lamindb_setup 1.18.1__tar.gz → 1.19.0__tar.gz

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/.github/workflows/build.yml

@@ -91,8 +91,7 @@ jobs:
           path: .coverage
           include-hidden-files: true
 
-  # test user access to storage
-  storage:
+  core:
     runs-on: ubuntu-latest
     timeout-minutes: 13
     steps:
@@ -103,15 +102,15 @@ jobs:
           cache: "pip"
           cache-dependency-path: ".github/workflows/build.yml"
       - run: pip install "laminci@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci"
-      - run: nox -s "install(group='storage')"
+      - run: nox -s "install(group='core')"
       - run: nox -s lint
-      - run: nox -s storage
+      - run: nox -s core
         env:
           TMP_AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
           TMP_AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
       - uses: actions/upload-artifact@v4
         with:
-          name: coverage--storage
+          name: coverage--core
           path: .coverage
           include-hidden-files: true
 
@@ -137,7 +136,7 @@ jobs:
           touch .env.local
           echo "AWS_ACCESS_KEY_ID_HOSTED_S3=${{ secrets.AWS_ACCESS_KEY_ID }}" >> .env.local
           echo "AWS_SECRET_ACCESS_KEY_HOSTED_S3=${{ secrets.AWS_SECRET_ACCESS_KEY }}" >> .env.local
-        working-directory: laminhub/backend/central/supabase
+        working-directory: laminhub/backend/services/central/supabase
       - uses: actions/setup-python@v6
         with:
           python-version: "3.11" # we need to run everything for coverage on 3.11
@@ -152,7 +151,7 @@ jobs:
           key: cache-supabase
       - uses: supabase/setup-cli@v1
         with:
-          version: "2.6.8"
+          version: "2.72.7"
       - run: nox -s hub_local
         env:
           LAMIN_ENV: "local"
@@ -216,8 +215,35 @@ jobs:
       - name: run tests
         run: nox -s connectivity
 
+  profile:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    env:
+      LAMIN_API_KEY: ${{ secrets.LAMIN_API_KEY_TESTUSER1 }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - uses: actions/setup-python@v6
+        with:
+          python-version: |
+            ${{ github.ref == 'refs/heads/release' && '3.11' ||
+                '3.13'
+                }}
+      - run: pip install git+https://github.com/laminlabs/laminci
+      - run: uv pip install --system git+https://github.com/laminlabs/lamin-cli
+      - run: uv pip install --system git+https://github.com/laminlabs/lamindb
+      - run: uv pip install --system git+https://github.com/laminlabs/laminprofiler
+      - run: uv pip install --system -e .
+      - run: lamin login
+      - run: lamin connect laminlabs/lamindata
+      - run: laminprofiler check tests/profiling/import_lamindb_setup.py --threshold 0.25
+      - run: laminprofiler check tests/profiling/print_lamindb_setup_settings.py --threshold 0.4
+      - run: laminprofiler check tests/profiling/connect_cli.py --threshold 2.0
+
   coverage:
-    needs: [hub-prod, hub-cloud, storage, hub-local]
+    needs: [hub-prod, hub-cloud, core, hub-local]
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/PKG-INFO

@@ -1,11 +1,12 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.18.1
+Version: 1.19.0
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 Requires-Dist: lamin_utils>=0.3.3
+Requires-Dist: python-dotenv
 Requires-Dist: django>=5.2,<5.3
 Requires-Dist: dj_database_url>=1.3.0,<3.0.0
 Requires-Dist: django-pgtrigger

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/docs/hub-cloud/02-connect-local-instance.ipynb

@@ -94,10 +94,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# wetlab is not in the (schema) modules of mydata\n",
+    "# pertdb is not in the (schema) modules of mydata\n",
     "with pytest.raises(ModuleWasntConfigured):\n",
     "    # _check_instance_setup is called inside\n",
-    "    import wetlab"
+    "    import pertdb"
    ]
   },
   {

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/docs/hub-cloud/03-add-managed-storage.ipynb

@@ -48,11 +48,22 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "33c2bb76-d61f-4866-87e2-780e61600022",
+   "id": "cc2ba3c0",
    "metadata": {},
    "outputs": [],
    "source": [
     "import os\n",
+    "\n",
+    "os.environ[\"LAMINHUB_ID\"] = \"00000000-0000-0000-0000-000000000000\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "33c2bb76-d61f-4866-87e2-780e61600022",
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "import laminci\n",
     "import pytest\n",
     "from pathlib import Path\n",

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/docs/hub-prod/test-cache-management.ipynb

@@ -239,7 +239,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "exit_status = os.system(\"lamin cache clear\")\n",
+    "exit_status = os.system(\"lamin settings cache-dir clear\")\n",
     "assert exit_status == 0"
    ]
   },
@@ -346,7 +346,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "exit_status = os.system(\"lamin cache get\")\n",
+    "exit_status = os.system(\"lamin settings cache-dir get\")\n",
     "assert exit_status == 0"
    ]
   },
@@ -357,7 +357,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "exit_status = os.system(\"lamin cache set 'null'\")\n",
+    "exit_status = os.system(\"lamin settings cache-dir set 'null'\")\n",
     "assert exit_status == 0"
    ]
   },
@@ -397,7 +397,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.16"
+   "version": "3.11.14"
   }
  },
  "nbformat": 4,

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/docs/hub-prod/test-import-schema.ipynb

@@ -27,7 +27,7 @@
    },
    "outputs": [],
    "source": [
-    "!lamin init --storage test-implicit-load --modules wetlab,bionty"
+    "!lamin init --storage test-implicit-load --modules pertdb,bionty"
    ]
   },
   {
@@ -49,7 +49,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import wetlab as wl"
+    "import pertdb"
    ]
   },
   {
@@ -69,7 +69,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "wl.Compound"
+    "pertdb.Compound"
    ]
   },
   {

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/__init__.py

@@ -35,7 +35,7 @@ Migration management
 
 """
 
-__version__ = "1.18.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "1.19.0"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os
 import warnings
@@ -48,9 +48,9 @@ warnings.filterwarnings(
 )
 warnings.filterwarnings("ignore", category=DeprecationWarning, module="postgrest")
 
-from packaging import version as packaging_version
-
-from . import core, errors, io, types
+# do not import io by default to reduce import time
+# it's not immediately needed in the default user workflows
+from . import core, errors, types
 from ._check_setup import _check_instance_setup
 from ._connect_instance import connect
 from ._delete import delete
@@ -63,20 +63,6 @@ from ._register_instance import register
 from ._setup_user import login, logout
 from .core._settings import settings
 
-# check that the version of s3fs is higher than the lower bound
-# needed because spatialdata installs old versions of s3fs
-try:
-    from s3fs import __version__ as s3fs_version
-
-    if packaging_version.parse(s3fs_version) < packaging_version.parse("2023.12.2"):
-        raise RuntimeError(
-            f"The version of s3fs you have ({s3fs_version}) is impompatible "
-            "with lamindb, please upgrade it: pip install s3fs>=2023.12.2"
-        )
-except ImportError:
-    # might be not installed
-    pass
-
 
 def _is_CI_environment() -> bool:
     ci_env_vars = [
@@ -112,5 +98,4 @@ _call_registered_entry_points("lamindb_setup.on_import")
 
 settings.__doc__ = """Global :class:`~lamindb.setup.core.SetupSettings`."""
 
-
 close = disconnect  # backward compatibility

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/_connect_instance.py

@@ -13,8 +13,6 @@ from ._check_setup import _check_instance_setup
 from ._disconnect import disconnect
 from ._init_instance import load_from_isettings
 from ._silence_loggers import silence_loggers
-from .core._hub_core import connect_instance_hub
-from .core._hub_utils import LaminDsnModel
 from .core._settings import settings
 from .core._settings_instance import InstanceSettings
 from .core._settings_load import load_instance_settings
@@ -66,6 +64,9 @@ def update_db_using_local(
             # read directly from the environment
             db_updated = db_env
         else:
+            # dynamic import to avoid importing the heavy LaminDsnModel at root
+            from .core._hub_utils import LaminDsnModel
+
             db_hub = hub_instance_result["db"]
             db_dsn_hub = LaminDsnModel(db=db_hub)
             # read from a cached settings file in case the hub result is inexistent
@@ -113,6 +114,8 @@ def _connect_instance(
         # the following will return a string if the instance does not exist on the hub
         # do not call hub if the user is anonymous
         if owner != "anonymous":
+            from .core._hub_core import connect_instance_hub
+
             hub_result = connect_instance_hub(
                 owner=owner,
                 name=name,
@@ -233,7 +236,8 @@ def reset_django_module_variables():
 
 
 def _connect_cli(
-    instance: str, use_root_db_user: bool = False, use_proxy_db: bool = False
+    instance: str,
+    use_root_db_user: bool = False,
 ) -> None:
     from lamindb_setup import settings as settings_
 
@@ -242,7 +246,6 @@ def _connect_cli(
         owner,
         name,
         use_root_db_user=use_root_db_user,
-        use_proxy_db=use_proxy_db,
         raise_systemexit=True,
     )
     isettings._persist(write_to_disk=True)

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/_delete.py

@@ -8,8 +8,6 @@ from lamin_utils import logger
 
 from ._connect_instance import _connect_instance, get_owner_name_from_identifier
 from .core._aws_options import HOSTED_BUCKETS
-from .core._hub_core import delete_instance as delete_instance_on_hub
-from .core._hub_core import get_storage_records_for_instance
 from .core._settings import settings
 from .core._settings_load import load_instance_settings
 from .core._settings_storage import StorageSettings
@@ -120,6 +118,9 @@ def delete(slug: str, force: bool = False, require_empty: bool = True) -> int |
         )
     # now everything that's on the hub
     if settings.user.handle != "anonymous":
+        # dynamic import to avoid importing hub logic at root
+        from .core._hub_core import get_storage_records_for_instance
+
         storage_records = get_storage_records_for_instance(isettings._id)
         for storage_record in storage_records:
             if storage_record["root"] == isettings.storage.root_as_str:
@@ -139,7 +140,10 @@ def delete(slug: str, force: bool = False, require_empty: bool = True) -> int |
     if settings.user.handle != "anonymous" and isettings.is_on_hub:
         # start with deleting things on the hub
         # this will error if the user doesn't have permission
-        delete_instance_on_hub(isettings._id, require_empty=False)
+        # dynamic import to avoid importing hub logic at root
+        from .core._hub_core import delete_instance
+
+        delete_instance(isettings._id, require_empty=False)
     delete_by_isettings(isettings)
     # if lamin.db file was delete, then we might count -1
     if n_files <= 0 and isettings.storage.type == "local":

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/_init_instance.py

@@ -6,7 +6,6 @@ import uuid
 from typing import TYPE_CHECKING, Literal
 from uuid import UUID
 
-import click
 from lamin_utils import logger
 
 from ._disconnect import disconnect
@@ -17,7 +16,7 @@ from .core._settings import settings
 from .core._settings_instance import check_is_instance_remote
 from .core._settings_storage import StorageSettings, init_storage
 from .core.upath import UPath
-from .errors import CannotSwitchDefaultInstance
+from .errors import CannotSwitchDefaultInstance, InstanceNotCreated
 
 if TYPE_CHECKING:
     from lamindb.models import Storage
@@ -27,11 +26,6 @@ if TYPE_CHECKING:
     from .types import UPathStr
 
 
-class InstanceNotCreated(click.ClickException):
-    def show(self, file=None):
-        pass
-
-
 def get_schema_module_name(module_name, raise_import_error: bool = True) -> str | None:
     import importlib.util
 

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/_migrate.py

@@ -2,9 +2,7 @@ from __future__ import annotations
 
 import os
 
-import httpx
 from django.db import connection
-from django.db.migrations.loader import MigrationLoader
 from lamin_utils import logger
 from packaging import version
 
@@ -111,6 +109,9 @@ class migrate:
         isettings = settings.instance
 
         if isettings.is_on_hub and LAMIN_MIGRATE_ON_LAMBDA:
+            # dynamic import to avoid importing the heavy httpx at root
+            import httpx
+
             response = httpx.post(
                 f"{isettings.api_url}/instances/{isettings._id}/migrate",
                 headers={"Authorization": f"Bearer {settings.user.access_token}"},
@@ -300,6 +301,9 @@ class migrate:
 
             return latest_migrations
         else:
+            # import dynamically to avoid importing the heavy django.db.migrations at the root
+            from django.db.migrations.loader import MigrationLoader
+
             # Load all migrations using Django's migration loader
             loader = MigrationLoader(connection)
             squashed_replacements = set()

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/_set_managed_storage.py

@@ -5,7 +5,6 @@ from typing import TYPE_CHECKING
 from lamin_utils import logger
 
 from ._init_instance import register_storage_in_instance
-from .core._hub_core import delete_storage_record
 from .core._settings import settings
 from .core._settings_storage import StorageSettings, init_storage
 
@@ -65,6 +64,8 @@ def set_managed_storage(root: UPathStr, host: str | None = None, **fs_kwargs):
         register_storage_in_instance(ssettings)
     except Exception as e:
         if hub_record_status == "hub-record-created" and ssettings._uuid is not None:
+            from .core._hub_core import delete_storage_record
+
             delete_storage_record(ssettings)
         raise e
 

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/core/_aws_options.py

@@ -58,7 +58,17 @@ class AWSOptionsManager:
         self._parameters_cache = {}  # this is not refreshed
 
         from aiobotocore.session import AioSession
+        from packaging import version as packaging_version
+
+        # takes 100ms to import, so keep it here to avoid delaying the import of the main module
         from s3fs import S3FileSystem
+        from s3fs import __version__ as s3fs_version
+
+        if packaging_version.parse(s3fs_version) < packaging_version.parse("2023.12.2"):
+            raise RuntimeError(
+                f"The version of s3fs you have ({s3fs_version}) is impompatible "
+                "with lamindb, please upgrade it: pip install s3fs>=2023.12.2"
+            )
 
         anon_env = os.getenv("LAMIN_S3_ANON") == "true"
         # this is cached so will be resued with the connection initialized

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/core/_aws_storage.py

@@ -1,10 +1,12 @@
 from __future__ import annotations
 
-import httpx
 from lamin_utils import logger
 
 
 def get_location(ip="ipinfo.io"):
+    # dynamic import to avoid importing the heavy httpx at root
+    import httpx
+
     response = httpx.get(f"http://{ip}/json").json()
     loc = response["loc"].split(",")
     return {"latitude": float(loc[0]), "longitude": float(loc[1])}

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/core/_hub_client.py

@@ -10,26 +10,20 @@ from urllib.request import urlretrieve
 import httpx
 from httpx_retries import Retry, RetryTransport
 from lamin_utils import logger
-from pydantic_settings import BaseSettings
 from supabase import Client, ClientOptions, create_client
 
 from ._settings_save import save_user_settings
-
-
-class Connector(BaseSettings):
-    url: str
-    key: str
+from ._settings_store import Connector
 
 
 def load_fallback_connector() -> Connector:
     url = "https://lamin-site-assets.s3.amazonaws.com/connector.env"
     connector_file, _ = urlretrieve(url)
-    connector = Connector(_env_file=connector_file)
-    return connector
+    return Connector.from_env_file(connector_file, "")
 
 
 PROD_URL = "https://hub.lamin.ai"
-PROD_ANON_KEY = "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJzdXBhYmFzZSIsInJlZiI6ImxhZXNhdW1tZHlkbGxwcGdmY2h1Iiwicm9sZSI6ImFub24iLCJpYXQiOjE2NTY4NDA1NTEsImV4cCI6MTk3MjQxNjU1MX0.WUeCRiun0ExUxKIv5-CtjF6878H8u26t0JmCWx3_2-c"
+PROD_ANON_KEY = "sb_publishable_YVa4h8hQ-yBhXpfa2cP39w_PhoLW6Nu"
 
 
 class Environment:
@@ -48,13 +42,13 @@ class Environment:
                 key = connector.key
         elif lamin_env == "staging":
             url = "https://amvrvdwndlqdzgedrqdv.supabase.co"
-            key = "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJzdXBhYmFzZSIsInJlZiI6ImFtdnJ2ZHduZGxxZHpnZWRycWR2Iiwicm9sZSI6ImFub24iLCJpYXQiOjE2NzcxNTcxMzMsImV4cCI6MTk5MjczMzEzM30.Gelt3dQEi8tT4j-JA36RbaZuUvxRnczvRr3iyRtzjY0"
+            key = "sb_publishable_amVjtilv_Yj4VmGLmxtq6A_sYlLoQx5"
         elif lamin_env == "staging-test":
             url = "https://iugyyajllqftbpidapak.supabase.co"
-            key = "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJzdXBhYmFzZSIsInJlZiI6Iml1Z3l5YWpsbHFmdGJwaWRhcGFrIiwicm9sZSI6ImFub24iLCJpYXQiOjE2OTQyMjYyODMsImV4cCI6MjAwOTgwMjI4M30.s7B0gMogFhUatMSwlfuPJ95kWhdCZMn1ROhZ3t6Og90"
+            key = "sb_publishable_XmXroXqTLQw-eeT5kysCww_k8vJv-4L"
         elif lamin_env == "prod-test":
             url = "https://xtdacpwiqwpbxsatoyrv.supabase.co"
-            key = "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJzdXBhYmFzZSIsInJlZiI6Inh0ZGFjcHdpcXdwYnhzYXRveXJ2Iiwicm9sZSI6ImFub24iLCJpYXQiOjE2OTQyMjYxNDIsImV4cCI6MjAwOTgwMjE0Mn0.Dbi27qujTt8Ei9gfp9KnEWTYptE5KUbZzEK6boL46k4"
+            key = "sb_publishable_G-pyO5aW6VFErTzJyVvM5w_NAv1_Mf7"
         else:
             url = os.environ["SUPABASE_API_URL"]
             key = os.environ["SUPABASE_ANON_KEY"]

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/core/_hub_core.py

@@ -627,8 +627,6 @@ def access_aws(storage_root: str, access_token: str | None = None) -> dict[str,
 
 
 def _access_aws(*, storage_root: str, client: Client) -> dict[str, dict]:
-    import lamindb_setup
-
     storage_root_info: dict[str, dict] = {"credentials": {}, "accessibility": {}}
     response = client.functions.invoke(
         "get-cloud-access-v1",

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/core/_settings_instance.py

@@ -5,14 +5,9 @@ import shutil
 from pathlib import Path
 from typing import TYPE_CHECKING, Literal
 
-from django.db import connection
-from django.db.utils import ProgrammingError
 from lamin_utils import logger
 
 from ._deprecated import deprecated
-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 (
     LEGACY_STORAGE_UID_FILE_KEY,
@@ -85,6 +80,7 @@ class InstanceSettings:
         _locker_user: UserSettings | None = None,  # user to lock for if cloud sqlite,
         _is_clone: bool = False,
     ):
+        # dynamic import to avoid importing pydantic at root
         from ._hub_utils import validate_db_arg
 
         self._id_: UUID = id
@@ -135,6 +131,9 @@ class InstanceSettings:
                     )
             elif attr == "db":
                 if self.dialect != "sqlite":
+                    # dynamic import to avoid importing pydantic at root
+                    from ._hub_utils import LaminDsn, LaminDsnModel
+
                     model = LaminDsnModel(db=value)
                     db_print = LaminDsn.build(
                         scheme=model.db.scheme,
@@ -166,6 +165,7 @@ class InstanceSettings:
     def _search_local_root(
         self, local_root: str | None = None, mute_warning: bool = False
     ) -> StorageSettings | None:
+        from django.db.utils import ProgrammingError
         from lamindb.models import Storage
 
         if local_root is not None:
@@ -375,6 +375,7 @@ class InstanceSettings:
         if self._db_permissions != "jwt":
             return None
 
+        from django.db import connection
         from lamindb.models import Space
 
         spaces: dict = {"admin": [], "write": [], "read": []}
@@ -452,6 +453,9 @@ class InstanceSettings:
             sqlite_file.synchronize_to(cache_file, print_progress=True)  # type: ignore
 
     def _check_sqlite_lock(self):
+        from ._hub_client import call_with_fallback
+        from ._hub_crud import select_account_handle_name_by_lnid
+
         if not self._cloud_sqlite_locker.has_lock:
             locked_by = self._cloud_sqlite_locker._locked_by
             lock_msg = "Cannot load the instance, it is locked by "
@@ -560,7 +564,7 @@ class InstanceSettings:
         Will return `False` in case the user token can't find the instance.
         """
         if self._is_on_hub is None:
-            from ._hub_client import call_with_fallback_auth
+            from ._hub_client import call_with_fallback, call_with_fallback_auth
             from ._hub_crud import select_instance_by_id
             from ._settings import settings
 

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/core/_settings_load.py

@@ -8,7 +8,6 @@ from uuid import UUID, uuid4
 
 from dotenv import dotenv_values
 from lamin_utils import logger
-from pydantic import ValidationError
 
 from lamindb_setup.errors import CurrentInstanceNotConfigured, SettingsEnvFileOutdated
 
@@ -49,7 +48,7 @@ def load_cache_path_from_settings(storage_settings: Path | None = None) -> Path
 
 def find_module_candidates():
     """Find all local packages that depend on lamindb."""
-    candidates = ["bionty", "wetlab"]
+    candidates = ["bionty", "pertdb"]
     return [c for c in candidates if find_spec(c) is not None]
 
 
@@ -72,8 +71,10 @@ def load_instance_settings(instance_settings_file: Path | None = None):
         # this errors only if the file was explicitly provided
         raise CurrentInstanceNotConfigured
     try:
-        settings_store = InstanceSettingsStore(_env_file=isettings_file)
-    except (ValidationError, TypeError) as error:
+        settings_store = InstanceSettingsStore.from_env_file(
+            isettings_file, "lamindb_instance_"
+        )
+    except (ValueError, KeyError, TypeError) as error:
         raise SettingsEnvFileOutdated(
             f"\n\n{error}\n\nYour instance settings file with\n\n{isettings_file.read_text()}\nis invalid"
             f" (likely outdated), see validation error. Please delete {isettings_file} &"
@@ -108,8 +109,10 @@ def load_or_create_user_settings(api_key: str | None = None) -> UserSettings:
 
 def load_user_settings(user_settings_file: Path):
     try:
-        settings_store = UserSettingsStore(_env_file=user_settings_file)
-    except (ValidationError, TypeError) as error:
+        settings_store = UserSettingsStore.from_env_file(
+            user_settings_file, "lamin_user_"
+        )
+    except (ValueError, KeyError, TypeError) as error:
         msg = (
             "Your user settings file is invalid, please delete"
             f" {user_settings_file} and log in again."
@@ -121,7 +124,7 @@ def load_user_settings(user_settings_file: Path):
 
 
 def _null_to_value(field, value=None):
-    return field if field != "null" else value
+    return value if field in (None, "null") else field
 
 
 def setup_instance_from_store(store: InstanceSettingsStore) -> InstanceSettings:
@@ -155,5 +158,5 @@ def setup_user_from_store(store: UserSettingsStore) -> UserSettings:
     settings.uid = store.uid
     settings.handle = _null_to_value(store.handle, value="anonymous")
     settings.name = _null_to_value(store.name)
-    settings._uuid = UUID(store.uuid) if store.uuid != "null" else None
+    settings._uuid = UUID(store.uuid) if store.uuid not in (None, "null") else None
     return settings

{lamindb_setup-1.18.1 → lamindb_setup-1.19.0}/lamindb_setup/core/_settings_save.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Optional, get_type_hints
+from typing import TYPE_CHECKING, Any, Optional, get_args, get_type_hints
 from uuid import UUID
 
 from ._settings_store import (
@@ -33,6 +33,21 @@ def save_user_settings(settings: UserSettings):
         )
 
 
+def _coerce_type_for_write(type_: Any) -> Any:
+    """Resolve union types to the non-None part for coercion when value is not None."""
+    if type_ in (str, bool):
+        return type_
+    if type_ == Optional[str]:  # noqa: UP045
+        return str
+    if type_ == Optional[bool]:  # noqa: UP045
+        return bool
+    args = get_args(type_) or ()
+    if type(None) in args:
+        non_none = next((a for a in args if a is not type(None)), type_)
+        return non_none if non_none in (str, bool) else type_
+    return type_
+
+
 def save_settings(
     settings: Any,
     settings_file: Path,
@@ -41,10 +56,7 @@ def save_settings(
 ):
     with open(settings_file, "w") as f:
         for store_key, type_ in type_hints.items():
-            if type_ == Optional[str]:  # noqa: UP045
-                type_ = str
-            if type_ == Optional[bool]:  # noqa: UP045
-                type_ = bool
+            type_ = _coerce_type_for_write(type_)
             if "__" not in store_key:
                 if store_key == "model_config":
                     continue