lamindb_setup 1.18.0__tar.gz → 1.18.2__tar.gz

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/.github/workflows/build.yml

@@ -137,7 +137,7 @@ jobs:
           touch .env.local
           echo "AWS_ACCESS_KEY_ID_HOSTED_S3=${{ secrets.AWS_ACCESS_KEY_ID }}" >> .env.local
           echo "AWS_SECRET_ACCESS_KEY_HOSTED_S3=${{ secrets.AWS_SECRET_ACCESS_KEY }}" >> .env.local
-        working-directory: laminhub/backend/central/supabase
+        working-directory: laminhub/backend/services/central/supabase
       - uses: actions/setup-python@v6
         with:
           python-version: "3.11" # we need to run everything for coverage on 3.11

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.18.0
+Version: 1.18.2
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/docs/hub-cloud/02-connect-local-instance.ipynb

@@ -94,10 +94,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# wetlab is not in the (schema) modules of mydata\n",
+    "# pertdb is not in the (schema) modules of mydata\n",
     "with pytest.raises(ModuleWasntConfigured):\n",
     "    # _check_instance_setup is called inside\n",
-    "    import wetlab"
+    "    import pertdb"
    ]
   },
   {

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/docs/hub-cloud/03-add-managed-storage.ipynb

@@ -48,11 +48,22 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "33c2bb76-d61f-4866-87e2-780e61600022",
+   "id": "cc2ba3c0",
    "metadata": {},
    "outputs": [],
    "source": [
     "import os\n",
+    "\n",
+    "os.environ[\"LAMINHUB_ID\"] = \"00000000-0000-0000-0000-000000000000\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "33c2bb76-d61f-4866-87e2-780e61600022",
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "import laminci\n",
     "import pytest\n",
     "from pathlib import Path\n",

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/docs/hub-prod/test-import-schema.ipynb

@@ -27,7 +27,7 @@
    },
    "outputs": [],
    "source": [
-    "!lamin init --storage test-implicit-load --modules wetlab,bionty"
+    "!lamin init --storage test-implicit-load --modules pertdb,bionty"
    ]
   },
   {
@@ -49,7 +49,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import wetlab as wl"
+    "import pertdb"
    ]
   },
   {
@@ -69,7 +69,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "wl.Compound"
+    "pertdb.Compound"
    ]
   },
   {

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/lamindb_setup/__init__.py

@@ -35,7 +35,7 @@ Migration management
 
 """
 
-__version__ = "1.18.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "1.18.2"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os
 import warnings

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/lamindb_setup/core/_settings_load.py

@@ -49,7 +49,7 @@ def load_cache_path_from_settings(storage_settings: Path | None = None) -> Path
 
 def find_module_candidates():
     """Find all local packages that depend on lamindb."""
-    candidates = ["bionty", "wetlab"]
+    candidates = ["bionty", "pertdb"]
     return [c for c in candidates if find_spec(c) is not None]
 
 

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/lamindb_setup/core/django.py

@@ -276,6 +276,27 @@ def setup_django(
                 ],
                 STATIC_URL="static/",
             )
+        if logger._verbosity == 5:  # debug-level verbosity
+            kwargs.update(
+                {
+                    "DEBUG": True,
+                    "LOGGING": {
+                        "version": 1,
+                        "handlers": {
+                            "console": {
+                                "level": "DEBUG",
+                                "class": "logging.StreamHandler",
+                            }
+                        },
+                        "loggers": {
+                            "django.db.backends": {
+                                "level": "DEBUG",
+                                "handlers": ["console"],
+                            }
+                        },
+                    },
+                }
+            )
         settings.configure(**kwargs)
         # this isn't needed the first time django.setup() is called, but for unknown reason it's needed the second time
         # the first time, it already defaults to true

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/lamindb_setup/io.py

@@ -156,7 +156,7 @@ def export_db(
     Ensure that you connect to postgres instances using `use_root_db_user=True`.
 
     Args:
-        module_names: Module names to export (e.g., ["lamindb", "bionty", "wetlab"]).
+        module_names: Module names to export (e.g., ["lamindb", "bionty", "pertdb"]).
             Defaults to "lamindb" if not provided.
         output_dir: Directory path for exported parquet files.
         max_workers: Number of parallel processes.
@@ -345,7 +345,7 @@ def import_db(
 
     Args:
         input_dir: Directory containing parquet files to import.
-        module_names: Module names to import (e.g., ["lamindb", "bionty", "wetlab"]).
+        module_names: Module names to import (e.g., ["lamindb", "bionty", "pertdb"]).
         if_exists: How to behave if table exists: 'fail', 'replace', or 'append'.
             If set to 'replace', existing data is deleted and new data is imported. All PKs and indices are not guaranteed to be preserved which can lead to write errors.
             If set to 'append', new data is added to existing data without clearing the table. All PKs and indices are preserved allowing write operations but database size will greatly increase.

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/noxfile.py

@@ -27,7 +27,7 @@ def lint(session: nox.Session) -> None:
     ["hub-local", "hub-prod", "hub-cloud", "storage", "connectivity", "docs"],
 )
 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"
+    no_deps_packages = "git+https://github.com/laminlabs/lamindb git+https://github.com/laminlabs/pertdb git+https://github.com/laminlabs/lamin-cli"
     modules_deps = f"""uv pip install --system --no-deps {no_deps_packages}
 uv pip install --system git+https://github.com/laminlabs/bionty
 """
@@ -37,9 +37,10 @@ uv pip install --system git+https://github.com/laminlabs/bionty
             + "uv pip install --system sentry_sdk line_profiler wheel==0.45.1 flit"
             + "\nuv pip install --system ./laminhub/backend --no-build-isolation"
             + "\nuv pip install --system ./laminhub/backend/utils"
-            + "\nuv pip install --system ./laminhub/backend/central"
-            + "\nuv pip install --system ./laminhub/backend/dbinstance"
-            + "\nuv pip install --system ./laminhub/backend/aws"
+            + "\nuv pip install --system ./laminhub/backend/services/central"
+            + "\nuv pip install --system ./laminhub/backend/services/instancedb"
+            + "\nuv pip install --system ./laminhub/backend/services/aws"
+            + "\nuv pip install --system --no-deps ./laminhub/backend/services/instancedb/hubmodule"
         )
     elif group == "docs":
         cmds = modules_deps.strip()
@@ -62,10 +63,10 @@ uv pip install --system git+https://github.com/laminlabs/bionty
         cmds += "\nuv pip install --system sentry_sdk line_profiler wheel==0.45.1 flit"
         cmds += "\nuv pip install --system -e ./laminhub/backend --no-build-isolation"
         cmds += "\nuv pip install --system -e ./laminhub/backend/utils"
-        cmds += "\nuv pip install --system -e ./laminhub/backend/central"
-        cmds += "\nuv pip install --system -e ./laminhub/backend/dbinstance"
-        cmds += "\nuv pip install --system -e ./laminhub/backend/aws"
-        cmds += "\nuv pip install --system --no-deps -e ./laminhub/backend/laminhub_rest/hubmodule"
+        cmds += "\nuv pip install --system -e ./laminhub/backend/services/central"
+        cmds += "\nuv pip install --system -e ./laminhub/backend/services/instancedb"
+        cmds += "\nuv pip install --system -e ./laminhub/backend/services/aws"
+        cmds += "\nuv pip install --system --no-deps -e ./laminhub/backend/services/instancedb/hubmodule"
         # check that just installing psycopg (psycopg3) doesn't break fine-grained access
         cmds += "\nuv pip install --system psycopg[binary]"
         # force new supabase

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/tests/hub-cloud/test_edge_request.py

@@ -43,7 +43,7 @@ def test_edge_request():
         assert instance["owner"] == "laminlabs"
         assert instance["name"] == "lamindata"
         assert instance["api_url"] == "https://aws.us-east-1.lamin.ai/api"
-        assert instance["schema_str"].startswith("bionty,wetlab")
+        assert instance["schema_str"].startswith("bionty,pertdb")
         assert "schema_id" in instance
         # check that schema_id is well-formed UUID
         # if not, throws ValueError

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/tests/hub-local/conftest.py

@@ -9,6 +9,7 @@ from lamincentral.client import SupabaseClientWrapper, connect_central
 from lamincentral.dev._local_supabase import (
     _remove_lamin_local_settings,
     _SupabaseLocalResources,
+    start_supabase,
 )
 from lamindb_setup.core._hub_client import (
     connect_hub_with_auth,
@@ -27,7 +28,7 @@ from lamindb_setup.core._settings_save import save_user_settings
 from lamindb_setup.core._settings_storage import base62
 from lamindb_setup.core._settings_storage import init_storage as init_storage_base
 from lamindb_setup.core._settings_user import UserSettings
-from laminhub_rest.dev import seed_local_test
+from laminhub_rest.dev._seed import LocalSeed
 from laminhub_rest.test.instance import create_instance
 from supabase_auth.errors import AuthApiError
 
@@ -42,11 +43,9 @@ def pytest_configure():
     os.environ["LAMIN_TEST_INSTANCE_SCHEMA_STR"] = "bionty"
     # Disable redis, it is not deployed here
     os.environ["EXTERNAL_CACHE_DISABLED"] = "true"
-    _remove_lamin_local_settings()
-    supabase_resources.start()
-    supabase_resources.reset()
-    supabase_resources.migrate()
-    seed_local_test()
+    # _remove_lamin_local_settings()
+    start_supabase()
+    LocalSeed.populate()
     # reset user
     del os.environ["LAMIN_API_KEY"]
     ln_setup.settings._user_settings = None

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/tests/hub-local/test_update_schema_in_hub.py

@@ -7,7 +7,7 @@ from lamindb_setup._schema_metadata import _dict_to_uuid, update_schema_in_hub
 def setup_instance():
     ln_setup.init(
         storage="./test_storage",
-        modules="bionty,wetlab",
+        modules="bionty,pertdb",
         db="postgresql://postgres:postgres@127.0.0.1:54322/postgres",
         name="test-update-modules",
     )
@@ -34,12 +34,12 @@ def test_update_schema_in_hub(setup_instance):
     assert module_set_info[1]["id"] == 0
     assert module_set_info[1]["name"] == "core"
     assert module_set_info[2]["id"] == 0
-    assert module_set_info[2]["name"] == "wetlab"
+    assert module_set_info[2]["name"] == "pertdb"
 
     assert len(schema["schema_json"].keys()) == 3
     assert "core" in schema["schema_json"]
     assert "bionty" in schema["schema_json"]
-    assert "wetlab" in schema["schema_json"]
+    assert "pertdb" in schema["schema_json"]
 
     assert not schema["schema_json"]["core"]["artifact"]["is_link_table"]
     assert not schema["schema_json"]["core"]["artifact"]["is_auto_created"]
@@ -149,7 +149,7 @@ def test_update_schema_in_hub(setup_instance):
         "related_schema_name": "bionty",
     }
 
-    assert schema["schema_json"]["wetlab"]["compound"]["fields"]["artifacts"] == {
+    assert schema["schema_json"]["pertdb"]["compound"]["fields"]["artifacts"] == {
         "type": "ManyToManyField",
         "column_name": None,
         "through": {
@@ -159,7 +159,7 @@ def test_update_schema_in_hub(setup_instance):
         },
         "field_name": "artifacts",
         "model_name": "compound",
-        "schema_name": "wetlab",
+        "schema_name": "pertdb",
         "is_link_table": False,
         "is_primary_key": False,
         "is_editable": False,

{lamindb_setup-1.18.0 → lamindb_setup-1.18.2}/tests/storage/conftest.py

@@ -5,6 +5,6 @@ import pytest
 def simple_instance():
     import lamindb_setup as ln_setup
 
-    ln_setup.init(storage="./testdb", modules="bionty,wetlab")
+    ln_setup.init(storage="./testdb", modules="bionty,pertdb")
     yield
     ln_setup.delete("testdb", force=True)