lamindb_setup 1.0a5__tar.gz → 1.0.2__tar.gz

{lamindb_setup-1.0a5 → lamindb_setup-1.0.2}/.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-1.0a5 → lamindb_setup-1.0.2}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.0a5
+Version: 1.0.2
 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-1.0a5 → lamindb_setup-1.0.2}/lamindb_setup/__init__.py

@@ -33,10 +33,9 @@ Modules & settings:
 
 """
 
-__version__ = "1.0a5"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "1.0.2"  # 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-1.0a5 → lamindb_setup-1.0.2}/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-1.0a5 → lamindb_setup-1.0.2}/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-1.0a5 → lamindb_setup-1.0.2}/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,
@@ -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:
@@ -331,6 +339,25 @@ def migrate_lnschema_core(
     """Migrate lnschema_core tables to lamindb tables."""
     from urllib.parse import urlparse
 
+    if isettings.is_on_hub:
+        from lamindb_setup.core._hub_client import call_with_fallback_auth
+        from lamindb_setup.core._hub_crud import (
+            select_collaborator,
+        )
+
+        # double check that user is an admin, otherwise will fail below
+        # due to insufficient SQL permissions with cryptic error
+        collaborator = call_with_fallback_auth(
+            select_collaborator,
+            instance_id=settings.instance._id,
+            account_id=settings.user._uuid,
+        )
+        if collaborator is None or collaborator["role"] != "admin":
+            raise SystemExit(
+                "❌ Only admins can deploy migrations, please ensure that you're an"
+                f" admin: https://lamin.ai/{settings.instance.slug}/settings"
+            )
+
     parsed_uri = urlparse(isettings.db)
     db_type = parsed_uri.scheme
 
@@ -381,7 +408,7 @@ 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-1.0a5 → lamindb_setup-1.0.2}/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-1.0a5 → lamindb_setup-1.0.2}/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-1.0a5 → lamindb_setup-1.0.2}/lamindb_setup/core/django.py

@@ -54,7 +54,8 @@ def setup_django(
 
         module_names = ["core"] + list(isettings.modules)
         raise_import_error = True if init else False
-        installed_apps = [
+        installed_apps = ["django.contrib.contenttypes"]
+        installed_apps += [
             package_name
             for name in module_names
             if (
@@ -113,9 +114,7 @@ def setup_django(
     elif init:
         global IS_MIGRATING
         IS_MIGRATING = True
-        call_command(
-            "migrate", verbosity=2
-        )  # may change back to verbosity 0 in the future
+        call_command("migrate", verbosity=0)
         IS_MIGRATING = False
 
     global IS_SETUP

{lamindb_setup-1.0a5 → lamindb_setup-1.0.2}/lamindb_setup/core/hashing.py

@@ -119,7 +119,7 @@ def hash_dir(path: Path):
             hashes_sizes = pool.map(hash_size, files)
     else:
         hashes_sizes = map(hash_size, files)
-    hashes, sizes = zip(*hashes_sizes)
+    hashes, sizes = zip(*hashes_sizes, strict=False)
 
     hash, hash_type = hash_from_hashes_list(hashes), "md5-d"
     n_files = len(hashes)

{lamindb_setup-1.0a5 → lamindb_setup-1.0.2}/lamindb_setup/core/upath.py

@@ -549,7 +549,7 @@ def compute_file_tree(
         pointers = [tee] * (len(contents) - 1) + [last]
         n_files_per_dir_and_type = defaultdict(lambda: 0)  # type: ignore
         # TODO: pass strict=False to zip with python > 3.9
-        for pointer, child_path in zip(pointers, contents):  # type: ignore
+        for pointer, child_path in zip(pointers, contents, strict=False):  # type: ignore
             if child_path.is_dir():
                 if include_dirs and child_path not in include_dirs:
                     continue

{lamindb_setup-1.0a5 → lamindb_setup-1.0.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "lamindb_setup"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 authors = [{name = "Lamin Labs", email = "open-source@lamin.ai"}]
 readme = "README.md"
 dynamic = ["version", "description"]
@@ -71,6 +71,9 @@ lint.select = [
     "PTH"  # Use pathlib
 ]
 lint.ignore = [
+    # this needs to be refactored as we dropped 3.9
+    # todo: refactor types and remove this
+    "UP007",
     # Do not catch blind exception: `Exception`
     "BLE001",
     # Errors from function calls in argument defaults. These are fine when the result is immutable.

{lamindb_setup-1.0a5 → lamindb_setup-1.0.2}/tests/hub-cloud/test_connect_instance.py

@@ -10,12 +10,14 @@ from lamindb_setup.core._hub_crud import update_instance
 from laminhub_rest.core.instance.collaborator import InstanceCollaboratorHandler
 from postgrest.exceptions import APIError
 
-# @pytest.fixture
-# def create_remote_test_instance():
-#     ln_setup.login("testuser1")
-#     ln_setup.init(storage="s3://lamindb-ci/load_remote_instance", _test=True)
-#     yield
-#     ln_setup.delete("load_remote_instance", force=True)
+
+def test_connect_pass_none():
+    with pytest.raises(SystemExit) as err:
+        ln_setup.connect(_test=True)
+    assert (
+        err.exconly()
+        == "SystemExit: No instance was connected through the CLI, pass a value to `instance` or connect via the CLI."
+    )
 
 
 # do not call hub if the owner is set to anonymous

{lamindb_setup-1.0a5 → lamindb_setup-1.0.2}/tests/hub-local/test_all.py

@@ -325,7 +325,10 @@ def test_connect_instance_hub_corrupted_or_expired_credentials(
     create_myinstance, create_testadmin1_session
 ):
     # assume token & password are corrupted or expired
-    ln_setup.settings.user.access_token = "corrupted_or_expired_token"
+    # make realisticly looking token that passes
+    # supafunc is_valid_jwt but is actually not a real token
+    invalid_token = "header1.payload1.signature1"
+    ln_setup.settings.user.access_token = invalid_token
     correct_password = ln_setup.settings.user.password
     ln_setup.settings.user.password = "corrupted_password"
     with pytest.raises(FunctionsHttpError):
@@ -336,7 +339,7 @@ def test_connect_instance_hub_corrupted_or_expired_credentials(
     # now, let's assume only the token is expired or corrupted
     # re-creating the auth client triggers a re-generated token because it
     # excepts the error assuming the token is expired
-    ln_setup.settings.user.access_token = "corrupted_or_expired_token"
+    ln_setup.settings.user.access_token = invalid_token
     ln_setup.settings.user.password = correct_password
     connect_instance_hub(
         owner="testadmin1",
@@ -344,7 +347,7 @@ def test_connect_instance_hub_corrupted_or_expired_credentials(
     )
     # check access_token renewal
     access_token = ln_setup.settings.user.access_token
-    assert access_token != "corrupted_or_expired_token"
+    assert access_token != invalid_token
     # check that the access_token was written to the settings
     ln_setup.settings._user_settings = None
     assert ln_setup.settings.user.access_token == access_token

{lamindb_setup-1.0a5 → lamindb_setup-1.0.2}/tests/hub-prod/test_upath.py

@@ -32,7 +32,7 @@ def test_progress_callback_size():
     pcb.set_size(10)
 
     cwd = str(Path.cwd())
-    paths = zip([cwd, cwd], [cwd, cwd])
+    paths = zip([cwd, cwd], [cwd, cwd], strict=False)
     # adjust size for directories in path list
     assert pcb.wrap(paths) == [(cwd, cwd), (cwd, cwd)]
     assert pcb.size == 8