lamindb_setup 0.76.1__tar.gz → 0.76.3__tar.gz

{lamindb_setup-0.76.1 → lamindb_setup-0.76.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.76.1
+Version: 0.76.3
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Description-Content-Type: text/markdown

{lamindb_setup-0.76.1 → lamindb_setup-0.76.3}/lamindb_setup/__init__.py

@@ -34,7 +34,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.76.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.76.3"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import sys
 from os import name as _os_name

{lamindb_setup-0.76.1 → lamindb_setup-0.76.3}/lamindb_setup/_schema_metadata.py

@@ -22,6 +22,13 @@ from lamindb_setup import settings
 from lamindb_setup._init_instance import get_schema_module_name
 from lamindb_setup.core._hub_client import call_with_fallback_auth
 
+# surpress pydantic warning about `model_` namespace
+try:
+    BaseModel.model_config["protected_namespaces"] = ()
+except Exception:
+    pass
+
+
 if TYPE_CHECKING:
     from supabase import Client
 
@@ -349,7 +356,9 @@ class _SchemaHandler:
         return self.to_dict(include_django_objects=False)
 
     def _get_modules_metadata(self):
-        return {
+        from lnschema_core.models import Record, Registry
+
+        all_models = {
             module_name: {
                 model._meta.model_name: _ModelHandler(
                     model, module_name, self.included_modules
@@ -357,13 +366,15 @@ class _SchemaHandler:
                 for model in self._get_schema_module(
                     module_name
                 ).models.__dict__.values()
-                if model.__class__.__name__ == "RecordMeta"
-                and model.__name__ not in ["Record", "ORM"]
+                if model.__class__ is Registry
+                and model is not Record
                 and not model._meta.abstract
                 and model.__get_schema_name__() == module_name
             }
             for module_name in self.included_modules
         }
+        assert all_models
+        return all_models
 
     def _get_module_set_info(self):
         # TODO: rely on schemamodule table for this

{lamindb_setup-0.76.1 → lamindb_setup-0.76.3}/lamindb_setup/core/upath.py

@@ -28,7 +28,7 @@ LocalPathClasses = (PosixUPath, WindowsUPath, LocalPath)
 # also see https://gist.github.com/securifera/e7eed730cbe1ce43d0c29d7cd2d582f4
 #    ".gz" is not listed here as it typically occurs with another suffix
 # the complete list is at lamindb.core.storage._suffixes
-VALID_SUFFIXES = {
+VALID_SIMPLE_SUFFIXES = {
     #
     # without readers
     #
@@ -56,11 +56,8 @@ VALID_SUFFIXES = {
     ".zarr",
     ".json",
 }
-VALID_COMPOSITE_SUFFIXES = {
-    ".anndata.zarr",
-    ".spatialdata.zarr",
-    ".ome.zarr",
-}
+# below gets updated within lamindb because it's frequently changing
+VALID_COMPOSITE_SUFFIXES = {".anndata.zarr"}
 
 TRAILING_SEP = (os.sep, os.altsep) if os.altsep is not None else os.sep
 
@@ -76,7 +73,7 @@ def extract_suffix_from_path(path: Path, arg_name: str | None = None) -> str:
         return process_digits(path.suffix)
 
     total_suffix = "".join(path.suffixes)
-    if total_suffix in VALID_SUFFIXES:
+    if total_suffix in VALID_SIMPLE_SUFFIXES:
         return total_suffix
     elif total_suffix.endswith(tuple(VALID_COMPOSITE_SUFFIXES)):
         # below seems slow but OK for now
@@ -94,7 +91,7 @@ def extract_suffix_from_path(path: Path, arg_name: str | None = None) -> str:
         # in COMPRESSION_SUFFIXES to detect something like .random.gz and then
         # add ".random.gz" but concluded it's too dangerous it's safer to just
         # use ".gz" in such a case
-        if path.suffixes[-2] in VALID_SUFFIXES:
+        if path.suffixes[-2] in VALID_SIMPLE_SUFFIXES:
             suffix = "".join(path.suffixes[-2:])
             msg += f"inferring: '{suffix}'"
             # do not print a warning for things like .tar.gz, .fastq.gz
@@ -105,7 +102,7 @@ def extract_suffix_from_path(path: Path, arg_name: str | None = None) -> str:
             msg += (
                 f"using only last suffix: '{suffix}' - if you want your composite"
                 " suffix to be recognized add it to"
-                " lamindb.core.storage.VALID_SUFFIXES.add()"
+                " lamindb.core.storage.VALID_SIMPLE_SUFFIXES.add()"
             )
         if print_hint:
             logger.hint(msg)

{lamindb_setup-0.76.1 → lamindb_setup-0.76.3}/tests/hub-local/test_update_schema_in_hub.py

@@ -57,7 +57,7 @@ def test_update_schema_in_hub(setup_instance):
 
     assert schema["schema_json"]["core"]["artifact"]["fields"]["_accessor"] == {
         "type": "CharField",
-        "column_name": "accessor",
+        "column_name": "_accessor",
         "through": None,
         "field_name": "_accessor",
         "model_name": "artifact",

{lamindb_setup-0.76.1 → lamindb_setup-0.76.3}/tests/storage/test_storage_basis.py

@@ -19,7 +19,7 @@ def test_extract_suffix_from_path():
         ("logs/date.log.123", ""),  # digits are no valid suffixes
         ("salmon.merged.gene_counts.tsv", ".tsv"),
         ("salmon.merged.gene_counts.tsv.gz", ".tsv.gz"),
-        ("filename.v1.1.0.spatialdata.zarr", ".spatialdata.zarr"),
+        ("filename.v1.1.0.anndata.zarr", ".anndata.zarr"),
     ]
     for path, suffix in collection:
         filepath = Path(path)