lamindb_setup 0.73.2__tar.gz → 0.73.3__tar.gz

{lamindb_setup-0.73.2 → lamindb_setup-0.73.3}/.gitignore

@@ -108,3 +108,4 @@ lamin_sphinx
 docs/conf.py
 _docs_tmp*
 *.lndb
+_is_initialized

{lamindb_setup-0.73.2 → lamindb_setup-0.73.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.73.2
+Version: 0.73.3
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <laminlabs@gmail.com>
 Description-Content-Type: text/markdown

{lamindb_setup-0.73.2 → lamindb_setup-0.73.3}/docs/changelog.md

@@ -3,6 +3,10 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+💚 Fix test | [784](https://github.com/laminlabs/lamindb-setup/pull/784) | [falexwolf](https://github.com/falexwolf) | 2024-06-26 | 0.73.3
+♻️ Save schema to hub upon init | [782](https://github.com/laminlabs/lamindb-setup/pull/782) | [falexwolf](https://github.com/falexwolf) | 2024-06-24 |
+💚 Fix schema serialization test | [781](https://github.com/laminlabs/lamindb-setup/pull/781) | [falexwolf](https://github.com/falexwolf) | 2024-06-24 |
+Better error message | [780](https://github.com/laminlabs/lamindb-setup/pull/780) | [falexwolf](https://github.com/falexwolf) | 2024-06-20 |
 🐛 Fix permission error when screening for local storage root | [778](https://github.com/laminlabs/lamindb-setup/pull/778) | [falexwolf](https://github.com/falexwolf) | 2024-06-19 | 0.73.2
 🐛 Fix same root check in get_locker | [777](https://github.com/laminlabs/lamindb-setup/pull/777) | [Koncopd](https://github.com/Koncopd) | 2024-06-13 |
 ✨ Add .ome.zarr as composite suffix | [775](https://github.com/laminlabs/lamindb-setup/pull/775) | [sunnyosun](https://github.com/sunnyosun) | 2024-06-05 |

{lamindb_setup-0.73.2 → lamindb_setup-0.73.3}/lamindb_setup/__init__.py

@@ -34,7 +34,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.73.2"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.73.3"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import sys
 from os import name as _os_name

{lamindb_setup-0.73.2 → lamindb_setup-0.73.3}/lamindb_setup/_init_instance.py

@@ -33,8 +33,7 @@ def get_schema_module_name(schema_name) -> str:
         if module_spec is not None:
             return name
     raise ImportError(
-        f"Python package for '{schema_name}' is not installed, tried two package names:"
-        f" {name_attempts}\nHave you installed the schema package using `pip install`?"
+        f"Python package for '{schema_name}' is not installed.\nIf your package is on PyPI, run `pip install {schema_name}`"
     )
 
 
@@ -256,7 +255,10 @@ def init(
             schema=schema,
             uid=ssettings.uid,
         )
-        if isettings.is_remote and instance_state != "instance-corrupted-or-deleted":
+        register_on_hub = (
+            isettings.is_remote and instance_state != "instance-corrupted-or-deleted"
+        )
+        if register_on_hub:
             init_instance_hub(isettings)
         validate_sqlite_state(isettings)
         isettings._persist()
@@ -270,8 +272,10 @@ def init(
                 "locked instance (to unlock and push changes to the cloud SQLite file,"
                 " call: lamin close)"
             )
-        # we can debate whether this is the right setting, but this is how
-        # things have been and we'd like to not easily break backward compat
+        if register_on_hub and isettings.dialect != "sqlite":
+            from ._schema_metadata import update_schema_in_hub
+
+            update_schema_in_hub()
         settings.auto_connect = True
     except Exception as e:
         from ._delete import delete_by_isettings

{lamindb_setup-0.73.2 → lamindb_setup-0.73.3}/lamindb_setup/_migrate.py

@@ -75,21 +75,15 @@ class migrate:
         from lamindb_setup.core._hub_client import call_with_fallback_auth
         from lamindb_setup.core._hub_crud import (
             select_collaborator,
-            select_instance_by_id,
             update_instance,
         )
 
-        instance_id_str = settings.instance._id.hex
-        instance = call_with_fallback_auth(
-            select_instance_by_id, instance_id=instance_id_str
-        )
-        instance_is_on_hub = instance is not None
-        if instance_is_on_hub:
+        if settings.instance.is_on_hub:
             # double check that user is an admin, otherwise will fail below
-            # without idempotence
+            # due to insufficient SQL permissions with cryptic error
             collaborator = call_with_fallback_auth(
                 select_collaborator,
-                instance_id=instance_id_str,
+                instance_id=settings.instance._id,
                 account_id=settings.user._uuid,
             )
             if collaborator is None or collaborator["role"] != "admin":
@@ -104,7 +98,7 @@ class migrate:
         # this sets up django and deploys the migrations
         setup_django(settings.instance, deploy_migrations=True)
         # this populates the hub
-        if instance_is_on_hub:
+        if settings.instance.is_on_hub:
             logger.important(f"updating lamindb version in hub: {lamindb.__version__}")
             # TODO: integrate update of instance table within update_schema_in_hub & below
             if settings.instance.dialect != "sqlite":

{lamindb_setup-0.73.2 → lamindb_setup-0.73.3}/lamindb_setup/_register_instance.py

@@ -27,3 +27,7 @@ def register(_test: bool = False):
     init_instance_hub(isettings)
     isettings._is_on_hub = True
     isettings._persist()
+    if isettings.dialect != "sqlite" and not _test:
+        from ._schema_metadata import update_schema_in_hub
+
+        update_schema_in_hub()

{lamindb_setup-0.73.2 → lamindb_setup-0.73.3}/lamindb_setup/core/_settings.py

@@ -51,7 +51,11 @@ class SetupSettings:
     @property
     def user(self) -> UserSettings:
         """:class:`~lamindb.setup.core.UserSettings`."""
-        if self._user_settings is None or self._user_settings_env != get_env_name():
+        env_changed = (
+            self._user_settings_env is not None
+            and self._user_settings_env != get_env_name()
+        )
+        if self._user_settings is None or env_changed:
             self._user_settings = load_or_create_user_settings()
             self._user_settings_env = get_env_name()
             if self._user_settings and self._user_settings.uid is None:
@@ -61,10 +65,11 @@ class SetupSettings:
     @property
     def instance(self) -> InstanceSettings:
         """:class:`~lamindb.setup.core.InstanceSettings`."""
-        if (
-            self._instance_settings is None
-            or self._instance_settings_env != get_env_name()
-        ):
+        env_changed = (
+            self._instance_settings_env is not None
+            and self._instance_settings_env != get_env_name()
+        )
+        if self._instance_settings is None or env_changed:
             self._instance_settings = load_instance_settings()
             self._instance_settings_env = get_env_name()
         return self._instance_settings  # type: ignore

{lamindb_setup-0.73.2 → lamindb_setup-0.73.3}/lamindb_setup/core/_settings_storage.py

@@ -121,6 +121,8 @@ def init_storage(
         init_storage_hub(ssettings)
     # below comes last only if everything else was successful
     try:
+        # (federated) credentials for AWS access are provisioned under-the-hood
+        # discussion: https://laminlabs.slack.com/archives/C04FPE8V01W/p1719260587167489
         mark_storage_root(ssettings.root, ssettings.uid)  # type: ignore
     except Exception:
         logger.important(

{lamindb_setup-0.73.2 → lamindb_setup-0.73.3}/tests/hub-local/conftest.py

@@ -14,10 +14,8 @@ local_setup_state = setup_local_hub()
 
 
 def pytest_configure():
-    if os.environ["LAMIN_ENV"] == "local":
-        local_setup_state.__enter__()
-    else:
-        logger.warning("you're running non-local tests")
+    assert os.environ["LAMIN_ENV"] == "local"
+    local_setup_state.__enter__()
 
 
 def pytest_unconfigure():

{lamindb_setup-0.73.2 → lamindb_setup-0.73.3}/tests/hub-local/test_update_schema_in_hub.py

@@ -9,17 +9,20 @@ def setup_instance():
         storage="./test_storage",
         schema="bionty,wetlab",
         db="postgresql://postgres:postgres@127.0.0.1:54322/postgres",
-        name="testdb",
+        name="test-update-schema",
     )
     ln_setup.register()
     yield
-    ln_setup.delete("testdb", force=True)
+    ln_setup.delete("test-update-schema", force=True)
 
 
 def test_update_schema_in_hub(setup_instance):
     is_new, schema_uuid, schema = update_schema_in_hub()
 
-    assert is_new is True
+    # TODO: construct a test in which is_new is true
+    # currently it's false because the schema is already registered
+    # via `lamin register` earlier in the test
+    assert not is_new
     assert _dict_to_uuid(schema["json"]) == schema_uuid
 
     assert len(schema["module_set_info"]) == 3
@@ -38,6 +41,7 @@ def test_update_schema_in_hub(setup_instance):
     assert "bionty" in schema["json"]
     assert "wetlab" in schema["json"]
 
+    print(schema["json"]["core"]["artifact"]["fields"]["id"])
     assert schema["json"]["core"]["artifact"]["fields"]["id"] == {
         "type": "AutoField",
         "column": "id",
@@ -53,6 +57,7 @@ def test_update_schema_in_hub(setup_instance):
         "through": None,
     }
 
+    print(schema["json"]["core"]["artifact"]["fields"]["created_by"])
     assert schema["json"]["core"]["artifact"]["fields"]["created_by"] == {
         "type": "ForeignKey",
         "column": "created_by_id",
@@ -68,6 +73,7 @@ def test_update_schema_in_hub(setup_instance):
         "through": None,
     }
 
+    print(schema["json"]["bionty"]["gene"]["fields"]["pathways"])
     assert schema["json"]["bionty"]["gene"]["fields"]["pathways"] == {
         "type": "ManyToManyField",
         "column": None,
@@ -87,23 +93,24 @@ def test_update_schema_in_hub(setup_instance):
         },
     }
 
+    print(schema["json"]["wetlab"]["well"]["fields"]["artifacts"])
     assert schema["json"]["wetlab"]["well"]["fields"]["artifacts"] == {
         "type": "ManyToManyField",
         "column": None,
+        "through": {
+            "wetlab_well": "well_id",
+            "link_table_name": "wetlab_well_artifacts",
+            "lnschema_core_artifact": "artifact_id",
+        },
         "field_name": "artifacts",
         "model_name": "well",
         "schema_name": "wetlab",
-        "select_term": 'ARRAY(SELECT JSONB_BUILD_OBJECT((\'version\')::text, U0."version", (\'created_at\')::text, U0."created_at", (\'updated_at\')::text, U0."updated_at", (\'id\')::text, U0."id", (\'uid\')::text, U0."uid", (\'description\')::text, U0."description", (\'key\')::text, U0."key", (\'suffix\')::text, U0."suffix", (\'accessor\')::text, U0."accessor", (\'size\')::text, U0."size", (\'hash\')::text, U0."hash", (\'hash_type\')::text, U0."hash_type", (\'n_objects\')::text, U0."n_objects", (\'n_observations\')::text, U0."n_observations", (\'visibility\')::text, U0."visibility", (\'key_is_virtual\')::text, U0."key_is_virtual") AS "data" FROM "lnschema_core_artifact" U0 INNER JOIN "wetlab_well_artifacts" U1 ON (U0."id" = U1."artifact_id") WHERE U1."well_id" = ("wetlab_well"."id") LIMIT 5) AS "artifacts"',
+        "select_term": 'ARRAY(SELECT JSONB_BUILD_OBJECT((\'version\')::text, U0."version", (\'created_at\')::text, U0."created_at", (\'updated_at\')::text, U0."updated_at", (\'id\')::text, U0."id", (\'uid\')::text, U0."uid", (\'description\')::text, U0."description", (\'key\')::text, U0."key", (\'suffix\')::text, U0."suffix", (\'type\')::text, U0."type", (\'accessor\')::text, U0."accessor", (\'size\')::text, U0."size", (\'hash\')::text, U0."hash", (\'hash_type\')::text, U0."hash_type", (\'n_objects\')::text, U0."n_objects", (\'n_observations\')::text, U0."n_observations", (\'visibility\')::text, U0."visibility", (\'key_is_virtual\')::text, U0."key_is_virtual") AS "data" FROM "lnschema_core_artifact" U0 INNER JOIN "wetlab_well_artifacts" U1 ON (U0."id" = U1."artifact_id") WHERE U1."well_id" = ("wetlab_well"."id") LIMIT 5) AS "artifacts"',
         "is_link_table": False,
         "relation_type": "many-to-many",
         "related_field_name": "wells",
         "related_model_name": "artifact",
         "related_schema_name": "core",
-        "through": {
-            "wetlab_well": "well_id",
-            "link_table_name": "wetlab_well_artifacts",
-            "lnschema_core_artifact": "artifact_id",
-        },
     }