lamindb_setup 0.77.5__tar.gz → 0.77.6__tar.gz

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.77.5
+Version: 0.77.6
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Description-Content-Type: text/markdown
@@ -13,12 +13,13 @@ 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: gotrue>=2.1.0,<2.9.0
 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,<=2024.6.1 ; extra == "aws"
+Requires-Dist: line_profiler ; extra == "dev"
 Requires-Dist: pyjwt<3.0.0 ; extra == "dev"
 Requires-Dist: psycopg2-binary ; extra == "dev"
 Requires-Dist: python-dotenv ; extra == "dev"

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/lamindb_setup/__init__.py

@@ -21,7 +21,6 @@ Instance operations:
    :toctree:
 
    migrate
-   register
 
 Modules & settings:
 
@@ -34,7 +33,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.77.5"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.77.6"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 import sys as _sys

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/lamindb_setup/_check_setup.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import importlib as il
 import os
 from typing import TYPE_CHECKING, Optional
 
@@ -52,9 +53,18 @@ def _get_current_instance_settings() -> InstanceSettings | None:
 
 
 # we make this a private function because in all the places it's used,
-# users should see it
-def _check_instance_setup(from_lamindb: bool = False) -> bool:
+# users should not see it
+def _check_instance_setup(
+    from_lamindb: bool = False, from_module: str | None = None
+) -> bool:
+    reload_module = from_lamindb or from_module is not None
+    from ._init_instance import get_schema_module_name, reload_schema_modules
+
     if django.IS_SETUP:
+        # reload logic here because module might not yet have been imported
+        # upon first setup
+        if from_module is not None:
+            il.reload(il.import_module(from_module))
         return True
     silence_loggers()
     if os.environ.get("LAMINDB_MULTI_INSTANCE") == "true":
@@ -65,15 +75,18 @@ def _check_instance_setup(from_lamindb: bool = False) -> bool:
         return True
     isettings = _get_current_instance_settings()
     if isettings is not None:
-        if from_lamindb and settings.auto_connect:
+        if reload_module and settings.auto_connect:
             if not django.IS_SETUP:
-                from ._init_instance import reload_schema_modules
-
                 django.setup_django(isettings)
-                reload_schema_modules(isettings)
+                if from_module is not None:
+                    # this only reloads `from_module`
+                    il.reload(il.import_module(from_module))
+                else:
+                    # this bulk reloads all schema modules
+                    reload_schema_modules(isettings)
                 logger.important(f"connected lamindb: {isettings.slug}")
         return django.IS_SETUP
     else:
-        if from_lamindb and settings.auto_connect:
+        if reload_module and settings.auto_connect:
             logger.warning(InstanceNotSetupError.default_message)
         return False

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/lamindb_setup/_connect_instance.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import os
+import sys
 from typing import TYPE_CHECKING
 from uuid import UUID
 
@@ -9,10 +10,8 @@ from lamin_utils import logger
 from ._check_setup import _check_instance_setup
 from ._close import close as close_instance
 from ._init_instance import MESSAGE_NO_MULTIPLE_INSTANCE, load_from_isettings
-from ._migrate import check_whether_migrations_in_sync
 from ._silence_loggers import silence_loggers
-from .core._hub_core import connect_instance as load_instance_from_hub
-from .core._hub_core import connect_instance_new as load_instance_from_hub_edge
+from .core._hub_core import connect_instance as connect_instance_from_hub
 from .core._hub_utils import (
     LaminDsn,
     LaminDsnModel,
@@ -129,14 +128,9 @@ def _connect_instance(
         # on the hub
         # do not call hub if the user is anonymous
         if owner != "anonymous":
-            if settings.user.handle in {"Koncopd", "sunnyosun", "falexwolf"}:
-                hub_result = load_instance_from_hub_edge(
-                    owner=owner, name=name, access_token=access_token
-                )
-            else:
-                hub_result = load_instance_from_hub(
-                    owner=owner, name=name, access_token=access_token
-                )
+            hub_result = connect_instance_from_hub(
+                owner=owner, name=name, access_token=access_token
+            )
         else:
             hub_result = "anonymous-user"
         # if hub_result is not a string, it means it made a request
@@ -167,7 +161,6 @@ def _connect_instance(
                 keep_artifacts_local=bool(instance_result["keep_artifacts_local"]),
                 is_on_hub=True,
             )
-            check_whether_migrations_in_sync(instance_result["lamindb_version"])
         else:
             if hub_result != "anonymous-user":
                 message = INSTANCE_NOT_FOUND_MESSAGE.format(
@@ -313,6 +306,7 @@ def load(slug: str) -> str | tuple | None:
     This is exactly the same as ``ln.connect()`` except for that
     ``ln.connect()`` doesn't change the state of ``auto-connect``.
     """
+    print("Warning: This is deprecated and will be removed.")
     result = connect(slug)
     settings.auto_connect = True
     return result

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/lamindb_setup/_init_instance.py

@@ -97,8 +97,9 @@ def register_user_and_storage_in_instance(isettings: InstanceSettings, usettings
         logger.warning(f"instance seems not set up ({error})")
 
 
-def reload_schema_modules(isettings: InstanceSettings):
-    schema_names = ["core"] + list(isettings.schema)
+def reload_schema_modules(isettings: InstanceSettings, include_core: bool = True):
+    schema_names = ["core"] if include_core else []
+    # schema_names += list(isettings.schema)
     schema_module_names = [get_schema_module_name(n) for n in schema_names]
 
     for schema_module_name in schema_module_names:
@@ -114,16 +115,10 @@ def reload_lamindb_itself(isettings) -> bool:
 
         importlib.reload(lamindb)
         reloaded = True
-    if "bionty" in isettings.schema and "bionty" in sys.modules:
-        schema_module = importlib.import_module("bionty")
-        importlib.reload(schema_module)
-        reloaded = True
     return reloaded
 
 
 def reload_lamindb(isettings: InstanceSettings):
-    # only touch lamindb if we're operating from lamindb
-    reload_schema_modules(isettings)
     log_message = settings.auto_connect
     if not reload_lamindb_itself(isettings):
         log_message = True
@@ -214,7 +209,7 @@ def validate_init_args(
 MESSAGE_NO_MULTIPLE_INSTANCE = """
 Currently don't support subsequent connection to different databases in the same
 Python session.\n
-Try running on the CLI: lamin set auto-connect false
+Try running on the CLI: lamin settings set auto-connect false
 """
 
 
@@ -352,7 +347,7 @@ def load_from_isettings(
     user: UserSettings | None = None,
     write_settings: bool = True,
 ) -> None:
-    from .core._setup_bionty_sources import load_bionty_sources, write_bionty_sources
+    from .core._setup_bionty_sources import write_bionty_sources
 
     user = settings.user if user is None else user
 
@@ -370,7 +365,6 @@ def load_from_isettings(
         # yet be registered
         if not isettings._get_settings_file().exists():
             register_user(user)
-        load_bionty_sources(isettings)
     isettings._persist(write_to_disk=write_settings)
     reload_lamindb(isettings)
 

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/lamindb_setup/_migrate.py

@@ -30,7 +30,7 @@ def check_whether_migrations_in_sync(db_version_str: str):
         db_version_lower = f"{db_version.major}.{db_version.minor}"
         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"the database ({db_version_str}) is ahead of your installed lamindb"
             f" package ({installed_version_str})"
         )
         logger.important(
@@ -42,10 +42,10 @@ def check_whether_migrations_in_sync(db_version_str: str):
         or installed_version.minor > db_version.minor
     ):
         logger.warning(
-            f"your database ({db_version_str}) is behind your installed lamindb package"
+            f"the database ({db_version_str}) is behind your installed lamindb package"
             f" ({installed_version_str})"
         )
-        logger.important("please migrate your database: lamin migrate deploy")
+        logger.important("consider migrating your database: lamin migrate deploy")
 
 
 # for tests, see lamin-cli

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/lamindb_setup/core/_hub_client.py

@@ -95,7 +95,7 @@ def get_access_token(
     try:
         if api_key is not None:
             auth_response = hub.functions.invoke(
-                "create-jwt",
+                "get-jwt-v1",
                 invoke_options={"body": {"api_key": api_key}},
             )
             return json.loads(auth_response)["accessToken"]

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/lamindb_setup/core/_hub_core.py

@@ -10,6 +10,8 @@ from uuid import UUID
 from lamin_utils import logger
 from postgrest.exceptions import APIError
 
+from lamindb_setup._migrate import check_whether_migrations_in_sync
+
 from ._hub_client import (
     call_with_fallback,
     call_with_fallback_auth,
@@ -381,6 +383,7 @@ def _connect_instance(
             database=instance["db_database"],
         )
         instance["db"] = db_dsn
+    check_whether_migrations_in_sync(instance["lamindb_version"])
     return instance, storage  # type: ignore
 
 
@@ -390,7 +393,8 @@ def _connect_instance_new(
     client: Client,
 ) -> tuple[dict, dict] | str:
     response = client.functions.invoke(
-        "get-instance-settings", invoke_options={"body": {"owner": owner, "name": name}}
+        "get-instance-settings-v1",
+        invoke_options={"body": {"owner": owner, "name": name}},
     )
     # no instance found, check why is that
     if response == b"{}":
@@ -471,7 +475,7 @@ def _access_aws(*, storage_root: str, client: Client) -> dict[str, dict]:
 
     storage_root_info: dict[str, dict] = {"credentials": {}, "accessibility": {}}
     response = client.functions.invoke(
-        "access-aws",
+        "get-cloud-access-v1",
         invoke_options={"body": {"storage_root": storage_root}},
     )
     if response is not None and response != b"{}":
@@ -563,7 +567,7 @@ def sign_in_hub(
 
 def _sign_in_hub_api_key(api_key: str, client: Client):
     response = client.functions.invoke(
-        "create-jwt",
+        "get-jwt-v1",
         invoke_options={"body": {"api_key": api_key}},
     )
     access_token = json.loads(response)["accessToken"]
@@ -599,7 +603,7 @@ def sign_in_hub_api_key(
 
 def _create_api_key(body: dict, client: Client) -> str:
     response = client.functions.invoke(
-        "create-api-key",
+        "create-api-key-v1",
         invoke_options={"body": body},
     )
     api_key = json.loads(response)["apiKey"]

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/lamindb_setup/core/_settings.py

@@ -40,11 +40,18 @@ class SetupSettings:
 
     @property
     def auto_connect(self) -> bool:
-        """Auto-connect to loaded instance upon lamindb import.
+        """Auto-connect to current instance upon `import lamindb`.
 
-        `lamin init` and `lamin load` switch this to `True`.
+        Upon installing `lamindb`, this setting is `False`.
+
+        Upon calling `lamin init` or `lamin connect` on the CLI, this setting is switched to `True`.
 
         `ln.connect()` doesn't change the value of this setting.
+
+        You can manually change this setting
+
+        - in Python: `ln.setup.settings.auto_connect = True/False`
+        - via the CLI: `lamin settings set auto-connect true/false`
         """
         return self._auto_connect_path.exists()
 

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/lamindb_setup/core/_settings_user.py

@@ -50,4 +50,6 @@ class UserSettings:
         """Integer id valid in current intance."""
         from lnschema_core.users import current_user_id
 
+        # there is no cache needed here because current_user_id()
+        # has its own cache
         return current_user_id()

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/lamindb_setup/core/django.py

@@ -8,6 +8,7 @@ import time
 from lamin_utils import logger
 from ._settings_store import current_instance_settings_file
 from ._settings_instance import InstanceSettings
+import sys
 
 IS_RUN_FROM_IPYTHON = getattr(builtins, "__IPYTHON__", False)
 IS_SETUP = False

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/noxfile.py

@@ -27,8 +27,8 @@ def lint(session: nox.Session) -> None:
     ["hub-local", "hub-prod", "hub-cloud", "storage", "docs"],
 )
 def install(session: nox.Session, group: str) -> None:
-    no_deps_packages = "git+https://github.com/laminlabs/lnschema-core git+https://github.com/laminlabs/wetlab git+https://github.com/laminlabs/lamin-cli"
-    schema_deps = f"""uv pip install --system git+https://github.com/laminlabs/bionty git+https://github.com/laminlabs/lamindb@main
+    no_deps_packages = "git+https://github.com/laminlabs/lnschema-core git+https://github.com/laminlabs/wetlab@lazyreload git+https://github.com/laminlabs/lamin-cli"
+    schema_deps = f"""uv pip install --system git+https://github.com/laminlabs/bionty@lazyconnect git+https://github.com/laminlabs/lamindb@improvelaminconnect
 uv pip install --system --no-deps {no_deps_packages}
 """
     if group == "hub-cloud":

{lamindb_setup-0.77.5 → lamindb_setup-0.77.6}/pyproject.toml

@@ -18,7 +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
+    "gotrue>=2.1.0,<2.9.0", # lower - for options in auth.sign_out, upper - 2.9.0 fails
     "supabase==2.2.1",
     "psutil"
 ]
@@ -39,6 +39,7 @@ erdiagram = [
     "django-schema-graph",
 ]
 dev = [
+    "line_profiler",
     "pyjwt<3.0.0",
     "psycopg2-binary",
     "python-dotenv",