lamindb_setup 1.18.1__py3-none-any.whl → 1.19.0__py3-none-any.whl

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/_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/_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/_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/_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/_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/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/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/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/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/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/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/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

lamindb_setup/core/_settings_store.py

@@ -1,26 +1,25 @@
+from __future__ import annotations
+
 import os
+from dataclasses import MISSING, dataclass, fields
 from pathlib import Path
-from typing import Optional
+from typing import Any, get_args, get_type_hints
 
+from dotenv import dotenv_values
 from lamin_utils import logger
 from platformdirs import site_config_dir
-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
+    # Needed for AWS Lambda, as only tmp/ has write access
     settings_dir = Path(f"{os.environ['LAMIN_SETTINGS_DIR']}/.lamin")
 else:
-    # user_config_dir is weird on MacOS!
-    # hence, let's take home/.lamin
     settings_dir = Path.home() / ".lamin"
 
-
 try:
     settings_dir.mkdir(parents=True, exist_ok=True)
 except Exception as e:
     logger.warning(f"Failed to create lamin settings directory at {settings_dir}: {e}")
 
-
 system_settings_dir = Path(site_config_dir(appname="lamindb", appauthor="laminlabs"))
 
 
@@ -53,7 +52,6 @@ def user_settings_file_handle(handle: str):
     return settings_dir / f"{get_settings_file_name_prefix()}user--{handle}.env"
 
 
-# here user means the user directory on os, not a lamindb user
 def platform_user_storage_settings_file():
     return settings_dir / "storage.env"
 
@@ -62,31 +60,103 @@ def system_settings_file():
     return system_settings_dir / "system.env"
 
 
-class InstanceSettingsStore(BaseSettings):
-    api_url: str | None = None
+def _load_env_to_kwargs(
+    cls: type,
+    path: Path | str,
+    prefix: str,
+) -> dict[str, Any]:
+    path = Path(path) if isinstance(path, str) else path
+    raw = dotenv_values(path)
+    type_hints = get_type_hints(cls)
+    flds = {f.name: f for f in fields(cls)}
+    optional = {
+        n
+        for n, f in flds.items()
+        if f.default is not MISSING or f.default_factory is not MISSING
+    }
+
+    kwargs: dict[str, Any] = {}
+    for store_key in type_hints:
+        if store_key.startswith("__"):
+            continue
+        env_key = f"{prefix}{store_key}"
+        has_key = env_key in raw
+        raw_val = raw.get(env_key) if has_key else None
+        is_opt = store_key in optional
+
+        if not has_key:
+            if not is_opt:
+                raise ValueError(f"Missing required key {env_key!r} in env file {path}")
+            kwargs[store_key] = None
+            continue
+        if raw_val is None or raw_val == "" or raw_val == "null":
+            kwargs[store_key] = None
+            continue
+        type_ = type_hints[store_key]
+        args = get_args(type_) or ()
+        if type_ is bool:
+            kwargs[store_key] = raw_val.lower() in ("true", "1", "yes")
+        elif type(None) in args:
+            non_none = next((a for a in args if a is not type(None)), type_)
+            if non_none is bool:
+                kwargs[store_key] = raw_val.lower() in ("true", "1", "yes")
+            else:
+                kwargs[store_key] = raw_val
+        else:
+            kwargs[store_key] = raw_val
+    return kwargs
+
+
+@dataclass
+class InstanceSettingsStore:
+    # Required (no default) — must come first
     owner: str
     name: str
     storage_root: str
     storage_region: str | None
     db: str | None
     schema_str: str | None
-    schema_id: str | None = None
-    fine_grained_access: bool = False
-    db_permissions: str | None = None
     id: str
     git_repo: str | None
     keep_artifacts_local: bool | None
+    # Optional
+    api_url: str | None = None
+    schema_id: str | None = None
+    fine_grained_access: bool = False
+    db_permissions: str | None = None
     is_clone: bool = False
-    model_config = SettingsConfigDict(env_prefix="lamindb_instance_", env_file=".env")
+
+    @classmethod
+    def from_env_file(cls, path: Path | str, prefix: str) -> InstanceSettingsStore:
+        kwargs = _load_env_to_kwargs(cls, path, prefix)
+        return cls(**kwargs)
 
 
-class UserSettingsStore(BaseSettings):
+@dataclass
+class UserSettingsStore:
+    # Required (no default)
     email: str
     password: str
     access_token: str
-    api_key: str | None = None
     uid: str
     uuid: str
     handle: str
     name: str
-    model_config = SettingsConfigDict(env_prefix="lamin_user_", env_file=".env")
+    # Optional
+    api_key: str | None = None
+
+    @classmethod
+    def from_env_file(cls, path: Path | str, prefix: str) -> UserSettingsStore:
+        kwargs = _load_env_to_kwargs(cls, path, prefix)
+        return cls(**kwargs)
+
+
+@dataclass
+class Connector:
+    url: str
+    key: str
+
+    @classmethod
+    def from_env_file(cls, path: Path | str, prefix: str) -> Connector:
+        kwargs = _load_env_to_kwargs(cls, path, prefix)
+        return cls(**kwargs)

lamindb_setup/core/django.py

@@ -276,6 +276,27 @@ def setup_django(
                 ],
                 STATIC_URL="static/",
             )
+        if logger._verbosity == 5:  # debug-level verbosity
+            kwargs.update(
+                {
+                    "DEBUG": True,
+                    "LOGGING": {
+                        "version": 1,
+                        "handlers": {
+                            "console": {
+                                "level": "DEBUG",
+                                "class": "logging.StreamHandler",
+                            }
+                        },
+                        "loggers": {
+                            "django.db.backends": {
+                                "level": "DEBUG",
+                                "handlers": ["console"],
+                            }
+                        },
+                    },
+                }
+            )
         settings.configure(**kwargs)
         # this isn't needed the first time django.setup() is called, but for unknown reason it's needed the second time
         # the first time, it already defaults to true

lamindb_setup/errors.py

@@ -8,13 +8,12 @@
 .. autoexception:: SettingsEnvFileOutdated
 .. autoexception:: CannotSwitchDefaultInstance
 .. autoexception:: InstanceNotFoundError
+.. autoexception:: InstanceNotCreated
 
 """
 
 from __future__ import annotations
 
-import click
-
 
 class DefaultMessageException(Exception):
     default_message: str | None = None
@@ -47,15 +46,18 @@ class StorageAlreadyManaged(Exception):
     pass
 
 
-class StorageNotEmpty(click.ClickException):
-    def show(self, file=None):
-        pass
+class StorageNotEmpty(Exception):
+    pass
 
 
 class InstanceNotFoundError(Exception):
     pass
 
 
+class InstanceNotCreated(Exception):
+    pass
+
+
 # raise if a cloud SQLite instance is already locked
 # ignored by unlock_cloud_sqlite_upon_exception
 class InstanceLockedException(Exception):

lamindb_setup/io.py

@@ -8,10 +8,7 @@ from importlib import import_module
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-import numpy as np
-import pandas as pd
 from django.db import models, transaction
-from rich.progress import Progress
 
 if TYPE_CHECKING:
     from collections.abc import Iterable
@@ -59,6 +56,7 @@ def _export_full_table(
     Returns:
         String identifier for single-file exports, or list of (table_name, chunk_path) tuples for chunked exports that need merging.
     """
+    import pandas as pd
     from django.db import connection
 
     import lamindb_setup as ln_setup
@@ -156,12 +154,15 @@ def export_db(
     Ensure that you connect to postgres instances using `use_root_db_user=True`.
 
     Args:
-        module_names: Module names to export (e.g., ["lamindb", "bionty", "wetlab"]).
+        module_names: Module names to export (e.g., ["lamindb", "bionty", "pertdb"]).
             Defaults to "lamindb" if not provided.
         output_dir: Directory path for exported parquet files.
         max_workers: Number of parallel processes.
         chunk_size: Number of rows per chunk for large tables.
     """
+    import pandas as pd
+    from rich.progress import Progress
+
     import lamindb_setup as ln_setup
 
     if output_dir is None:
@@ -212,6 +213,9 @@ def export_db(
 
 def _serialize_value(val):
     """Convert value to JSON string if it's a dict, list, or numpy array, otherwise return as-is."""
+    # keep dynamic import to minimize import time
+    import numpy as np
+
     if isinstance(val, (dict, list, np.ndarray)):
         return json.dumps(
             val, default=lambda o: o.tolist() if isinstance(o, np.ndarray) else None
@@ -232,6 +236,8 @@ def _import_registry(
     For SQLite, uses multi-row INSERTs with dynamic chunking to stay under the 999
     variable limit (2-5x faster than single-row INSERTs).
     """
+    import numpy as np
+    import pandas as pd
     from django.db import connection
 
     table_name = registry._meta.db_table
@@ -345,13 +351,14 @@ def import_db(
 
     Args:
         input_dir: Directory containing parquet files to import.
-        module_names: Module names to import (e.g., ["lamindb", "bionty", "wetlab"]).
+        module_names: Module names to import (e.g., ["lamindb", "bionty", "pertdb"]).
         if_exists: How to behave if table exists: 'fail', 'replace', or 'append'.
             If set to 'replace', existing data is deleted and new data is imported. All PKs and indices are not guaranteed to be preserved which can lead to write errors.
             If set to 'append', new data is added to existing data without clearing the table. All PKs and indices are preserved allowing write operations but database size will greatly increase.
             If set to 'fail', raises an error if the table contains any data.
     """
     from django.db import connection
+    from rich.progress import Progress
 
     import lamindb_setup as ln_setup
 

{lamindb_setup-1.18.1.dist-info → lamindb_setup-1.19.0.dist-info}/METADATA

@@ -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.dist-info → lamindb_setup-1.19.0.dist-info}/RECORD

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