lamindb 0.67.0__tar.gz → 0.67.1__tar.gz

{lamindb-0.67.0 → lamindb-0.67.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.67.0
+Version: 0.67.1
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -12,7 +12,7 @@ Classifier: Programming Language :: Python :: 3.11
 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==0.38.3 ; 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-0.67.0 → lamindb-0.67.1}/docs/changelog.md

@@ -7,6 +7,14 @@
 
 ## 0.67
 
+### 0.67.1 {small}`2024-01-12`
+
+- 🐛 Fix idempotency of `collection.save()` [PR](https://github.com/laminlabs/lamindb/pull/1401) [@falexwolf](https://github.com/falexwolf)
+- 🩹 Also amend run [PR](https://github.com/laminlabs/lamindb/pull/1399) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Disallow bulk-delete for Artifact, Transform & Collection [PR](https://github.com/laminlabs/lamindb/pull/1398) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Init transform versions at 1 [PR](https://github.com/laminlabs/lamindb/pull/1397) [@falexwolf](https://github.com/falexwolf)
+- ✨ Load json and html files [PR](https://github.com/laminlabs/lamindb/pull/1396) [@falexwolf](https://github.com/falexwolf)
+
 ### 0.67.0 {small}`2024-01-11`
 
 - 🚚 Rename `.bionty` to `.public`, `.from_bionty` to `.from_public` [PR](https://github.com/laminlabs/lamindb/pull/1394) [@sunnyosun](https://github.com/sunnyosun)

{lamindb-0.67.0 → lamindb-0.67.1}/lamindb/__init__.py

@@ -54,7 +54,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.67.0"  # 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-0.67.0 → lamindb-0.67.1}/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-0.67.0 → lamindb-0.67.1}/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-0.67.0 → lamindb-0.67.1}/lamindb/_from_values.py

@@ -173,20 +173,20 @@ def create_records_from_public(
 
     # create the corresponding bionty object from model
     try:
-        bionty_object = model.public(
+        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 public_source record to the kwargs
-    kwargs.update({"public_source": get_public_source_record(bionty_object)})
+    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-0.67.0 → lamindb-0.67.1}/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-0.67.0 → lamindb-0.67.1}/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-0.67.0 → lamindb-0.67.1}/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-0.67.0 → lamindb-0.67.1}/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-0.67.0 → lamindb-0.67.1}/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-0.67.0 → lamindb-0.67.1}/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-0.67.0 → lamindb-0.67.1}/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-0.67.0 → lamindb-0.67.1}/pyproject.toml

@@ -19,7 +19,7 @@ dependencies = [
     "lnschema_core==0.61.1",
     "lamindb_setup==0.64.2",
     "lamin_utils==0.13.0",
-    "lamin_cli==0.6.0",
+    "lamin_cli==0.6.1",
     # others
     "rapidfuzz",
     "pyarrow",
@@ -37,7 +37,7 @@ Home = "https://github.com/laminlabs/lamindb"
 
 [project.optional-dependencies]
 bionty = [
-    "lnschema_bionty==0.38.3",
+    "lnschema_bionty==0.39.0",
 ]
 aws = [
     "botocore==1.31.17",  # for aiobotocore inside s3fs, to fix deps resolution
@@ -51,7 +51,7 @@ gcp = [
     "fsspec[gs]==2023.9.0"
 ]
 jupyter = [
-    "nbproject==0.9.2",  # keep pinning
+    "nbproject==0.10.0",  # keep pinning
     "nbstripout",
     "nbconvert",
 ]

lamindb-0.67.1/sub/lamin-cli/lamin_cli/__init__.py

@@ -0,0 +1,3 @@
+"""Lamin CLI."""
+
+__version__ = "0.6.1"

{lamindb-0.67.0 → lamindb-0.67.1}/sub/lamin-cli/lamin_cli/_transform.py

@@ -13,7 +13,7 @@ def init_script_metadata(script_path: str):
     from lnschema_core.ids import base62_12
 
     stem_uid = base62_12()
-    version = "0"
+    version = "1"
 
     with open(script_path) as f:
         content = f.read()
@@ -331,7 +331,7 @@ def save(filepath: str) -> Optional[str]:
         else:
             report_file = ln.Artifact(
                 filepath_html,
-                description=f"Report of transform {transform.uid}",
+                description=f"Report of run {run.uid}",
                 is_new_version_of=initial_report,
                 visibility=0,  # hidden file
             )

{lamindb-0.67.0 → lamindb-0.67.1}/sub/lnschema-bionty/docs/changelog.md

@@ -3,6 +3,8 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+⬆️ Rename Bionty to PublicOntology | [214](https://github.com/laminlabs/lnschema-bionty/pull/214) | [sunnyosun](https://github.com/sunnyosun) | 2024-01-12 | 0.39.0
+✏️ Fix encoding | [213](https://github.com/laminlabs/lnschema-bionty/pull/213) | [sunnyosun](https://github.com/sunnyosun) | 2024-01-12 | 0.38.4
 🚑️ Re-encode PublicSource | [212](https://github.com/laminlabs/lnschema-bionty/pull/212) | [sunnyosun](https://github.com/sunnyosun) | 2024-01-10 | 0.38.3
 🔊 Remove logging | [211](https://github.com/laminlabs/lnschema-bionty/pull/211) | [sunnyosun](https://github.com/sunnyosun) | 2024-01-10 | 0.38.2
 ⚡️ Speed up previous migration | [210](https://github.com/laminlabs/lnschema-bionty/pull/210) | [sunnyosun](https://github.com/sunnyosun) | 2024-01-10 | 0.38.1

{lamindb-0.67.0 → lamindb-0.67.1}/sub/lnschema-bionty/lnschema_bionty/__init__.py

@@ -79,7 +79,7 @@ Developer API:
    dev
 """
 
-__version__ = "0.38.3"  # Denote a release candidate of version 0.1.0 with 0.1rc1
+__version__ = "0.39.0"  # Denote a release candidate of version 0.1.0 with 0.1rc1
 
 from lamindb_setup import _check_instance_setup
 

{lamindb-0.67.0 → lamindb-0.67.1}/sub/lnschema-bionty/lnschema_bionty/_bionty.py

@@ -44,12 +44,12 @@ def create_or_get_organism_record(organism: Optional[Union[str, Registry]], orm:
     return organism_record
 
 
-def get_public_source_record(bionty_object: bt.Bionty):
+def get_public_source_record(public_ontology: bt.PublicOntology):
     kwargs = dict(
-        entity=bionty_object.__class__.__name__,
-        organism=bionty_object.organism,
-        source=bionty_object.source,
-        version=bionty_object.version,
+        entity=public_ontology.__class__.__name__,
+        organism=public_ontology.organism,
+        source=public_ontology.source,
+        version=public_ontology.version,
     )
     from .models import PublicSource
 
@@ -66,36 +66,36 @@ def encode_uid(orm: Registry, kwargs: dict):
     except AttributeError:
         name = orm.__class__.__name__.lower()
     ontology = False
-    str_to_encode = ""
+    str_to_encode = None
     if name == "gene":
-        str_to_encode = kwargs.get("ensembl_gene_id", "")
-        if str_to_encode == "":
-            str_to_encode = kwargs.get("stable_id", "")
-        if str_to_encode == "":
-            str_to_encode = kwargs.get("symbol", "")
-        if str_to_encode == "":
+        str_to_encode = kwargs.get("ensembl_gene_id")
+        if str_to_encode is None or str_to_encode == "":
+            str_to_encode = kwargs.get("stable_id")
+        if str_to_encode is None or str_to_encode == "":
+            str_to_encode = kwargs.get("symbol")
+        if str_to_encode is None or str_to_encode == "":
             raise AssertionError("must provide ensembl_gene_id, stable_id or symbol")
     elif name == "protein":
-        str_to_encode = kwargs.get("uniprotkb_id", "")
-        if str_to_encode == "":
-            str_to_encode = kwargs.get("name", "")
-        if str_to_encode == "":
+        str_to_encode = kwargs.get("uniprotkb_id")
+        if str_to_encode is None or str_to_encode == "":
+            str_to_encode = kwargs.get("name")
+        if str_to_encode is None or str_to_encode == "":
             raise AssertionError("must provide uniprotkb_id or name")
     elif name == "cellmarker":
-        str_to_encode = kwargs.get("name", "")
-        if str_to_encode == "":
+        str_to_encode = kwargs.get("name")
+        if str_to_encode is None or str_to_encode == "":
             raise AssertionError("must provide name")
     elif name == "publicsource":
         str_to_encode = f'{kwargs.get("entity", "")}{kwargs.get("source", "")}{kwargs.get("organism", "")}{kwargs.get("version", "")}'  # noqa
     else:
-        str_to_encode = kwargs.get("ontology_id", "")
-        if str_to_encode == "":
-            str_to_encode = kwargs.get("name", "")
-        if str_to_encode == "":
+        str_to_encode = kwargs.get("ontology_id")
+        if str_to_encode is None or str_to_encode == "":
+            str_to_encode = kwargs.get("name")
+        if str_to_encode is None or str_to_encode == "":
             raise AssertionError("must provide ontology_id or name")
         ontology = True
 
-    if len(str_to_encode) > 0:
+    if str_to_encode is not None and len(str_to_encode) > 0:
         if ontology:
             id_encoder = ids.ontology
         else:
@@ -122,8 +122,8 @@ def lookup2kwargs(orm: Registry, *args, **kwargs) -> Dict:
         organism_record = create_or_get_organism_record(orm=orm.__class__, organism=kwargs.get("organism"))
         if organism_record is not None:
             bionty_kwargs["organism"] = organism_record
-        bionty_object = getattr(bt, orm.__class__.__name__)(organism=organism_record.name if organism_record is not None else None)
-        bionty_kwargs["public_source"] = get_public_source_record(bionty_object)
+        public_ontology = getattr(bt, orm.__class__.__name__)(organism=organism_record.name if organism_record is not None else None)
+        bionty_kwargs["public_source"] = get_public_source_record(public_ontology)
 
         model_field_names = {i.name for i in orm._meta.fields}
         model_field_names.add("parents")

{lamindb-0.67.0 → lamindb-0.67.1}/sub/lnschema-bionty/lnschema_bionty/models.py

@@ -1,7 +1,8 @@
-from typing import List, Optional, Tuple, TypeAlias, Union, overload  # noqa
+from typing import List, Optional, Tuple, Union, overload  # noqa
 
 import bionty as bt
 import numpy as np
+from bionty import PublicOntology
 from django.db import models
 from lamin_utils import logger
 from lnschema_core.models import CanValidate, HasParents, Registry, User
@@ -10,8 +11,6 @@ from lnschema_core.users import current_user_id
 from . import ids
 from ._bionty import encode_uid, lookup2kwargs
 
-PublicOntology: TypeAlias = bt.Bionty
-
 
 class BioRegistry(Registry, HasParents, CanValidate):
     """Base Registry of lnschema_bionty.
@@ -88,28 +87,28 @@ class BioRegistry(Registry, HasParents, CanValidate):
         public_source: Optional["PublicSource"] = None,
         **kwargs,
     ) -> "PublicOntology":
-        """The corresponding Bionty object.
+        """The corresponding PublicOntology object.
 
-        e.g. lnschema_bionty.CellType.public() is equivalent to bionty.CellType().
         Note that the public source is auto-configured and tracked via :meth:`lnschema_bionty.PublicSource`.
 
         See Also:
-            `Bionty <https://lamin.ai/docs/public-ontologies>`__
+            `PublicOntology <https://lamin.ai/docs/public-ontologies>`__
 
         Examples:
             >>> celltype_pub = lb.CellType.public()
             >>> celltype_pub
-            CellType
+            PublicOntology
+            Entity: CellType
             Organism: all
             Source: cl, 2023-04-20
             #terms: 2698
             ...
-            📖 CellType.df(): ontology reference table
-            🔎 CellType.lookup(): autocompletion of terms
-            🎯 CellType.search(): free text search of terms
-            🧐 CellType.inspect(): check if identifiers are mappable
-            👽 CellType.standardize(): map synonyms to standardized names
-            🔗 CellType.ontology: Pronto.Ontology object
+            📖 .df(): ontology reference table
+            🔎 .lookup(): autocompletion of terms
+            🎯 .search(): free text search of terms
+            🧐 .inspect(): check if identifiers are mappable
+            👽 .standardize(): map synonyms to standardized names
+            🔗 .to_pronto(): Pronto.Ontology object
         """
         if cls.__module__.startswith("lnschema_bionty."):
             # backward compat with renaming species to organism
@@ -129,9 +128,8 @@ class BioRegistry(Registry, HasParents, CanValidate):
                     organism = organism if lb.settings.organism is None else lb.settings.organism.name
                 source = None
                 version = None
-            bionty_object = getattr(bt, cls.__name__)(organism=organism, source=source, version=version)
 
-            return bionty_object
+            return getattr(bt, cls.__name__)(organism=organism, source=source, version=version)
 
     @classmethod
     def from_public(cls, **kwargs) -> Optional[Union["BioRegistry", List["BioRegistry"]]]:

{lamindb-0.67.0 → lamindb-0.67.1}/sub/lnschema-bionty/pyproject.toml

@@ -15,7 +15,7 @@ classifiers = [
 ]
 dependencies = [
     "lnschema_core>=0.58.0",
-    "bionty==0.35.2",
+    "bionty==0.36.0",
 ]
 
 [project.urls]