lamindb_setup 1.16.0__py3-none-any.whl → 1.18.0__py3-none-any.whl

lamindb_setup/core/upath.py

@@ -1005,13 +1005,22 @@ def check_storage_is_empty(
         objects = [o for o in objects if "/.lamindb/_exclusion/" not in o]
     n_files = len(objects)
     n_diff = n_files - n_offset_objects
-    ask_for_deletion = (
-        "delete them prior to deleting the storage location"
-        if raise_error
-        else "consider deleting them"
-    )
-    message = f"'{directory_string}' contains {n_diff} objects - {ask_for_deletion}"
     if n_diff > 0:
+        ask_for_deletion = (
+            "delete them prior to deleting the storage location"
+            if raise_error
+            else "consider deleting them"
+        )
+        message = f"'{directory_string}' contains {n_diff} objects:\n"
+        message += "\n".join(
+            [
+                o
+                for o in objects
+                if not o.endswith(".lamindb/storage_uid.txt")
+                and not (account_for_sqlite_file and o.endswith(".lamindb/lamin.db"))
+            ]
+        )
+        message += f"\n{ask_for_deletion}"
         if raise_error:
             raise StorageNotEmpty(message) from None
         else:

lamindb_setup/errors.py

@@ -1,13 +1,13 @@
 """Errors.
 
 .. autoexception:: CurrentInstanceNotConfigured
-.. autoexception:: InstanceNotSetupError
 .. autoexception:: ModuleWasntConfigured
 .. autoexception:: StorageAlreadyManaged
 .. autoexception:: StorageNotEmpty
 .. autoexception:: InstanceLockedException
 .. autoexception:: SettingsEnvFileOutdated
 .. autoexception:: CannotSwitchDefaultInstance
+.. autoexception:: InstanceNotFoundError
 
 """
 
@@ -25,17 +25,6 @@ class DefaultMessageException(Exception):
         super().__init__(message)
 
 
-# TODO: remove this exception sooner or later because we don't have a need for it anymore
-class InstanceNotSetupError(DefaultMessageException):
-    default_message = """\
-To use lamindb, you need to connect to an instance.
-
-Connect to an instance: `ln.connect()`. Init an instance: `ln.setup.init()`.
-
-If you used the CLI to set up lamindb in a notebook, restart the Python session.
-"""
-
-
 class CurrentInstanceNotConfigured(DefaultMessageException):
     default_message = """\
 No instance is connected! Call
@@ -63,6 +52,10 @@ class StorageNotEmpty(click.ClickException):
         pass
 
 
+class InstanceNotFoundError(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

@@ -14,7 +14,7 @@ from django.db import models, transaction
 from rich.progress import Progress
 
 if TYPE_CHECKING:
-    from collections.abc import Iterable, Sequence
+    from collections.abc import Iterable
     from typing import Literal
 
 
@@ -22,6 +22,9 @@ def _get_registries(module_name: str) -> list[str]:
     """Get registry class names from a module."""
     schema_module = import_module(module_name)
 
+    # Ensure that models are loaded; we've observed empty exports otherwise
+    from django.db import models
+
     return [
         name
         for name in dir(schema_module.models)
@@ -142,9 +145,9 @@ def _export_full_table(
 
 
 def export_db(
-    module_names: Sequence[str] | None = None,
+    module_names: Iterable[str] | None = None,
     *,
-    output_dir: str | Path = "./lamindb_export/",
+    output_dir: str | Path | None = None,
     max_workers: int = 8,
     chunk_size: int = 500_000,
 ) -> None:
@@ -159,6 +162,11 @@ def export_db(
         max_workers: Number of parallel processes.
         chunk_size: Number of rows per chunk for large tables.
     """
+    import lamindb_setup as ln_setup
+
+    if output_dir is None:
+        output_dir = f"./{ln_setup.settings.instance.name}_export/"
+
     directory = Path(output_dir)
     directory.mkdir(parents=True, exist_ok=True)
 
@@ -332,12 +340,15 @@ def import_db(
     Temporarily disables FK constraints to allow insertion in arbitrary order.
     Requires superuser/RDS admin privileges for postgres databases.
 
+    Note: When running in a subprocess, add a short delay or explicit connection close after `import_db()`
+    to ensure all SQLite writes are flushed to disk before process termination.
+
     Args:
         input_dir: Directory containing parquet files to import.
         module_names: Module names to import (e.g., ["lamindb", "bionty", "wetlab"]).
         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. 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. PKs and indices are preserved but database size will greatly increase.
+            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

{lamindb_setup-1.16.0.dist-info → lamindb_setup-1.18.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.16.0
+Version: 1.18.0
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10
@@ -15,14 +15,13 @@ Requires-Dist: httpx_retries<1.0.0
 Requires-Dist: requests
 Requires-Dist: universal_pathlib==0.2.6
 Requires-Dist: botocore<2.0.0
-Requires-Dist: supabase>=2.8.1,<=2.16.0
-Requires-Dist: gotrue<=2.12.0
-Requires-Dist: storage3!=0.11.2; python_version < '3.11'
+Requires-Dist: supabase>=2.20.0,<=2.24.0
+Requires-Dist: websockets>=13.0
 Requires-Dist: pyjwt<3.0.0
 Requires-Dist: psutil
 Requires-Dist: packaging
 Requires-Dist: aiobotocore[boto3]>=2.12.4,<3.0.0 ; extra == "aws"
-Requires-Dist: s3fs>=2023.12.2,<=2025.9.0,!=2024.10.0 ; extra == "aws"
+Requires-Dist: s3fs>=2023.12.2,<=2025.12.0,!=2024.10.0 ; extra == "aws"
 Requires-Dist: line_profiler ; extra == "dev"
 Requires-Dist: psycopg2-binary ; extra == "dev"
 Requires-Dist: python-dotenv ; extra == "dev"
@@ -33,7 +32,7 @@ Requires-Dist: pytest-xdist ; extra == "dev"
 Requires-Dist: nbproject-test>=0.4.3 ; extra == "dev"
 Requires-Dist: pandas ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
-Requires-Dist: gcsfs>=2023.12.2,<=2025.9.0 ; extra == "gcp"
+Requires-Dist: gcsfs>=2023.12.2,<=2025.12.0 ; extra == "gcp"
 Project-URL: Home, https://github.com/laminlabs/lamindb-setup
 Provides-Extra: aws
 Provides-Extra: dev

lamindb_setup-1.18.0.dist-info/RECORD

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lamindb_setup-1.16.0.dist-info/RECORD

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