lamindb_setup 0.81.1__py3-none-any.whl → 0.81.3__py3-none-any.whl

lamindb_setup/__init__.py

@@ -33,7 +33,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.81.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.81.3"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 import sys as _sys

lamindb_setup/core/_settings.py

@@ -195,27 +195,30 @@ class SetupPaths:
         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):
+        if not isinstance(filepath, UPath):
+            filepath = UPath(filepath)
+        # cache_key is ignored if filepath is a local path
+        if 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
+                filepath.path if cache_key is None else cache_key  # type: ignore
             )
         else:
             local_filepath = filepath
-        return UPath(local_filepath)
+        return 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
+        if not isinstance(filepath, UPath):
+            filepath = UPath(filepath)
+        # cache_key is ignored in cloud_to_local_no_update if filepath is local
         local_filepath = SetupPaths.cloud_to_local_no_update(filepath, cache_key)
-        if isinstance(filepath, UPath) and not isinstance(filepath, LocalPathClasses):
+        if not isinstance(filepath, LocalPathClasses):
             local_filepath.parent.mkdir(parents=True, exist_ok=True)
-            filepath.synchronize(local_filepath, **kwargs)
+            filepath.synchronize(local_filepath, **kwargs)  # type: ignore
         return local_filepath
 
 

lamindb_setup/core/_setup_bionty_sources.py

@@ -1,8 +1,12 @@
 from __future__ import annotations
 
+import os
 from typing import TYPE_CHECKING
 
 from django.db.utils import OperationalError, ProgrammingError
+from lamin_utils import logger
+
+from ._settings import settings as setup_settings
 
 if TYPE_CHECKING:
     from ._settings_instance import InstanceSettings
@@ -63,10 +67,21 @@ def write_bionty_sources(isettings: InstanceSettings) -> None:
     Source.objects.bulk_create(all_records, ignore_conflicts=True)
 
 
-def load_bionty_sources(isettings: InstanceSettings):
+def load_bionty_sources(isettings: InstanceSettings | None = None):
     """Write currently_used bionty sources to LAMINDB_VERSIONS_PATH in bionty."""
-    if "bionty" not in isettings.schema:
-        return None
+    if isettings is None:
+        if setup_settings._instance_settings is not None:
+            isettings = setup_settings.instance
+        else:
+            logger.warning(
+                f"Ignoring bionty setup because running in LAMINDB_MULTI_INSTANCE mode = {os.environ.get('LAMINDB_MULTI_INSTANCE')}"
+            )
+            # not setting up bionty sources
+            return None
+    if isettings is not None:
+        if "bionty" not in isettings.schema:
+            # no need to setup anything
+            return None
 
     import bionty.base as bionty_base
     from bionty.base.dev._handle_sources import parse_currently_used_sources

lamindb_setup/core/upath.py

@@ -46,6 +46,8 @@ VALID_SIMPLE_SUFFIXES = {
     ".tsv",
     ".zip",
     ".xml",
+    ".qs",  # https://cran.r-project.org/web/packages/qs/vignettes/vignette.html
+    ".rds",
     #
     # with readers (see below)
     #

{lamindb_setup-0.81.1.dist-info → lamindb_setup-0.81.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.81.1
+Version: 0.81.3
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.9
@@ -14,12 +14,11 @@ Requires-Dist: appdirs<2.0.0
 Requires-Dist: requests
 Requires-Dist: universal_pathlib==0.2.5
 Requires-Dist: botocore<2.0.0
-Requires-Dist: gotrue>=2.1.0,<2.9.0
-Requires-Dist: supabase==2.2.1
+Requires-Dist: supabase>=2.8.1,<=2.10.0
 Requires-Dist: psutil
 Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: aiobotocore[boto3]>=2.5.4,<3.0.0 ; extra == "aws"
-Requires-Dist: s3fs>=2023.12.2,<=2024.10.0 ; extra == "aws"
+Requires-Dist: s3fs>=2023.12.2,<=2024.10.0,!=2024.10.0 ; extra == "aws"
 Requires-Dist: line_profiler ; extra == "dev"
 Requires-Dist: pyjwt<3.0.0 ; extra == "dev"
 Requires-Dist: psycopg2-binary ; extra == "dev"

{lamindb_setup-0.81.1.dist-info → lamindb_setup-0.81.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-lamindb_setup/__init__.py,sha256=dFAjI0r6-lM4WoJ3n0uo6iCdKHvnV-20y76RufgIFCQ,1714
+lamindb_setup/__init__.py,sha256=xPpghv8_6NLAzTOyEbqSg4UsrBIVXl-wFpemsz9p40o,1714
 lamindb_setup/_cache.py,sha256=1XnM-V_KprbjpgPY7Bg3FYn53Iz_2_fEgcMOaSdKKbg,1332
 lamindb_setup/_check.py,sha256=28PcG8Kp6OpjSLSi1r2boL2Ryeh6xkaCL87HFbjs6GA,129
 lamindb_setup/_check_setup.py,sha256=6cSfpmVOSgU7YiVHfJpBTGTQ7rrnwunt1pJT_jkgNM8,3196
@@ -27,21 +27,21 @@ lamindb_setup/core/_hub_core.py,sha256=eUxRz9iJj6RA5-MWgQqqZYAU-di5LQDamRZn6t-VO
 lamindb_setup/core/_hub_crud.py,sha256=eZErpq9t1Cp2ULBSi457ekrcqfesw4Y6IJgaqyrINMY,5276
 lamindb_setup/core/_hub_utils.py,sha256=08NwQsb53-tXa_pr-f0tPTN0FeeVf_i1p3dEbEWD0F4,3016
 lamindb_setup/core/_private_django_api.py,sha256=KIn43HOhiRjkbTbddyJqv-WNTTa1bAizbM1tWXoXPBg,2869
-lamindb_setup/core/_settings.py,sha256=mpGsSb98UsBedLsW2RuowZ17EP2tI2XRGPztqrJtrV4,7952
+lamindb_setup/core/_settings.py,sha256=RostEkf87oC8E4D8LMxb5NcnFKu9I8YFDMehLbwlwhE,7988
 lamindb_setup/core/_settings_instance.py,sha256=ajcq9zRNE598tTqyMkMqaEOubVfFeE998DPtbgyzK3A,18801
 lamindb_setup/core/_settings_load.py,sha256=5OpghcbkrK9KBM_0Iu-61FTI76UbOpPkkJpUittXS-w,4098
 lamindb_setup/core/_settings_save.py,sha256=rxGxgaK5i9exKqSJERQQyY1WZio20meoQJoYXlVW-1w,3138
 lamindb_setup/core/_settings_storage.py,sha256=CYwGZm0fKYN7eLLsU-sOtOKG7HzswQVjTWb0ooHKcNg,11990
 lamindb_setup/core/_settings_store.py,sha256=WcsgOmgnu9gztcrhp-N4OONNZyxICHV8M0HdJllTaEo,2219
 lamindb_setup/core/_settings_user.py,sha256=iz0MqFLKXqm8LYx_CHmr02_oNvYWFLIxKkJLdpS5W08,1476
-lamindb_setup/core/_setup_bionty_sources.py,sha256=o2L5Ww8TKgSqJtL4cGUcpJwLNYxA9BZgddhCMCu_E2g,3428
+lamindb_setup/core/_setup_bionty_sources.py,sha256=jZOPXpipW_5IjMO-bLMk-_wVwk7-5MLd72K2rnqqy7U,4001
 lamindb_setup/core/cloud_sqlite_locker.py,sha256=i6TrT7HG0lqliPvZTlsZ_uplPaqhPBbabyfeR32SkA8,7107
 lamindb_setup/core/django.py,sha256=E4U9nUlV2kHd-G5v6iSdFGAAWixlQDxOFwMwOMG9xfw,3864
 lamindb_setup/core/exceptions.py,sha256=4NpLUNUIfXYVTFX2FvLZF8RW34exk2Vn2X3G4YhnTRg,276
 lamindb_setup/core/hashing.py,sha256=26dtak7XgmrWa_D1zuDyxObRQcriMtnc1yEigkKASmM,3142
 lamindb_setup/core/types.py,sha256=zJii2le38BJUmsNVvzDrbzGYr0yaeb-9Rw9IKmsBr3k,523
-lamindb_setup/core/upath.py,sha256=4rCC0EOe-UaCexRDReQ5D_zs13Zi626pqn1slYNvISE,28945
-lamindb_setup-0.81.1.dist-info/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
-lamindb_setup-0.81.1.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb_setup-0.81.1.dist-info/METADATA,sha256=yvD9AXAL_lFbagwrcvhId-DMCbgFHtWxZ8fVxobspDM,1745
-lamindb_setup-0.81.1.dist-info/RECORD,,
+lamindb_setup/core/upath.py,sha256=a0yxP9dmujTn_hkDC0E2UuVsX-Img4i0kVNB-OV5K1s,29038
+lamindb_setup-0.81.3.dist-info/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
+lamindb_setup-0.81.3.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb_setup-0.81.3.dist-info/METADATA,sha256=VPKC024x5sheF1oT-iZRMb4k77WARFy2Y2PwA4Z_S9E,1730
+lamindb_setup-0.81.3.dist-info/RECORD,,