lamindb_setup 1.3.1__tar.gz → 1.4.0__tar.gz

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/.gitignore

@@ -107,6 +107,6 @@ _build
 lamin_sphinx
 docs/conf.py
 _docs_tmp*
-*.lndb
-_is_initialized
+*.db
+storage_uid.txt
 test.ipynb

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.3.1
+Version: 1.4.0
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10
@@ -15,13 +15,13 @@ Requires-Dist: universal_pathlib==0.2.6
 Requires-Dist: botocore<2.0.0
 Requires-Dist: supabase>=2.8.1,<=2.11.0
 Requires-Dist: storage3!=0.11.2; python_version < '3.11'
+Requires-Dist: pyjwt<3.0.0
 Requires-Dist: psutil
 Requires-Dist: packaging
 Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: aiobotocore[boto3]>=2.5.4,<3.0.0 ; extra == "aws"
 Requires-Dist: s3fs>=2023.12.2,<=2025.2.0,!=2024.10.0 ; extra == "aws"
 Requires-Dist: line_profiler ; extra == "dev"
-Requires-Dist: pyjwt<3.0.0 ; extra == "dev"
 Requires-Dist: psycopg2-binary ; extra == "dev"
 Requires-Dist: python-dotenv ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/docs/hub-cloud/01-init-local-instance.ipynb

@@ -58,7 +58,7 @@
     "assert ln_setup.settings.storage.id is not None\n",
     "assert (\n",
     "    ln_setup.settings.instance.db\n",
-    "    == f\"sqlite:///{Path('./mydata').resolve().as_posix()}/{ln_setup.settings.instance._id.hex}.lndb\"\n",
+    "    == f\"sqlite:///{Path('./mydata').resolve().as_posix()}/.lamindb/lamin.db\"\n",
     ")\n",
     "assert ln_setup.settings.storage._instance_id == ln_setup.settings.instance._id\n",
     "assert (\n",

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/docs/hub-cloud/02-connect-local-instance.ipynb

@@ -128,7 +128,7 @@
     "assert ln_setup.settings.instance.storage.root == root_path\n",
     "assert (\n",
     "    ln_setup.settings.instance.db\n",
-    "    == f\"sqlite:///{root_path.as_posix()}/{ln_setup.settings.instance._id.hex}.lndb\"\n",
+    "    == f\"sqlite:///{root_path.as_posix()}/.lamindb/lamin.db\"\n",
     ")"
    ]
   },

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/docs/hub-cloud/03-add-managed-storage.ipynb

@@ -133,7 +133,7 @@
     "storage2_uid = ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.root_as_str == f\"{Path.cwd()}/storage2\"\n",
     "assert (\n",
-    "    ln_setup.settings.storage.root / \".lamindb/_is_initialized\"\n",
+    "    ln_setup.settings.storage.root / \".lamindb/storage_uid.txt\"\n",
     ").read_text() == ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.is_on_hub"
    ]
@@ -165,7 +165,7 @@
    "source": [
     "assert ln_setup.settings.storage.root_as_str == f\"{Path.cwd()}/storage1\"\n",
     "assert (\n",
-    "    ln_setup.settings.storage.root / \".lamindb/_is_initialized\"\n",
+    "    ln_setup.settings.storage.root / \".lamindb/storage_uid.txt\"\n",
     ").read_text() == ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.is_on_hub\n",
     "assert ln_setup.settings.storage.uid == storage1_uid"
@@ -198,7 +198,7 @@
    "source": [
     "assert ln_setup.settings.storage.root_as_str == f\"{Path.cwd()}/storage1\"\n",
     "assert (\n",
-    "    ln_setup.settings.storage.root / \".lamindb/_is_initialized\"\n",
+    "    ln_setup.settings.storage.root / \".lamindb/storage_uid.txt\"\n",
     ").read_text() == ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.is_on_hub\n",
     "assert ln_setup.settings.storage.uid == storage1_uid"
@@ -224,7 +224,7 @@
     "storage2_uid = ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.root_as_str == f\"{Path.cwd()}/storage2\"\n",
     "assert (\n",
-    "    ln_setup.settings.storage.root / \".lamindb/_is_initialized\"\n",
+    "    ln_setup.settings.storage.root / \".lamindb/storage_uid.txt\"\n",
     ").read_text() == ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.is_on_hub\n",
     "assert ln_setup.settings.storage.uid == storage2_uid"
@@ -263,7 +263,7 @@
     "assert ln_setup.settings.storage.root_as_str == \"s3://lamindb-ci/storage3\"\n",
     "assert ln_setup.settings.storage.region == \"us-west-1\"\n",
     "assert (\n",
-    "    ln_setup.settings.storage.root / \".lamindb/_is_initialized\"\n",
+    "    ln_setup.settings.storage.root / \".lamindb/storage_uid.txt\"\n",
     ").read_text() == ln_setup.settings.storage.uid\n",
     "# root.fs contains the underlying fsspec filesystem\n",
     "assert (\n",
@@ -338,13 +338,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from laminhub_rest.core.instance.collaborator import InstanceCollaboratorHandler\n",
-    "from laminhub_rest.core.account.user import UserAccountHandler\n",
+    "from laminhub_rest.core.legacy._instance_collaborator import InstanceCollaboratorHandler\n",
+    "from laminhub_rest.core.account import AccountHandler\n",
     "from lamindb_setup.core._hub_client import connect_hub_with_auth\n",
     "from lamindb.models import User\n",
     "\n",
     "admin_hub = connect_hub_with_auth()\n",
-    "testuser2 = UserAccountHandler(admin_hub).get_by_handle(\"testuser2\")\n",
+    "testuser2 = AccountHandler(admin_hub).get_by_handle(\"testuser2\")\n",
     "InstanceCollaboratorHandler(admin_hub).add(\n",
     "    instance_id=instance_id,\n",
     "    account_id=testuser2.id,\n",
@@ -457,7 +457,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.17"
+   "version": "3.10.16"
   },
   "vscode": {
    "interpreter": {

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/docs/hub-cloud/04-test-bionty.ipynb

@@ -70,10 +70,7 @@
    },
    "outputs": [],
    "source": [
-    "from bionty.base import settings as bionty_base_settings\n",
-    "\n",
-    "assert sources_df.shape[0] > 0\n",
-    "assert bionty_base_settings.lamindb_sources.exists()"
+    "assert sources_df.shape[0] > 0"
    ]
   },
   {
@@ -140,7 +137,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "py310",
    "language": "python",
    "name": "python3"
   },
@@ -155,11 +152,6 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.10.13"
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "61b4062b24dfb1010f420dad5aa3bd73a4d2af47d0ec44eafec465a35a9d7239"
-   }
   }
  },
  "nbformat": 4,

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/docs/hub-cloud/07-keep-artifacts-local.ipynb

@@ -31,8 +31,7 @@
     "assert ln_setup.settings.instance.storage.type_is_cloud\n",
     "assert ln_setup.settings.instance.storage.root_as_str == storage\n",
     "assert (\n",
-    "    ln_setup.settings.instance._sqlite_file.as_posix()\n",
-    "    == f\"{storage}/{ln_setup.settings.instance._id.hex}.lndb\"\n",
+    "    ln_setup.settings.instance._sqlite_file.as_posix() == f\"{storage}/.lamindb/lamin.db\"\n",
     ")"
    ]
   },
@@ -75,7 +74,7 @@
     "    == UPath(\"./my_storage_local\").resolve().as_posix()\n",
     ")\n",
     "assert (\n",
-    "    ln_setup.settings.instance.storage_local.root / \".lamindb/_is_initialized\"\n",
+    "    ln_setup.settings.instance.storage_local.root / \".lamindb/storage_uid.txt\"\n",
     ").read_text() == ln_setup.settings.instance.storage_local.uid\n",
     "assert ln_setup.settings.instance.storage_local is not None\n",
     "# the remote storage location is still in the regular slot\n",
@@ -109,7 +108,7 @@
     "    == UPath(\"./my_storage_local2\").resolve().as_posix()\n",
     ")\n",
     "assert (\n",
-    "    ln_setup.settings.instance.storage_local.root / \".lamindb/_is_initialized\"\n",
+    "    ln_setup.settings.instance.storage_local.root / \".lamindb/storage_uid.txt\"\n",
     ").read_text() == ln_setup.settings.instance.storage_local.uid"
    ]
   },

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/docs/hub-prod/test-empty-init.ipynb

@@ -74,10 +74,7 @@
     "assert ln_setup.settings.storage.type_is_cloud\n",
     "assert ln_setup.settings.storage.root_as_str == root_str\n",
     "assert ln_setup.settings.storage.region == \"us-east-1\"\n",
-    "assert (\n",
-    "    str(ln_setup.settings.instance._sqlite_file)\n",
-    "    == f\"{root_str}/{ln_setup.settings.instance._id.hex}.lndb\"\n",
-    ")"
+    "assert str(ln_setup.settings.instance._sqlite_file) == f\"{root_str}/.lamindb/lamin.db\""
    ]
   },
   {

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/lamindb_setup/__init__.py

@@ -33,7 +33,7 @@ Modules & settings:
 
 """
 
-__version__ = "1.3.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "1.4.0"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os
 

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/lamindb_setup/_close.py

@@ -4,7 +4,6 @@ from lamin_utils import logger
 
 from .core._settings import settings
 from .core._settings_store import current_instance_settings_file
-from .core._setup_bionty_sources import delete_bionty_sources_yaml
 from .core.cloud_sqlite_locker import clear_locker
 
 
@@ -24,8 +23,6 @@ def close(mute: bool = False) -> None:
                 logger.warning("did not upload cache file - not enough permissions")
             else:
                 raise e
-        if "bionty" in settings.instance.modules:
-            delete_bionty_sources_yaml()
         current_instance_settings_file().unlink()
         clear_locker()
         if not mute:

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/lamindb_setup/_connect_instance.py

@@ -169,6 +169,7 @@ def _connect_instance(
                 if (schema_id := instance_result["schema_id"]) is None
                 else UUID(schema_id),
                 fine_grained_access=instance_result.get("fine_grained_access", False),
+                db_permissions=instance_result.get("db_permissions", None),
             )
         else:
             if hub_result != "anonymous-user":

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/lamindb_setup/_delete.py

@@ -131,7 +131,7 @@ def delete(slug: str, force: bool = False, require_empty: bool = True) -> int |
         # this will error if the user doesn't have permission
         delete_instance_on_hub(isettings._id, require_empty=False)
     delete_by_isettings(isettings)
-    # if .lndb file was delete, then we might count -1
+    # if lamin.db file was delete, then we might count -1
     if n_files <= 0 and isettings.storage.type == "local":
         # dir is only empty after sqlite file was delete via delete_by_isettings
         if (isettings.storage.root / ".lamindb").exists():

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/lamindb_setup/_init_instance.py

@@ -14,6 +14,7 @@ from lamin_utils import logger
 from ._close import close as close_instance
 from ._silence_loggers import silence_loggers
 from .core import InstanceSettings
+from .core._docs import doc_args
 from .core._settings import settings
 from .core._settings_instance import is_local_db_url
 from .core._settings_storage import StorageSettings, init_storage
@@ -95,11 +96,16 @@ def register_user(usettings):
         pass
 
 
-def register_user_and_storage_in_instance(isettings: InstanceSettings, usettings):
-    """Register user & storage in DB."""
+def register_initial_records(isettings: InstanceSettings, usettings):
+    """Register space, user & storage in DB."""
     from django.db.utils import OperationalError
+    from lamindb.models import Space
 
     try:
+        Space.objects.get_or_create(
+            name="All",
+            description="Every team & user with access to the instance has access.",
+        )
         register_user(usettings)
         register_storage_in_instance(isettings.storage)
     except OperationalError as error:
@@ -208,22 +214,32 @@ ln.Artifact.using("laminlabs/cellxgene").filter()
 Or do you want to switch off auto-connect via `lamin settings set auto-connect false`?
 """
 
+DOC_STORAGE_ARG = "A local or remote folder (`'s3://...'` or `'gs://...'`). Defaults to current working directory."
+DOC_INSTANCE_NAME = (
+    "Instance name. If not passed, it will equal the folder name passed to `storage`."
+)
+DOC_DB = "Database connection URL. Defaults to `None`, which implies an SQLite file in the storage location."
+DOC_MODULES = "Comma-separated string of schema modules."
+DOC_LOW_LEVEL_KWARGS = "Keyword arguments for low-level control."
+
 
+@doc_args(DOC_STORAGE_ARG, DOC_INSTANCE_NAME, DOC_DB, DOC_MODULES, DOC_LOW_LEVEL_KWARGS)
 def init(
     *,
-    storage: UPathStr,
+    storage: UPathStr = ".",
     name: str | None = None,
     db: PostgresDsn | None = None,
     modules: str | None = None,
     **kwargs,
 ) -> None:
-    """Create and load a LaminDB instance.
+    """Init a LaminDB instance.
 
     Args:
-        storage: Either local or remote folder (`"s3://..."` or `"gs://..."`).
-        name: Instance name.
-        db: Database connection url, do not pass for SQLite.
-        modules: Comma-separated string of modules. None if the lamindb registries are enough.
+        storage: {}
+        name: {}
+        db: {}
+        modules: {}
+        **kwargs: {}
     """
     isettings = None
     ssettings = None
@@ -359,8 +375,8 @@ def load_from_isettings(
     user = settings.user if user is None else user
 
     if init:
-        # during init both user and storage need to be registered
-        register_user_and_storage_in_instance(isettings, user)
+        # during init space, user and storage need to be registered
+        register_initial_records(isettings, user)
         write_bionty_sources(isettings)
         isettings._update_cloud_sqlite_file(unlock_cloud_sqlite=False)
     else:

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/lamindb_setup/_migrate.py

@@ -47,16 +47,20 @@ def check_whether_migrations_in_sync(db_version_str: str):
             f"the database ({db_version_str}) is far behind your installed lamindb package"
             f" ({installed_version_str})"
         )
-        logger.important("migrate your database: lamin migrate deploy")
+        logger.important(
+            "if you are an admin, migrate your database: lamin migrate deploy"
+        )
     elif (
         installed_version.major == db_version.major
         and installed_version.minor > db_version.minor
     ):
-        logger.important(
-            f"the database ({db_version_str}) is behind your installed lamindb package"
-            f" ({installed_version_str})"
-        )
-        logger.important("consider migrating your database: lamin migrate deploy")
+        pass
+        # if the database is behind by a minor version, we don't want to spam the user
+        # logger.important(
+        #     f"the database ({db_version_str}) is behind your installed lamindb package"
+        #     f" ({installed_version_str})"
+        # )
+        # logger.important("consider migrating your database: lamin migrate deploy")
 
 
 # for tests, see lamin-cli

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/lamindb_setup/_set_managed_storage.py

@@ -31,7 +31,7 @@ def set_managed_storage(root: UPathStr, **fs_kwargs):
         )
     # here the storage is registered in the hub
     # hub_record_status="hub-record-created" if a new record is created
-    # "hub-record-retireved" if the storage is in the hub already
+    # "hub-record-retrieved" if the storage is in the hub already
     ssettings, hub_record_status = init_storage(
         root=root, instance_id=settings.instance._id, register_hub=True
     )

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/lamindb_setup/core/_hub_client.py

@@ -69,7 +69,9 @@ def connect_hub(
         # function_client_timeout=5 by default
         # increase to avoid rare timeouts for edge functions
         client_options = ClientOptions(
-            auto_refresh_token=False, function_client_timeout=10
+            auto_refresh_token=False,
+            function_client_timeout=20,
+            postgrest_client_timeout=20,
         )
     return create_client(env.supabase_api_url, env.supabase_anon_key, client_options)
 

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/lamindb_setup/core/_hub_core.py

@@ -7,6 +7,7 @@ from importlib import metadata
 from typing import TYPE_CHECKING, Literal
 from uuid import UUID
 
+import jwt
 from lamin_utils import logger
 from postgrest.exceptions import APIError
 
@@ -121,7 +122,7 @@ def init_storage_hub(
     auto_populate_instance: bool = True,
     created_by: UUID | None = None,
     access_token: str | None = None,
-) -> Literal["hub-record-retireved", "hub-record-created"]:
+) -> Literal["hub-record-retrieved", "hub-record-created"]:
     if settings.user.handle != "anonymous" or access_token is not None:
         return call_with_fallback_auth(
             _init_storage_hub,
@@ -135,7 +136,7 @@ def init_storage_hub(
             _select_storage, ssettings=ssettings, update_uid=True
         )
         if storage_exists:
-            return "hub-record-retireved"
+            return "hub-record-retrieved"
         else:
             raise ValueError("Log in to create a storage location on the hub.")
 
@@ -145,7 +146,7 @@ def _init_storage_hub(
     ssettings: StorageSettings,
     auto_populate_instance: bool,
     created_by: UUID | None = None,
-) -> Literal["hub-record-retireved", "hub-record-created"]:
+) -> Literal["hub-record-retrieved", "hub-record-created"]:
     from lamindb_setup import settings
 
     created_by = settings.user._uuid if created_by is None else created_by
@@ -153,7 +154,7 @@ def _init_storage_hub(
     # database
     root = ssettings.root_as_str
     if _select_storage(ssettings, update_uid=True, client=client):
-        return "hub-record-retireved"
+        return "hub-record-retrieved"
     if ssettings.type_is_cloud:
         id = uuid.uuid5(uuid.NAMESPACE_URL, root)
     else:
@@ -548,7 +549,7 @@ def _sign_in_hub_api_key(api_key: str, client: Client):
     access_token = json.loads(response)["accessToken"]
     # probably need more info here to avoid additional queries
     # like handle, uid etc
-    account_id = client.auth._decode_jwt(access_token)["sub"]
+    account_id = jwt.decode(access_token, options={"verify_signature": False})["sub"]
     client.postgrest.auth(access_token)
     # normally public.account.id is equal to auth.user.id
     data = client.table("account").select("*").eq("id", account_id).execute().data

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/lamindb_setup/core/_settings_instance.py

@@ -13,7 +13,12 @@ from ._hub_client import call_with_fallback
 from ._hub_crud import select_account_handle_name_by_lnid
 from ._hub_utils import LaminDsn, LaminDsnModel
 from ._settings_save import save_instance_settings
-from ._settings_storage import StorageSettings, init_storage, mark_storage_root
+from ._settings_storage import (
+    LEGACY_STORAGE_UID_FILE_KEY,
+    STORAGE_UID_FILE_KEY,
+    StorageSettings,
+    init_storage,
+)
 from ._settings_store import current_instance_settings_file, instance_settings_file
 from .cloud_sqlite_locker import (
     EXPIRATION_TIME,
@@ -60,6 +65,7 @@ class InstanceSettings:
         api_url: str | None = None,
         schema_id: UUID | None = None,
         fine_grained_access: bool = False,
+        db_permissions: str | None = None,
         _locker_user: UserSettings | None = None,  # user to lock for if cloud sqlite
     ):
         from ._hub_utils import validate_db_arg
@@ -83,6 +89,8 @@ class InstanceSettings:
         # private, whether fine grained access is used
         # needed to be set to request jwt etc
         self._fine_grained_access = fine_grained_access
+        # permissions for db such as jwt, read, write etc.
+        self._db_permissions = db_permissions
         # if None then settings.user is used
         self._locker_user = _locker_user
 
@@ -144,32 +152,27 @@ class InstanceSettings:
         for record in all_local_records:
             root_path = Path(record.root)
             if root_path.exists():
-                marker_path = root_path / ".lamindb/_is_initialized"
-                if marker_path.exists():
-                    try:
-                        uid = marker_path.read_text()
-                    except PermissionError:
+                marker_path = root_path / STORAGE_UID_FILE_KEY
+                if not marker_path.exists():
+                    legacy_filepath = root_path / LEGACY_STORAGE_UID_FILE_KEY
+                    if legacy_filepath.exists():
                         logger.warning(
-                            f"ignoring the following location because no permission to read it: {marker_path}"
+                            f"found legacy marker file, renaming it from {legacy_filepath} to {marker_path}"
                         )
-                        continue
-                    if uid == record.uid:
-                        found = True
-                        break
-                    elif uid == "":
-                        try:
-                            # legacy instance that was not yet marked properly
-                            mark_storage_root(record.root, record.uid)
-                        except PermissionError:
-                            logger.warning(
-                                f"ignoring the following location because no permission to write to it: {marker_path}"
-                            )
-                            continue
+                        legacy_filepath.rename(marker_path)
                     else:
-                        continue
-                else:
-                    # legacy instance that was not yet marked at all
-                    mark_storage_root(record.root, record.uid)
+                        raise ValueError(
+                            f"local storage location '{root_path}' is corrupted, cannot find marker file with storage uid"
+                        )
+                try:
+                    uid = marker_path.read_text()
+                except PermissionError:
+                    logger.warning(
+                        f"ignoring the following location because no permission to read it: {marker_path}"
+                    )
+                    continue
+                if uid == record.uid:
+                    found = True
                     break
         if found:
             return StorageSettings(record.root)
@@ -295,7 +298,8 @@ class InstanceSettings:
     @property
     def _sqlite_file(self) -> UPath:
         """SQLite file."""
-        return self.storage.key_to_filepath(f"{self._id.hex}.lndb")
+        filepath = self.storage.root / ".lamindb/lamin.db"
+        return filepath
 
     @property
     def _sqlite_file_local(self) -> Path:
@@ -477,24 +481,18 @@ class InstanceSettings:
 
         disable_auto_connect(setup_django)(self, init=True)
 
-        from lamindb.models import Space
-
-        Space.objects.get_or_create(
-            name="All",
-            description="Every team & user with access to the instance has access.",
-        )
-
     def _load_db(self) -> tuple[bool, str]:
         # Is the database available and initialized as LaminDB?
         # returns a tuple of status code and message
         if self.dialect == "sqlite" and not self._sqlite_file.exists():
-            legacy_file = self.storage.key_to_filepath(f"{self.name}.lndb")
+            legacy_file = self.storage.key_to_filepath(f"{self._id.hex}.lndb")
             if legacy_file.exists():
-                raise RuntimeError(
-                    "The SQLite file has been renamed!\nPlease rename your SQLite file"
-                    f" {legacy_file} to {self._sqlite_file}"
+                logger.warning(
+                    f"The SQLite file is being renamed from {legacy_file} to {self._sqlite_file}"
                 )
-            return False, f"SQLite file {self._sqlite_file} does not exist"
+                legacy_file.rename(self._sqlite_file)
+            else:
+                return False, f"SQLite file {self._sqlite_file} does not exist"
         # we need the local sqlite to setup django
         self._update_local_sqlite_file()
         # setting up django also performs a check for migrations & prints them

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/lamindb_setup/core/_settings_load.py

@@ -104,6 +104,7 @@ def setup_instance_from_store(store: InstanceSettingsStore) -> InstanceSettings:
         api_url=_null_to_value(store.api_url),
         schema_id=None if store.schema_id == "null" else UUID(store.schema_id),
         fine_grained_access=store.fine_grained_access,
+        db_permissions=_null_to_value(store.db_permissions),
     )
 
 

{lamindb_setup-1.3.1 → lamindb_setup-1.4.0}/lamindb_setup/core/_settings_save.py

@@ -61,6 +61,7 @@ def save_settings(
                         "api_url",
                         "schema_id",
                         "fine_grained_access",
+                        "db_permissions",
                     }:
                         settings_key = f"_{store_key.rstrip('_')}"
                     else: