lamindb 0.48a2__py3-none-any.whl → 0.48.1__py3-none-any.whl

lamindb/_manager.py

@@ -8,38 +8,45 @@ class Manager(models.Manager):
 
     See Also:
 
+        :class:`lamindb.dev.QuerySet`
         `django Manager <https://docs.djangoproject.com/en/4.2/topics/db/managers/>`__
 
     Examples:
 
-        >>> ln.save(ln.Tag.from_values(["Tag1", "Tag2", "Tag3"], field="name"))
-        >>> tags = ln.Tag.select(name__icontains = "tag").all()
-        >>> ln.Project(name="Project1").save()
-        >>> project = ln.Project.select(name="Project1").one()
-        >>> project.tags.set(tags)
-        >>> manager = project.tags
+        >>> ln.save(ln.Label.from_values(["Label1", "Label2", "Label3"], field="name"))
+        >>> labels = ln.Label.select(name__icontains = "label").all()
+        >>> ln.Label(name="Label1").save()
+        >>> label = ln.Label.select(name="Label1").one()
+        >>> label.parents.set(labels)
+        >>> manager = label.parents
+        >>> manager.df()
     """
 
     def list(self, field: Optional[str] = None):
         """Populate a list with the results.
 
         Examples:
-            >>> ln.save(ln.Tag.from_values(["Tag1", "Tag2", "Tag3"], field="name"))
-            >>> tags = ln.Tag.select(name__icontains = "tag").all()
-            >>> ln.Project(name="Project1").save()
-            >>> project = ln.Project.select(name="Project1").one()
-            >>> project.tags.set(tags)
-            >>> project.tags.list()
-            [Tag(id=sFMcPepC, name=Tag1, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse), # noqa
-            Tag(id=2SscQvsM, name=Tag2, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse), # noqa
-            Tag(id=lecV87vi, name=Tag3, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse)] # noqa
-            >>> project.tags.list("name")
-            ['Tag1', 'Tag2', 'Tag3']
+            >>> ln.save(ln.Label.from_values(["Label1", "Label2", "Label3"], field="name"))
+            >>> labels = ln.Label.select(name__icontains = "label").all()
+            >>> ln.Label(name="Label1").save()
+            >>> label = ln.Label.select(name="Label1").one()
+            >>> label.parents.set(labels)
+            >>> label.parents.list()
+            [Label(id=sFMcPepC, name=Label1, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse), # noqa
+            Label(id=2SscQvsM, name=Label2, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse), # noqa
+            Label(id=lecV87vi, name=Label3, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse)] # noqa
+            >>> label.parents.list("name")
+            ['Label1', 'Label2', 'Label3']
         """
         if field is None:
             return [item for item in self.all()]
         else:
             return [item for item in self.values_list(field, flat=True)]
 
+    def df(self, **kwargs):
+        """Convert to DataFrame."""
+        return self.all().df(**kwargs)
+
 
 setattr(models.Manager, "list", Manager.list)
+setattr(models.Manager, "df", Manager.df)

lamindb/_orm.py

@@ -5,9 +5,9 @@ import pandas as pd
 from django.core.exceptions import FieldDoesNotExist
 from django.db.models import Manager, QuerySet
 from django.db.models.query_utils import DeferredAttribute as Field
-from lamin_logger import logger
-from lamin_logger._lookup import Lookup
-from lamin_logger._search import search as base_search
+from lamin_utils import colors, logger
+from lamin_utils._lookup import Lookup
+from lamin_utils._search import search as base_search
 from lamindb_setup.dev._docs import doc_args
 from lnschema_core import ORM
 from lnschema_core.models import format_datetime
@@ -16,7 +16,9 @@ from lnschema_core.types import ListLike, StrField
 from lamindb.dev.utils import attach_func_to_class_method
 
 from . import _TESTING
+from ._feature_manager import create_features_df
 from ._from_values import _has_species_field, get_or_create_records
+from .dev._settings import settings
 
 IPYTHON = getattr(builtins, "__IPYTHON__", False)
 
@@ -105,7 +107,12 @@ def __init__(orm: ORM, *args, **kwargs):
         super(ORM, orm).__init__(*args, **kwargs)
 
 
-def view_parents(self, field: Optional[StrField] = None, distance: int = 100):
+def view_parents(
+    self,
+    field: Optional[StrField] = None,
+    with_children: bool = False,
+    distance: int = 100,
+):
     from lamindb.dev._view_parents import view_parents as _view_parents
 
     if field is None:
@@ -113,7 +120,9 @@ def view_parents(self, field: Optional[StrField] = None, distance: int = 100):
     if not isinstance(field, str):
         field = field.field.name
 
-    return _view_parents(record=self, field=field, distance=distance)
+    return _view_parents(
+        record=self, field=field, with_children=with_children, distance=distance
+    )
 
 
 @classmethod  # type:ignore
@@ -281,7 +290,7 @@ def _inspect(
     **kwargs,
 ) -> Union["pd.DataFrame", Dict[str, List[str]]]:
     """{}"""
-    from lamin_logger._inspect import inspect
+    from lamin_utils._inspect import inspect
 
     if not isinstance(field, str):
         field = field.field.name
@@ -337,7 +346,7 @@ def _map_synonyms(
     **kwargs,
 ) -> Union[List[str], Dict[str, str]]:
     """{}"""
-    from lamin_logger._map_synonyms import map_synonyms
+    from lamin_utils._map_synonyms import map_synonyms
 
     if field is None:
         field = get_default_str_field(cls)
@@ -388,9 +397,40 @@ def map_synonyms(
     )
 
 
+def _labels_with_feature_names(labels: Union[QuerySet, Manager]) -> Dict:
+    from django.db.models import F
+
+    df = labels.annotate(feature_name=F("feature__name")).df()
+    return df.groupby("feature_name")["name"].apply(list).to_dict()
+
+
 def describe(self):
-    model_name = self.__class__.__name__
+    model_name = colors.green(self.__class__.__name__)
     msg = ""
+
+    def dict_related_model_to_related_name(orm):
+        d: Dict = {
+            f"{i.related_model.__get_schema_name__()}.{i.related_model.__name__}": (
+                i.related_name
+            )
+            for i in orm._meta.related_objects
+            if i.related_name is not None
+        }
+        d.update(
+            {
+                f"{i.related_model.__get_schema_name__()}.{i.related_model.__name__}": (
+                    i.name
+                )
+                for i in orm._meta.many_to_many
+                if i.name is not None
+            }
+        )
+
+        return d
+
+    file_related_models = dict_related_model_to_related_name(self)
+
+    # Display the file record
     fields = self._meta.fields
     direct_fields = []
     foreign_key_fields = []
@@ -399,42 +439,126 @@ def describe(self):
             foreign_key_fields.append(f.name)
         else:
             direct_fields.append(f.name)
+
+    # Display Provenance
     # display line by line the foreign key fields
+    emojis = {"storage": "💾", "created_by": "👤", "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"
 
-        msg += "One/Many-to-One:\n    "
+        msg += f"{colors.green('Provenance')}:\n    "
         related_msg = "".join(
-            [f"🔗 {i}: {self.__getattribute__(i)}\n    " for i in foreign_key_fields]
+            [
+                f"{emojis.get(i, '📎')} {i}: {self.__getattribute__(i)}\n    "
+                for i in foreign_key_fields
+            ]
         )
         msg += related_msg
+    # input of
+    if self.input_of.exists():
+        values = [format_datetime(i.run_at) for i in self.input_of.all()]
+        msg += f"⬇️ input_of ({colors.italic('core.Run')}): {values}\n    "
     msg = msg.rstrip("    ")
 
-    # display many-to-many relationship objects
-    # fields in the model definition
-    related_names = [i.name for i in self._meta.many_to_many]
-    # fields back linked
-    related_names += [i.related_name for i in self._meta.related_objects]
-    msg += "Many-to-Many:\n"
-    for related_name in related_names:
-        related_objects = self.__getattribute__(related_name)
-        count = related_objects.count()
-        if count > 0:
-            try:
-                field = get_default_str_field(related_objects)
-            except ValueError:
-                field = "id"
-            objects_list = list(related_objects.values_list(field, flat=True)[:10])
-            if field == "created_at":
-                objects_list = [format_datetime(i) for i in objects_list]
-            msg_objects = f"    🔗 {related_name} ({count}): {objects_list}\n"
-            if count > 10:
-                msg_objects = msg_objects.replace("]", " ... ]")
-            msg += msg_objects
+    if not self.feature_sets.exists():
+        print(msg)
+        return
+    else:
+        feature_sets_related_models = dict_related_model_to_related_name(
+            self.feature_sets.first()
+        )
+    # Display Features by slot
+    msg += f"{colors.green('Features')}:\n"
+    # var
+    feature_sets = self.feature_sets.exclude(ref_orm="Feature")
+    if feature_sets.exists():
+        for feature_set in feature_sets.all():
+            key = f"{feature_set.ref_schema}.{feature_set.ref_orm}"
+            related_name = feature_sets_related_models.get(key)
+            values = (
+                feature_set.__getattribute__(related_name)
+                .all()[:5]
+                .list(feature_set.ref_field)
+            )
+            slots = self.feature_sets.through.objects.filter(
+                file=self, feature_set=feature_set
+            ).list("slot")
+            for slot in slots:
+                if slot == "var":
+                    slot += " (X)"
+                msg += f"  🗺️ {colors.bold(slot)}:\n"
+                ref = colors.italic(f"{key}.{feature_set.ref_field}")
+                msg += f"    🔗 index ({feature_set.n}, {ref}): {values}\n".replace(
+                    "]", "...]"
+                )
+
+    # obs
+    # ref_orm=Feature, combine all features into one dataframe
+    feature_sets = self.feature_sets.filter(ref_orm="Feature").all()
+    if feature_sets.exists():
+        features_df = create_features_df(
+            file=self, feature_sets=feature_sets.all(), exclude=True
+        )
+        for slot in features_df["slot"].unique():
+            df_slot = features_df[features_df.slot == slot]
+            if slot == "obs":
+                slot += " (metadata)"
+            msg += f"  🗺️ {colors.bold(slot)}:\n"
+            df_label_index = df_slot[
+                (df_slot["labels_orm"] == "Label")
+                & (df_slot["labels_schema"] == "core")
+            ].index
+
+            # for labels
+            if len(df_label_index) > 0:
+                labels_schema = "core"
+                labels_orm = "Label"
+                key = f"{labels_schema}.{labels_orm}"
+                related_name = file_related_models.get(key)
+                related_objects = self.__getattribute__(related_name)
+                labels = _labels_with_feature_names(related_objects)
+                msg_objects = ""
+                for k, v in labels.items():
+                    msg_objects_k = (
+                        f"    🔗 {k} ({len(v)}, {colors.italic(key)}): {v[:5]}\n"
+                    )
+                    if len(v) > 5:
+                        msg_objects_k = msg_objects_k.replace("]", " ... ]")
+                    msg_objects += msg_objects_k
+                msg += msg_objects
+
+            # for non-labels
+            nonlabel_index = df_slot.index.difference(df_label_index)
+            if len(nonlabel_index) == 0:
+                continue
+            df_nonlabels = df_slot.loc[nonlabel_index]
+            df_nonlabels = (
+                df_nonlabels.groupby(["labels_schema", "labels_orm"], group_keys=False)[
+                    "name"
+                ]
+                .apply(lambda x: "|".join(x))
+                .reset_index()
+            )
+            for _, row in df_nonlabels.iterrows():
+                key = f"{row.labels_schema}.{row.labels_orm}"
+                related_name = file_related_models.get(key)
+                related_objects = self.__getattribute__(related_name)
+                count = related_objects.count()
+                count_str = f"{count}, {colors.italic(f'{key}')}"
+                try:
+                    field = get_default_str_field(related_objects)
+                except ValueError:
+                    field = "id"
+                values = list(related_objects.values_list(field, flat=True)[:5])
+                msg_objects = f"    🔗 {row['name']} ({count_str}): {values}\n"
+                msg += msg_objects
     msg = msg.rstrip("\n")
-    msg = msg.rstrip("Many-to-Many:")
-    print(msg)
+    msg = msg.rstrip("Features:")
+    verbosity = settings.verbosity
+    settings.verbosity = 2
+    logger.info(msg)
+    settings.verbosity = verbosity
 
 
 def set_abbr(self, value: str):

lamindb/_queryset.py

@@ -36,10 +36,10 @@ class QuerySet(models.QuerySet):
 
     Examples:
 
-        >>> ln.Tag(name="my tag").save()
-        >>> queryset = ln.Tag.select(name="my tag")
+        >>> ln.Label(name="my label").save()
+        >>> queryset = ln.Label.select(name="my label")
         >>> queryset
-        <QuerySet [Tag(id=MIeZISeF, name=my tag, updated_at=2023-07-19 19:53:34, created_by_id=DzTjkKse)]> # noqa
+        <QuerySet [Label(id=MIeZISeF, name=my label, updated_at=2023-07-19 19:53:34, created_by_id=DzTjkKse)]> # noqa
     """
 
     def df(self, include: Optional[List[str]] = None):
@@ -52,27 +52,27 @@ class QuerySet(models.QuerySet):
 
         Args:
             include: ``Optional[List[str]] = None`` Additional (many-to-many)
-                fields to include. Takes expressions like ``"tags__name"``
+                fields to include. Takes expressions like ``"labels__name"``
                 ``"cell_types__name"``.
 
         Examples:
 
-            >>> ln.save(ln.Project.from_values(["Project1", "Project2", "Project3"], field="name")) # noqa
-            >>> ln.Project.select().df()
+            >>> ln.save(ln.Label.from_values(["Label1", "Label2", "Label3"], field="name")) # noqa
+            >>> ln.Label.select().df()
                           name  external_id           updated_at  created_by_id
                   id
-            wsCyIq2Z  Project1         None  2023-07-19 19:14:08       DzTjkKse
-            MvpDP8Y3  Project2         None  2023-07-19 19:14:08       DzTjkKse
-            zKFFabCu  Project3         None  2023-07-19 19:14:08       DzTjkKse
-            >>> project = ln.Project.select(name="Project1").one()
-            >>> tag = ln.Tag.select(name="benchmark").one()
-            >>> project.tags.add(tag)
-            >>> ln.Project.select().df(include=["tags__name", "tags__created_by_id"])
-                      tags__name  tags__created_by_id      name  external_id           updated_at  created_by_id # noqa
+            wsCyIq2Z  Label1         None  2023-07-19 19:14:08       DzTjkKse
+            MvpDP8Y3  Label2         None  2023-07-19 19:14:08       DzTjkKse
+            zKFFabCu  Label3         None  2023-07-19 19:14:08       DzTjkKse
+            >>> label = ln.Label.select(name="Label1").one()
+            >>> label = ln.Label.select(name="benchmark").one()
+            >>> label.parents.add(label)
+            >>> ln.Label.select().df(include=["labels__name", "labels__created_by_id"])
+                      labels__name  labels__created_by_id      name  external_id           updated_at  created_by_id # noqa
                   id
-            wsCyIq2Z  [benchmark]          [DzTjkKse]  Project1         None  2023-07-19 19:14:08       DzTjkKse # noqa
-            MvpDP8Y3         None                None  Project2         None  2023-07-19 19:14:08       DzTjkKse # noqa
-            zKFFabCu         None                None  Project3         None  2023-07-19 19:14:08       DzTjkKse # noqa
+            wsCyIq2Z  [benchmark]          [DzTjkKse]  Label1         None  2023-07-19 19:14:08       DzTjkKse # noqa
+            MvpDP8Y3         None                None  Label2         None  2023-07-19 19:14:08       DzTjkKse # noqa
+            zKFFabCu         None                None  Label3         None  2023-07-19 19:14:08       DzTjkKse # noqa
         """
         data = self.values()
         if len(data) > 0:
@@ -100,6 +100,8 @@ class QuerySet(models.QuerySet):
             df.run_at = format_and_convert_to_local_time(df.run_at)
         if "id" in df.columns:
             df = df.set_index("id")
+        if len(df) == 0:
+            return df
         if include is not None:
             if isinstance(include, str):
                 include = [include]
@@ -121,7 +123,7 @@ class QuerySet(models.QuerySet):
                     if field.field.model != ORM
                     else field.field.related_model
                 )
-                if field.field.model == related_ORM:
+                if ORM == related_ORM:
                     left_side_link_model = f"from_{ORM.__name__.lower()}"
                     values_expression = f"to_{ORM.__name__.lower()}__{lookup_str}"
                 else:
@@ -135,7 +137,7 @@ class QuerySet(models.QuerySet):
                 link_groupby = link_df.groupby(left_side_link_model)[
                     values_expression
                 ].apply(list)
-                df = pd.concat((link_groupby, df), axis=1)
+                df = pd.concat((link_groupby, df), axis=1, join="inner")
                 df.rename(columns={values_expression: expression}, inplace=True)
         return df
 
@@ -144,14 +146,14 @@ class QuerySet(models.QuerySet):
 
         Examples:
 
-            >>> ln.save(ln.Project.from_values(["Project1", "Project2", "Project3"], field="name")) # noqa
-            >>> queryset = ln.Project.select(name__icontains = "project")
+            >>> ln.save(ln.Label.from_values(["Label1", "Label2", "Label3"], field="name")) # noqa
+            >>> queryset = ln.Label.select(name__icontains = "project")
             >>> queryset.list()
-            [Project(id=NAgTZxoo, name=Project1, updated_at=2023-07-19 19:25:48, created_by_id=DzTjkKse), # noqa
-            Project(id=bnsAgKRC, name=Project2, updated_at=2023-07-19 19:25:48, created_by_id=DzTjkKse), # noqa
-            Project(id=R8xhAJNE, name=Project3, updated_at=2023-07-19 19:25:48, created_by_id=DzTjkKse)] # noqa
+            [Label(id=NAgTZxoo, name=Label1, updated_at=2023-07-19 19:25:48, created_by_id=DzTjkKse), # noqa
+            Label(id=bnsAgKRC, name=Label2, updated_at=2023-07-19 19:25:48, created_by_id=DzTjkKse), # noqa
+            Label(id=R8xhAJNE, name=Label3, updated_at=2023-07-19 19:25:48, created_by_id=DzTjkKse)] # noqa
             >>> queryset.list("name")
-            ['Project1', 'Project2', 'Project3']
+            ['Label1', 'Label2', 'Label3']
         """
         if field is None:
             return [item for item in self]
@@ -162,10 +164,10 @@ class QuerySet(models.QuerySet):
         """If non-empty, the first result in the query set, otherwise None.
 
         Examples:
-            >>> ln.save(ln.Project.from_values(["Project1", "Project2", "Project3"], field="name")) # noqa
-            >>> queryset = ln.Project.select(name__icontains = "project")
+            >>> ln.save(ln.Label.from_values(["Label1", "Label2", "Label3"], field="name")) # noqa
+            >>> queryset = ln.Label.select(name__icontains = "project")
             >>> queryset.first()
-            Project(id=NAgTZxoo, name=Project1, updated_at=2023-07-19 19:25:48, created_by_id=DzTjkKse) # noqa
+            Label(id=NAgTZxoo, name=Label1, updated_at=2023-07-19 19:25:48, created_by_id=DzTjkKse) # noqa
         """
         if len(self) == 0:
             return None
@@ -175,9 +177,9 @@ class QuerySet(models.QuerySet):
         """Exactly one result. Throws error if there are more or none.
 
         Examples:
-            >>> ln.Tag(name="benchmark").save()
-            >>> ln.Tag.select(name="benchmark").one()
-            Tag(id=gznl0GZk, name=benchmark, updated_at=2023-07-19 19:39:01, created_by_id=DzTjkKse) # noqa
+            >>> ln.Label(name="benchmark").save()
+            >>> ln.Label.select(name="benchmark").one()
+            Label(id=gznl0GZk, name=benchmark, updated_at=2023-07-19 19:39:01, created_by_id=DzTjkKse) # noqa
         """
         if len(self) == 0:
             raise NoResultFound
@@ -190,10 +192,10 @@ class QuerySet(models.QuerySet):
         """At most one result. Returns it if there is one, otherwise returns None.
 
         Examples:
-            >>> ln.Tag(name="benchmark").save()
-            >>> ln.Tag.select(name="benchmark").one_or_none()
-            Tag(id=gznl0GZk, name=benchmark, updated_at=2023-07-19 19:39:01, created_by_id=DzTjkKse) # noqa
-            >>> ln.Tag.select(name="non existing tag").one_or_none()
+            >>> ln.Label(name="benchmark").save()
+            >>> ln.Label.select(name="benchmark").one_or_none()
+            Label(id=gznl0GZk, name=benchmark, updated_at=2023-07-19 19:39:01, created_by_id=DzTjkKse) # noqa
+            >>> ln.Label.select(name="non existing label").one_or_none()
             None
         """
         if len(self) == 0:

lamindb/_save.py

@@ -7,7 +7,7 @@ from typing import Iterable, List, Optional, Tuple, Union, overload  # noqa
 
 import lamindb_setup
 from django.db import transaction
-from lamin_logger import logger
+from lamin_utils import logger
 from lnschema_core.models import ORM, File
 
 from lamindb.dev.storage import store_object
@@ -45,7 +45,7 @@ def save(records: Iterable[ORM], **kwargs) -> None:  # type: ignore
         Save a collection of records in one transaction, which is much faster
         than writing a loop over calls ``projects.save()``:
 
-        >>> projects = [ln.Project(f"Project {i}") for i in range(10)]
+        >>> labels = [ln.Label(f"Label {i}") for i in range(10)]
         >>> ln.save(projects)
 
         For a single record, use ``.save()``:
@@ -76,13 +76,23 @@ def save(records: Iterable[ORM], **kwargs) -> None:  # type: ignore
         non_files_with_parents = {r for r in non_files if hasattr(r, "_parents")}
 
         if len(non_files_with_parents) > 0 and kwargs.get("parents") is not False:
-            # save the record with parents one by one
-            logger.warning(
-                "Now recursing through parents: "
-                "this only happens once, but is much slower than bulk saving"
-            )
-            for record in non_files_with_parents:
-                record._save_ontology_parents()
+            # this can only happen within lnschema_bionty right now!!
+            # we might extend to core lamindb later
+            import lnschema_bionty as lb
+
+            if kwargs.get("parents") or (
+                kwargs.get("parents") is None and lb.settings.auto_save_parents
+            ):
+                # save the record with parents one by one
+                logger.warning(
+                    "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"
+                )
+                for record in non_files_with_parents:
+                    record._save_ontology_parents()
 
     if files:
         with transaction.atomic():

lamindb/_transform.py

@@ -1,19 +1,28 @@
+import hashlib
+
 from lnschema_core.ids import base62
 from lnschema_core.models import Transform
 
+from .dev.hashing import to_b64_str
+
 
 def __init__(transform, *args, **kwargs):
     if len(args) > 0:  # initialize with all fields from db as args
         super(Transform, transform).__init__(*args, **kwargs)
         return None
     else:  # user-facing calling signature
+        if "version" not in kwargs:
+            kwargs["version"] = "0"
+        elif not isinstance(kwargs["version"], str):
+            raise ValueError("version must be str, e.g., '0', '1', etc.")
+        id_ext = to_b64_str(hashlib.md5(kwargs["version"].encode()).digest())[:2]
         # set default ids
         if "id" not in kwargs and "stem_id" not in kwargs:
-            kwargs["id"] = base62(14)
-            kwargs["stem_id"] = kwargs["id"][:12]
+            kwargs["stem_id"] = base62(12)
+            kwargs["id"] = kwargs["stem_id"] + id_ext
         elif "stem_id" in kwargs:
             assert isinstance(kwargs["stem_id"], str) and len(kwargs["stem_id"]) == 12
-            kwargs["id"] = kwargs["stem_id"] + base62(2)
+            kwargs["id"] = kwargs["stem_id"] + id_ext
         elif "id" in kwargs:
             assert isinstance(kwargs["id"], str) and len(kwargs["id"]) == 14
             kwargs["stem_id"] = kwargs["id"][:12]

lamindb/_view.py

@@ -3,7 +3,7 @@ import inspect
 from typing import List, Optional
 
 from IPython.display import display
-from lamin_logger import colors
+from lamin_utils import colors
 from lamindb_setup import settings
 from lamindb_setup.dev._setup_schema import get_schema_module_name
 from lnschema_core import ORM

lamindb/dev/__init__.py

@@ -6,16 +6,20 @@
    ORM
    QuerySet
    Manager
+   FeatureManager
    datasets
    hashing
    storage
    Settings
+   run_context
 """
 
 from lnschema_core.models import ORM
 
+from lamindb._feature_manager import FeatureManager
 from lamindb._manager import Manager
 from lamindb._queryset import QuerySet
 
+from .._context import run_context
 from . import datasets  # noqa
 from ._settings import Settings

lamindb/dev/_settings.py

@@ -2,7 +2,7 @@ from pathlib import Path
 from typing import Literal, Mapping, Tuple, Union
 
 import lamindb_setup as ln_setup
-from lamin_logger import logger
+from lamin_utils import logger
 from upath import UPath