lamindb 1.3.1__tar.gz → 1.3.2__tar.gz

{lamindb-1.3.1 → lamindb-1.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.3.1
+Version: 1.3.2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10,<3.14
@@ -11,7 +11,7 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: lamin_utils==0.13.11
 Requires-Dist: lamin_cli==1.2.0
-Requires-Dist: lamindb_setup[aws]==1.4.0
+Requires-Dist: lamindb_setup[aws]==1.4.1
 Requires-Dist: pyyaml
 Requires-Dist: pyarrow
 Requires-Dist: pandera
@@ -23,7 +23,7 @@ Requires-Dist: anndata>=0.8.0,<=0.11.3
 Requires-Dist: fsspec
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
-Requires-Dist: bionty>=1.2a1 ; extra == "bionty"
+Requires-Dist: bionty>=1.2.1 ; extra == "bionty"
 Requires-Dist: cellregistry ; extra == "cellregistry"
 Requires-Dist: clinicore ; extra == "clinicore"
 Requires-Dist: tomlkit ; extra == "dev"

{lamindb-1.3.1 → lamindb-1.3.2}/lamindb/__init__.py

@@ -72,7 +72,7 @@ Backward compatibility.
 
 # ruff: noqa: I001
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "1.3.1"
+__version__ = "1.3.2"
 
 import warnings
 

{lamindb-1.3.1 → lamindb-1.3.2}/lamindb/models/record.py

@@ -612,9 +612,11 @@ class Registry(ModelBase):
                     f"Failed to load instance {instance}, please check your permissions!"
                 )
             iresult, _ = result
-            source_module = {
-                modules for modules in iresult["schema_str"].split(",") if modules != ""
-            }  # type: ignore
+            # do not use {} syntax below, it gives rise to a dict if the schema modules
+            # are empty and then triggers a TypeError in missing_members = source_module - target_module
+            source_module = set(  # noqa
+                [mod for mod in iresult["schema_str"].split(",") if mod != ""]
+            )
             target_module = ln_setup.settings.instance.modules
             if not source_module.issubset(target_module):
                 missing_members = source_module - target_module

{lamindb-1.3.1 → lamindb-1.3.2}/pyproject.toml

@@ -18,7 +18,7 @@ dependencies = [
     # Lamin PINNED packages
     "lamin_utils==0.13.11",
     "lamin_cli==1.2.0",
-    "lamindb_setup[aws]==1.4.0",
+    "lamindb_setup[aws]==1.4.1",
     # others
     "pyyaml",
     "pyarrow",
@@ -38,7 +38,7 @@ Home = "https://github.com/laminlabs/lamindb"
 
 [project.optional-dependencies]
 bionty = [
-    "bionty>=1.2a1",   # do not pin, is bounded in bionty
+    "bionty>=1.2.1",   # do not pin, is bounded in bionty
 ]
 gcp = [
     "lamindb_setup[gcp]",

{lamindb-1.3.1 → lamindb-1.3.2}/sub/bionty/bionty/__init__.py

@@ -89,7 +89,7 @@ Submodules:
 
 """
 
-__version__ = "1.2a1"
+__version__ = "1.2.1"
 
 from lamindb_setup._check_setup import _check_instance_setup
 

{lamindb-1.3.1 → lamindb-1.3.2}/sub/bionty/bionty/_organism.py

@@ -82,8 +82,10 @@ def organism_from_ensembl_id(id: str, using_key: str | None) -> Organism | None:
     import bionty as bt
     from bionty.base.dev._io import s3_bionty_assets
 
+    # below has to consume a file path and NOT a directory because otherwise it fails on reticulate
     localpath = s3_bionty_assets(
-        ".lamindb/0QeqXlKq9aqW8aqe0000.parquet", bt.base.settings.dynamicdir
+        ".lamindb/0QeqXlKq9aqW8aqe0000.parquet",
+        bt.base.settings.dynamicdir / "ensembl_prefix.parquet",
     )
     ensembl_prefixes = pd.read_parquet(localpath).set_index("gene_prefix")
 

{lamindb-1.3.1 → lamindb-1.3.2}/sub/bionty/bionty/base/dev/_io.py

@@ -103,8 +103,9 @@ def s3_bionty_assets(
 
     if localpath is None:
         localpath = settings.datasetdir / filename
-    elif localpath.is_dir():
-        localpath = localpath / filename
+    else:  # it errors on reticulate if we pass a directory
+        if localpath.exists():
+            assert localpath.is_file(), f"localpath {localpath} has to be a file path"
 
     bucket = assets_base_url.replace("s3://", "")
     s3_client = session.get_session().create_client(

{lamindb-1.3.1 → lamindb-1.3.2}/sub/lamindb-setup/lamindb_setup/__init__.py

@@ -33,7 +33,7 @@ Modules & settings:
 
 """
 
-__version__ = "1.4.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "1.4.1"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os
 

{lamindb-1.3.1 → lamindb-1.3.2}/sub/lamindb-setup/lamindb_setup/_init_instance.py

@@ -42,10 +42,9 @@ def get_schema_module_name(module_name, raise_import_error: bool = True) -> str
         module_spec = importlib.util.find_spec(name)
         if module_spec is not None:
             return name
-    message = f"schema module '{module_name}' is not installed → no access to its labels & registries (resolve via `pip install {module_name}`)"
+    message = f"schema module '{module_name}' is not installed → resolve via `pip install {module_name}`"
     if raise_import_error:
         raise ImportError(message)
-    logger.warning(message.lower())
     return None
 
 

{lamindb-1.3.1 → lamindb-1.3.2}/sub/lamindb-setup/pyproject.toml

@@ -18,7 +18,8 @@ dependencies = [
     "requests",
     "universal_pathlib==0.2.6",  # is still experimental, need pinning
     "botocore<2.0.0",
-    "supabase>=2.8.1,<=2.11.0", # from 2.8.1 has correct bounds on gotrue
+    "supabase>=2.8.1,<2.12.0", # from 2.8.1 has correct lower bounds on gotrue
+    "gotrue<2.12.0", # supabase doesn't have this upper bound
     "storage3!=0.11.2; python_version < '3.11'", # 0.11.2 breaks python 3.10 through usage of new types
     "pyjwt<3.0.0", # needed to decode jwt for sign in with the new api key
     "psutil",