lamindb_setup 0.78.0__py3-none-any.whl → 0.80.0__py3-none-any.whl

lamindb_setup/__init__.py

@@ -33,7 +33,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.78.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.80.0"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 import sys as _sys

lamindb_setup/_connect_instance.py

@@ -9,7 +9,11 @@ from lamin_utils import logger
 
 from ._check_setup import _check_instance_setup
 from ._close import close as close_instance
-from ._init_instance import MESSAGE_NO_MULTIPLE_INSTANCE, load_from_isettings
+from ._init_instance import (
+    MESSAGE_CANNOT_SWITCH_DEFAULT_INSTANCE,
+    CannotSwitchDefaultInstance,
+    load_from_isettings,
+)
 from ._silence_loggers import silence_loggers
 from .core._hub_core import connect_instance_hub
 from .core._hub_utils import (
@@ -224,7 +228,9 @@ def connect(slug: str, **kwargs) -> str | tuple | None:
                 logger.info(f"connected lamindb: {settings.instance.slug}")
                 return None
             else:
-                raise RuntimeError(MESSAGE_NO_MULTIPLE_INSTANCE)
+                raise CannotSwitchDefaultInstance(
+                    MESSAGE_CANNOT_SWITCH_DEFAULT_INSTANCE
+                )
         elif (
             _write_settings
             and settings._instance_exists

lamindb_setup/_init_instance.py

@@ -26,7 +26,7 @@ if TYPE_CHECKING:
     from .core.types import UPathStr
 
 
-def get_schema_module_name(schema_name) -> str:
+def get_schema_module_name(schema_name, raise_import_error: bool = True) -> str | None:
     import importlib.util
 
     name_attempts = [f"lnschema_{schema_name.replace('-', '_')}", schema_name]
@@ -34,9 +34,11 @@ def get_schema_module_name(schema_name) -> str:
         module_spec = importlib.util.find_spec(name)
         if module_spec is not None:
             return name
-    raise ImportError(
-        f"Python package for '{schema_name}' is not installed.\nIf your package is on PyPI, run `pip install {schema_name}`"
-    )
+    message = f"Schema module '{schema_name}' is not installed → no access to its labels & registries (resolve via `pip install {schema_name}`)"
+    if raise_import_error:
+        raise ImportError(message)
+    logger.warning(message.lower())
+    return None
 
 
 def register_storage_in_instance(ssettings: StorageSettings):
@@ -180,6 +182,8 @@ def validate_init_args(
         validate_schema_arg,
     )
 
+    if storage is None:
+        raise SystemExit("✗ `storage` argument can't be `None`")
     # should be called as the first thing
     name_str = infer_instance_name(storage=storage, name=name, db=db)
     owner_str = settings.user.handle if _user is None else _user.handle
@@ -206,10 +210,18 @@ def validate_init_args(
     return name_str, instance_id, instance_state, instance_slug
 
 
-MESSAGE_NO_MULTIPLE_INSTANCE = """
-Currently don't support subsequent connection to different databases in the same
-Python session.\n
-Try running on the CLI: lamin settings set auto-connect false
+class CannotSwitchDefaultInstance(SystemExit):
+    pass
+
+
+MESSAGE_CANNOT_SWITCH_DEFAULT_INSTANCE = """
+You cannot write to different instances in the same Python session.
+
+Do you want to read from another instance via `Record.using()`? For example:
+
+ln.Artifact.using("laminlabs/cellxgene").filter()
+
+Or do you want to switch off auto-connect via `lamin settings set auto-connect false`?
 """
 
 
@@ -248,7 +260,7 @@ def init(
         from ._check_setup import _check_instance_setup
 
         if _check_instance_setup() and not _test:
-            raise RuntimeError(MESSAGE_NO_MULTIPLE_INSTANCE)
+            raise CannotSwitchDefaultInstance(MESSAGE_CANNOT_SWITCH_DEFAULT_INSTANCE)
         elif _write_settings:
             close_instance(mute=True)
         from .core._hub_core import init_instance as init_instance_hub

lamindb_setup/_setup_user.py

@@ -48,14 +48,14 @@ def load_user(email: str | None = None, handle: str | None = None) -> UserSettin
 
 
 def login(
-    user: str | None = None, *, key: str | None = None, api_key: str | None = None
+    user: str | None = None, *, api_key: str | None = None, key: str | None = None
 ) -> None:
     """Log in user.
 
     Args:
         user: handle or email
-        key: API key
-        api_key: Beta API key
+        api_key: API key
+        key: legacy API key
     """
     if user is None and api_key is None:
         if "LAMIN_API_KEY" in os.environ:

lamindb_setup/core/_hub_client.py

@@ -10,6 +10,8 @@ from pydantic_settings import BaseSettings
 from supabase import Client, create_client  # type: ignore
 from supabase.lib.client_options import ClientOptions
 
+from ._settings_save import save_user_settings
+
 
 class Connector(BaseSettings):
     url: str
@@ -129,14 +131,17 @@ def call_with_fallback_auth(
 
     for renew_token, fallback_env in [(False, False), (True, False), (False, True)]:
         try:
-            if renew_token:
-                logger.warning(
-                    "renewing expired lamin token: call `lamin login <your-handle>` to avoid this"
-                )
             client = connect_hub_with_auth(
                 renew_token=renew_token, fallback_env=fallback_env
             )
             result = callable(**kwargs, client=client)
+            # we update access_token here
+            # because at this point the call has been successfully resolved
+            if renew_token:
+                from lamindb_setup import settings
+
+                # here settings.user contains an updated access_token
+                save_user_settings(settings.user)
             break
         # we use Exception here as the ways in which the client fails upon 401
         # are not consistent and keep changing

lamindb_setup/core/_settings.py

@@ -161,6 +161,15 @@ class SetupSettings:
         cache_dir.mkdir(parents=True, exist_ok=True)
         return cache_dir
 
+    @property
+    def paths(self) -> type[SetupPaths]:
+        """Convert cloud paths to lamidb local paths.
+
+        Use `settings.paths.cloud_to_local_no_update`
+        or `settings.paths.cloud_to_local`.
+        """
+        return SetupPaths
+
     def __repr__(self) -> str:
         """Rich string representation."""
         repr = self.user.__repr__()
@@ -174,6 +183,38 @@ class SetupSettings:
         return repr
 
 
+class SetupPaths:
+    """A static class for conversion of cloud paths to lamindb local paths."""
+
+    @staticmethod
+    def cloud_to_local_no_update(
+        filepath: UPathStr, cache_key: str | None = None
+    ) -> UPath:
+        """Local (or local cache) filepath from filepath without synchronization."""
+        # cache_key is ignored if filepath is a string or a local path
+        # ignores a mere string even if it represents a cloud path
+        if isinstance(filepath, UPath) and not isinstance(filepath, LocalPathClasses):
+            # settings is defined further in this file
+            local_filepath = settings.cache_dir / (
+                filepath.path if cache_key is None else cache_key
+            )
+        else:
+            local_filepath = filepath
+        return UPath(local_filepath)
+
+    @staticmethod
+    def cloud_to_local(
+        filepath: UPathStr, cache_key: str | None = None, **kwargs
+    ) -> UPath:
+        """Local (or local cache) filepath from filepath."""
+        # cache_key is ignored in cloud_to_local_no_update if filepath is local or a string
+        local_filepath = SetupPaths.cloud_to_local_no_update(filepath, cache_key)
+        if isinstance(filepath, UPath) and not isinstance(filepath, LocalPathClasses):
+            local_filepath.parent.mkdir(parents=True, exist_ok=True)
+            filepath.synchronize(local_filepath, **kwargs)
+        return local_filepath
+
+
 def get_env_name():
     if "LAMIN_ENV" in os.environ:
         return os.environ["LAMIN_ENV"]

lamindb_setup/core/_settings_storage.py

@@ -85,8 +85,8 @@ def init_storage(
     StorageSettings,
     Literal["hub-record-not-created", "hub-record-retireved", "hub-record-created"],
 ]:
-    if root is None:
-        raise ValueError("`storage` argument can't be `None`")
+    assert root is not None, "`root` argument can't be `None`"
+
     root_str = str(root)  # ensure we have a string
     if ".lamindb" in root_str:
         raise ValueError(
@@ -322,24 +322,20 @@ class StorageSettings:
         self, filepath: UPathStr, cache_key: str | None = None, **kwargs
     ) -> UPath:
         """Local (or local cache) filepath from filepath."""
-        # cache_key is ignored in cloud_to_local_no_update if filepath is local
-        local_filepath = self.cloud_to_local_no_update(filepath, cache_key)
-        if isinstance(filepath, UPath) and not isinstance(filepath, LocalPathClasses):
-            local_filepath.parent.mkdir(parents=True, exist_ok=True)
-            filepath.synchronize(local_filepath, **kwargs)
-        return local_filepath
+        from lamindb_setup import settings
+
+        return settings.paths.cloud_to_local(
+            filepath=filepath, cache_key=cache_key, **kwargs
+        )
 
     def cloud_to_local_no_update(
         self, filepath: UPathStr, cache_key: str | None = None
     ) -> UPath:
-        # cache_key is ignored if filepath is local
-        if isinstance(filepath, UPath) and not isinstance(filepath, LocalPathClasses):
-            local_filepath = self.cache_dir / (
-                filepath.path if cache_key is None else cache_key
-            )
-        else:
-            local_filepath = filepath
-        return UPath(local_filepath)
+        from lamindb_setup import settings
+
+        return settings.paths.cloud_to_local_no_update(
+            filepath=filepath, cache_key=cache_key
+        )
 
     def key_to_filepath(self, filekey: UPathStr) -> UPath:
         """Cloud or local filepath from filekey."""

lamindb_setup/core/_settings_user.py

@@ -24,9 +24,9 @@ class UserSettings:
     email: str | None = None
     """User email."""
     api_key: str | None = None
-    """Beta API key."""
+    """API key."""
     password: str | None = None
-    """API key or legacy password."""
+    """legacy API key or legacy password."""
     access_token: str | None = None
     """User access token."""
     uid: str = "null"

lamindb_setup/core/django.py

@@ -55,7 +55,17 @@ def setup_django(
         from .._init_instance import get_schema_module_name
 
         schema_names = ["core"] + list(isettings.schema)
-        installed_apps = [get_schema_module_name(n) for n in schema_names]
+        raise_import_error = True if init else False
+        installed_apps = [
+            package_name
+            for n in schema_names
+            if (
+                package_name := get_schema_module_name(
+                    n, raise_import_error=raise_import_error
+                )
+            )
+            is not None
+        ]
         if view_schema:
             installed_apps = installed_apps[::-1]  # to fix how apps appear
             installed_apps += ["schema_graph", "django.contrib.staticfiles"]

lamindb_setup/core/upath.py

@@ -763,13 +763,9 @@ def check_storage_is_empty(
         if raise_error
         else "consider deleting them"
     )
-    hint = "'_is_initialized'"
-    if n_offset_objects == 2:
-        hint += " & SQLite file"
-    hint += " ignored"
     message = (
-        f"Storage {directory_string} contains {n_objects - n_offset_objects} objects "
-        f"({hint}) - {ask_for_deletion}"
+        f"Storage '{directory_string}' contains {n_objects - n_offset_objects} objects"
+        f" - {ask_for_deletion}"
     )
     if n_diff > 0:
         if raise_error:

{lamindb_setup-0.78.0.dist-info → lamindb_setup-0.80.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.78.0
+Version: 0.80.0
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.9

{lamindb_setup-0.78.0.dist-info → lamindb_setup-0.80.0.dist-info}/RECORD

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