lamindb_setup 1.13.0__py3-none-any.whl → 1.14.0__py3-none-any.whl

lamindb_setup/__init__.py

@@ -4,25 +4,17 @@ Many functions in this "setup API" have a matching command in the :doc:`docs:cli
 
 Guide: :doc:`docs:setup`.
 
-Basic operations:
+Basic operations
+----------------
 
-.. autosummary::
-   :toctree:
+.. autofunction:: login
+.. autofunction:: logout
+.. autofunction:: init
+.. autofunction:: disconnect
+.. autofunction:: delete
 
-   login
-   logout
-   init
-   disconnect
-   delete
-
-Instance operations:
-
-.. autosummary::
-   :toctree:
-
-   migrate
-
-Modules & settings:
+Modules & settings
+------------------
 
 .. autosummary::
    :toctree:
@@ -33,9 +25,17 @@ Modules & settings:
    errors
    types
 
+Migration management
+--------------------
+
+.. autosummary::
+   :toctree:
+
+   migrate
+
 """
 
-__version__ = "1.13.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "1.14.0"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os
 import warnings

lamindb_setup/_migrate.py

@@ -109,6 +109,7 @@ class migrate:
             response = httpx.post(
                 f"{settings.instance.api_url}/instances/{settings.instance._id}/migrate",
                 headers={"Authorization": f"Bearer {settings.user.access_token}"},
+                timeout=None,  # this can take time
             )
             if response.status_code != 200:
                 raise Exception(f"Failed to migrate instance: {response.text}")

lamindb_setup/core/__init__.py

@@ -1,21 +1,16 @@
 """Core setup library.
 
-Settings:
-
-.. autosummary::
-   :toctree:
-
-   SetupSettings
-   UserSettings
-   InstanceSettings
-   StorageSettings
+.. autoclass:: SetupSettings
+.. autoclass:: UserSettings
+.. autoclass:: InstanceSettings
+.. autoclass:: StorageSettings
 
 """
 
 from . import django, upath
 from ._clone import connect_local_sqlite, init_local_sqlite
-from ._deprecated import deprecated
-from ._docs import doc_args
+from ._deprecated import deprecated  # documented in lamindb.base
+from ._docs import doc_args  # documented in lamindb.base
 from ._settings import SetupSettings
 from ._settings_instance import InstanceSettings
 from ._settings_storage import StorageSettings

lamindb_setup/core/_hub_core.py

@@ -551,6 +551,9 @@ def _connect_instance_hub(
                     db_user["password" if fine_grained_access else "db_user_password"],
                 )
 
+        db_user_name = "none" if db_user_name is None else db_user_name
+        db_user_password = "none" if db_user_password is None else db_user_password
+
         if use_proxy_db:
             host = instance.get("proxy_host", None)
             assert host is not None, (
@@ -560,14 +563,16 @@ def _connect_instance_hub(
             assert port is not None, (
                 "Database proxy port is not available, please do not pass 'use_proxy_db'."
             )
+            # remove supabase project id if present
+            db_user_name = db_user_name.rsplit(".", 1)[0]
         else:
             host = instance["db_host"]
             port = instance["db_port"]
 
         db_dsn = LaminDsn.build(
             scheme=instance["db_scheme"],
-            user=db_user_name if db_user_name is not None else "none",
-            password=db_user_password if db_user_password is not None else "none",
+            user=db_user_name,
+            password=db_user_password,
             host=host,
             port=port,
             database=instance["db_database"],

lamindb_setup/core/_settings.py

@@ -5,6 +5,7 @@ import sys
 from pathlib import Path
 from typing import TYPE_CHECKING
 
+import jwt
 from lamin_utils import logger
 from platformdirs import user_cache_dir
 
@@ -319,6 +320,35 @@ class SetupSettings:
         """
         return SetupPaths
 
+    def _debug_db_access(self):
+        """Debug database access problems."""
+        instance = self.instance
+        db_permissions = instance._db_permissions
+        print("db connection: ", instance.db)
+        print("db permissions: ", db_permissions)
+        if db_permissions != "jwt":
+            return
+        # sets the token if not present yet
+        print("available spaces: ", instance.available_spaces)
+
+        from lamindb_setup.core.django import db_token_manager
+
+        tokens = db_token_manager.tokens
+        if tokens:
+            for conn, token in tokens.items():
+                token_encoded = token._token
+                if token_encoded is None:
+                    token._refresh_token()
+                    token_encoded = token._token
+                token_decoded = jwt.decode(
+                    token_encoded, options={"verify_signature": False}
+                )
+                print(
+                    f"db token for the connection '{conn}' is '{token_encoded}': {token_decoded}"
+                )
+        else:
+            print("no db tokens are present")
+
     def __repr__(self) -> str:
         """Rich string representation."""
         from lamin_utils import colors

lamindb_setup/core/upath.py

@@ -737,25 +737,30 @@ UPath.exists.__doc__ = Path.exists.__doc__
 UPath.is_dir.__doc__ = Path.is_dir.__doc__
 UPath.is_file.__doc__ = Path.is_file.__doc__
 UPath.unlink.__doc__ = Path.unlink.__doc__
-UPath.rename.__doc__ = """Move file, see fsspec.AbstractFileSystem.mv.
+UPath.rename.__doc__ = """Move file, see `fsspec.AbstractFileSystem.mv`.
 
->>> upath = Upath("s3://my-bucket/my-file")
->>> upath.rename(UPath("s3://my-bucket/my-file-renamed"))
->>> upath.rename("my-file-renamed")
+For example::
 
->>> upath = Upath("local-folder/my-file")
->>> upath.rename("local-folder/my-file-renamed")
+    upath = UPath("s3://my-bucket/my-file")
+    upath.rename(UPath("s3://my-bucket/my-file-renamed"))
+    upath.rename("my-file-renamed")
 """
-UPath.__doc__ = """Paths: low-level key-value access to files/objects.
+UPath.__doc__ = """Paths: low-level key-value access to files.
 
-Paths are based on keys that offer the typical access patterns of file systems
- and object stores.
+Offers the typical access patterns of file systems and object stores, for instance::
 
->>> upath = UPath("s3://my-bucket/my-folder")
->>> upath.exists()
+    upath = UPath("s3://my-bucket/my-folder/my-file.txt")
+    upath.exists()  # file exists in storage
+
+LaminDB exposes `universal_pathlib.UPath` and adds functionality related to authentication and the following methods::
+
+    upath.view_tree()  # view a file tree
+    upath.upload_from("local-file.txt") # upload a local file
+    upath.download_to("local-file.txt") # download a file
+    upath.synchronize_to("local-folder/") # synchronize a folder
 
 Args:
-    pathlike: A string or Path to a local/cloud file/directory/folder.
+    pathlike: A string or `Path` to a local or cloud file/directory/folder.
 """
 
 logger.debug("upath.UPath has been patched")

lamindb_setup/errors.py

@@ -1,16 +1,13 @@
 """Errors.
 
-.. autosummary::
-   :toctree: .
-
-   CurrentInstanceNotConfigured
-   InstanceNotSetupError
-   ModuleWasntConfigured
-   StorageAlreadyManaged
-   StorageNotEmpty
-   InstanceLockedException
-   SettingsEnvFileOutdated
-   CannotSwitchDefaultInstance
+.. autoexception:: CurrentInstanceNotConfigured
+.. autoexception:: InstanceNotSetupError
+.. autoexception:: ModuleWasntConfigured
+.. autoexception:: StorageAlreadyManaged
+.. autoexception:: StorageNotEmpty
+.. autoexception:: InstanceLockedException
+.. autoexception:: SettingsEnvFileOutdated
+.. autoexception:: CannotSwitchDefaultInstance
 
 """
 

lamindb_setup/types.py

@@ -1,10 +1,7 @@
 """Types.
 
-.. autosummary::
-   :toctree: .
-
-   UPathStr
-   StorageType
+.. autoclass:: UPathStr
+.. autoclass:: StorageType
 """
 
 from __future__ import annotations

{lamindb_setup-1.13.0.dist-info → lamindb_setup-1.14.0.dist-info}/METADATA

@@ -1,12 +1,12 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.13.0
+Version: 1.14.0
 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: django>=5.1,<5.2
+Requires-Dist: django>=5.2,<5.3
 Requires-Dist: dj_database_url>=1.3.0,<3.0.0
 Requires-Dist: pydantic-settings
 Requires-Dist: platformdirs<5.0.0

{lamindb_setup-1.13.0.dist-info → lamindb_setup-1.14.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-lamindb_setup/__init__.py,sha256=SV2P-RJAPRv_l-GGuqpUGnfTTGxuutqh1UgzIgNjQTM,3112
+lamindb_setup/__init__.py,sha256=sxtG8b-Ej77NblAXc9qHKSUFtAnWUSSzNsDtUCwxjTY,3211
 lamindb_setup/_cache.py,sha256=pGvDNVHGx4HWr_6w5ajqEJOdysmaGc6F221qFnXkT-k,2747
 lamindb_setup/_check.py,sha256=28PcG8Kp6OpjSLSi1r2boL2Ryeh6xkaCL87HFbjs6GA,129
 lamindb_setup/_check_setup.py,sha256=ToKMxsUq8dQBQh8baOrNVlSb1iC8h4zTg5dV8wMu0W4,6760
@@ -10,28 +10,28 @@ lamindb_setup/_entry_points.py,sha256=sKwXPX9xjOotoAjvgkU5LBwjjHLWVkh0ZGdiSsrch9
 lamindb_setup/_exportdb.py,sha256=QLjoH4dEwqa01A12naKaDPglCCzl2_VLKWFfJRE_uSg,2113
 lamindb_setup/_importdb.py,sha256=fKv9ev5OOj_-bmzC8XZ1GxOcjIjI486yrHSHDWQrJeI,1874
 lamindb_setup/_init_instance.py,sha256=8ejD6zjV0eF7KR-DvnmDAVJb9Ty0hjaPtIkFbyLDvA0,14806
-lamindb_setup/_migrate.py,sha256=nkTzzNlUMqCAPujIgYK-A6Eg08r6LQAhm3rtbNtKZnU,11212
+lamindb_setup/_migrate.py,sha256=SN8uphuQX-8XShH5odLyzV8-eyXATDxB5hWoxwxmgBU,11264
 lamindb_setup/_register_instance.py,sha256=RdUZxZWHLdbvdNZWpF8e0UWROb_T0cStWbzc5yUw34I,1047
 lamindb_setup/_schema.py,sha256=b3uzhhWpV5mQtDwhMINc2MabGCnGLESy51ito3yl6Wc,679
 lamindb_setup/_schema_metadata.py,sha256=af1Es7qFKGPRdNmk48384HiB2r-cDTdBPu0wB9qrga4,15526
 lamindb_setup/_set_managed_storage.py,sha256=y5YQASsWNYVWUYeLgh3N2YBETYP7mBtbpxe3X_Vgb5I,2699
 lamindb_setup/_setup_user.py,sha256=DapdzT3u0f5LN5W9W9A6PWw-n8ejcJciQtHN9b5lidA,5889
 lamindb_setup/_silence_loggers.py,sha256=AKF_YcHvX32eGXdsYK8MJlxEaZ-Uo2f6QDRzjKFCtws,1568
-lamindb_setup/errors.py,sha256=qZTfSL0rpbY8AIG-Z4-3-_EbLW5zyo2CFEJrVU02-3A,1863
+lamindb_setup/errors.py,sha256=lccF3X3M2mcbHVG_0HxfuJRFFpUE-42paccIxFOfefQ,1958
 lamindb_setup/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-lamindb_setup/types.py,sha256=XlXLb4nmbc68uBj5Hp3xpDRezYGJIBZv6jAAqqN0p10,614
-lamindb_setup/core/__init__.py,sha256=qPSHqJoRKoG9542Au7EfTRFUHBPrKaCoXmNNwQEonMY,470
+lamindb_setup/types.py,sha256=fuQxZJnrGYe7a_Ju9n1RqO-HhkOAr1l1xjpAg9dmBu8,605
+lamindb_setup/core/__init__.py,sha256=z3Gy27SfnbO1gUMi-fVrL0yeLzUQ4K14vHOpw10hENo,536
 lamindb_setup/core/_aws_options.py,sha256=NtDLfR2BIz3MiR4rGrBu4uW70MFy2p3hjxCnN1sGDB8,9414
 lamindb_setup/core/_aws_storage.py,sha256=QEtV-riQrwfivcwqHnXBbkJ-9YyNEXL4fLoCmOHZ1BI,2003
 lamindb_setup/core/_clone.py,sha256=2NlXV04yykqg_k7z59C_kD1F1Hi4H-55H-JtNjhenQ0,3691
 lamindb_setup/core/_deprecated.py,sha256=M3vpM4fZPOncxY2qsXQAPeaEph28xWdv7tYaueaUyAA,2554
 lamindb_setup/core/_docs.py,sha256=3k-YY-oVaJd_9UIY-LfBg_u8raKOCNfkZQPA73KsUhs,276
 lamindb_setup/core/_hub_client.py,sha256=J0x43at0zb0yWP-RoT2lyqaHV66ewUP3OiYVYQCjxe8,9974
-lamindb_setup/core/_hub_core.py,sha256=ii7IZ_CVw_-GRgFgfvnXhVL6KI3UiuGKnMeIwTgiMd4,28907
+lamindb_setup/core/_hub_core.py,sha256=GAQK5XkHROIuqA-H8sOQZVlxvN4QIH_cmHY0TENnq2U,29090
 lamindb_setup/core/_hub_crud.py,sha256=j6516H82kLjFUNPqFGUINbDw9YbofMgjxadGzYb0OS4,6362
 lamindb_setup/core/_hub_utils.py,sha256=6dyDGyzYFgVfR_lE3VN3CP1jGp98gxPtr-T91PAP05U,2687
 lamindb_setup/core/_private_django_api.py,sha256=By63l3vIEtK1pq246FhHq3tslxsaTJGKm5VakYluWp4,2656
-lamindb_setup/core/_settings.py,sha256=QrxSClRK2GgP1-xgNSi0I0hp-wCTUsCs40CnFsncBts,14175
+lamindb_setup/core/_settings.py,sha256=FRHqCVmKjSqH4Y-33-LHUY9fLx6fEe88gXYUtiyqvmU,15289
 lamindb_setup/core/_settings_instance.py,sha256=7VXd1W88fgqEnAfzFQKUlDnTr3pmA_e8aIag7FqPrJI,23899
 lamindb_setup/core/_settings_load.py,sha256=j20cy3J56ZBHLDfB2A8oKjekNetMNsy0_W3eWD36pWI,5161
 lamindb_setup/core/_settings_save.py,sha256=jh412jXIAbIYvnSoW9riBFePRAa4vmPm-ScYD0smlnw,3292
@@ -44,8 +44,8 @@ lamindb_setup/core/django.py,sha256=2HwhtfUEX4peSkczc0VSfA-CpfCGL4vNgkPe9Pwu5kw,
 lamindb_setup/core/exceptions.py,sha256=qjMzqy_uzPA7mCOdnoWnS_fdA6OWbdZGftz-YYplrY0,84
 lamindb_setup/core/hashing.py,sha256=Y8Uc5uSGTfU6L2R_gb5w8DdHhGRog7RnkK-e9FEMjPY,3680
 lamindb_setup/core/types.py,sha256=T7NwspfRHgIIpYsXDcApks8jkOlGeGRW-YbVLB7jNIo,67
-lamindb_setup/core/upath.py,sha256=J43wCLFLRxNAUFN1bAtm6y6Mgt168JKq-wnhhG048Us,35486
-lamindb_setup-1.13.0.dist-info/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
-lamindb_setup-1.13.0.dist-info/WHEEL,sha256=CpUCUxeHQbRN5UGRQHYRJorO5Af-Qy_fHMctcQ8DSGI,82
-lamindb_setup-1.13.0.dist-info/METADATA,sha256=80aqYu5D3oJTyPh7GbZwC29u0m8fWNRL_BNLiRkZSJM,1798
-lamindb_setup-1.13.0.dist-info/RECORD,,
+lamindb_setup/core/upath.py,sha256=bi3k8AYeiGB_NtVTO9e9gHsfs2AFB4fXiVHcbNpnlpI,35780
+lamindb_setup-1.14.0.dist-info/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
+lamindb_setup-1.14.0.dist-info/WHEEL,sha256=CpUCUxeHQbRN5UGRQHYRJorO5Af-Qy_fHMctcQ8DSGI,82
+lamindb_setup-1.14.0.dist-info/METADATA,sha256=r0iCqy4CfmQ5hL_EExFqA32kGvZ3Rq8oQYZ7PcBjAEU,1798
+lamindb_setup-1.14.0.dist-info/RECORD,,