lamindb_setup 0.76.6__tar.gz → 0.76.8__tar.gz

{lamindb_setup-0.76.6 → lamindb_setup-0.76.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.76.6
+Version: 0.76.8
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Description-Content-Type: text/markdown
@@ -13,11 +13,12 @@ Requires-Dist: appdirs<2.0.0
 Requires-Dist: requests
 Requires-Dist: universal_pathlib==0.2.2
 Requires-Dist: botocore<2.0.0
+Requires-Dist: gotrue>=2.1.0
 Requires-Dist: supabase==2.2.1
 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,<=2024.3.1 ; extra == "aws"
+Requires-Dist: s3fs>=2023.12.2,<=2024.6.1 ; extra == "aws"
 Requires-Dist: pyjwt<3.0.0 ; extra == "dev"
 Requires-Dist: psycopg2-binary ; extra == "dev"
 Requires-Dist: python-dotenv ; extra == "dev"
@@ -28,7 +29,7 @@ Requires-Dist: pytest-xdist ; extra == "dev"
 Requires-Dist: nbproject-test>=0.4.3 ; extra == "dev"
 Requires-Dist: pandas ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
-Requires-Dist: gcsfs>=2023.12.2,<=2024.3.1 ; extra == "gcp"
+Requires-Dist: gcsfs>=2023.12.2,<=2024.6.1 ; extra == "gcp"
 Project-URL: Home, https://github.com/laminlabs/lamindb-setup
 Provides-Extra: aws
 Provides-Extra: dev

{lamindb_setup-0.76.6 → lamindb_setup-0.76.8}/docs/hub-cloud/03-add-managed-storage.ipynb

@@ -324,14 +324,20 @@
    "outputs": [],
    "source": [
     "from laminhub_rest.core.instance.collaborator import InstanceCollaboratorHandler\n",
+    "from laminhub_rest.core.account.user import UserAccountHandler\n",
     "from lamindb_setup.core._hub_client import connect_hub_with_auth\n",
+    "from lnschema_core.models import User\n",
     "\n",
     "admin_hub = connect_hub_with_auth()\n",
-    "InstanceCollaboratorHandler(admin_hub).add_by_slug(\n",
-    "    \"testuser1/test-add-managed-storage\",\n",
-    "    \"testuser2\",\n",
-    "    \"write\"\n",
+    "testuser2 = UserAccountHandler(admin_hub).get_by_handle(\"testuser2\")\n",
+    "InstanceCollaboratorHandler(admin_hub).add(\n",
+    "    instance_id=instance_id,\n",
+    "    account_id=testuser2.id,\n",
+    "    role=\"write\",\n",
+    "    schema_id=None,\n",
+    "    skip_insert_user_table=True\n",
     ")\n",
+    "User.objects.create(uid=testuser2.lnid, handle=testuser2.handle, name=testuser2.name)\n",
     "admin_hub.auth.close()"
    ]
   },

{lamindb_setup-0.76.6 → lamindb_setup-0.76.8}/lamindb_setup/__init__.py

@@ -34,7 +34,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.76.6"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.76.8"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import sys
 from os import name as _os_name

{lamindb_setup-0.76.6 → lamindb_setup-0.76.8}/lamindb_setup/_migrate.py

@@ -31,7 +31,10 @@ def check_whether_migrations_in_sync(db_version_str: str):
         db_version_upper = f"{db_version.major}.{db_version.minor + 1}"
         logger.warning(
             f"your database ({db_version_str}) is ahead of your installed lamindb"
-            f" package ({installed_version_str}) \n❗ please update lamindb: pip install"
+            f" package ({installed_version_str})"
+        )
+        logger.important(
+            "please update lamindb: pip install"
             f' "lamindb>={db_version_lower},<{db_version_upper}"'
         )
     elif (
@@ -40,9 +43,9 @@ def check_whether_migrations_in_sync(db_version_str: str):
     ):
         logger.warning(
             f"your database ({db_version_str}) is behind your installed lamindb package"
-            f" ({installed_version_str}) \n❗ please migrate your database: lamin"
-            " migrate deploy"
+            f" ({installed_version_str})"
         )
+        logger.important("please migrate your database: lamin migrate deploy")
 
 
 # for tests, see lamin-cli

{lamindb_setup-0.76.6 → lamindb_setup-0.76.8}/lamindb_setup/_schema_metadata.py

@@ -95,22 +95,42 @@ def _dict_to_uuid(dict: dict):
 RelationType = Literal["many-to-one", "one-to-many", "many-to-many", "one-to-one"]
 Type = Literal[
     "ForeignKey",
-    "CharField",
-    "DateTimeField",
+    # the following are generated with `from django.db import models; [attr for attr in dir(models) if attr.endswith('Field')]`
     "AutoField",
-    "BooleanField",
-    "BigIntegerField",
-    "SmallIntegerField",
-    "TextField",
     "BigAutoField",
-    "ManyToManyField",
-    "IntegerField",
-    "OneToOneField",
-    "JSONField",
+    "BigIntegerField",
+    "BinaryField",
+    "BooleanField",
+    "CharField",
+    "CommaSeparatedIntegerField",
     "DateField",
+    "DateTimeField",
+    "DecimalField",
+    "DurationField",
+    "EmailField",
+    "Field",
+    "FileField",
+    "FilePathField",
     "FloatField",
-    "PositiveIntegerField",
+    "GeneratedField",
+    "GenericIPAddressField",
+    "IPAddressField",
+    "ImageField",
+    "IntegerField",
+    "JSONField",
+    "ManyToManyField",
+    "NullBooleanField",
+    "OneToOneField",
     "PositiveBigIntegerField",
+    "PositiveIntegerField",
+    "PositiveSmallIntegerField",
+    "SlugField",
+    "SmallAutoField",
+    "SmallIntegerField",
+    "TextField",
+    "TimeField",
+    "URLField",
+    "UUIDField",
 ]
 
 

{lamindb_setup-0.76.6 → lamindb_setup-0.76.8}/lamindb_setup/core/_hub_client.py

@@ -98,7 +98,7 @@ def get_access_token(email: str | None = None, password: str | None = None):
         )
         return auth_response.session.access_token
     finally:
-        hub.auth.sign_out()
+        hub.auth.sign_out(options={"scope": "local"})
 
 
 def call_with_fallback_auth(
@@ -113,7 +113,7 @@ def call_with_fallback_auth(
             result = callable(**kwargs, client=client)
         finally:
             try:
-                client.auth.sign_out()
+                client.auth.sign_out(options={"scope": "local"})
             except NameError:
                 pass
         return result
@@ -137,7 +137,7 @@ def call_with_fallback_auth(
                 raise e
         finally:
             try:
-                client.auth.sign_out()
+                client.auth.sign_out(options={"scope": "local"})
             except NameError:
                 pass
     return result
@@ -156,6 +156,9 @@ def call_with_fallback(
             if fallback_env:
                 raise e
         finally:
-            # in case there was sign in
-            client.auth.sign_out()
+            try:
+                # in case there was sign in
+                client.auth.sign_out(options={"scope": "local"})
+            except NameError:
+                pass
     return result

{lamindb_setup-0.76.6 → lamindb_setup-0.76.8}/lamindb_setup/core/_settings_instance.py

@@ -161,8 +161,9 @@ class InstanceSettings:
         elif not mute_warning:
             logger.warning(
                 f"none of the registered local storage locations were found in your environment: {local_records}"
-                "\n❗ please register a new local storage location via `ln.settings.storage_local = local_root_path` "
-                "and re-load/connect the instance"
+            )
+            logger.important(
+                "please register a new local storage location via `ln.settings.storage_local = local_root_path` and re-load/connect the instance"
             )
         return None
 

{lamindb_setup-0.76.6 → lamindb_setup-0.76.8}/lamindb_setup/core/_setup_bionty_sources.py

@@ -75,7 +75,9 @@ def load_bionty_sources(isettings: InstanceSettings):
 
     try:
         # need try except because of integer primary key migration
-        active_records = Source.objects.filter(currently_used=True).all().values()
+        active_records = (
+            Source.objects.filter(currently_used=True).order_by("id").all().values()
+        )
         for kwargs in active_records:
             for db_field, base_col in RENAME.items():
                 kwargs[base_col] = kwargs.pop(db_field)

{lamindb_setup-0.76.6 → lamindb_setup-0.76.8}/noxfile.py

@@ -32,7 +32,7 @@ def install(session: nox.Session, group: str) -> None:
 uv pip install --system --no-deps {no_deps_packages}
 """
     if group == "hub-cloud":
-        cmds = schema_deps + "uv pip install --system ./laminhub/rest-hub"
+        cmds = schema_deps + "uv pip install --system ./laminhub/rest-hub line_profiler"
     elif group == "docs":
         cmds = (
             """uv pip install --system git+https://github.com/laminlabs/lnschema-core"""
@@ -51,7 +51,7 @@ uv pip install --system --no-deps {no_deps_packages}
 
     # above downgrades django, I don't understand why, try this
     if group == "hub-local":
-        cmds += "\nuv pip install --system -e ./laminhub/rest-hub"
+        cmds += "\nuv pip install --system -e ./laminhub/rest-hub line_profiler"
 
     [run(session, line) for line in cmds.splitlines()]
 

{lamindb_setup-0.76.6 → lamindb_setup-0.76.8}/pyproject.toml

@@ -18,6 +18,7 @@ dependencies = [
     "requests",
     "universal_pathlib==0.2.2",  # is still experimental, need pinning
     "botocore<2.0.0",
+    "gotrue>=2.1.0", # for options in auth.sign_out
     "supabase==2.2.1",
     "psutil"
 ]
@@ -29,10 +30,10 @@ Home = "https://github.com/laminlabs/lamindb-setup"
 aws = [
     "urllib3<2", # for botocore, TODO: check that really required
     "aiobotocore[boto3]>=2.5.4,<3.0.0",
-    "s3fs>=2023.12.2,<=2024.3.1"
+    "s3fs>=2023.12.2,<=2024.6.1"
 ]
 gcp = [
-    "gcsfs>=2023.12.2,<=2024.3.1"
+    "gcsfs>=2023.12.2,<=2024.6.1"
 ]
 erdiagram = [
     "django-schema-graph",

{lamindb_setup-0.76.6 → lamindb_setup-0.76.8}/tests/hub-local/test_all.py

@@ -201,6 +201,7 @@ def test_db_user(
         account_id=reader_settings._uuid,
         instance_id=instance_id,
         role="read",
+        schema_id=None,
         skip_insert_user_table=True,
     )
     # check that this was successful and can be read by the reader