "_artifacts"):
         if self._artifacts is not None and len(self._artifacts) > 0:
             links = [
                 CollectionArtifact(collection_id=self.id, artifact_id=artifact.id)

lamindb/_from_values.py

@@ -14,7 +14,7 @@ def get_or_create_records(
     iterable: ListLike,
     field: StrField,
     *,
-    from_bionty: bool = False,
+    from_public: bool = False,
     **kwargs,
 ) -> List[Registry]:
     """Get or create records from iterables."""
@@ -32,14 +32,14 @@ def get_or_create_records(
 
         # new records to be created based on new values
         if len(nonexist_values) > 0:
-            if from_bionty:
-                records_bionty, unmapped_values = create_records_from_bionty(
+            if from_public:
+                records_bionty, unmapped_values = create_records_from_public(
                     iterable_idx=nonexist_values, field=field, msg=msg, **kwargs
                 )
                 if len(records_bionty) > 0:
                     msg = ""
                 for record in records_bionty:
-                    record._from_bionty = True
+                    record._from_public = True
                 records += records_bionty
             else:
                 unmapped_values = nonexist_values
@@ -81,8 +81,8 @@ def get_existing_records(
     model = field.field.model
     condition: Dict = {} if len(kwargs) == 0 else kwargs.copy()
     # existing records matching is agnostic to the bionty source
-    if "bionty_source" in condition:
-        condition.pop("bionty_source")
+    if "public_source" in condition:
+        condition.pop("public_source")
 
     if _has_organism_field(model):
         from lnschema_bionty._bionty import create_or_get_organism_record
@@ -160,7 +160,7 @@ def get_existing_records(
     return records, nonexist_values, msg
 
 
-def create_records_from_bionty(
+def create_records_from_public(
     iterable_idx: pd.Index,
     field: StrField,
     msg: str = "",
@@ -169,24 +169,24 @@ def create_records_from_bionty(
     model = field.field.model
     records: List = []
     # populate additional fields from bionty
-    from lnschema_bionty._bionty import get_bionty_source_record
+    from lnschema_bionty._bionty import get_public_source_record
 
     # create the corresponding bionty object from model
     try:
-        bionty_object = model.bionty(
-            organism=kwargs.get("organism"), bionty_source=kwargs.get("bionty_source")
+        public_ontology = model.public(
+            organism=kwargs.get("organism"), public_source=kwargs.get("public_source")
         )
     except Exception:
         # for custom records that are not created from bionty sources
         return records, iterable_idx
-    # add bionty_source record to the kwargs
-    kwargs.update({"bionty_source": get_bionty_source_record(bionty_object)})
+    # add public_source record to the kwargs
+    kwargs.update({"public_source": get_public_source_record(public_ontology)})
 
     # filter the columns in bionty df based on fields
-    bionty_df = _filter_bionty_df_columns(model=model, bionty_object=bionty_object)
+    bionty_df = _filter_bionty_df_columns(model=model, public_ontology=public_ontology)
 
     # standardize in the bionty reference
-    result = bionty_object.inspect(iterable_idx, field=field.field.name, mute=True)
+    result = public_ontology.inspect(iterable_idx, field=field.field.name, mute=True)
     syn_mapper = result.synonyms_mapper
 
     msg_syn: str = ""
@@ -254,13 +254,13 @@ def _print_values(names: List, n: int = 20) -> str:
     return print_values
 
 
-def _filter_bionty_df_columns(model: Registry, bionty_object: Any) -> pd.DataFrame:
+def _filter_bionty_df_columns(model: Registry, public_ontology: Any) -> pd.DataFrame:
     bionty_df = pd.DataFrame()
-    if bionty_object is not None:
+    if public_ontology is not None:
         model_field_names = {i.name for i in model._meta.fields}
         # parents needs to be added here as relationships aren't in fields
         model_field_names.add("parents")
-        bionty_df = bionty_object.df().reset_index()
+        bionty_df = public_ontology.df().reset_index()
         if model.__name__ == "Gene":
             # groupby ensembl_gene_id and concat ncbi_gene_ids
             groupby_id_col = (

lamindb/_query_manager.py

@@ -46,14 +46,11 @@ class QueryManager(models.Manager):
 
         Examples:
             >>> ln.save(ln.ULabel.from_values(["ULabel1", "ULabel2", "ULabel3"], field="name"))
-            >>> labels = ln.ULabel.filter(name__icontains = "label").all()
+            >>> labels = ln.ULabel.filter(name__icontains="label").all()
             >>> ln.ULabel(name="ULabel1").save()
             >>> label = ln.ULabel.filter(name="ULabel1").one()
             >>> label.parents.set(labels)
             >>> label.parents.list()
-            [ULabel(id=sFMcPepC, name=ULabel1, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse), # noqa
-            ULabel(id=2SscQvsM, name=ULabel2, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse), # noqa
-            ULabel(id=lecV87vi, name=ULabel3, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse)] # noqa
             >>> label.parents.list("name")
             ['ULabel1', 'ULabel2', 'ULabel3']
         """
@@ -76,7 +73,7 @@ class QueryManager(models.Manager):
         For `**kwargs`, see :meth:`lamindb.dev.QuerySet.df`.
         """
         self._track_run_input_manager()
-        return self.all_base_class()
+        return self._all_base_class()
 
     @doc_args(Registry.search.__doc__)
     def search(self, string: str, **kwargs):
@@ -115,5 +112,5 @@ models.Manager.__getitem__ = QueryManager.__getitem__
 models.Manager._track_run_input_manager = QueryManager._track_run_input_manager
 # the two lines below would be easy if we could actually inherit; like this,
 # they're suboptimal
-models.Manager.all_base_class = models.Manager.all
+models.Manager._all_base_class = models.Manager.all
 models.Manager.all = QueryManager.all

lamindb/_query_set.py

@@ -4,7 +4,14 @@ from typing import Dict, Iterable, List, NamedTuple, Optional, Union
 import pandas as pd
 from django.db import models
 from lamindb_setup.dev._docs import doc_args
-from lnschema_core.models import CanValidate, IsTree, Registry
+from lnschema_core.models import (
+    Artifact,
+    CanValidate,
+    Collection,
+    IsTree,
+    Registry,
+    Transform,
+)
 from lnschema_core.types import ListLike, StrField
 
 
@@ -147,6 +154,13 @@ class QuerySet(models.QuerySet, CanValidate, IsTree):
                 df.rename(columns={values_expression: expression}, inplace=True)
         return df
 
+    def delete(self, *args, **kwargs):
+        if self.model in {Artifact, Collection, Transform}:
+            for record in self:
+                record.delete(*args, **kwargs)
+        else:
+            self._delete_base_class(*args, **kwargs)
+
     def list(self, field: Optional[str] = None) -> List[Registry]:
         """Populate a list with the results.
 
@@ -282,3 +296,5 @@ models.QuerySet.lookup = QuerySet.lookup
 models.QuerySet.validate = QuerySet.validate
 models.QuerySet.inspect = QuerySet.inspect
 models.QuerySet.standardize = QuerySet.standardize
+models.QuerySet._delete_base_class = models.QuerySet.delete
+models.QuerySet.delete = QuerySet.delete

lamindb/_registry.py

@@ -129,12 +129,12 @@ def from_values(
     cls, values: ListLike, field: Optional[StrField] = None, **kwargs
 ) -> List["Registry"]:
     """{}."""
-    from_bionty = True if cls.__module__.startswith("lnschema_bionty.") else False
+    from_public = True if cls.__module__.startswith("lnschema_bionty.") else False
     field_str = get_default_str_field(cls, field=field)
     return get_or_create_records(
         iterable=values,
         field=getattr(cls, field_str),
-        from_bionty=from_bionty,
+        from_public=from_public,
         **kwargs,
     )
 
@@ -412,7 +412,7 @@ def update_fk_to_default_db(
 def transfer_fk_to_default_db_bulk(records: Union[List, QuerySet]):
     for fk in [
         "organism",
-        "bionty_source",
+        "public_source",
         "initial_version",
         "latest_report",  # Transform
         "source_code",  # Transform

lamindb/_run.py

@@ -30,4 +30,27 @@ def __init__(run: Run, *args, **kwargs):
     )
 
 
+def delete_run_artifacts(run: Run) -> None:
+    environment = None
+    if run.environment is not None:
+        environment = run.environment
+        run.environment = None
+    report = None
+    if run.report is not None:
+        report = run.report
+        run.report = None
+    if environment is not None or report is not None:
+        run.save()
+    if environment is not None:
+        environment.delete(permanent=True)
+    if report is not None:
+        report.delete(permanent=True)
+
+
+def delete(self) -> None:
+    delete_run_artifacts(self)
+    super(Run, self).delete()
+
+
 Run.__init__ = __init__
+Run.delete = delete

lamindb/_transform.py

@@ -1,7 +1,8 @@
 from typing import TYPE_CHECKING, Optional
 
-from lnschema_core.models import TRANSFORM_TYPE_DEFAULT, Transform
+from lnschema_core.models import TRANSFORM_TYPE_DEFAULT, Artifact, Run, Transform
 
+from ._run import delete_run_artifacts
 from .dev.versioning import get_uid_from_old_version, init_uid
 
 if TYPE_CHECKING:
@@ -63,4 +64,28 @@ def __init__(transform: Transform, *args, **kwargs):
     )
 
 
+def delete(self) -> None:
+    # set latest_report to None, it's tracked through the latest run
+    latest_report = None
+    if self.latest_report is not None:
+        latest_report = self.latest_report
+        self.latest_report = None
+    source_code = None
+    if self.source_code is not None:
+        source_code = self.source_code
+        self.source_code = None
+    if latest_report is not None or source_code is not None:
+        self.save()
+    if source_code is not None:
+        source_code.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()
+
+
 Transform.__init__ = __init__
+Transform.delete = delete

lamindb/_validate.py

@@ -84,7 +84,7 @@ def _inspect(
 
     if len(nonval) > 0 and orm.__get_schema_name__() == "bionty":
         try:
-            bionty_result = orm.bionty(organism=kwargs.get("organism")).inspect(
+            bionty_result = orm.public(organism=kwargs.get("organism")).inspect(
                 values=nonval, field=field, mute=True, **kwargs
             )
             bionty_validated = bionty_result.validated
@@ -186,7 +186,7 @@ def standardize(
     return_mapper: bool = False,
     case_sensitive: bool = False,
     mute: bool = False,
-    bionty_aware: bool = True,
+    public_aware: bool = True,
     keep: Literal["first", "last", False] = "first",
     synonyms_field: str = "synonyms",
     **kwargs,
@@ -200,7 +200,7 @@ def standardize(
         return_mapper=return_mapper,
         case_sensitive=case_sensitive,
         mute=mute,
-        bionty_aware=bionty_aware,
+        public_aware=public_aware,
         keep=keep,
         synonyms_field=synonyms_field,
         **kwargs,
@@ -248,7 +248,7 @@ def _standardize(
     return_mapper: bool = False,
     case_sensitive: bool = False,
     mute: bool = False,
-    bionty_aware: bool = True,
+    public_aware: bool = True,
     keep: Literal["first", "last", False] = "first",
     synonyms_field: str = "synonyms",
     **kwargs,
@@ -308,7 +308,7 @@ def _standardize(
             return result
 
     # map synonyms in Bionty
-    if orm.__get_schema_name__() == "bionty" and bionty_aware:
+    if orm.__get_schema_name__() == "bionty" and public_aware:
         mapper = {}
         if return_mapper:
             mapper = std_names_db
@@ -321,7 +321,7 @@ def _standardize(
             return _return(result=std_names_db, mapper=mapper)
 
         nonval = np.array(std_names_db)[~val_res]
-        std_names_bt_mapper = orm.bionty(organism=organism).standardize(
+        std_names_bt_mapper = orm.public(organism=organism).standardize(
             nonval, return_mapper=True, mute=True, **_kwargs
         )
 

lamindb/dev/_label_manager.py

@@ -23,7 +23,7 @@ def get_labels_as_dict(self: Data):
     ).items():
         if related_name in {
             "feature_sets",
-            "artifacts",
+            "unordered_artifacts",
             "input_of",
             "collections",
             "source_of",

lamindb/dev/_run_context.py

@@ -27,9 +27,9 @@ msg_path_failed = (
 
 msg_manual_init = (
     "\n(1) save your notebook!"
-    "\n(2) attach metadata to the notebook by running the CLI:\n"
+    "\n(2) add stem_uid & version to your notebook file by running the CLI:\n"
     "lamin track {notebook_path}"
-    "\n(3) reload or re-open your notebook"
+    "\n(3) reload your notebook from disk"
 )
 
 

lamindb/dev/datasets/_core.py

@@ -38,10 +38,10 @@ def file_fcs_alpert19(populate_registries: bool = False) -> Path:  # pragma: no
         verbosity = ln.settings.verbosity
         ln.settings.verbosity = "error"
         adata = readfcs.read(filepath)
-        std = lb.CellMarker.bionty().standardize(adata.var.index)
+        std = lb.CellMarker.public().standardize(adata.var.index)
         ln.save(
             lb.CellMarker.from_values(
-                lb.CellMarker.bionty().inspect(std, "name").validated, "name"
+                lb.CellMarker.public().inspect(std, "name").validated, "name"
             )
         )
         ln.Feature(
@@ -86,7 +86,7 @@ def file_tsv_rnaseq_nfcore_salmon_merged_gene_counts(
             name="assay", type="category", registries=[lb.ExperimentalFactor]
         ).save()
         ln.Feature(name="organism", type="category", registries=[lb.Organism]).save()
-        lb.ExperimentalFactor.from_bionty(ontology_id="EFO:0008896").save()
+        lb.ExperimentalFactor.from_public(ontology_id="EFO:0008896").save()
         ln.settings.verbosity = verbosity
 
     return Path(filepath)
@@ -191,20 +191,20 @@ def anndata_mouse_sc_lymph_node(
         auto_save_parents = lb.settings.auto_save_parents
         lb.settings.auto_save_parents = False
         # strain
-        lb.ExperimentalFactor.from_bionty(ontology_id="EFO:0004472").save()
+        lb.ExperimentalFactor.from_public(ontology_id="EFO:0004472").save()
         # developmental stage
-        lb.ExperimentalFactor.from_bionty(ontology_id="EFO:0001272").save()
+        lb.ExperimentalFactor.from_public(ontology_id="EFO:0001272").save()
         # tissue
-        lb.Tissue.from_bionty(ontology_id="UBERON:0001542").save()
+        lb.Tissue.from_public(ontology_id="UBERON:0001542").save()
         # cell types
         ln.save(lb.CellType.from_values(["CL:0000115", "CL:0000738"], "ontology_id"))
         # assays
         ln.Feature(
             name="assay", type="category", registries=[lb.ExperimentalFactor]
         ).save()
-        lb.ExperimentalFactor.from_bionty(ontology_id="EFO:0008913").save()
+        lb.ExperimentalFactor.from_public(ontology_id="EFO:0008913").save()
         # genes
-        validated = lb.Gene.bionty(organism="mouse").validate(
+        validated = lb.Gene.public(organism="mouse").validate(
             adata.var.index, field="ensembl_gene_id"
         )
         ln.save(
@@ -335,7 +335,7 @@ def anndata_human_immune_cells(
         ln.Feature(name="tissue", type="category", registries=[lb.Tissue]).save()
         ln.Feature(name="organism", type="category", registries=[lb.Organism]).save()
         ln.Feature(name="donor", type="category", registries=[ln.ULabel]).save()
-        lb.ExperimentalFactor.from_bionty(ontology_id="EFO:0008913").save()
+        lb.ExperimentalFactor.from_public(ontology_id="EFO:0008913").save()
         ln.save([ln.ULabel(name=name) for name in adata.obs.donor.unique()])
         ln.settings.verbosity = verbosity
         lb.settings.auto_save_parents = auto_save_parents

lamindb/dev/storage/file.py

@@ -1,6 +1,8 @@
+import builtins
+import re
 import shutil
 from pathlib import Path
-from typing import Union
+from typing import Optional, Union
 
 import anndata as ad
 import pandas as pd
@@ -24,6 +26,7 @@ except ImportError:
 
 
 AUTO_KEY_PREFIX = ".lamindb/"
+is_run_from_ipython = getattr(builtins, "__IPYTHON__", False)
 
 
 # add type annotations back asap when re-organizing the module
@@ -143,6 +146,33 @@ def read_tsv(path: Union[str, Path, UPath]) -> pd.DataFrame:
     return pd.read_csv(path_sanitized, sep="\t")
 
 
+def load_html(path: Union[str, Path, UPath]):
+    if is_run_from_ipython:
+        with open(path, encoding="utf-8") as f:
+            html_content = f.read()
+        # Extract the body content using regular expressions
+        body_content = re.findall(
+            r"<body(?:.*?)>(?:.*?)</body>", html_content, re.DOTALL
+        )
+        # Remove any empty body tags
+        if body_content:
+            body_content = body_content[0]
+            body_content = body_content.strip()  # type: ignore
+        from IPython.display import HTML, display
+
+        display(HTML(data=body_content))
+    else:
+        return path
+
+
+def load_json(path: Union[str, Path, UPath]):
+    import json
+
+    with open(path) as f:
+        data = json.load(f)
+    return data
+
+
 def load_to_memory(filepath: Union[str, Path, UPath], stream: bool = False, **kwargs):
     """Load a file into memory.
 
@@ -170,6 +200,8 @@ def load_to_memory(filepath: Union[str, Path, UPath], stream: bool = False, **kw
         ".fcs": read_fcs,
         ".zarr": read_adata_zarr,
         ".zrad": read_adata_zarr,
+        ".html": load_html,
+        ".json": load_json,
     }
 
     reader = READER_FUNCS.get(filepath.suffix)

{lamindb-0.66.1.dist-info → lamindb-0.67.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.66.1
+Version: 0.67.1
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,10 +9,10 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.61.0
-Requires-Dist: lamindb_setup==0.64.1
+Requires-Dist: lnschema_core==0.61.1
+Requires-Dist: lamindb_setup==0.64.2
 Requires-Dist: lamin_utils==0.13.0
-Requires-Dist: lamin_cli==0.6.0
+Requires-Dist: lamin_cli==0.6.1
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -28,7 +28,7 @@ Requires-Dist: boto3==1.28.17 ; extra == "aws"
 Requires-Dist: aiobotocore==2.5.4 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.9.0 ; extra == "aws"
 Requires-Dist: s3fs>=2023.9.0 ; extra == "aws"
-Requires-Dist: lnschema_bionty==0.37.2 ; extra == "bionty"
+Requires-Dist: lnschema_bionty==0.39.0 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
@@ -42,7 +42,7 @@ Requires-Dist: lamin_vault ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=1.1.7 ; extra == "fcs"
 Requires-Dist: fsspec[gs]==2023.9.0 ; extra == "gcp"
-Requires-Dist: nbproject==0.9.2 ; extra == "jupyter"
+Requires-Dist: nbproject==0.10.0 ; extra == "jupyter"
 Requires-Dist: nbstripout ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"

{lamindb-0.66.1.dist-info → lamindb-0.67.1.dist-info}/RECORD

@@ -1,29 +1,28 @@
-lamindb/__init__.py,sha256=QoJov2BScjf_-bnCnlA4PlHMRHSh0YHN_fpscdyyB70,2691
-lamindb/_artifact.py,sha256=eWsLj8x6Cqy8MR7LxKyScxozM52MaqOTCK8gplloP2c,38087
-lamindb/_collection.py,sha256=gVcs3A200JZilfdYd0zrX29UrAmhP9Eovu6r_SIxXQ4,17634
-lamindb/_delete.py,sha256=jO6kcIoxY6EFgqiVF2vlbXaCaqlI25AvBo7nre3JXkQ,1968
+lamindb/__init__.py,sha256=hMge9XlaVuCCh6oLRPJWy1lAE4u58fiIrWHxORYbIv0,2530
+lamindb/_artifact.py,sha256=4GIo987_3AJgQRFDC7LwokXBYFKPwmnOUeGcFxG8zjI,38110
+lamindb/_collection.py,sha256=Y-GU-MOvlLmqlcBhfGVojDbnZFD7V_FZEbrsF37rvqI,17850
 lamindb/_feature.py,sha256=tEcqFoEj5yp4LSJfMGyiVvxDUuLoZaik6lo05ZKcCtE,6036
 lamindb/_feature_set.py,sha256=KYgdmMdXb21pfpir1J1O21in3nJvUeznECOB38qfTvk,8654
 lamindb/_filter.py,sha256=YwWqviJ34kHTMJ8NYlrEw-vsrXkKrVIPsEZSBVvMcrI,1163
-lamindb/_from_values.py,sha256=dKz4cTUBRkXOOzFX2Ix2cKhK2Lw9PyTgi7d0PI-kh3c,11869
+lamindb/_from_values.py,sha256=WMyD2FiEgxgpSYpj8fFChv7Mdz8Y--2a8RoEZjLFR30,11885
 lamindb/_parents.py,sha256=UVvCOR9CUkEWc2_qr3iHJUM_j7s88L5H6F3Xz5Ni5gY,14240
-lamindb/_query_manager.py,sha256=m4WUScviuNlMHeNEPZ8H8y0YsMXSbwWyfIgS4L00wBY,4332
-lamindb/_query_set.py,sha256=tItL2YNdycpbXklYd8aW4jJX6Z-kGcNclscg0v3l8t4,10495
-lamindb/_registry.py,sha256=z0Wy9gEU6Ldw5vB4bYoYw3cwHD5zMpNgytpakfHMIu0,17535
-lamindb/_run.py,sha256=659lqY32GW7F41rFUUo37OftUa38-p8yaV9Z0oF32CE,1120
+lamindb/_query_manager.py,sha256=OGBFv-l16t2g0TqBIUvMjfEZhu0a5AT0LsFBHVEOyv8,4001
+lamindb/_query_set.py,sha256=LOHuiGok0FRrG_CBOHVkIsVTDdw406eJalsNwI0MNng,10904
+lamindb/_registry.py,sha256=56ax7_mrUbmQveGCkHypvQrGlrw5LMF3yFZPqj8_gkk,17535
+lamindb/_run.py,sha256=O5TcVPZqgdUvk4nBmI_HXzvWOG_Zr3B_HMDaw228w-4,1719
 lamindb/_save.py,sha256=UlRHJGUiHGOXv90wmawZVsOqhJIqk8f1wj8MW3Rlq_c,10535
 lamindb/_storage.py,sha256=mz2Cy0CTaeJGA03A1FPQmmH0Vt2ib_KlXklaLqtN1mU,394
-lamindb/_transform.py,sha256=VcfdhfaUsFS-TZCNdgJgf9Kg9KAAwjA3c679ayn6nUI,2478
+lamindb/_transform.py,sha256=O5fJ6X-sHicoGj3aHTikYjd3Nsru0mstlI6gRMgRamQ,3360
 lamindb/_ulabel.py,sha256=HALoy6HerRnehR-u8zPH-qmiFQHWxeAwkZ31jxjrfgI,1893
 lamindb/_utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
-lamindb/_validate.py,sha256=fS2685MYX9h6iAWymEorJJmDYA2CGNOSmJpesbG6faU,14400
+lamindb/_validate.py,sha256=KFzU3aLEd5RcimT61FWDlX7_uojFyEL0BaVZVzmoyow,14400
 lamindb/_view.py,sha256=yFMu4vnt0YqvN1q11boAkwigxCH1gdliDUSbzh3IuDw,2175
 lamindb/dev/__init__.py,sha256=LLqivujL8c-oKWC15SJepAYyrTlLNvql5Vdwunc0qvE,1174
 lamindb/dev/_data.py,sha256=YPZ664qGKMl34LbZCMCEFIxQ-E81iAt_b3lvMiTe-oc,17066
 lamindb/dev/_feature_manager.py,sha256=jn8x_JbrtLFelmaFh4noOXqGSCfqVuVX0quoa7gTJtM,9366
-lamindb/dev/_label_manager.py,sha256=6E_pSQicqfTWDGEGe4WPn_3GZl_CCIMTZ6xJDh4EkC0,8740
+lamindb/dev/_label_manager.py,sha256=eViJrKRnVqbO4zUPZk0yW4IP224sbTcGFL-UHSE1otg,8750
 lamindb/dev/_mapped_collection.py,sha256=UhlDRuXOySQNqNabcJQ3dXmSz-zPwYxk2VZzdLikc4Y,13754
-lamindb/dev/_run_context.py,sha256=03VvW7x8bIyumnmw6PZ-q82m6HihdMfkr0Ga2BxA7dU,22961
+lamindb/dev/_run_context.py,sha256=3p-2GdxNREKvUW86gW79MtDHLZ0IxuruYJJ_7MbfZwI,22973
 lamindb/dev/_settings.py,sha256=nixk8lVijCbq_fRlUpkX5gvO9AdgUFjbXzFThAJhGBA,3824
 lamindb/dev/_track_environment.py,sha256=QjHWbyl2u8J4hbJG8Q_ToFaZIgS-H15Ej6syJgk-dvY,662
 lamindb/dev/_view_tree.py,sha256=K-C1BsOiEupwgkhyrsGxLFxHU45SAkiKsQbeOV9PbaY,3421
@@ -33,17 +32,17 @@ lamindb/dev/hashing.py,sha256=wmioFBv_5G-Gjnm-QU_UtofpB0wBjeEkycof_V9F454,1745
 lamindb/dev/types.py,sha256=dzzoSaxjtJ1zJ_C9LZJcydiULf9XfZji1KI2DvO6S8g,224
 lamindb/dev/versioning.py,sha256=NlwOH7Vf4bad5iC1l9erkuE7MBcj1vQd-AfgAZRpNew,2499
 lamindb/dev/datasets/__init__.py,sha256=zRP98oqUAaXhqWyKMiH0s_ImVIuNeziQQ2kQ_t0f-DI,1353
-lamindb/dev/datasets/_core.py,sha256=0VCCQ_LAj7lTkK0JjdO0WE0t53R0uyMNskSKXeXcVPI,18882
+lamindb/dev/datasets/_core.py,sha256=pdJn25vlX9NQ0AaPo2E9LYGHQqH02rQnjHgZ8U-5Z6o,18882
 lamindb/dev/datasets/_fake.py,sha256=S8mNho-oSh1M9x9oOSsUBLLHmBAegsOLlFk6LnF81EA,942
 lamindb/dev/storage/__init__.py,sha256=P6LYolhSu4QNtvp4hEnVpLpW1GueX2BTewbUE8A12ak,368
 lamindb/dev/storage/_anndata_sizes.py,sha256=0XVzA6AQeVGPaGPrhGusKyxFgFjeo3qSN29hxb8D5E8,993
 lamindb/dev/storage/_backed_access.py,sha256=NFMS--MZHjh1obyNjUG_wIe9NGpYhv9G08sr8PslafI,22794
 lamindb/dev/storage/_zarr.py,sha256=FEwAkOhAp_1PcgBCJF2q-OxZsr2iVFQQ88svuAJ_AKU,2815
-lamindb/dev/storage/file.py,sha256=jalzFQ8q110UUu_GGQBkU-g3M04h5g4LJ3nLjCzJ4pU,5740
+lamindb/dev/storage/file.py,sha256=4PVxVzPGzoSizODRPW1cejbyVG_7ur5qNKWYHa_BjUw,6654
 lamindb/dev/storage/object.py,sha256=KGuOwwYuN2yCJxTXn9v0LanC0fjKwy_62P-WksHcf40,1140
 lamindb/setup/__init__.py,sha256=WaWKO-2XT67S65lSbS80hUojL-Mr_Wms9UxH6U54TsY,289
 lamindb/setup/dev/__init__.py,sha256=tBty426VGF2PGqqt2XuNU-WgvOrbOp1aZBDowjLuzgA,242
-lamindb-0.66.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.66.1.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb-0.66.1.dist-info/METADATA,sha256=QPfOsgiVpthQ3qnq8Yo_SW831XoRVlTPpMqsBhMbKJI,3076
-lamindb-0.66.1.dist-info/RECORD,,
+lamindb-0.67.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.67.1.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.67.1.dist-info/METADATA,sha256=qwqkIHZP36qqzxe9xe3rwEM924X5eYlyLEgihVjuPgU,3077
+lamindb-0.67.1.dist-info/RECORD,,

lamindb/_delete.py

@@ -1,65 +0,0 @@
-from typing import List, Union, overload
-
-from lamin_utils import colors, logger
-from lnschema_core import Registry
-
-
-@overload
-def delete(
-    record: Registry,
-) -> None:
-    ...  # pragma: no cover
-
-
-@overload
-def delete(
-    records: List[Registry],
-) -> None:  # type: ignore
-    ...  # pragma: no cover
-
-
-def delete(  # type: ignore
-    records: Union[Registry, List[Registry]],
-) -> None:
-    """Delete metadata records & files.
-
-    Args:
-        records: `Union[Registry, List[Registry]]` One or multiple records.
-
-    Returns:
-        `None`
-
-    Examples:
-
-        Delete by record:
-
-        >>> experiment = ln.filter(Experiment, id=experiment_id).one()
-        >>> ln.delete(experiment)
-
-        Delete files (delete the metadata record and the file in storage):
-
-        >>> file = ln.filter(File, id=artifact_id).one()
-        >>> ln.delete(file)
-        >>> # deleting the record occurs automatically
-        >>> # you will be asked whether to delete the file in storage
-        >>> # for more control, use:
-        >>> artifact.delete(storage=True)
-
-        Bulk delete via QuerySet:
-
-        >>> ln.save(ln.ULabel.from_values(["ULabel1", "ULabel2", "ULabel3"], field="name"))
-        >>> queryset = ln.ULabel.filter(name__icontains = "label")
-        >>> queryset.list()
-        [ULabel(id=o3FY3c5n, name=ULabel2, updated_at=2023-07-19 18:28:16, created_by_id=kmvZDIX9), # noqa
-        ULabel(id=Qi3c4utq, name=ULabel3, updated_at=2023-07-19 18:28:16, created_by_id=kmvZDIX9), # noqa
-        ULabel(id=CcFPLmpq, name=ULabel1, updated_at=2023-07-19 18:28:16, created_by_id=kmvZDIX9)] # noqa
-        >>> queryset.delete()
-    """
-    logger.warning("for efficient bulk delete, use `queryset.delete` instead")
-    if isinstance(records, list):
-        records = records
-    elif isinstance(records, Registry):
-        records = [records]
-    for record in records:
-        record.delete()
-        logger.success(f"deleted {colors.yellow(f'{record}')}")