lamindb_setup 1.0a1__tar.gz → 1.0.1__tar.gz

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/.github/workflows/build.yml

@@ -12,7 +12,7 @@ jobs:
   # tests only on production hub
   hub-prod:
     runs-on: ubuntu-latest
-    timeout-minutes: 8
+    timeout-minutes: 12
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
@@ -44,7 +44,7 @@ jobs:
             python-version: "3.11"
           - lamin_env: "staging"
             python-version: "3.10" # test on 3.9
-    timeout-minutes: 8
+    timeout-minutes: 12
     steps:
       - uses: aws-actions/configure-aws-credentials@v4
         with:
@@ -94,7 +94,7 @@ jobs:
   # test user access to storage
   storage:
     runs-on: ubuntu-latest
-    timeout-minutes: 8
+    timeout-minutes: 12
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
@@ -119,7 +119,7 @@ jobs:
   # test low-level hub functionality
   hub-local:
     runs-on: ubuntu-latest
-    timeout-minutes: 8
+    timeout-minutes: 12
     steps:
       - uses: aws-actions/configure-aws-credentials@v4
         with:
@@ -152,6 +152,8 @@ jobs:
           path: /var/lib/docker
           key: cache-supabase
       - uses: supabase/setup-cli@v1
+        with:
+          version: "2.6.8"
       - run: nox -s hub_local
         env:
           LAMIN_ENV: "local"

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.0a1
+Version: 1.0.1
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 Requires-Dist: lamin_utils>=0.3.3
 Requires-Dist: django>=5,<5.2

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/docs/hub-cloud/04-test-bionty.ipynb

@@ -33,7 +33,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln_setup.init(storage=\"mydata2\", schema=\"bionty\")"
+    "ln_setup.init(storage=\"mydata2\", modules=\"bionty\")"
    ]
   },
   {
@@ -89,7 +89,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "output = getoutput(\"lamin init --storage mydata2 --schema bionty\")\n",
+    "output = getoutput(\"lamin init --storage mydata2 --modules bionty\")\n",
     "print(output)"
    ]
   },
@@ -107,7 +107,7 @@
    "outputs": [],
    "source": [
     "ln_setup.settings.instance._get_settings_file().unlink()\n",
-    "output = getoutput(\"lamin init --storage mydata2 --schema bionty\")\n",
+    "output = getoutput(\"lamin init --storage mydata2 --modules bionty\")\n",
     "print(output)"
    ]
   },

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/docs/hub-prod/test-import-schema.ipynb

@@ -14,7 +14,7 @@
    "id": "3e5867b4",
    "metadata": {},
    "source": [
-    "Also see the corresponding FAQ notebook in lamindb: `import-schema`.\n",
+    "Also see the corresponding FAQ notebook in lamindb: `import-modules`.\n",
     "\n",
     "If you try to access an attribute (other than `model`), you'll load the instance in the same way as calling `import lamindb`."
    ]
@@ -28,7 +28,7 @@
    },
    "outputs": [],
    "source": [
-    "!lamin init --storage test-implicit-load --schema wetlab,bionty"
+    "!lamin init --storage test-implicit-load --modules wetlab,bionty"
    ]
   },
   {

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/docs/hub-prod/test-init-load-local-anonymously.ipynb

@@ -64,7 +64,7 @@
    "outputs": [],
    "source": [
     "!lamin disconnect\n",
-    "!lamin init --storage ./test-anonymous-init --schema bionty"
+    "!lamin init --storage ./test-anonymous-init --modules bionty"
    ]
   },
   {

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/docs/hub-prod/test-invalid-schema.ipynb

@@ -24,7 +24,9 @@
    "outputs": [],
    "source": [
     "with pytest.raises(ImportError):\n",
-    "    ln_setup.init(storage=\"./test-invalid-schema\", schema=\"bionty,invalid_module_name\")"
+    "    ln_setup.init(\n",
+    "        storage=\"./test-invalid-modules\", modules=\"bionty,invalid_module_name\"\n",
+    "    )"
    ]
   }
  ],

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/docs/notebooks.md

@@ -14,8 +14,8 @@ hub-cloud/test-multi-session
 
 hub-prod/test-cache-management
 hub-prod/test-empty-init
-hub-prod/test-import-schema
-hub-prod/test-invalid-schema
+hub-prod/test-import-modules
+hub-prod/test-invalid-modules
 hub-prod/test-insufficient-user-info
 hub-prod/test-init-load-local-anonymously
 hub-prod/test-connect-anonymously

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/lamindb_setup/__init__.py

@@ -33,10 +33,9 @@ Modules & settings:
 
 """
 
-__version__ = "1.0a1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "1.0.1"  # denote a release candidate for 0.1.0 with 0.1rc1
 
-import os as _os
-import sys as _sys
+import os
 
 from . import core
 from ._check_setup import _check_instance_setup
@@ -76,27 +75,11 @@ def _is_CI_environment() -> bool:
         "SEMAPHORE",  # Semaphore CI
         "BUILD_ID",  # Generic build environments
     ]
-    return any(env_var in _os.environ for env_var in ci_env_vars)
+    return any(env_var in os.environ for env_var in ci_env_vars)
 
 
 _TESTING = _is_CI_environment()
 
-
-# hide the supabase error in a thread on windows
-if _os.name == "nt":
-    if _sys.version_info.minor > 7:
-        import threading
-
-        _original_excepthook = threading.excepthook
-
-        def _except_hook(args):
-            is_overflow = args.exc_type is OverflowError
-            for_timeout = str(args.exc_value) == "timeout value is too large"
-            if not (is_overflow and for_timeout):
-                _original_excepthook(args)
-
-        threading.excepthook = _except_hook
-
 # provide a way for other packages to run custom code on import
 _call_registered_entry_points("lamindb_setup.on_import")
 

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/lamindb_setup/_cache.py

@@ -10,11 +10,15 @@ from .core._settings_save import save_system_storage_settings
 def clear_cache_dir():
     from lamindb_setup import close, settings
 
-    if settings.instance._is_cloud_sqlite:
-        logger.warning(
-            "Closing the current instance to update the cloud sqlite database."
-        )
-        close()
+    try:
+        if settings.instance._is_cloud_sqlite:
+            logger.warning(
+                "Closing the current instance to update the cloud sqlite database."
+            )
+            close()
+    except SystemExit as e:
+        if str(e) != "No instance is loaded! Call `lamin init` or `lamin connect`":
+            raise e
 
     cache_dir = settings.cache_dir
     shutil.rmtree(cache_dir)

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/lamindb_setup/_check_setup.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import functools
 import importlib as il
 import os
 from typing import TYPE_CHECKING
@@ -13,6 +14,8 @@ from .core._settings_store import current_instance_settings_file
 from .core.exceptions import DefaultMessageException
 
 if TYPE_CHECKING:
+    from collections.abc import Callable
+
     from .core._settings_instance import InstanceSettings
 
 
@@ -30,6 +33,20 @@ CURRENT_ISETTINGS: InstanceSettings | None = None
 IS_LOADING: bool = False
 
 
+# decorator to disable auto-connect when importing a module such as lamindb
+def _loading(func: Callable):
+    @functools.wraps(func)
+    def wrapper(*args, **kwargs):
+        global IS_LOADING
+        IS_LOADING = True
+        try:
+            return func(*args, **kwargs)
+        finally:
+            IS_LOADING = False
+
+    return wrapper
+
+
 def _get_current_instance_settings() -> InstanceSettings | None:
     global CURRENT_ISETTINGS
 

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/lamindb_setup/_close.py

@@ -24,7 +24,7 @@ def close(mute: bool = False) -> None:
                 logger.warning("did not upload cache file - not enough permissions")
             else:
                 raise e
-        if "bionty" in settings.instance.schema:
+        if "bionty" in settings.instance.modules:
             delete_bionty_sources_yaml()
         current_instance_settings_file().unlink()
         clear_locker()

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/lamindb_setup/_connect_instance.py

@@ -7,7 +7,7 @@ from uuid import UUID
 
 from lamin_utils import logger
 
-from ._check_setup import _check_instance_setup
+from ._check_setup import _check_instance_setup, _get_current_instance_settings
 from ._close import close as close_instance
 from ._init_instance import (
     MESSAGE_CANNOT_SWITCH_DEFAULT_INSTANCE,
@@ -160,7 +160,7 @@ def _connect_instance(
                 name=name,
                 storage=ssettings,
                 db=db_updated,
-                schema=instance_result["schema_str"],
+                modules=instance_result["schema_str"],
                 git_repo=instance_result["git_repo"],
                 keep_artifacts_local=bool(instance_result["keep_artifacts_local"]),
                 is_on_hub=True,
@@ -186,12 +186,12 @@ def _connect_instance(
 
 
 @unlock_cloud_sqlite_upon_exception(ignore_prev_locker=True)
-def connect(slug: str, **kwargs) -> str | tuple | None:
-    """Connect to instance.
+def connect(instance: str | None = None, **kwargs) -> str | tuple | None:
+    """Connect to an instance.
 
     Args:
-        slug: The instance slug `account_handle/instance_name` or URL.
-            If the instance is owned by you, it suffices to pass the instance name.
+        instance: `None` or an instance identifier (URL, slug `account/name`, or `name` if the instance is local or in your account).
+            If `None`, it will connect to the instance that was connected via the CLI.
     """
     # validate kwargs
     valid_kwargs = {
@@ -220,39 +220,46 @@ def connect(slug: str, **kwargs) -> str | tuple | None:
         access_token = _user.access_token
 
     try:
-        owner, name = get_owner_name_from_identifier(slug)
-
-        if _check_instance_setup() and not _test:
-            if (
-                settings._instance_exists
-                and f"{owner}/{name}" == settings.instance.slug
+        if instance is None:
+            isettings_or_none = _get_current_instance_settings()
+            if isettings_or_none is None:
+                raise SystemExit(
+                    "No instance was connected through the CLI, pass a value to `instance` or connect via the CLI."
+                )
+            isettings = isettings_or_none
+        else:
+            owner, name = get_owner_name_from_identifier(instance)
+            if _check_instance_setup() and not _test:
+                if (
+                    settings._instance_exists
+                    and f"{owner}/{name}" == settings.instance.slug
+                ):
+                    logger.important(f"connected lamindb: {settings.instance.slug}")
+                    return None
+                else:
+                    raise CannotSwitchDefaultInstance(
+                        MESSAGE_CANNOT_SWITCH_DEFAULT_INSTANCE
+                    )
+            elif (
+                _write_settings
+                and settings._instance_exists
+                and f"{owner}/{name}" != settings.instance.slug
             ):
-                logger.info(f"connected lamindb: {settings.instance.slug}")
-                return None
-            else:
-                raise CannotSwitchDefaultInstance(
-                    MESSAGE_CANNOT_SWITCH_DEFAULT_INSTANCE
+                close_instance(mute=True)
+
+            try:
+                isettings = _connect_instance(
+                    owner, name, db=_db, access_token=access_token
                 )
-        elif (
-            _write_settings
-            and settings._instance_exists
-            and f"{owner}/{name}" != settings.instance.slug
-        ):
-            close_instance(mute=True)
-
-        try:
-            isettings = _connect_instance(
-                owner, name, db=_db, access_token=access_token
-            )
-        except InstanceNotFoundError as e:
-            if _raise_not_found_error:
-                raise e
-            else:
-                return "instance-not-found"
-        if isinstance(isettings, str):
-            return isettings
+            except InstanceNotFoundError as e:
+                if _raise_not_found_error:
+                    raise e
+                else:
+                    return "instance-not-found"
+            if isinstance(isettings, str):
+                return isettings
         # at this point we have checked already that isettings is not a string
-        # _user is passed to lock cloud sqite for this user in isettings._load_db()
+        # _user is passed to lock cloud sqlite for this user in isettings._load_db()
         # has no effect if _user is None or if not cloud sqlite instance
         isettings._locker_user = _user
         isettings._persist(write_to_disk=_write_settings)
@@ -304,6 +311,7 @@ def connect(slug: str, **kwargs) -> str | tuple | None:
         load_from_isettings(isettings, user=_user, write_settings=_write_settings)
         if _reload_lamindb:
             importlib.reload(importlib.import_module("lamindb"))
+        logger.important(f"connected lamindb: {isettings.slug}")
     except Exception as e:
         if isettings is not None:
             if _write_settings:
@@ -381,7 +389,7 @@ def migrate_lnschema_core(
         else:
             try:
                 response = input(
-                    f"Do you want to migrate to lamindb 0.78 (integrate lnschema_core into lamindb)? (y/n) -- Will rename {tables_to_rename}"
+                    f"Do you want to migrate to lamindb 1.0 (integrate lnschema_core into lamindb)? (y/n) -- Will rename {tables_to_rename}"
                 )
                 if response != "y":
                     print("Aborted.")

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/lamindb_setup/_entry_points.py

@@ -5,10 +5,7 @@ from importlib.metadata import entry_points
 
 def call_registered_entry_points(group, **kwargs):
     """load and call entry points registered under group."""
-    if sys.version_info >= (3, 10):
-        eps = entry_points(group=group)
-    else:
-        eps = entry_points().get(group, [])
+    eps = entry_points(group=group)
 
     for ep in eps:
         func = ep.load()

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/lamindb_setup/_exportdb.py

@@ -12,7 +12,7 @@ MODELS = {
         "User": False,
         "Storage": False,
         "Feature": False,
-        "FeatureSet": False,
+        "Schema": False,
         "ULabel": False,
     },
     # "bionty": {
@@ -57,9 +57,9 @@ def exportdb() -> None:
 
     # export data to parquet files
     print(f"\nexporting data to parquet files in: {directory}\n")
-    for schema_name, models in MODELS.items():
+    for module_name, models in MODELS.items():
         for model_name in models.keys():
-            schema_module = import_module(f"lnschema_{schema_name}")
+            schema_module = import_module(f"lnschema_{module_name}")
             registry = getattr(schema_module, model_name)
             export_registry(registry, directory)
             many_to_many_names = [field.name for field in registry._meta.many_to_many]

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/lamindb_setup/_importdb.py

@@ -36,10 +36,10 @@ def importdb() -> None:
     with engine.begin() as connection:
         if ln_setup.settings.instance.dialect == "postgresql":
             connection.execute(text("SET CONSTRAINTS ALL DEFERRED;"))
-        for schema_name, models in MODELS.items():
+        for module_name, models in MODELS.items():
             for model_name in models.keys():
                 print(model_name)
-                schema_module = import_module(f"lnschema_{schema_name}")
+                schema_module = import_module(f"lnschema_{module_name}")
                 registry = getattr(schema_module, model_name)
                 import_registry(registry, directory, connection)
                 many_to_many_names = [

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/lamindb_setup/_init_instance.py

@@ -25,17 +25,17 @@ if TYPE_CHECKING:
     from .core.types import UPathStr
 
 
-def get_schema_module_name(schema_name, raise_import_error: bool = True) -> str | None:
+def get_schema_module_name(module_name, raise_import_error: bool = True) -> str | None:
     import importlib.util
 
-    if schema_name == "core":
+    if module_name == "core":
         return "lamindb"
-    name_attempts = [f"lnschema_{schema_name.replace('-', '_')}", schema_name]
+    name_attempts = [f"lnschema_{module_name.replace('-', '_')}", module_name]
     for name in name_attempts:
         module_spec = importlib.util.find_spec(name)
         if module_spec is not None:
             return name
-    message = f"Schema module '{schema_name}' is not installed → no access to its labels & registries (resolve via `pip install {schema_name}`)"
+    message = f"schema module '{module_name}' is not installed → no access to its labels & registries (resolve via `pip install {module_name}`)"
     if raise_import_error:
         raise ImportError(message)
     logger.warning(message.lower())
@@ -129,12 +129,21 @@ def process_connect_response(
     return instance_id, instance_state
 
 
+def process_modules_arg(modules: str | None = None) -> str:
+    if modules is None or modules == "":
+        return ""
+    # currently no actual validation, can add back if we see a need
+    # the following just strips white spaces
+    to_be_validated = [s.strip() for s in modules.split(",")]
+    return ",".join(to_be_validated)
+
+
 def validate_init_args(
     *,
     storage: UPathStr,
     name: str | None = None,
     db: PostgresDsn | None = None,
-    schema: str | None = None,
+    modules: str | None = None,
     _test: bool = False,
     _write_settings: bool = True,
     _user: UserSettings | None = None,
@@ -150,9 +159,6 @@ def validate_init_args(
     str,
 ]:
     from ._connect_instance import connect
-    from .core._hub_utils import (
-        validate_schema_arg,
-    )
 
     if storage is None:
         raise SystemExit("✗ `storage` argument can't be `None`")
@@ -178,7 +184,7 @@ def validate_init_args(
     instance_id = None
     if response is not None:
         instance_id, instance_state = process_connect_response(response, instance_slug)
-    schema = validate_schema_arg(schema)
+    modules = process_modules_arg(modules)
     return name_str, instance_id, instance_state, instance_slug
 
 
@@ -202,22 +208,23 @@ def init(
     storage: UPathStr,
     name: str | None = None,
     db: PostgresDsn | None = None,
-    schema: str | None = None,
+    modules: str | None = None,
     **kwargs,
 ) -> None:
     """Create and load a LaminDB instance.
 
     Args:
-        storage: Either ``"create-s3"``, local or
-            remote folder (``"s3://..."`` or ``"gs://..."``).
+        storage: Either local or remote folder (`"s3://..."` or `"gs://..."`).
         name: Instance name.
         db: Database connection url, do not pass for SQLite.
-        schema: Comma-separated string of schema modules. None if not set.
+        modules: Comma-separated string of modules. None if the lamindb registries are enough.
     """
     isettings = None
     ssettings = None
 
     _write_settings: bool = kwargs.get("_write_settings", True)
+    if modules is None:
+        modules = kwargs.get("schema", None)
     _test: bool = kwargs.get("_test", False)
 
     # use this user instead of settings.user
@@ -241,7 +248,7 @@ def init(
             storage=storage,
             name=name,
             db=db,
-            schema=schema,
+            modules=modules,
             _test=_test,
             _write_settings=_write_settings,
             _user=_user,  # will get from settings.user if _user is None
@@ -268,7 +275,7 @@ def init(
             name=name_str,
             storage=ssettings,
             db=db,
-            schema=schema,
+            modules=modules,
             uid=ssettings.uid,
             # to lock passed user in isettings._cloud_sqlite_locker.lock()
             _locker_user=_user,  # only has effect if cloud sqlite

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/lamindb_setup/_migrate.py

@@ -5,7 +5,7 @@ from django.db.migrations.loader import MigrationLoader
 from lamin_utils import logger
 from packaging import version
 
-from . import _check_setup
+from ._check_setup import _check_instance_setup, _loading
 from .core._settings import settings
 from .core.django import setup_django
 
@@ -23,9 +23,9 @@ def check_whether_migrations_in_sync(db_version_str: str):
         return None
     installed_version = version.parse(installed_version_str)
     db_version = version.parse(db_version_str)
-    if (
-        installed_version.major < db_version.major
-        or installed_version.minor < db_version.minor
+    if installed_version.major < db_version.major or (
+        installed_version.major == db_version.major
+        and installed_version.minor < db_version.minor
     ):
         db_version_lower = f"{db_version.major}.{db_version.minor}"
         db_version_upper = f"{db_version.major}.{db_version.minor + 1}"
@@ -37,9 +37,9 @@ def check_whether_migrations_in_sync(db_version_str: str):
             "please update lamindb: pip install"
             f' "lamindb>={db_version_lower},<{db_version_upper}"'
         )
-    elif (
-        installed_version.major > db_version.major
-        or installed_version.minor > db_version.minor
+    elif installed_version.major > db_version.major or (
+        installed_version.major == db_version.major
+        and installed_version.minor > db_version.minor
     ):
         logger.warning(
             f"the database ({db_version_str}) is behind your installed lamindb package"
@@ -62,20 +62,20 @@ class migrate:
     """
 
     @classmethod
+    @_loading
     def create(cls) -> None:
         """Create a migration."""
-        if _check_setup._check_instance_setup():
+        if _check_instance_setup():
             raise RuntimeError("Restart Python session to create migration or use CLI!")
-        _check_setup.IS_LOADING = True
         setup_django(settings.instance, create_migrations=True)
-        _check_setup.IS_LOADING = False
 
     @classmethod
+    @_loading
     def deploy(cls) -> None:
         """Deploy a migration."""
         from ._schema_metadata import update_schema_in_hub
 
-        if _check_setup._check_instance_setup():
+        if _check_instance_setup():
             raise RuntimeError("Restart Python session to migrate or use CLI!")
         from lamindb_setup.core._hub_client import call_with_fallback_auth
         from lamindb_setup.core._hub_crud import (
@@ -115,6 +115,7 @@ class migrate:
             )
 
     @classmethod
+    @_loading
     def check(cls) -> bool:
         """Check whether Registry definitions are in sync with migrations."""
         from django.core.management import call_command
@@ -131,6 +132,7 @@ class migrate:
         return True
 
     @classmethod
+    @_loading
     def squash(
         cls, package_name, migration_nr, start_migration_nr: str | None = None
     ) -> None:
@@ -146,6 +148,7 @@ class migrate:
             call_command("squashmigrations", package_name, migration_nr)
 
     @classmethod
+    @_loading
     def show(cls) -> None:
         """Show migrations."""
         from django.core.management import call_command

{lamindb_setup-1.0a1 → lamindb_setup-1.0.1}/lamindb_setup/_schema_metadata.py

@@ -238,15 +238,15 @@ class _ModelHandler:
         model_name = field.model._meta.model_name
         relation_type = self._get_relation_type(model, field)
         if field.related_model is None:
-            schema_name = field.model.__get_schema_name__()
+            schema_name = field.model.__get_module_name__()
             related_model_name = None
             related_schema_name = None
             related_field_name = None
             field_name = field.name
         else:
             related_model_name = field.related_model._meta.model_name
-            related_schema_name = field.related_model.__get_schema_name__()
-            schema_name = field.model.__get_schema_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
 
@@ -362,7 +362,7 @@ class _ModelHandler:
 
 class _SchemaHandler:
     def __init__(self) -> None:
-        self.included_modules = ["core"] + list(settings.instance.schema)
+        self.included_modules = ["core"] + list(settings.instance.modules)
         self.modules = self._get_modules_metadata()
 
     def to_dict(self, include_django_objects: bool = True):
@@ -391,7 +391,7 @@ class _SchemaHandler:
                 if model.__class__ is Registry
                 and model is not Record
                 and not model._meta.abstract
-                and model.__get_schema_name__() == module_name
+                and model.__get_module_name__() == module_name
             }
             for module_name in self.included_modules
         }