lamindb_setup 0.81.0__py3-none-any.whl → 0.81.2__py3-none-any.whl

lamindb_setup/__init__.py

@@ -33,7 +33,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.81.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.81.2"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 import sys as _sys

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

@@ -4,6 +4,7 @@
 from __future__ import annotations
 
 import os
+import warnings
 from collections import defaultdict
 from datetime import datetime, timezone
 from functools import partial
@@ -45,6 +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)
     #
@@ -708,6 +711,12 @@ Args:
     pathlike: A string or Path to a local/cloud file/directory/folder.
 """
 
+# suppress the warning from upath about hf (huggingface) filesystem
+# not being explicitly implemented in upath
+warnings.filterwarnings(
+    "ignore", module="upath", message=".*'hf' filesystem not explicitly implemented.*"
+)
+
 
 def create_path(path: UPath, access_token: str | None = None) -> UPath:
     path = UPath(path)

{lamindb_setup-0.81.0.dist-info → lamindb_setup-0.81.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.81.0
+Version: 0.81.2
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.9

{lamindb_setup-0.81.0.dist-info → lamindb_setup-0.81.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-lamindb_setup/__init__.py,sha256=Xm__DIYPUbJSjykjcT4bC-mR75b1GFYVGZ0owhVfCyI,1714
+lamindb_setup/__init__.py,sha256=o71S_vO9_RpZ91eHTH0FZG57w9nwWR54OUufTiq-aN8,1714
 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
@@ -34,14 +34,14 @@ lamindb_setup/core/_settings_save.py,sha256=rxGxgaK5i9exKqSJERQQyY1WZio20meoQJoY
 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=GD-EW9QSqJH023ox53hPDvjE86hFjXVhb0MSEU02HeY,28702
-lamindb_setup-0.81.0.dist-info/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
-lamindb_setup-0.81.0.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb_setup-0.81.0.dist-info/METADATA,sha256=mEUNPAf6Q4NfqeO2YuUIlADbKkLQLOFFzL-BNkvk3dY,1745
-lamindb_setup-0.81.0.dist-info/RECORD,,
+lamindb_setup/core/upath.py,sha256=a0yxP9dmujTn_hkDC0E2UuVsX-Img4i0kVNB-OV5K1s,29038
+lamindb_setup-0.81.2.dist-info/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
+lamindb_setup-0.81.2.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb_setup-0.81.2.dist-info/METADATA,sha256=qUDiU989EwoOfdbfJ8jXPCiGLXc1TLwgXQQAN5H1Iu0,1745
+lamindb_setup-0.81.2.dist-info/RECORD,,