lamindb 0.50.0__py3-none-any.whl → 0.50.1__py3-none-any.whl

lamindb/__init__.py

@@ -85,7 +85,7 @@ Static classes & modules:
 
 """
 
-__version__ = "0.50.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.50.1"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 

lamindb/_context.py

@@ -15,16 +15,16 @@ from lnschema_core.types import TransformType
 is_run_from_ipython = getattr(builtins, "__IPYTHON__", False)
 
 msg_path_failed = (
-    "Failed to infer notebook path.\nFix: Either track manually via"
+    "failed to infer notebook path.\nfix: either track manually via"
     " `ln.track(ln.Transform(name='My notebook'))` or pass"
-    " `notebook_path` to ln.track()."
+    " `notebook_path` to ln.track()"
 )
 
 msg_manual_init = (
-    "\n(1) Save your notebook!"
-    "\n(2) Attach metadata to the notebook by running the CLI:\n"
+    "\n(1) save your notebook!"
+    "\n(2) attach metadata to the notebook by running the CLI:\n"
     "lamin track {notebook_path}"
-    "\n(3) Reload or re-open your notebook"
+    "\n(3) reload or re-open your notebook"
 )
 
 
@@ -204,20 +204,20 @@ class run_context:
                 except Exception as e:
                     if isinstance(e, ImportError):
                         logger.info(
-                            "It looks like you are running ln.track() from a "
-                            "notebook!\nPlease install nbproject: pip install nbproject"
+                            "it looks like you are running ln.track() from a "
+                            "notebook!\nplease install nbproject: pip install nbproject"
                         )
                     elif isinstance(e, UpdateNbWithNonInteractiveEditorError):
                         raise e
                     elif isinstance(e, (NotebookNotSavedError, NoTitleError)):
                         raise e
                     else:
-                        logger.warning(f"Automatic tracking of notebook failed: {e}")
+                        logger.warning(f"automatic tracking of notebook failed: {e}")
                     is_tracked_notebook = False
 
             if not is_tracked_notebook:
                 logger.warning(
-                    "No automatic metadata detection, consider passing transform"
+                    "no automatic metadata detection, consider passing transform"
                 )
                 return None
         else:
@@ -227,7 +227,7 @@ class run_context:
                 transform_exists = Transform.filter(id=transform.id).first()
             if transform_exists is None:
                 transform.save()
-                logger.info(f"saved: {transform}")
+                logger.save(f"saved: {transform}")
                 transform_exists = transform
             else:
                 logger.success(f"loaded: {transform_exists}")
@@ -253,17 +253,17 @@ class run_context:
         if run is None:  # create new run
             run = ln.Run(transform=cls.transform)
             run.save()
-            logger.info(f"saved: {run}")
+            logger.save(f"saved: {run}")
         cls.run = run
 
         # at this point, we have a transform can display its parents if there are any
         parents = cls.transform.parents.all() if cls.transform is not None else []
         if len(parents) > 0:
             if len(parents) == 1:
-                logger.info(f"parent transform: {parents[0]}")
+                logger.info(f"  parent transform: {parents[0]}")
             else:
                 parents_formatted = "\n   - ".join([f"{parent}" for parent in parents])
-                logger.info(f"parent transforms:\n   - {parents_formatted}")
+                logger.info(f"  parent transforms:\n   - {parents_formatted}")
 
         # only for newly intialized notebooks
         if hasattr(cls, "_notebook_meta"):
@@ -405,9 +405,9 @@ class run_context:
                 type=TransformType.notebook,
             )
             transform.save()
-            logger.success(f"saved: {transform}")
+            logger.save(f"saved: {transform}")
         else:
-            logger.info(f"loaded: {transform}")
+            logger.success(f"loaded: {transform}")
             if transform.name != title or transform.short_name != filestem:
                 response = input(
                     "Updated notebook name and/or title: Do you want to assign a"
@@ -427,7 +427,7 @@ class run_context:
                 transform.short_name = filestem
                 transform.save()
                 if response == "y":
-                    logger.success(f"saved: {transform}")
+                    logger.save(f"saved: {transform}")
                 else:
                     logger.success(f"updated: {transform}")
 

lamindb/_delete.py

@@ -55,11 +55,11 @@ def delete(  # type: ignore
         Label(id=CcFPLmpq, name=Label1, 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")
+    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}')}")
+        logger.success(f"deleted {colors.yellow(f'{record}')}")

lamindb/_feature_set.py

@@ -62,7 +62,7 @@ def get_validated_features(features: List[Registry], field: Field) -> List[Regis
     if non_validated_features:
         non_validated_features_display = ",".join(non_validated_features)
         logger.warning(
-            f"ignoring unvalidated features: {non_validated_features_display}"
+            f"ignoring non-validated features: {non_validated_features_display}"
         )
     return validated_features
 
@@ -96,7 +96,7 @@ def __init__(self, *args, **kwargs):
         features_hash = hash_set({feature.id for feature in features})
         feature_set = FeatureSet.filter(hash=features_hash).one_or_none()
         if feature_set is not None:
-            logger.info(f"loaded: {feature_set}")
+            logger.success(f"loaded: {feature_set}")
             init_self_from_db(self, feature_set)
             return None
         else:
@@ -181,7 +181,7 @@ def from_values(
     features_hash = hash_set(set(validated_feature_ids))
     feature_set = FeatureSet.filter(hash=features_hash).one_or_none()
     if feature_set is not None:
-        logger.info(f"loaded {feature_set}")
+        logger.success(f"loaded {feature_set}")
     else:
         if type is not None:
             type_str = type.__name__ if not isinstance(type, str) else type
@@ -213,7 +213,7 @@ def from_df(
     if validated_features:
         feature_set = FeatureSet(validated_features, name=name)
     else:
-        logger.warning("no validated features, not creating feature set")
+        logger.warning("no validated features, skip creating feature set")
         feature_set = None
         # raise ValidationError("Dataframe columns contain no validated feature names")
     return feature_set

lamindb/_file.py

@@ -171,9 +171,9 @@ def get_hash(
     result = File.filter(hash=hash).list()
     if len(result) > 0:
         if settings.upon_file_create_if_hash_exists == "error":
-            msg = f"File with same hash exists: {result[0]}"
+            msg = f"file with same hash exists: {result[0]}"
             hint = (
-                "💡 You can make this error a warning:\n"
+                "💡 you can make this error a warning:\n"
                 "    ln.settings.upon_file_create_if_hash_exists"
             )
             raise RuntimeError(f"{msg}\n{hint}")
@@ -381,9 +381,9 @@ def log_storage_hint(
     else:
         hint += "file will be copied to default storage upon `save()`"
     if key is None:
-        hint += f" with key = '{id}{suffix}'"
+        hint += f" with key '{id}{suffix}'"
     else:
-        hint += f" with key = '{key}'"
+        hint += f" with key '{key}'"
     logger.hint(hint)
 
 
@@ -557,24 +557,25 @@ def from_anndata(
     else:
         type = convert_numpy_dtype_to_lamin_feature_type(adata.X.dtype)
     feature_sets = {}
-    logger.info("parsing feature names of X, stored in slot 'var'")
+    logger.info("parsing feature names of X stored in slot 'var'")
     logger.indent = "   "
     feature_set_var = FeatureSet.from_values(
         data_parse.var.index,
         var_ref,
         type=type,
     )
+
     if feature_set_var is not None:
-        logger.info(f"linking: {feature_set_var}")
         feature_sets["var"] = feature_set_var
+        logger.save(f"linked: {feature_set_var}")
     logger.indent = ""
     if len(data_parse.obs.columns) > 0:
         logger.info("parsing feature names of slot 'obs'")
         logger.indent = "   "
         feature_set_obs = FeatureSet.from_df(data_parse.obs)
         if feature_set_obs is not None:
-            logger.info(f"linking: {feature_set_obs}")
             feature_sets["obs"] = feature_set_obs
+            logger.save(f"linked: {feature_set_obs}")
         logger.indent = ""
     file._feature_sets = feature_sets
     return file
@@ -663,7 +664,7 @@ def replace(
             self._clear_storagekey = self.key
             self.key = str(key_path.with_name(new_filename))
             logger.warning(
-                f"Replacing the file will replace key '{key_path}' with '{self.key}'"
+                f"replacing the file will replace key '{key_path}' with '{self.key}'"
                 f" and delete '{key_path}' upon `save()`"
             )
     else:
@@ -812,7 +813,7 @@ def _save_skip_storage(file, *args, **kwargs) -> None:
         for feature_set in file._feature_sets.values():
             feature_set.save()
         s = "s" if len(file._feature_sets) > 1 else ""
-        logger.info(
+        logger.save(
             f"saved {len(file._feature_sets)} feature set{s} for slot{s}:"
             f" {list(file._feature_sets.keys())}"
         )

lamindb/_registry.py

@@ -19,6 +19,7 @@ from . import _TESTING
 from ._from_values import get_or_create_records
 from .dev._feature_manager import create_features_df
 from .dev._settings import settings
+from .dev._view_parents import _transform_emoji
 
 IPYTHON = getattr(builtins, "__IPYTHON__", False)
 
@@ -65,9 +66,10 @@ def suggest_objects_with_same_name(orm: Registry, kwargs) -> Optional[str]:
             if results.index[0] == kwargs["name"]:
                 return "object-with-same-name-exists"
             else:
+                s = "" if results.shape[0] == 1 else "s"
+                it = "it" if results.shape[0] == 1 else "one of them"
                 msg = (
-                    "Records with similar names exist! Did you mean to load one of"
-                    " them?"
+                    f"record{s} with similar name{s} exist! did you mean to load {it}?"
                 )
                 if IPYTHON:
                     from IPython.display import display
@@ -97,13 +99,13 @@ def __init__(orm: Registry, *args, **kwargs):
                     existing_record = orm.filter(name=kwargs["name"]).one()
                 if existing_record is not None:
                     logger.success(
-                        f"Loaded record with exact same name{version_comment}"
+                        f"loaded record with exact same name{version_comment}"
                     )
                     init_self_from_db(orm, existing_record)
                     return None
         super(Registry, orm).__init__(**kwargs)
     elif len(args) != len(orm._meta.concrete_fields):
-        raise ValueError("Please provide keyword arguments, not plain arguments")
+        raise ValueError("please provide keyword arguments, not plain arguments")
     else:
         # object is loaded from DB (**kwargs could be omitted below, I believe)
         super(Registry, orm).__init__(*args, **kwargs)
@@ -317,7 +319,12 @@ def describe(self):
 
     # Display Provenance
     # display line by line the foreign key fields
-    emojis = {"storage": "💾", "created_by": "👤", "transform": "💫", "run": "🚗"}
+    emojis = {
+        "storage": "🗃️",
+        "created_by": "👤",
+        "transform": _transform_emoji(self.transform),
+        "run": "🚗",
+    }
     if len(foreign_key_fields) > 0:
         record_msg = f"{model_name}({''.join([f'{i}={self.__getattribute__(i)}, ' for i in direct_fields])})"  # noqa
         msg += f"{record_msg.rstrip(', )')})\n\n"
@@ -352,7 +359,7 @@ def describe(self):
             key_split = feature_set.registry.split(".")
             if len(key_split) == 3:
                 logger.warning(
-                    "You have a legacy entry in feature_set.field, should be just"
+                    "you have a legacy entry in feature_set.field, should be just"
                     " 'bionty.Gene'"
                 )
             orm_name_with_schema = f"{key_split[0]}.{key_split[1]}"
@@ -474,7 +481,7 @@ def __get_name_with_schema__(cls) -> str:
 
 
 def select_backward(cls, **expressions):
-    logger.warning("select() is deprecated! Please rename: Registry.filter()")
+    logger.warning("select() is deprecated! please use: Registry.filter()")
     return cls.filter(**expressions)
 
 

lamindb/_save.py

@@ -86,11 +86,11 @@ def save(records: Iterable[Registry], **kwargs) -> None:  # type: ignore
             ):
                 # save the record with parents one by one
                 logger.warning(
-                    "Now recursing through parents: "
+                    "now recursing through parents: "
                     "this only happens once, but is much slower than bulk saving"
                 )
                 logger.hint(
-                    "You can switch this off via: lb.settings.auto_save_parents = False"
+                    "you can switch this off via: lb.settings.auto_save_parents = False"
                 )
                 for record in non_files_with_parents:
                     record._save_ontology_parents()
@@ -123,7 +123,7 @@ def check_and_attempt_upload(file: File) -> Optional[Exception]:
         try:
             upload_data_object(file)
         except Exception as exception:
-            logger.warning(f"Could not upload file: {file}")
+            logger.warning(f"could not upload file: {file}")
             return exception
         # copies (if ob-disk) or moves the temporary file (if in-memory) to the cache
         copy_or_move_to_cache(file)
@@ -173,7 +173,7 @@ def check_and_attempt_clearing(file: File) -> Optional[Exception]:
             if file._clear_storagekey is not None:
                 delete_storage_using_key(file, file._clear_storagekey)
                 logger.success(
-                    f"Deleted stale object at storage key {file._clear_storagekey}"
+                    f"deleted stale object at storage key {file._clear_storagekey}"
                 )
                 file._clear_storagekey = None
         except Exception as exception:
@@ -238,20 +238,16 @@ def upload_data_object(file) -> None:
     """Store and add file and its linked entries."""
     # do NOT hand-craft the storage key!
     file_storage_key = auto_storage_key_from_file(file)
+    msg = f"storing file '{file.id}' with key '{file_storage_key}'"
     if hasattr(file, "_to_store") and file._to_store and file.suffix != ".zarr":
-        display_key = (
-            f"`{file.key}` ('{file_storage_key}')"
-            if file.key is None
-            else f"'{file_storage_key}'"
-        )
-        logger.hint(f"storing file '{file.id}' with key {display_key}")
+        logger.save(msg)
         store_object(file._local_filepath, file_storage_key)
     elif (
         file.suffix in {".zarr", ".zrad"}
         and hasattr(file, "_memory_rep")
         and file._memory_rep is not None
     ):
-        logger.hint(f"storing file {file.id} with key {file_storage_key}")
+        logger.save(msg)
         storagepath = lamindb_setup.settings.storage.key_to_filepath(file_storage_key)
         print_progress = partial(
             print_hook, filepath=file_storage_key, action="uploading"

lamindb/_synonym.py

@@ -94,8 +94,8 @@ def _add_or_remove_synonyms(
         if matches_df.shape[0] > 0:
             records_df = pd.DataFrame(syns_all.filter(id__in=matches_df["id"]).values())
             logger.error(
-                f"Input synonyms {matches_df['synonyms'].unique()} already associated"
-                " with the following records:\n(Pass `force=True` to ignore this error)"
+                f"input synonyms {matches_df['synonyms'].unique()} already associated"
+                " with the following records:\n"
             )
             display(records_df)
             raise SystemExit(AssertionError)
@@ -110,7 +110,7 @@ def _add_or_remove_synonyms(
         return
     # because we use | as the separator
     if any(["|" in i for i in syn_new_set]):
-        raise AssertionError("A synonym can't contain '|'!")
+        raise AssertionError("a synonym can't contain '|'!")
 
     # existing synonyms
     syns_exist = record.synonyms

lamindb/_validate.py

@@ -3,6 +3,7 @@ from typing import Dict, List, Optional, Union
 import numpy as np
 import pandas as pd
 from django.db.models import QuerySet
+from lamin_utils._inspect import InspectResult
 from lamindb_setup.dev._docs import doc_args
 from lnschema_core import Registry, ValidationAware
 from lnschema_core.types import ListLike, StrField
@@ -20,16 +21,14 @@ def inspect(
     values: ListLike,
     field: StrField,
     *,
-    return_df: bool = False,
     mute: bool = False,
     **kwargs,
-) -> Union["pd.DataFrame", Dict[str, List[str]]]:
+) -> InspectResult:
     """{}"""
     return _inspect(
         cls=cls,
         values=values,
         field=field,
-        return_df=return_df,
         mute=mute,
         **kwargs,
     )
@@ -47,7 +46,6 @@ def _inspect(
     values: ListLike,
     field: StrField,
     *,
-    return_df: bool = False,
     mute: bool = False,
     **kwargs,
 ) -> Union["pd.DataFrame", Dict[str, List[str]]]:
@@ -66,8 +64,8 @@ def _inspect(
         identifiers=values,
         field=str(field),
         inspect_synonyms=True,
-        return_df=return_df,
-        logging=not mute,
+        mute=mute,
+        **kwargs,
     )
 
 
@@ -87,10 +85,7 @@ def _validate(cls, values: ListLike, field: StrField, **kwargs) -> np.ndarray[bo
         )
     )
     return validate(
-        identifiers=values,
-        field_values=field_values,
-        case_sensitive=True,
-        return_df=False,
+        identifiers=values, field_values=field_values, case_sensitive=True, **kwargs
     )
 
 

lamindb/dev/__init__.py

@@ -10,6 +10,7 @@
    FeatureManager
    ValidationAware
    SynonymsAware
+   InspectResult
    datasets
    hashing
    storage
@@ -18,6 +19,7 @@
    exc.ValidationError
 """
 
+from lamin_utils._inspect import InspectResult
 from lnschema_core.models import Data, Registry, SynonymsAware, ValidationAware
 
 from lamindb._query_manager import QueryManager

lamindb/dev/_data.py

@@ -43,12 +43,12 @@ def get_labels(
         feature_name = feature
         feature = Feature.filter(name=feature_name).one_or_none()
         if feature is None:
-            raise ValueError("Feature doesn't exist")
+            raise ValueError("feature doesn't exist")
     if feature.registries is None:
-        raise ValueError("Feature does not have linked labels")
+        raise ValueError("feature does not have linked labels")
     registries_to_check = feature.registries.split("|")
     if len(registries_to_check) > 1 and not mute:
-        logger.warning("Labels come from multiple registries!")
+        logger.warning("labels come from multiple registries!")
     qs_by_registry = {}
     for registry in registries_to_check:
         # currently need to distinguish between Label and non-Label, because
@@ -147,17 +147,18 @@ def add_labels(
                     for record in records
                 ]
             )
-            msg += f"linking labels {records_display} to feature '{feature.name}'"
-        if msg != "":
-            msg += ", "
+            msg += f"linked labels {records_display} to feature '{feature.name}'"
         if feature.registries is None or orm_name not in feature.registries:
-            msg += f"linking feature '{feature.name}' to registry '{orm_name}'"
+            if len(msg) > 0:
+                msg += ", "
+            msg += f"linked feature '{feature.name}' to registry '{orm_name}'"
             if feature.registries is None:
                 feature.registries = orm_name
             elif orm_name not in feature.registries:
                 feature.registries += f"|{orm_name}"
             feature.save()
-        logger.success(msg)
+        if len(msg) > 0:
+            logger.save(msg)
         # check whether we have to update the feature set that manages labels
         # (Feature) to account for a new feature
         found_feature = False
@@ -166,18 +167,18 @@ def add_labels(
                 found_feature = True
         if not found_feature:
             if "external" not in linked_features_by_slot:
-                logger.success("creating feature set for slot 'external'")
                 feature_set = FeatureSet([feature], modality="meta")
                 feature_set.save()
                 self.features.add_feature_set(feature_set, slot="external")
+                logger.save("created feature set for slot 'external'")
             else:
                 feature_set = self.features._feature_set_by_slot["external"]
-                logger.success(
-                    f"linking feature {feature.name} to feature set {feature_set}"
-                )
                 feature_set.features.add(feature)
                 feature_set.n += 1
                 feature_set.save()
+                logger.save(
+                    f"linked feature {feature.name} to feature set {feature_set}"
+                )
 
 
 @property  # type: ignore

lamindb/dev/_view_parents.py

@@ -1,11 +1,12 @@
 from typing import List, Set, Union
 
-from lnschema_core import File, Registry, Run
+from lnschema_core import File, Registry, Run, Transform
 from lnschema_core.models import format_field_value
 
 LAMIN_GREEN_LIGHTER = "#10b981"
 LAMIN_GREEN_DARKER = "#065f46"
 GREEN_FILL = "honeydew"
+TRANSFORM_EMOJIS = {"notebook": "📔", "app": "🖥️", "pipeline": "🧩"}
 
 
 def view_lineage(file: File, with_children: bool = True):
@@ -120,11 +121,11 @@ def view_parents(
     )
     u.node(
         record_label.replace(":", "_"),
-        label=record_label,
+        label=_add_emoji(record, record_label),
         fillcolor=LAMIN_GREEN_LIGHTER,
     )
     for _, row in df_edges.iterrows():
-        u.node(row["source"], label=row["source_label"])
+        u.node(row["source"], label=_add_emoji(record, row["source_label"]))
         u.edge(row["source"], row["target"], color="dimgrey")
 
     return u
@@ -182,6 +183,16 @@ def _df_edges_from_parents(
     return df_edges
 
 
+def _add_emoji(record: Registry, label: str):
+    if record.__class__.__name__ == "Transform":
+        emoji = TRANSFORM_EMOJIS.get(record.type, "💫")
+    elif record.__class__.__name__ == "Run":
+        emoji = TRANSFORM_EMOJIS.get(record.transform.type, "💫")
+    else:
+        emoji = ""
+    return f"{emoji} {label}"
+
+
 def _get_all_parent_runs(file: File):
     """Get all input file runs recursively."""
     all_runs = {file.run}
@@ -224,10 +235,9 @@ def _label_file_run(record: Union[File, Run]):
             rf' FACE="Monospace">id={record.id}<BR/>suffix={record.suffix}</FONT>>'
         )
     elif isinstance(record, Run):
-        emojis = {"notebook": "📔", "app": "🖥️"}
         name = f'{record.transform.name.replace("&", "&amp;")}'
         return (
-            rf'<{emojis.get(record.transform.type, "🧩")} {name}<BR/><FONT COLOR="GREY" POINT-SIZE="10"'  # noqa
+            rf'<{TRANSFORM_EMOJIS.get(str(record.transform.type), "💫")} {name}<BR/><FONT COLOR="GREY" POINT-SIZE="10"'  # noqa
             rf' FACE="Monospace">id={record.id}<BR/>type={record.transform.type},'
             rf" user={record.created_by.name}<BR/>run_at={format_field_value(record.run_at)}</FONT>>"  # noqa
         )
@@ -253,3 +263,7 @@ def _df_edges_from_runs(all_runs: List[Run]):
     df["source_label"] = df["source_record"].apply(_label_file_run)
     df["target_label"] = df["target_record"].apply(_label_file_run)
     return df
+
+
+def _transform_emoji(transform: Transform):
+    return TRANSFORM_EMOJIS.get(transform.type, "💫")

lamindb/dev/datasets/__init__.py

@@ -19,6 +19,7 @@
    anndata_mouse_sc_lymph_node
    anndata_human_immune_cells
    anndata_pbmc68k_reduced
+   anndata_file_pbmc68k_test
    anndata_pbmc3k_processed
    anndata_with_obs
    anndata_suo22_Visium10X
@@ -29,6 +30,7 @@
 """
 
 from ._core import (
+    anndata_file_pbmc68k_test,
     anndata_human_immune_cells,
     anndata_mouse_sc_lymph_node,
     anndata_pbmc3k_processed,

lamindb/dev/datasets/_core.py

@@ -132,6 +132,28 @@ def anndata_pbmc68k_reduced() -> ad.AnnData:
     return ad.read(filepath)
 
 
+def anndata_file_pbmc68k_test() -> Path:
+    """Modified from scanpy.datasets.pbmc68k_reduced().
+
+    Additional slots were added for testing purposes. Returns the filepath.
+
+    To reproduce::
+
+        pbmc68k = ln.dev.datasets.anndata_pbmc68k_reduced()
+        pbmc68k_test = pbmc68k[:30, :200].copy()
+        pbmc68k_test.raw = pbmc68k_test[:, :100]
+        pbmc68k_test.obsp["test"] = sparse.eye(pbmc68k_test.shape[0], format="csr")
+        pbmc68k_test.varp["test"] = sparse.eye(pbmc68k_test.shape[1], format="csr")
+        pbmc68k_test.layers["test"] = sparse.csr_matrix(pbmc68k_test.shape)
+        pbmc68k_test.layers["test"][0] = 1.
+        pbmc68k_test.write("pbmc68k_test.h5ad")
+    """
+    filepath, _ = urlretrieve(
+        "https://lamindb-test.s3.amazonaws.com/pbmc68k_test.h5ad", "pbmc68k_test.h5ad"
+    )
+    return Path(filepath)
+
+
 def anndata_pbmc3k_processed() -> ad.AnnData:
     """Modified from scanpy.pbmc3k_processed()."""
     filepath, _ = urlretrieve(

{lamindb-0.50.0.dist-info → lamindb-0.50.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.50.0
+Version: 0.50.1
 Summary: Open-source data platform for biology.
 Author-email: Lamin Labs <laminlabs@gmail.com>
 Requires-Python: >=3.8
@@ -8,9 +8,9 @@ Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
-Requires-Dist: lnschema_core==0.44.2
-Requires-Dist: lamindb_setup==0.49.5
-Requires-Dist: lamin_utils==0.9.4
+Requires-Dist: lnschema_core==0.44.3
+Requires-Dist: lamindb_setup==0.49.6
+Requires-Dist: lamin_utils==0.9.6
 Requires-Dist: erdiagram>=0.1.2
 Requires-Dist: rapidfuzz
 Requires-Dist: pydantic[dotenv]
@@ -24,7 +24,7 @@ Requires-Dist: botocore==1.29.76 ; extra == "aws"
 Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: boto3==1.26.76 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.5.0 ; extra == "aws"
-Requires-Dist: lnschema_bionty==0.29.1 ; extra == "bionty"
+Requires-Dist: lnschema_bionty==0.29.2 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"

{lamindb-0.50.0.dist-info → lamindb-0.50.1.dist-info}/RECORD

@@ -1,34 +1,34 @@
-lamindb/__init__.py,sha256=0qBsWU0Jt3I6d8NnvAEklA7Nxcl4_80o7FR5qvMDQMQ,3807
-lamindb/_context.py,sha256=yJW0RDzcHqjbbxBrZpoT2eEjkl1FkE1Wy3xlx7JNxjc,17837
+lamindb/__init__.py,sha256=oE18o68Zgr88aED7EbueNHqZ2JQApmGBUwiEcfqeXl0,3807
+lamindb/_context.py,sha256=bc-OpnQ5g_7ltx_qdj0Z1YYuNgeqm87T2jInjZX3iOY,17837
 lamindb/_dataset.py,sha256=w5Byx-9IwVsi2rZx1lKy-HuxTHq3f_Q-MF7t3zb0Msw,4884
-lamindb/_delete.py,sha256=oNvsdqJQQLDxJTHw6914fSCC--BIsLQ5dy7fGdO9Ris,1917
+lamindb/_delete.py,sha256=jvzDM_hbraBvOMhulibRziyDhoM1mqIX_MSLeC42c1M,1917
 lamindb/_feature.py,sha256=B3U9q-v_Bu9o3xrl2ScYefMEkNnDrlWpLzL4sdN4izQ,5479
-lamindb/_feature_set.py,sha256=eLlvysUs8f1kMmAkTXlN6ByQaIBzR9S1uG-bHUX0-cU,8483
-lamindb/_file.py,sha256=8Vwmbk_VrraShbB7Y-88kkEo4-AVJ9T6Y-c9OzfwNyo,35990
+lamindb/_feature_set.py,sha256=XBIGI2vuqECG9VegEzaiQm7iBNfqvpCq_WwJnL7h4ig,8492
+lamindb/_file.py,sha256=0W8mSiYhjl7Epvb87W3SJVFAgpEBlxZnS5r7zNgMyhY,35984
 lamindb/_filter.py,sha256=Rf5RSkglIhJhSdk3AIPfc83F5NIfZrdCZDpgcYNj5KY,351
 lamindb/_from_values.py,sha256=mezvC4d_b8ndRF8NNPl1vEj3O70qLv92b9ZjII5Qa3E,10532
 lamindb/_label.py,sha256=-gLa8WvD1mycruDEB67Zx_oewhO85KvOwVZ3SsKvSvs,1544
 lamindb/_logger.py,sha256=Q9ugUnZE4EwH0N6qFMG2HlILmu-SArnEEy-nafTPjRg,47
 lamindb/_query_manager.py,sha256=RSdPsANk4WBlKbu1DIoDto8HdSqCKbo8Q4CGyRqLd2U,1983
 lamindb/_query_set.py,sha256=yyzrU0ACqG0iebME5bah6ycj4HkvZ8_JigtyATHW3PA,9953
-lamindb/_registry.py,sha256=huNn6s4GbU7NiLh8BWDyaU9jriZJJPBZPdk9NrU_LmE,16271
-lamindb/_save.py,sha256=QfnCdLu_j1HYxT_K1mn3AWz4H0Ms8-aD1iUMrH642bA,9403
+lamindb/_registry.py,sha256=Jd0qb9sK1CO8ONMSN8MnF9UYofd-vvM1XszJQvNETNA,16486
+lamindb/_save.py,sha256=jC2a9JzQBZYVHHuq6NyIovFQI1Y6WT1q2C1dfiXKv_E,9216
 lamindb/_storage.py,sha256=a0ofo106NHNY2RBF3MB1PeeONZMc28aHFG2fbndn_80,246
-lamindb/_synonym.py,sha256=7I8JgEzb8cwFYe3rvCa1_eDxL61LWuWHoLmskx_UHp8,5910
+lamindb/_synonym.py,sha256=I7qL57F5a_Z3a_5hVIQKz5w55HGKEpgpBY9s-35Bg80,5870
 lamindb/_transform.py,sha256=K-Y37UqQPu06lsA3Jfnkyt5dssRpuMnpCDDHDbT40Z4,1251
-lamindb/_validate.py,sha256=OWXJ1QLqQFGX0hFjciRyEi0WqpA1r9PTX9IjwBKRQbQ,3726
+lamindb/_validate.py,sha256=W374jmKFvAy1wIfibz-C4sftxxtlWVwBHliIBy_YD1w,3606
 lamindb/_view.py,sha256=dxZ7BPrMAf0rJ8aKSprkQiO1O2OJsjtSaHBJfpKvVT4,2187
 lamindb/types.py,sha256=svg5S_aynuGfbEOsbmqkR_gF9d9YMzfOkcvGN37Rzvg,232
-lamindb/dev/__init__.py,sha256=i--O6zYzNZ2uK2mUXOU5ipfCPdVBDWUa243CjX8pdPw,592
-lamindb/dev/_data.py,sha256=-ggb6EZIUdP-B1xwtPT0O54IRnBdt8GTWlu4vDZAcKk,7779
+lamindb/dev/__init__.py,sha256=K8cgi474J2uIxbnQZeeeMrsDcWIPdsRXwjIrWcJ_qaQ,656
+lamindb/dev/_data.py,sha256=M5AGGCAvw7e_cDooAWA8_hUQFjxAC62QPs-vEQFqpD4,7806
 lamindb/dev/_feature_manager.py,sha256=laJRqKiL8Qlm5Jq60RoXXX6xYwgyL2MPd6OgS8eXs6A,3526
 lamindb/dev/_settings.py,sha256=WLweWZNAvBquybQYUlYyIehIlv3t5llgYhyNpL0obdg,2926
-lamindb/dev/_view_parents.py,sha256=oerfQHz5VTIoXZuP6GZ9jM3QxK8kt3keMms7j4ziVIw,8073
+lamindb/dev/_view_parents.py,sha256=pF0qTZirLwzgWFtqzRe-KksqASHjpFWLRkNK-0GsyGU,8590
 lamindb/dev/exc.py,sha256=xJ0QCeineZccjYKq-W-RXhU6fJH6JyFLtDyHKZTOoyU,96
 lamindb/dev/hashing.py,sha256=oYHDSEjINsmDYgCLasnhh_VHbB1dLag27ufVUwDgLyQ,1385
 lamindb/dev/utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
-lamindb/dev/datasets/__init__.py,sha256=FJyzXYPgeQuS898RX7f0NY3o3kZOy1Q6mkp4v2NxS50,1250
-lamindb/dev/datasets/_core.py,sha256=2vyCJ266n0gP084ps83vtsgTdFBApeqFfAbfRdt57_Y,11577
+lamindb/dev/datasets/__init__.py,sha256=0ObE_PmGsxOaCvMYZYkLQLo7zYD6Hr17Ixh53A-jqNs,1310
+lamindb/dev/datasets/_core.py,sha256=6GsgLPavWQPI0K7EIKJ5xq9JXKIxiF1ZNf_1GOABvD0,12426
 lamindb/dev/datasets/_fake.py,sha256=S8mNho-oSh1M9x9oOSsUBLLHmBAegsOLlFk6LnF81EA,942
 lamindb/dev/storage/__init__.py,sha256=S9BtWiqOj54Fiv213ThKqiyTVgEJpo91wVOkpzE1kEk,368
 lamindb/dev/storage/_anndata_sizes.py,sha256=0XVzA6AQeVGPaGPrhGusKyxFgFjeo3qSN29hxb8D5E8,993
@@ -40,8 +40,8 @@ lamindb/schema/__init__.py,sha256=PznznlFvbeNSZKpn1RS6Gv0JMXFkLmU2_ej_1hVLSTs,79
 lamindb/schema/_core.py,sha256=nWR3X_rNd1AbWw3naMiBi8ppAEpqIDyEYqM54feRB_s,766
 lamindb/setup/__init__.py,sha256=8-0F2C4Glx23-b8-D_1CBGgRBM5PppVhazhoXZYOLsg,275
 lamindb/setup/dev/__init__.py,sha256=iD0f2lx_Hgp-udkiPGal7si5waJSOgvnG6Id-g1mMOY,213
-lamindb-0.50.0.dist-info/entry_points.txt,sha256=MioM8vSpKwXxY3geNBwjo1wnwy1l15WjJYlI3lpKuZI,53
-lamindb-0.50.0.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.50.0.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb-0.50.0.dist-info/METADATA,sha256=TF_Yu8wTpbuH-cer9RSA-XY3-pGmF5oAtlDbz-zoy7s,12570
-lamindb-0.50.0.dist-info/RECORD,,
+lamindb-0.50.1.dist-info/entry_points.txt,sha256=MioM8vSpKwXxY3geNBwjo1wnwy1l15WjJYlI3lpKuZI,53
+lamindb-0.50.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.50.1.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.50.1.dist-info/METADATA,sha256=It6LNQR9QYgxitisJK1KcWhRfDhOq5CkcLpqpDhjLuY,12570
+lamindb-0.50.1.dist-info/RECORD,,