lamindb 0.74.2__tar.gz → 0.74.3__tar.gz

{lamindb-0.74.2 → lamindb-0.74.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.74.2
+Version: 0.74.3
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -10,7 +10,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Requires-Dist: lnschema_core==0.70.5
-Requires-Dist: lamindb_setup==0.74.1
+Requires-Dist: lamindb_setup==0.74.2
 Requires-Dist: lamin_utils==0.13.2
 Requires-Dist: lamin_cli==0.15.0
 Requires-Dist: rapidfuzz
@@ -24,7 +24,7 @@ Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.44.2 ; extra == "bionty"
+Requires-Dist: bionty==0.44.3 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"
@@ -37,7 +37,7 @@ Requires-Dist: faker-biology ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=1.1.8 ; extra == "fcs"
 Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
-Requires-Dist: nbproject==0.10.3 ; extra == "jupyter"
+Requires-Dist: nbproject==0.10.4 ; extra == "jupyter"
 Requires-Dist: nbstripout==0.6.1 ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"

{lamindb-0.74.2 → lamindb-0.74.3}/docs/api.md

@@ -34,6 +34,4 @@ wetlab
 
 bionty-base
 readfcs
-nbproject
-lamin-utils
 ```

{lamindb-0.74.2 → lamindb-0.74.3}/lamindb/__init__.py

@@ -42,7 +42,7 @@ Modules & settings:
 """
 
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "0.74.2"
+__version__ = "0.74.3"
 
 import os as _os
 

{lamindb-0.74.2 → lamindb-0.74.3}/lamindb/_record.py

@@ -529,12 +529,7 @@ def save(self, *args, **kwargs) -> Record:
     if result is not None:
         init_self_from_db(self, result)
     else:
-        # here, we can't use the parents argument
-        # parents are not saved for the self record
-        save_kwargs = kwargs.copy()
-        if "parents" in save_kwargs:
-            save_kwargs.pop("parents")
-        super(Record, self).save(*args, **save_kwargs)
+        super(Record, self).save(*args, **kwargs)
     # perform transfer of many-to-many fields
     # only supported for Artifact and Collection records
     if db is not None and db != "default" and using_key is None:
@@ -554,16 +549,8 @@ def save(self, *args, **kwargs) -> Record:
             self_on_db._state.db = db
             self_on_db.pk = pk_on_db  # manually set the primary key
             self_on_db.features = FeatureManager(self_on_db)
-            # by default, transfer parents of the labels to maintain ontological hierarchy
-            try:
-                import bionty as bt
-
-                parents = kwargs.get("parents", bt.settings.auto_save_parents)
-            except ImportError:
-                parents = kwargs.get("parents", True)
-            add_from_kwargs = {"parents": parents}
-            self.features._add_from(self_on_db, **add_from_kwargs)
-            self.labels.add_from(self_on_db, **add_from_kwargs)
+            self.features._add_from(self_on_db)
+            self.labels.add_from(self_on_db)
     return self
 
 

{lamindb-0.74.2 → lamindb-0.74.3}/lamindb/_save.py

@@ -27,9 +27,7 @@ if TYPE_CHECKING:
     from lamindb_setup.core.upath import UPath
 
 
-def save(
-    records: Iterable[Record], ignore_conflicts: bool | None = False, **kwargs
-) -> None:
+def save(records: Iterable[Record], ignore_conflicts: bool | None = False) -> None:
     """Bulk save to registries & storage.
 
     Note:
@@ -47,7 +45,6 @@ def save(
            unique or another constraint. However, it won't inplace update the id
            fields of records. If you need records with ids, you need to query
            them from the database.
-        **kwargs: Get kwargs related to parents.
 
     Examples:
 
@@ -87,27 +84,12 @@ def save(
         non_artifacts_with_parents = [
             r for r in non_artifacts_new if hasattr(r, "_parents")
         ]
-        if len(non_artifacts_with_parents) > 0 and kwargs.get("parents") is not False:
+        if len(non_artifacts_with_parents) > 0:
             # this can only happen within lnschema_bionty right now!!
             # we might extend to core lamindb later
-            import bionty as bt
-
-            if kwargs.get("parents") or (
-                kwargs.get("parents") is None and bt.settings.auto_save_parents
-            ):
-                mute = False if kwargs.get("mute") is None else kwargs.get("mute")
-                if not mute:
-                    # 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: bt.settings.auto_save_parents ="
-                        " False"
-                    )
-                for record in non_artifacts_with_parents:
-                    record._save_ontology_parents(mute=True)
+            from lnschema_bionty.core import add_ontology
+
+            add_ontology(non_artifacts_with_parents)
 
     if artifacts:
         with transaction.atomic():

{lamindb-0.74.2 → lamindb-0.74.3}/lamindb/core/_feature_manager.py

@@ -770,7 +770,7 @@ def _add_set_from_mudata(
     self._host.save()
 
 
-def _add_from(self, data: HasFeatures, parents: bool = True):
+def _add_from(self, data: HasFeatures):
     """Transfer features from a artifact or collection."""
     # This only covers feature sets, though.
     using_key = settings._using_key
@@ -782,23 +782,18 @@ def _add_from(self, data: HasFeatures, parents: bool = True):
         # note here the features are transferred based on an unique field
         field = REGISTRY_UNIQUE_FIELD.get(registry.__name__.lower(), "uid")
         # TODO: get a default ID field for the registry
-        if hasattr(registry, "ontology_id") and parents:
+        if hasattr(registry, "ontology_id"):
             field = "ontology_id"
         elif hasattr(registry, "ensembl_gene_id"):
             field = "ensembl_gene_id"
         elif hasattr(registry, "uniprotkb_id"):
             field = "uniprotkb_id"
-
-        if registry.__get_name_with_schema__() == "bionty.Organism":
-            parents = False
         # this will be e.g. be a list of ontology_ids or uids
         member_uids = list(members.values_list(field, flat=True))
-        # create records from ontology_id in order to populate parents
-        if field == "ontology_id" and len(member_uids) > 0 and parents:
+        # create records from ontology_id
+        if field == "ontology_id" and len(member_uids) > 0:
             # create from bionty
-            records = registry.from_values(member_uids, field=field)
-            if len(records) > 0:
-                save(records, parents=parents)
+            save(registry.from_values(member_uids, field=field))
         validated = registry.validate(member_uids, field=field, mute=True)
         new_members_uids = list(compress(member_uids, ~validated))
         new_members = members.filter(**{f"{field}__in": new_members_uids}).all()
@@ -814,7 +809,7 @@ def _add_from(self, data: HasFeatures, parents: bool = True):
                 # in the previous step transfer_fk_to_default_db_bulk
                 transfer_to_default_db(feature, using_key, mute=mute, transfer_fk=False)
             logger.info(f"saving {n_new_members} new {registry.__name__} records")
-            save(new_members, parents=parents)
+            save(new_members)
 
         # create a new feature set from feature values using the same uid
         feature_set_self = FeatureSet.from_values(

{lamindb-0.74.2 → lamindb-0.74.3}/lamindb/core/_label_manager.py

@@ -76,32 +76,28 @@ def print_labels(self: HasFeatures, field: str = "name", print_types: bool = Fal
 
 
 # Alex: is this a label transfer function?
-def validate_labels(labels: QuerySet | list | dict, parents: bool = True):
+def validate_labels(labels: QuerySet | list | dict):
     def validate_labels_registry(
-        labels: QuerySet | list | dict, parents: bool = True
+        labels: QuerySet | list | dict,
     ) -> tuple[list[str], list[str]]:
         if len(labels) == 0:
             return [], []
         registry = labels[0].__class__
         field = REGISTRY_UNIQUE_FIELD.get(registry.__name__.lower(), "uid")
-        if hasattr(registry, "ontology_id") and parents:
+        if hasattr(registry, "ontology_id"):
             field = "ontology_id"
         elif hasattr(registry, "ensembl_gene_id"):
             field = "ensembl_gene_id"
         elif hasattr(registry, "uniprotkb_id"):
             field = "uniprotkb_id"
-        if registry.__get_name_with_schema__() == "bionty.Organism":
-            parents = False
         # if the field value is None, use uid field
         label_uids = np.array(
             [getattr(label, field) for label in labels if label is not None]
         )
-        # save labels from ontology_ids so that parents are populated
+        # save labels from ontology_ids
         if field == "ontology_id" and len(label_uids) > 0:
             try:
-                records = registry.from_values(label_uids, field=field)
-                if len(records) > 0:
-                    save(records, parents=parents)
+                save(registry.from_values(label_uids, field=field))
             except Exception:  # noqa S110
                 pass
             field = "uid"
@@ -117,11 +113,9 @@ def validate_labels(labels: QuerySet | list | dict, parents: bool = True):
     if isinstance(labels, Dict):
         result = {}
         for registry, labels_registry in labels.items():
-            result[registry] = validate_labels_registry(
-                labels_registry, parents=parents
-            )
+            result[registry] = validate_labels_registry(labels_registry)
     else:
-        return validate_labels_registry(labels, parents=parents)
+        return validate_labels_registry(labels)
 
 
 class LabelManager:
@@ -176,7 +170,7 @@ class LabelManager:
 
         return get_labels(self._host, feature=feature, mute=mute, flat_names=flat_names)
 
-    def add_from(self, data: HasFeatures, parents: bool = True) -> None:
+    def add_from(self, data: HasFeatures) -> None:
         """Add labels from an artifact or collection to another artifact or collection.
 
         Examples:
@@ -202,7 +196,7 @@ class LabelManager:
                 data_name_lower = data.__class__.__name__.lower()
                 labels_by_features = defaultdict(list)
                 features = set()
-                _, new_labels = validate_labels(labels, parents=parents)
+                _, new_labels = validate_labels(labels)
                 if len(new_labels) > 0:
                     transfer_fk_to_default_db_bulk(new_labels, using_key)
                 for label in labels:
@@ -237,7 +231,7 @@ class LabelManager:
                         transfer_to_default_db(
                             feature, using_key, mute=True, transfer_fk=False
                         )
-                    save(new_features, parents=parents)
+                    save(new_features)
                 if hasattr(self._host, related_name):
                     for feature_name, labels in labels_by_features.items():
                         if feature_name is not None:

{lamindb-0.74.2 → lamindb-0.74.3}/lamindb/core/datasets/_core.py

@@ -185,8 +185,6 @@ def anndata_mouse_sc_lymph_node(
 
         verbosity = ln.settings.verbosity
         ln.settings.verbosity = "error"
-        auto_save_parents = bt.settings.auto_save_parents
-        bt.settings.auto_save_parents = False
         # strain
         bt.ExperimentalFactor.from_public(ontology_id="EFO:0004472").save()
         # developmental stage
@@ -215,7 +213,6 @@ def anndata_mouse_sc_lymph_node(
             labels += [ln.ULabel(name=name) for name in adata.obs[col]]
         ln.save(labels)
         ln.settings.verbosity = verbosity
-        bt.settings.auto_save_parents = auto_save_parents
 
     return adata
 
@@ -313,8 +310,6 @@ def anndata_human_immune_cells(
 
         verbosity = ln.settings.verbosity
         ln.settings.verbosity = "error"
-        auto_save_parents = bt.settings.auto_save_parents
-        bt.settings.auto_save_parents = False
         ln.save(
             bt.Gene.from_values(
                 adata.var.index, field="ensembl_gene_id", organism="human"
@@ -331,7 +326,6 @@ def anndata_human_immune_cells(
         bt.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
-        bt.settings.auto_save_parents = auto_save_parents
     return adata
 
 

{lamindb-0.74.2 → lamindb-0.74.3}/pyproject.toml

@@ -17,7 +17,7 @@ classifiers = [
 dependencies = [
     # Lamin PINNED packages
     "lnschema_core==0.70.5",
-    "lamindb_setup==0.74.1",
+    "lamindb_setup==0.74.2",
     "lamin_utils==0.13.2",
     "lamin_cli==0.15.0",
     # others
@@ -38,7 +38,7 @@ Home = "https://github.com/laminlabs/lamindb"
 
 [project.optional-dependencies]
 bionty = [
-    "bionty==0.44.2",
+    "bionty==0.44.3",
 ]
 aws = [
     "lamindb_setup[aws]",
@@ -47,7 +47,7 @@ gcp = [
     "lamindb_setup[gcp]",
 ]
 jupyter = [
-    "nbproject==0.10.3",  # keep pinning
+    "nbproject==0.10.4",  # keep pinning
     "nbstripout==0.6.1", # 0.7.0 seems to be broken, 0.6.2 incompatible with orjson
     "nbconvert",
 ]

{lamindb-0.74.2 → lamindb-0.74.3}/sub/bionty/bionty/__init__.py

@@ -122,7 +122,7 @@ Developer API:
    core
 """
 
-__version__ = "0.44.2"
+__version__ = "0.44.3"
 
 import lamindb  # this is needed as even the Record base class is defined in lamindb
 from lamindb_setup._check_setup import InstanceNotSetupError as _InstanceNotSetupError

{lamindb-0.74.2 → lamindb-0.74.3}/sub/bionty/pyproject.toml

@@ -8,7 +8,7 @@ authors = [{name = "Lamin Labs", email = "open-source@lamin.ai"}]
 readme = "README.md"
 dynamic = ["version", "description"]
 dependencies = [
-    "lnschema-bionty==0.43.2",
+    "lnschema-bionty==0.43.3",
 ]
 
 [project.urls]

{lamindb-0.74.2 → lamindb-0.74.3}/sub/lamindb-setup/.github/workflows/build.yml

@@ -43,7 +43,7 @@ jobs:
             python-version: "3.11"
           - lamin_env: "staging"
             python-version: "3.10" # test on 3.9
-    timeout-minutes: 6
+    timeout-minutes: 7
     steps:
       - uses: aws-actions/configure-aws-credentials@v2
         with:

{lamindb-0.74.2 → lamindb-0.74.3}/sub/lamindb-setup/.pre-commit-config.yaml

@@ -44,9 +44,3 @@ repos:
           (?x)(
               tests/hub-local/conftest.py
           )
-  - repo: https://github.com/pycqa/pydocstyle
-    rev: 6.1.1
-    hooks:
-      - id: pydocstyle
-        args: # google style + __init__, see http://www.pydocstyle.org/en/stable/error_codes.html
-          - --ignore=D100,D101,D102,D103,D104,D106,D107,D203,D204,D213,D215,D400,D401,D403,D404,D406,D407,D408,D409,D412,D413,D417

{lamindb-0.74.2 → lamindb-0.74.3}/sub/lamindb-setup/lamindb_setup/__init__.py

@@ -34,7 +34,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.74.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.74.2"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import sys
 from os import name as _os_name

{lamindb-0.74.2 → lamindb-0.74.3}/sub/lamindb-setup/lamindb_setup/_connect_instance.py

@@ -74,7 +74,8 @@ def update_db_using_local(
             # read from a cached settings file in case the hub result is only
             # read level or inexistent
             elif settings_file.exists() and (
-                "read" in db_dsn_hub.db.user or db_dsn_hub.db.user is None
+                db_dsn_hub.db.user is None
+                or (db_dsn_hub.db.user is not None and "read" in db_dsn_hub.db.user)
             ):
                 isettings = load_instance_settings(settings_file)
                 db_dsn_local = LaminDsnModel(db=isettings.db)
@@ -101,7 +102,7 @@ def update_db_using_local(
             scheme=db_dsn_hub.db.scheme,
             user=db_dsn_local.db.user,
             password=db_dsn_local.db.password,
-            host=db_dsn_hub.db.host,
+            host=db_dsn_hub.db.host,  # type: ignore
             port=db_dsn_hub.db.port,
             database=db_dsn_hub.db.database,
         )

{lamindb-0.74.2 → lamindb-0.74.3}/sub/lamindb-setup/lamindb_setup/_init_instance.py

@@ -245,7 +245,10 @@ def init(
         if instance_state == "connected":
             settings.auto_connect = True  # we can also debate this switch here
             return None
-        ssettings = init_storage(storage, instance_id=instance_id)
+        # cannot past instance_id here because instance does not yet exist!
+        # the instance_id field of the storage table is populated at the end of
+        # init_instance_hub
+        ssettings = init_storage(storage)
         isettings = InstanceSettings(
             id=instance_id,  # type: ignore
             owner=settings.user.handle,

{lamindb-0.74.2 → lamindb-0.74.3}/sub/lamindb-setup/lamindb_setup/core/_hub_client.py

@@ -5,7 +5,7 @@ from urllib.request import urlretrieve
 
 from gotrue.errors import AuthUnknownError
 from lamin_utils import logger
-from pydantic import BaseSettings
+from pydantic_settings import BaseSettings
 from supabase import Client, create_client  # type: ignore
 from supabase.lib.client_options import ClientOptions
 
@@ -59,9 +59,11 @@ class Environment:
 
 # runs ~0.5s
 def connect_hub(
-    fallback_env: bool = False, client_options: ClientOptions = ClientOptions()
+    fallback_env: bool = False, client_options: ClientOptions | None = None
 ) -> Client:
     env = Environment(fallback=fallback_env)
+    if client_options is None:
+        client_options = ClientOptions(auto_refresh_token=False)
     return create_client(env.supabase_api_url, env.supabase_anon_key, client_options)
 
 

{lamindb-0.74.2 → lamindb-0.74.3}/sub/lamindb-setup/lamindb_setup/core/_hub_core.py

@@ -93,20 +93,21 @@ def _select_storage(
         return False
     else:
         existing_storage = response.data[0]
-        if ssettings._instance_id is not None:
-            # consider storage settings that are meant to be managed by an instance
-            if UUID(existing_storage["instance_id"]) != ssettings._instance_id:
-                # everything is alright if the instance_id matches
-                # we're probably just switching storage locations
-                # below can be turned into a warning and then delegate the error
-                # to a unique constraint violation below
-                raise ValueError(
-                    f"Storage root {root} is already managed by instance {existing_storage['instance_id']}."
-                )
-        else:
-            # if the request is agnostic of the instance, that's alright,
-            # we'll update the instance_id with what's stored in the hub
-            ssettings._instance_id = UUID(existing_storage["instance_id"])
+        if existing_storage["instance_id"] is not None:
+            if ssettings._instance_id is not None:
+                # consider storage settings that are meant to be managed by an instance
+                if UUID(existing_storage["instance_id"]) != ssettings._instance_id:
+                    # everything is alright if the instance_id matches
+                    # we're probably just switching storage locations
+                    # below can be turned into a warning and then delegate the error
+                    # to a unique constraint violation below
+                    raise ValueError(
+                        f"Storage root {root} is already managed by instance {existing_storage['instance_id']}."
+                    )
+            else:
+                # if the request is agnostic of the instance, that's alright,
+                # we'll update the instance_id with what's stored in the hub
+                ssettings._instance_id = UUID(existing_storage["instance_id"])
         ssettings._uuid_ = UUID(existing_storage["id"])
         if update_uid:
             ssettings._uid = existing_storage["lnid"]
@@ -145,11 +146,14 @@ def _init_storage(ssettings: StorageSettings, client: Client) -> None:
         id = uuid.uuid5(uuid.NAMESPACE_URL, root)
     else:
         id = uuid.uuid4()
-    if ssettings._instance_id is None:
+    if ssettings._instance_id is None and settings._instance_exists:
         logger.warning(
             f"will manage storage location {ssettings.root_as_str} with instance {settings.instance.slug}"
         )
         ssettings._instance_id = settings.instance._id
+    instance_id_hex = (
+        None if ssettings._instance_id is None else ssettings._instance_id.hex
+    )
     fields = {
         "id": id.hex,
         "lnid": ssettings.uid,
@@ -157,7 +161,7 @@ def _init_storage(ssettings: StorageSettings, client: Client) -> None:
         "root": root,
         "region": ssettings.region,
         "type": ssettings.type,
-        "instance_id": ssettings._instance_id.hex,
+        "instance_id": instance_id_hex,
         # the empty string is important as we want the user flow to be through LaminHub
         # if this errors with unique constraint error, the user has to update
         # the description in LaminHub

lamindb-0.74.3/sub/lamindb-setup/lamindb_setup/core/_hub_utils.py

@@ -0,0 +1,109 @@
+from __future__ import annotations
+
+from typing import Any, ClassVar, Optional
+from urllib.parse import urlparse, urlunparse
+
+from pydantic import BaseModel, Field, GetCoreSchemaHandler
+from pydantic_core import CoreSchema, core_schema
+
+
+def validate_schema_arg(schema: str | None = None) -> str:
+    if schema is None or schema == "":
+        return ""
+    # currently no actual validation, can add back if we see a need
+    # the following just strips white spaces
+    to_be_validated = [s.strip() for s in schema.split(",")]
+    return ",".join(to_be_validated)
+
+
+def validate_db_arg(db: str | None) -> None:
+    if db is not None:
+        LaminDsnModel(db=db)
+
+
+class LaminDsn(str):
+    allowed_schemes: ClassVar[set[str]] = {
+        "postgresql",
+        # future enabled schemes
+        # "snowflake",
+        # "bigquery"
+    }
+
+    @classmethod
+    def __get_pydantic_core_schema__(
+        cls, source_type: Any, handler: GetCoreSchemaHandler
+    ) -> CoreSchema:
+        return core_schema.no_info_after_validator_function(
+            cls.validate,
+            core_schema.str_schema(),
+            serialization=core_schema.plain_serializer_function_ser_schema(str),
+        )
+
+    @classmethod
+    def validate(cls, v: Any) -> LaminDsn:
+        if isinstance(v, str):
+            parsed = urlparse(v)
+            if parsed.scheme not in cls.allowed_schemes:
+                raise ValueError(f"Invalid scheme: {parsed.scheme}")
+            return cls(v)
+        elif isinstance(v, cls):
+            return v
+        else:
+            raise ValueError(f"Invalid value for LaminDsn: {v}")
+
+    @property
+    def user(self) -> str | None:
+        return urlparse(self).username
+
+    @property
+    def password(self) -> str | None:
+        return urlparse(self).password
+
+    @property
+    def host(self) -> str | None:
+        return urlparse(self).hostname
+
+    @property
+    def port(self) -> int | None:
+        return urlparse(self).port
+
+    @property
+    def database(self) -> str:
+        return urlparse(self).path.lstrip("/")
+
+    @property
+    def scheme(self) -> str:
+        return urlparse(self).scheme
+
+    @classmethod
+    def build(
+        cls,
+        *,
+        scheme: str,
+        user: str | None = None,
+        password: str | None = None,
+        host: str,
+        port: int | None = None,
+        database: str | None = None,
+        query: str | None = None,
+        fragment: str | None = None,
+    ) -> LaminDsn:
+        netloc = host
+        if port is not None:
+            netloc = f"{netloc}:{port}"
+        if user is not None:
+            auth = user
+            if password is not None:
+                auth = f"{auth}:{password}"
+            netloc = f"{auth}@{netloc}"
+
+        path = f"/{database}" if database else ""
+
+        url = urlunparse((scheme, netloc, path, "", query or "", fragment or ""))
+        return cls(url)
+
+
+class LaminDsnModel(BaseModel):
+    db: LaminDsn = Field(..., description="The database DSN")
+
+    model_config = {"arbitrary_types_allowed": True}

{lamindb-0.74.2 → lamindb-0.74.3}/sub/lamindb-setup/lamindb_setup/core/_settings_load.py

@@ -4,7 +4,7 @@ from typing import TYPE_CHECKING, Optional
 from uuid import UUID, uuid4
 
 from lamin_utils import logger
-from pydantic.error_wrappers import ValidationError
+from pydantic import ValidationError
 
 from ._settings_instance import InstanceSettings
 from ._settings_storage import StorageSettings

{lamindb-0.74.2 → lamindb-0.74.3}/sub/lamindb-setup/lamindb_setup/core/_settings_save.py

@@ -44,6 +44,8 @@ def save_settings(
             if type == Optional[bool]:
                 type = bool
             if "__" not in store_key:
+                if store_key == "model_config":
+                    continue
                 if store_key == "storage_root":
                     value = settings.storage.root_as_str
                 elif store_key == "storage_region":

{lamindb-0.74.2 → lamindb-0.74.3}/sub/lamindb-setup/lamindb_setup/core/_settings_store.py

@@ -2,7 +2,7 @@ import os
 from pathlib import Path
 from typing import Optional
 
-from pydantic import BaseSettings
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 if "LAMIN_SETTINGS_DIR" in os.environ:
     # Needed when running with AWS Lambda, as only tmp/ directory has a write access
@@ -58,10 +58,7 @@ class InstanceSettingsStore(BaseSettings):
     id: str
     git_repo: Optional[str]
     keep_artifacts_local: Optional[bool]
-
-    class Config:
-        env_prefix = "lamindb_instance_"
-        env_file = ".env"
+    model_config = SettingsConfigDict(env_prefix="lamindb_instance_", env_file=".env")
 
 
 class UserSettingsStore(BaseSettings):
@@ -72,7 +69,4 @@ class UserSettingsStore(BaseSettings):
     uuid: str
     handle: str
     name: str
-
-    class Config:
-        env_prefix = "lamin_user_"
-        env_file = ".env"
+    model_config = SettingsConfigDict(env_prefix="lamin_user_", env_file=".env")