lamindb_setup 0.78.0__tar.gz → 0.80.0__tar.gz

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.78.0
+Version: 0.80.0
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.9

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/docs/hub-cloud/02-connect-local-instance.ipynb

@@ -85,29 +85,6 @@
     ")"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "0986a5f3",
-   "metadata": {},
-   "source": [
-    "You cannot load another instance in the same Python session:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "bc3568ae",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import pytest\n",
-    "\n",
-    "with pytest.raises(RuntimeError):\n",
-    "    ln_setup.connect(\"testuser2/mydata\")\n",
-    "\n",
-    "assert ln_setup.settings.instance.slug == \"testuser1/mydata\""
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "e3701120",

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/docs/hub-cloud/08-test-multi-session.ipynb

@@ -113,14 +113,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with pytest.raises(RuntimeError):\n",
+    "from lamindb_setup._init_instance import CannotSwitchDefaultInstance\n",
+    "\n",
+    "with pytest.raises(CannotSwitchDefaultInstance):\n",
     "    ln_setup.init(storage=\"./testsetup2\")\n",
-    "with pytest.raises(RuntimeError):\n",
+    "with pytest.raises(CannotSwitchDefaultInstance):\n",
     "    ln_setup.connect(\"testsetup\")\n",
     "with pytest.raises(RuntimeError):\n",
     "    ln_setup.migrate.create()\n",
     "with pytest.raises(RuntimeError):\n",
-    "    ln_setup.migrate.deploy()"
+    "    ln_setup.migrate.deploy()\n",
+    "\n",
+    "assert ln_setup.settings.instance.slug == \"testuser1/testsetup\""
    ]
   },
   {

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/docs/hub-prod/test-cloud-sync.ipynb

@@ -82,7 +82,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dir_sync_local = settings.storage.cloud_to_local_no_update(dir_sync)\n",
+    "dir_sync_local = settings.paths.cloud_to_local_no_update(dir_sync)\n",
     "if dir_sync_local.is_dir():\n",
     "    for file in dir_sync_local.iterdir():\n",
     "        file.unlink()\n",
@@ -118,9 +118,9 @@
    "outputs": [],
    "source": [
     "test_local_path = UPath(\"./some/local/path\")\n",
-    "assert settings.storage.cloud_to_local_no_update(test_local_path) == test_local_path\n",
-    "assert settings.storage.cloud_to_local_no_update(test_local_path.as_posix()) == test_local_path\n",
-    "assert settings.storage.cloud_to_local_no_update(test_local_path, cache_key=\"some/cache/key\") == test_local_path"
+    "assert settings.paths.cloud_to_local_no_update(test_local_path) == test_local_path\n",
+    "assert settings.paths.cloud_to_local_no_update(test_local_path.as_posix()) == test_local_path\n",
+    "assert settings.paths.cloud_to_local_no_update(test_local_path, cache_key=\"some/cache/key\") == test_local_path"
    ]
   },
   {
@@ -130,8 +130,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert settings.storage.cloud_to_local_no_update(dir_sync) == settings.cache_dir / f\"lamindb-ci/{instance_name}/dir_sync\"\n",
-    "assert settings.storage.cloud_to_local_no_update(dir_sync, cache_key=\"dir_cache/key\") == settings.cache_dir / \"dir_cache/key\""
+    "assert settings.paths.cloud_to_local_no_update(dir_sync) == settings.cache_dir / f\"lamindb-ci/{instance_name}/dir_sync\"\n",
+    "assert settings.paths.cloud_to_local_no_update(dir_sync, cache_key=\"dir_cache/key\") == settings.cache_dir / \"dir_cache/key\""
    ]
   },
   {
@@ -149,7 +149,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dir_sync_local = settings.storage.cloud_to_local(dir_sync, cache_key=\"dir_cache/key\")"
+    "dir_sync_local = settings.paths.cloud_to_local(dir_sync, cache_key=\"dir_cache/key\")"
    ]
   },
   {
@@ -191,7 +191,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dir_sync_local = settings.storage.cloud_to_local(dir_sync)"
+    "dir_sync_local = settings.paths.cloud_to_local(dir_sync)"
    ]
   },
   {
@@ -238,7 +238,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dir_sync_local = settings.storage.cloud_to_local(dir_sync)\n",
+    "dir_sync_local = settings.paths.cloud_to_local(dir_sync)\n",
     "assert local_file.exists()\n",
     "assert num_files(dir_sync_local) == 2"
    ]
@@ -267,7 +267,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dir_sync_local = settings.storage.cloud_to_local(dir_sync)\n",
+    "dir_sync_local = settings.paths.cloud_to_local(dir_sync)\n",
     "\n",
     "for file in (\"file1\", \"file2\"):\n",
     "    assert (dir_sync_local / file).stat().st_mtime == (\n",
@@ -298,7 +298,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dir_sync_local = settings.storage.cloud_to_local(dir_sync)\n",
+    "dir_sync_local = settings.paths.cloud_to_local(dir_sync)\n",
     "assert num_files(dir_sync_local) == 2\n",
     "assert local_file_new.exists()"
    ]
@@ -325,7 +325,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dir_sync_local = settings.storage.cloud_to_local(dir_sync)\n",
+    "dir_sync_local = settings.paths.cloud_to_local(dir_sync)\n",
     "\n",
     "assert num_files(dir_sync_local) == 2\n",
     "assert not local_file_new.exists()\n",
@@ -430,7 +430,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cache_file = settings.instance.storage.cloud_to_local_no_update(sqlite_file)"
+    "cache_file = settings.paths.cloud_to_local_no_update(sqlite_file)"
    ]
   },
   {

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/lamindb_setup/__init__.py

@@ -33,7 +33,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.78.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.80.0"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 import sys as _sys

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/lamindb_setup/_connect_instance.py

@@ -9,7 +9,11 @@ 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 ._init_instance import (
+    MESSAGE_CANNOT_SWITCH_DEFAULT_INSTANCE,
+    CannotSwitchDefaultInstance,
+    load_from_isettings,
+)
 from ._silence_loggers import silence_loggers
 from .core._hub_core import connect_instance_hub
 from .core._hub_utils import (
@@ -224,7 +228,9 @@ def connect(slug: str, **kwargs) -> str | tuple | None:
                 logger.info(f"connected lamindb: {settings.instance.slug}")
                 return None
             else:
-                raise RuntimeError(MESSAGE_NO_MULTIPLE_INSTANCE)
+                raise CannotSwitchDefaultInstance(
+                    MESSAGE_CANNOT_SWITCH_DEFAULT_INSTANCE
+                )
         elif (
             _write_settings
             and settings._instance_exists

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/lamindb_setup/_init_instance.py

@@ -26,7 +26,7 @@ if TYPE_CHECKING:
     from .core.types import UPathStr
 
 
-def get_schema_module_name(schema_name) -> str:
+def get_schema_module_name(schema_name, raise_import_error: bool = True) -> str | None:
     import importlib.util
 
     name_attempts = [f"lnschema_{schema_name.replace('-', '_')}", schema_name]
@@ -34,9 +34,11 @@ def get_schema_module_name(schema_name) -> str:
         module_spec = importlib.util.find_spec(name)
         if module_spec is not None:
             return name
-    raise ImportError(
-        f"Python package for '{schema_name}' is not installed.\nIf your package is on PyPI, run `pip install {schema_name}`"
-    )
+    message = f"Schema module '{schema_name}' is not installed → no access to its labels & registries (resolve via `pip install {schema_name}`)"
+    if raise_import_error:
+        raise ImportError(message)
+    logger.warning(message.lower())
+    return None
 
 
 def register_storage_in_instance(ssettings: StorageSettings):
@@ -180,6 +182,8 @@ def validate_init_args(
         validate_schema_arg,
     )
 
+    if storage is None:
+        raise SystemExit("✗ `storage` argument can't be `None`")
     # should be called as the first thing
     name_str = infer_instance_name(storage=storage, name=name, db=db)
     owner_str = settings.user.handle if _user is None else _user.handle
@@ -206,10 +210,18 @@ def validate_init_args(
     return name_str, instance_id, instance_state, instance_slug
 
 
-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 settings set auto-connect false
+class CannotSwitchDefaultInstance(SystemExit):
+    pass
+
+
+MESSAGE_CANNOT_SWITCH_DEFAULT_INSTANCE = """
+You cannot write to different instances in the same Python session.
+
+Do you want to read from another instance via `Record.using()`? For example:
+
+ln.Artifact.using("laminlabs/cellxgene").filter()
+
+Or do you want to switch off auto-connect via `lamin settings set auto-connect false`?
 """
 
 
@@ -248,7 +260,7 @@ def init(
         from ._check_setup import _check_instance_setup
 
         if _check_instance_setup() and not _test:
-            raise RuntimeError(MESSAGE_NO_MULTIPLE_INSTANCE)
+            raise CannotSwitchDefaultInstance(MESSAGE_CANNOT_SWITCH_DEFAULT_INSTANCE)
         elif _write_settings:
             close_instance(mute=True)
         from .core._hub_core import init_instance as init_instance_hub

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/lamindb_setup/_setup_user.py

@@ -48,14 +48,14 @@ def load_user(email: str | None = None, handle: str | None = None) -> UserSettin
 
 
 def login(
-    user: str | None = None, *, key: str | None = None, api_key: str | None = None
+    user: str | None = None, *, api_key: str | None = None, key: str | None = None
 ) -> None:
     """Log in user.
 
     Args:
         user: handle or email
-        key: API key
-        api_key: Beta API key
+        api_key: API key
+        key: legacy API key
     """
     if user is None and api_key is None:
         if "LAMIN_API_KEY" in os.environ:

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/lamindb_setup/core/_hub_client.py

@@ -10,6 +10,8 @@ from pydantic_settings import BaseSettings
 from supabase import Client, create_client  # type: ignore
 from supabase.lib.client_options import ClientOptions
 
+from ._settings_save import save_user_settings
+
 
 class Connector(BaseSettings):
     url: str
@@ -129,14 +131,17 @@ def call_with_fallback_auth(
 
     for renew_token, fallback_env in [(False, False), (True, False), (False, True)]:
         try:
-            if renew_token:
-                logger.warning(
-                    "renewing expired lamin token: call `lamin login <your-handle>` to avoid this"
-                )
             client = connect_hub_with_auth(
                 renew_token=renew_token, fallback_env=fallback_env
             )
             result = callable(**kwargs, client=client)
+            # we update access_token here
+            # because at this point the call has been successfully resolved
+            if renew_token:
+                from lamindb_setup import settings
+
+                # here settings.user contains an updated access_token
+                save_user_settings(settings.user)
             break
         # we use Exception here as the ways in which the client fails upon 401
         # are not consistent and keep changing

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/lamindb_setup/core/_settings.py

@@ -161,6 +161,15 @@ class SetupSettings:
         cache_dir.mkdir(parents=True, exist_ok=True)
         return cache_dir
 
+    @property
+    def paths(self) -> type[SetupPaths]:
+        """Convert cloud paths to lamidb local paths.
+
+        Use `settings.paths.cloud_to_local_no_update`
+        or `settings.paths.cloud_to_local`.
+        """
+        return SetupPaths
+
     def __repr__(self) -> str:
         """Rich string representation."""
         repr = self.user.__repr__()
@@ -174,6 +183,38 @@ class SetupSettings:
         return repr
 
 
+class SetupPaths:
+    """A static class for conversion of cloud paths to lamindb local paths."""
+
+    @staticmethod
+    def cloud_to_local_no_update(
+        filepath: UPathStr, cache_key: str | None = None
+    ) -> UPath:
+        """Local (or local cache) filepath from filepath without synchronization."""
+        # cache_key is ignored if filepath is a string or a local path
+        # ignores a mere string even if it represents a cloud path
+        if isinstance(filepath, UPath) and not isinstance(filepath, LocalPathClasses):
+            # settings is defined further in this file
+            local_filepath = settings.cache_dir / (
+                filepath.path if cache_key is None else cache_key
+            )
+        else:
+            local_filepath = filepath
+        return UPath(local_filepath)
+
+    @staticmethod
+    def cloud_to_local(
+        filepath: UPathStr, cache_key: str | None = None, **kwargs
+    ) -> UPath:
+        """Local (or local cache) filepath from filepath."""
+        # cache_key is ignored in cloud_to_local_no_update if filepath is local or a string
+        local_filepath = SetupPaths.cloud_to_local_no_update(filepath, cache_key)
+        if isinstance(filepath, UPath) and not isinstance(filepath, LocalPathClasses):
+            local_filepath.parent.mkdir(parents=True, exist_ok=True)
+            filepath.synchronize(local_filepath, **kwargs)
+        return local_filepath
+
+
 def get_env_name():
     if "LAMIN_ENV" in os.environ:
         return os.environ["LAMIN_ENV"]

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/lamindb_setup/core/_settings_storage.py

@@ -85,8 +85,8 @@ def init_storage(
     StorageSettings,
     Literal["hub-record-not-created", "hub-record-retireved", "hub-record-created"],
 ]:
-    if root is None:
-        raise ValueError("`storage` argument can't be `None`")
+    assert root is not None, "`root` argument can't be `None`"
+
     root_str = str(root)  # ensure we have a string
     if ".lamindb" in root_str:
         raise ValueError(
@@ -322,24 +322,20 @@ class StorageSettings:
         self, filepath: UPathStr, cache_key: str | None = None, **kwargs
     ) -> UPath:
         """Local (or local cache) filepath from filepath."""
-        # cache_key is ignored in cloud_to_local_no_update if filepath is local
-        local_filepath = self.cloud_to_local_no_update(filepath, cache_key)
-        if isinstance(filepath, UPath) and not isinstance(filepath, LocalPathClasses):
-            local_filepath.parent.mkdir(parents=True, exist_ok=True)
-            filepath.synchronize(local_filepath, **kwargs)
-        return local_filepath
+        from lamindb_setup import settings
+
+        return settings.paths.cloud_to_local(
+            filepath=filepath, cache_key=cache_key, **kwargs
+        )
 
     def cloud_to_local_no_update(
         self, filepath: UPathStr, cache_key: str | None = None
     ) -> UPath:
-        # cache_key is ignored if filepath is local
-        if isinstance(filepath, UPath) and not isinstance(filepath, LocalPathClasses):
-            local_filepath = self.cache_dir / (
-                filepath.path if cache_key is None else cache_key
-            )
-        else:
-            local_filepath = filepath
-        return UPath(local_filepath)
+        from lamindb_setup import settings
+
+        return settings.paths.cloud_to_local_no_update(
+            filepath=filepath, cache_key=cache_key
+        )
 
     def key_to_filepath(self, filekey: UPathStr) -> UPath:
         """Cloud or local filepath from filekey."""

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/lamindb_setup/core/_settings_user.py

@@ -24,9 +24,9 @@ class UserSettings:
     email: str | None = None
     """User email."""
     api_key: str | None = None
-    """Beta API key."""
+    """API key."""
     password: str | None = None
-    """API key or legacy password."""
+    """legacy API key or legacy password."""
     access_token: str | None = None
     """User access token."""
     uid: str = "null"

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/lamindb_setup/core/django.py

@@ -55,7 +55,17 @@ def setup_django(
         from .._init_instance import get_schema_module_name
 
         schema_names = ["core"] + list(isettings.schema)
-        installed_apps = [get_schema_module_name(n) for n in schema_names]
+        raise_import_error = True if init else False
+        installed_apps = [
+            package_name
+            for n in schema_names
+            if (
+                package_name := get_schema_module_name(
+                    n, raise_import_error=raise_import_error
+                )
+            )
+            is not None
+        ]
         if view_schema:
             installed_apps = installed_apps[::-1]  # to fix how apps appear
             installed_apps += ["schema_graph", "django.contrib.staticfiles"]

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/lamindb_setup/core/upath.py

@@ -763,13 +763,9 @@ def check_storage_is_empty(
         if raise_error
         else "consider deleting them"
     )
-    hint = "'_is_initialized'"
-    if n_offset_objects == 2:
-        hint += " & SQLite file"
-    hint += " ignored"
     message = (
-        f"Storage {directory_string} contains {n_objects - n_offset_objects} objects "
-        f"({hint}) - {ask_for_deletion}"
+        f"Storage '{directory_string}' contains {n_objects - n_offset_objects} objects"
+        f" - {ask_for_deletion}"
     )
     if n_diff > 0:
         if raise_error:

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/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://us-east-1.api.lamin.ai"
-        assert instance["schema_str"] == "bionty,wetlab"
+        assert instance["schema_str"].startswith("bionty,wetlab")
         assert "schema_id" in instance
         # check that schema_id is well-formed UUID
         # if not, throws ValueError

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/tests/hub-cloud/test_init_instance.py

@@ -32,6 +32,12 @@ def test_init_instance_postgres_default_name(get_hub_client):
         ln_setup.delete(instance_name, force=True)
     except InstanceNotFoundError:
         pass
+    # test init with storage=None
+    # this happens when calling CLI lamin init or lamin init --name smth
+    with pytest.raises(SystemExit):
+        ln_setup.init(storage=None, _test=True)
+    with pytest.raises(SystemExit):
+        ln_setup.init(storage=None, name="init-to-fail", _test=True)
     # now, run init
     ln_setup.init(storage="./mydatapg", db=pgurl, _test=True)
     assert ln_setup.settings.instance.slug == "testuser2/pgtest"

{lamindb_setup-0.78.0 → lamindb_setup-0.80.0}/tests/hub-local/test_all.py

@@ -342,6 +342,12 @@ def test_connect_instance_hub_corrupted_or_expired_credentials(
         owner="testadmin1",
         name=create_myinstance["name"],
     )
+    # check access_token renewal
+    access_token = ln_setup.settings.user.access_token
+    assert access_token != "corrupted_or_expired_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
 
 
 def test_init_storage_with_non_existing_bucket(create_testadmin1_session):