lamindb_setup 1.1.0__tar.gz → 1.2.0__tar.gz

{lamindb_setup-1.1.0 → lamindb_setup-1.2.0}/.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.4
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.5.1
     hooks:
       - id: prettier
         exclude: |

{lamindb_setup-1.1.0 → lamindb_setup-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.1.0
+Version: 1.2.0
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10

{lamindb_setup-1.1.0 → lamindb_setup-1.2.0}/lamindb_setup/__init__.py

@@ -33,7 +33,7 @@ Modules & settings:
 
 """
 
-__version__ = "1.1.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "1.2.0"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os
 

{lamindb_setup-1.1.0 → lamindb_setup-1.2.0}/lamindb_setup/_schema_metadata.py

@@ -148,6 +148,8 @@ class FieldMetadata(BaseModel):
     model_name: str
     schema_name: str
     is_link_table: bool
+    is_primary_key: bool
+    is_editable: bool
     relation_type: RelationType | None = None
     related_field_name: str | None = None
     related_model_name: str | None = None
@@ -156,6 +158,8 @@ class FieldMetadata(BaseModel):
 
 class _ModelHandler:
     def __init__(self, model, module_name: str, included_modules: list[str]) -> None:
+        from lamindb.models import LinkORM
+
         self.model = model
         self.class_name = model.__name__
         self.module_name = module_name
@@ -163,12 +167,14 @@ class _ModelHandler:
         self.table_name = model._meta.db_table
         self.included_modules = included_modules
         self.fields = self._get_fields_metadata(self.model)
+        self.is_link_table = issubclass(model, LinkORM)
 
     def to_dict(self, include_django_objects: bool = True):
         _dict = {
             "fields": self.fields.copy(),
             "class_name": self.class_name,
             "table_name": self.table_name,
+            "is_link_table": self.is_link_table,
         }
 
         for field_name in self.fields.keys():
@@ -242,13 +248,16 @@ class _ModelHandler:
             related_model_name = None
             related_schema_name = None
             related_field_name = None
-            field_name = field.name
+            is_editable = field.editable
         else:
             related_model_name = field.related_model._meta.model_name
             related_schema_name = field.related_model.__get_module_name__()
             schema_name = field.model.__get_module_name__()
             related_field_name = field.remote_field.name
-            field_name = field.name
+            is_editable = False
+
+        field_name = field.name
+        is_primary_key = getattr(field, "primary_key", False)
 
         if relation_type in ["one-to-many"]:
             # For a one-to-many relation, the field belong
@@ -278,6 +287,8 @@ class _ModelHandler:
             field_name=field_name,
             type=internal_type,
             is_link_table=issubclass(field.model, LinkORM),
+            is_primary_key=is_primary_key,
+            is_editable=is_editable,
             column_name=column,
             relation_type=relation_type,
             related_schema_name=related_schema_name

{lamindb_setup-1.1.0 → lamindb_setup-1.2.0}/lamindb_setup/core/_aws_options.py

@@ -125,7 +125,13 @@ class AWSOptionsManager:
 
     def enrich_path(self, path: UPath, access_token: str | None = None) -> UPath:
         # ignore paths with non-lamin-managed endpoints
-        if path.storage_options.get("endpoint_url", None) not in LAMIN_ENDPOINTS:
+        if (
+            endpoint_url := path.storage_options.get("endpoint_url", None)
+        ) not in LAMIN_ENDPOINTS:
+            if "r2.cloudflarestorage.com" in endpoint_url:
+                # fixed_upload_size should always be True for R2
+                # this option is needed for correct uploads to R2
+                path = UPath(path, fixed_upload_size=True)
             return path
         # trailing slash is needed to avoid returning incorrect results
         # with .startswith

{lamindb_setup-1.1.0 → lamindb_setup-1.2.0}/lamindb_setup/core/_private_django_api.py

@@ -34,7 +34,6 @@ def private_django_api(reverse=False):
     # the order here matters
     # changing it might break the tests
     attributes = [
-        "DoesNotExist",
         "MultipleObjectsReturned",
         "add_to_class",
         "adelete",
@@ -72,10 +71,6 @@ def private_django_api(reverse=False):
             new_name = attr if reverse else f"_{attr}"
             content = content.replace(old_name, new_name)
 
-        if not reverse:
-            content = content.replace("Field_DoesNotExist", "FieldDoesNotExist")
-            content = content.replace("Object_DoesNotExist", "ObjectDoesNotExist")
-
         if content != original_content:
             file_path.write_text(content, encoding=encoding)
 

{lamindb_setup-1.1.0 → lamindb_setup-1.2.0}/lamindb_setup/core/upath.py

@@ -517,7 +517,7 @@ def modified(self) -> datetime | None:
 
 
 def compute_file_tree(
-    path: Path,
+    path: UPath,
     *,
     level: int = -1,
     only_dirs: bool = False,
@@ -526,6 +526,11 @@ def compute_file_tree(
     include_paths: set[Any] | None = None,
     skip_suffixes: list[str] | None = None,
 ) -> tuple[str, int]:
+    # .exists() helps to separate files from folders for gcsfs
+    # otherwise sometimes it has is_dir() True and is_file() True
+    if path.protocol == "gs" and not path.exists():
+        raise FileNotFoundError
+
     space = "    "
     branch = "│   "
     tee = "├── "

{lamindb_setup-1.1.0 → lamindb_setup-1.2.0}/noxfile.py

@@ -28,8 +28,8 @@ def lint(session: nox.Session) -> None:
 )
 def install(session: nox.Session, group: str) -> None:
     no_deps_packages = "git+https://github.com/laminlabs/lamindb git+https://github.com/laminlabs/wetlab git+https://github.com/laminlabs/lamin-cli"
-    modules_deps = f"""uv pip install --system git+https://github.com/laminlabs/bionty
-uv pip install --system --no-deps {no_deps_packages}
+    modules_deps = f"""uv pip install --system --no-deps {no_deps_packages}
+uv pip install --system git+https://github.com/laminlabs/bionty
 """
     if group == "hub-cloud":
         cmds = (
@@ -44,7 +44,7 @@ uv pip install --system --no-deps {no_deps_packages}
         # cmds += "uv pip install --system -e ./django\n"
         cmds = ""
         cmds += modules_deps.strip()
-        cmds += """\nuv pip install --system huggingface_hub"""
+        cmds += """\nuv pip install --system gcsfs huggingface_hub"""
     elif group == "hub-local":
         cmds = modules_deps.strip()
     # current package

{lamindb_setup-1.1.0 → lamindb_setup-1.2.0}/tests/hub-cloud/test_edge_request.py

@@ -42,7 +42,7 @@ def test_edge_request():
         assert instance["lnid"] == hash_and_encode_as_b62(UUID(instance["id"]).hex)[:12]
         assert instance["owner"] == "laminlabs"
         assert instance["name"] == "lamindata"
-        assert instance["api_url"] == "https://us-east-1.api.lamin.ai"
+        assert instance["api_url"] == "https://aws.us-east-1.lamin.ai/api"
         assert instance["schema_str"].startswith("bionty,wetlab")
         assert "schema_id" in instance
         # check that schema_id is well-formed UUID

{lamindb_setup-1.1.0 → lamindb_setup-1.2.0}/tests/hub-local/test_update_schema_in_hub.py

@@ -41,6 +41,9 @@ def test_update_schema_in_hub(setup_instance):
     assert "bionty" in schema["schema_json"]
     assert "wetlab" in schema["schema_json"]
 
+    assert not schema["schema_json"]["core"]["artifact"]["is_link_table"]
+    assert schema["schema_json"]["core"]["artifactulabel"]["is_link_table"]
+
     assert schema["schema_json"]["core"]["artifact"]["fields"]["id"] == {
         "type": "AutoField",
         "column_name": "id",
@@ -49,6 +52,8 @@ def test_update_schema_in_hub(setup_instance):
         "model_name": "artifact",
         "schema_name": "core",
         "is_link_table": False,
+        "is_primary_key": True,
+        "is_editable": True,  # Primary key are read-only even if is_editable is True
         "relation_type": None,
         "related_field_name": None,
         "related_model_name": None,
@@ -63,6 +68,8 @@ def test_update_schema_in_hub(setup_instance):
         "model_name": "artifact",
         "schema_name": "core",
         "is_link_table": False,
+        "is_primary_key": False,
+        "is_editable": False,
         "relation_type": None,
         "related_field_name": None,
         "related_model_name": None,
@@ -81,6 +88,8 @@ def test_update_schema_in_hub(setup_instance):
         "model_name": "artifact",
         "schema_name": "core",
         "is_link_table": False,
+        "is_primary_key": False,
+        "is_editable": False,
         "relation_type": "many-to-one",
         "related_field_name": "created_artifacts",
         "related_model_name": "user",
@@ -99,6 +108,8 @@ def test_update_schema_in_hub(setup_instance):
         "model_name": "gene",
         "schema_name": "bionty",
         "is_link_table": False,
+        "is_primary_key": False,
+        "is_editable": False,
         "relation_type": "many-to-many",
         "related_field_name": "genes",
         "related_model_name": "pathway",
@@ -117,6 +128,8 @@ def test_update_schema_in_hub(setup_instance):
         "model_name": "well",
         "schema_name": "wetlab",
         "is_link_table": False,
+        "is_primary_key": False,
+        "is_editable": False,
         "relation_type": "many-to-many",
         "related_field_name": "wells",
         "related_model_name": "artifact",
@@ -135,6 +148,8 @@ def test_update_schema_in_hub(setup_instance):
         "model_name": "transform",
         "schema_name": "core",
         "is_link_table": False,
+        "is_primary_key": False,
+        "is_editable": False,
         "relation_type": "many-to-many",
         "related_field_name": "successors",
         "related_model_name": "transform",
@@ -153,6 +168,8 @@ def test_update_schema_in_hub(setup_instance):
         "model_name": "transform",
         "schema_name": "core",
         "is_link_table": False,
+        "is_primary_key": False,
+        "is_editable": False,
         "relation_type": "many-to-many",
         "related_field_name": "predecessors",
         "related_model_name": "transform",

{lamindb_setup-1.1.0 → lamindb_setup-1.2.0}/tests/hub-prod/test_upath.py

@@ -6,6 +6,11 @@ import pytest
 from lamindb_setup.core.upath import ProgressCallback, UPath, create_path
 
 
+def test_view_tree():
+    with pytest.raises(FileNotFoundError):
+        UPath("gs://no-such-bucket-surely-145/folder").view_tree()
+
+
 def test_trailing_slash():
     assert UPath("s3://bucket/key/").path[-1] != "/"
     assert (UPath("s3://bucket/") / "key/").path[-1] != "/"
@@ -51,6 +56,10 @@ def test_create_path():
     upath = create_path("http://some_url.com/")
     assert upath.storage_options["use_listings_cache"]
     assert "timeout" in upath.storage_options["client_kwargs"]
+    # test R2
+    upath = create_path("s3://bucket/key?endpoint_url=https://r2.cloudflarestorage.com")
+    assert upath.as_posix() == "s3://bucket/key"
+    assert upath.storage_options["fixed_upload_size"]
 
 
 def test_progress_callback_size():