lamindb_setup 0.77.5__tar.gz → 0.78.0__tar.gz

{lamindb_setup-0.77.5 → lamindb_setup-0.78.0}/PKG-INFO

@@ -1,8 +1,9 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.77.5
+Version: 0.78.0
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 Requires-Dist: lnschema_core>=0.51.0
 Requires-Dist: lamin_utils>=0.3.3
@@ -11,14 +12,15 @@ Requires-Dist: dj_database_url>=1.3.0,<3.0.0
 Requires-Dist: pydantic-settings
 Requires-Dist: appdirs<2.0.0
 Requires-Dist: requests
-Requires-Dist: universal_pathlib==0.2.2
+Requires-Dist: universal_pathlib==0.2.5
 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-0.78.0}/docs/hub-cloud/02-connect-local-instance.ipynb

@@ -19,10 +19,10 @@
    },
    "outputs": [],
    "source": [
-    "!lamin load --unload\n",
+    "!lamin disconnect\n",
     "!lamin delete --force mydata\n",
     "!lamin init --storage mydata\n",
-    "!lamin load --unload"
+    "!lamin disconnect"
    ]
   },
   {

{lamindb_setup-0.77.5 → lamindb_setup-0.78.0}/docs/hub-cloud/03-add-managed-storage.ipynb

@@ -21,7 +21,7 @@
    },
    "outputs": [],
    "source": [
-    "!lamin load --unload\n",
+    "!lamin disconnect\n",
     "!lamin login testuser1\n",
     "!lamin delete --force test-add-managed-storage\n",
     "!docker stop pgtest && docker rm pgtest"

{lamindb_setup-0.77.5 → lamindb_setup-0.78.0}/docs/hub-prod/test-cache-management.ipynb

@@ -15,7 +15,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import os\n",
     "import lamindb_setup as ln_setup\n",
+    "from lamindb_setup._cache import set_cache_dir\n",
     "from lamindb_setup.core._settings_store import system_storage_settings_file\n",
     "\n",
     "ln_setup.login(\"testuser2\")"
@@ -67,8 +69,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "save_cache_dir = ln_setup.settings.storage.cache_dir\n",
-    "set_cache_dir = save_cache_dir.parent / \"Cache1\""
+    "old_cache_dir = ln_setup.settings.cache_dir\n",
+    "new_cache_dir = old_cache_dir.parent / \"Cache1\""
    ]
   },
   {
@@ -78,7 +80,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln_setup.settings.storage.cache_dir = set_cache_dir"
+    "set_cache_dir(new_cache_dir)"
    ]
   },
   {
@@ -94,21 +96,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "df1a1396",
+   "id": "c1958c5b",
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert ln_setup.settings.storage.cache_dir != save_cache_dir"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5b5ca8a8",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "assert ln_setup.settings.storage.cache_dir == set_cache_dir"
+    "assert ln_setup.settings.cache_dir == new_cache_dir"
    ]
   },
   {
@@ -118,7 +110,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert set_cache_dir.exists()"
+    "assert new_cache_dir.exists()"
    ]
   },
   {
@@ -128,7 +120,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert set_cache_dir in ln_setup.settings.instance._sqlite_file_local.parents"
+    "assert new_cache_dir in ln_setup.settings.instance._sqlite_file_local.parents"
    ]
   },
   {
@@ -156,53 +148,35 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert not any(set_cache_dir.iterdir())"
+    "assert not any(new_cache_dir.iterdir())"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "14ffa755",
-   "metadata": {},
-   "source": [
-    "Check that the cache dir is preserved between`close` and `load`."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "a05bb5a2",
+   "id": "e2aeabb4",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "# ln_setup.connect(\"test-cache\")  # this isn't possible"
+    "Setting to `\"null\"` or `None` restores the default directory."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4f1c8dbe",
+   "id": "95aec7fd",
    "metadata": {},
    "outputs": [],
    "source": [
-    "# assert ln_setup.settings.storage.cache_dir == set_cache_dir"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "e2aeabb4",
-   "metadata": {},
-   "source": [
-    "Setting to `\"null\"` or `None` restores the default directory."
+    "set_cache_dir(\"null\")"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "95aec7fd",
+   "id": "f1923e4d",
    "metadata": {},
    "outputs": [],
    "source": [
-    "# ln_setup.settings.storage.cache_dir = None"
+    "assert ln_setup.settings.cache_dir == old_cache_dir"
    ]
   },
   {
@@ -212,7 +186,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# assert ln_setup.settings.storage.cache_dir == save_cache_dir"
+    "set_cache_dir(None)"
    ]
   },
   {
@@ -222,7 +196,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# assert ln_setup.settings.storage.cache_dir != set_cache_dir"
+    "assert ln_setup.settings.cache_dir == old_cache_dir"
    ]
   },
   {
@@ -248,7 +222,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!lamin cache"
+    "exit_status = os.system(\"lamin cache get\")\n",
+    "assert exit_status == 0"
    ]
   },
   {
@@ -258,7 +233,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!lamin cache set \"null\""
+    "exit_status = os.system(\"lamin cache set 'null'\")\n",
+    "assert exit_status == 0"
    ]
   },
   {
@@ -297,7 +273,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.9.17"
   }
  },
  "nbformat": 4,

{lamindb_setup-0.77.5 → lamindb_setup-0.78.0}/docs/hub-prod/test-cloud-sync.ipynb

@@ -18,7 +18,7 @@
     "import os\n",
     "\n",
     "instance_name = f\"test-sqlite-sync\"\n",
-    "!lamin load {instance_name}\n",
+    "!lamin connect {instance_name}\n",
     "!yes | lamin delete {instance_name}"
    ]
   },
@@ -130,8 +130,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert settings.storage.cloud_to_local_no_update(dir_sync) == settings.storage.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.storage.cache_dir / \"dir_cache/key\""
+    "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\""
    ]
   },
   {
@@ -159,7 +159,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert dir_sync_local == settings.storage.cache_dir / \"dir_cache/key\"\n",
+    "assert dir_sync_local == settings.cache_dir / \"dir_cache/key\"\n",
     "assert dir_sync_local.is_dir()\n",
     "assert num_files(dir_sync_local) == 2"
    ]
@@ -312,8 +312,8 @@
    "source": [
     "time.sleep(1)\n",
     "cloud_file = dir_sync / \"file1\"\n",
-    "# update cloud timestamp, exist_ok=False needed due to truncate=not exist_ok in upath\n",
-    "cloud_file.touch(exist_ok=False)  \n",
+    "# update cloud timestamp\n",
+    "cloud_file.fs.touch(cloud_file.as_posix(), truncate=True)  \n",
     "\n",
     "assert cloud_file.modified.timestamp() > local_file_new.stat().st_mtime"
    ]

{lamindb_setup-0.77.5 → lamindb_setup-0.78.0}/docs/hub-prod/test-init-load-local-anonymously.ipynb

@@ -63,7 +63,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!lamin load --unload\n",
+    "!lamin disconnect\n",
     "!lamin init --storage ./test-anonymous-init --schema bionty"
    ]
   },

{lamindb_setup-0.77.5 → lamindb_setup-0.78.0}/docs/hub-prod/test-insufficient-user-info.ipynb

@@ -13,7 +13,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!lamin load --unload"
+    "!lamin disconnect"
    ]
   },
   {

{lamindb_setup-0.77.5 → lamindb_setup-0.78.0}/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__ = "0.78.0"  # 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/_cache.py

@@ -0,0 +1,48 @@
+from __future__ import annotations
+
+import shutil
+
+from lamin_utils import logger
+
+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()
+
+    cache_dir = settings.cache_dir
+    shutil.rmtree(cache_dir)
+    cache_dir.mkdir()
+    logger.success("The cache directory was cleared.")
+
+
+def get_cache_dir():
+    from lamindb_setup import settings
+
+    return settings.cache_dir.as_posix()
+
+
+def set_cache_dir(cache_dir: str):
+    from lamindb_setup.core._settings import (
+        DEFAULT_CACHE_DIR,
+        _process_cache_path,
+        settings,
+    )
+
+    old_cache_dir = settings.cache_dir
+    new_cache_dir = _process_cache_path(cache_dir)
+    if new_cache_dir is None:
+        new_cache_dir = DEFAULT_CACHE_DIR
+    if new_cache_dir != old_cache_dir:
+        shutil.copytree(old_cache_dir, new_cache_dir, dirs_exist_ok=True)
+        shutil.rmtree(old_cache_dir)
+        logger.info("The current cache directory was moved to the specified location")
+    new_cache_dir = new_cache_dir.resolve()
+    save_system_storage_settings(new_cache_dir)
+    settings._cache_dir = new_cache_dir

{lamindb_setup-0.77.5 → lamindb_setup-0.78.0}/lamindb_setup/_check_setup.py

@@ -1,7 +1,8 @@
 from __future__ import annotations
 
+import importlib as il
 import os
-from typing import TYPE_CHECKING, Optional
+from typing import TYPE_CHECKING
 
 from lamin_utils import logger
 
@@ -41,9 +42,9 @@ def _get_current_instance_settings() -> InstanceSettings | None:
         except Exception as e:
             # user will get more detailed traceback once they run the CLI
             logger.error(
-                "Current instance cannot be reached, unload it: `lamin load --unload`\n"
+                "Current instance cannot be reached, disconnect from it: `lamin disconnect`\n"
                 "Alternatively, init or load a connectable instance on the"
-                " command line: `lamin load <instance>` or `lamin init <...>`"
+                " command line: `lamin connect <instance>` or `lamin init <...>`"
             )
             raise e
         return isettings
@@ -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-0.78.0}/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_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_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
@@ -166,8 +160,11 @@ def _connect_instance(
                 git_repo=instance_result["git_repo"],
                 keep_artifacts_local=bool(instance_result["keep_artifacts_local"]),
                 is_on_hub=True,
+                api_url=instance_result["api_url"],
+                schema_id=None
+                if (schema_id := instance_result["schema_id"]) is None
+                else UUID(schema_id),
             )
-            check_whether_migrations_in_sync(instance_result["lamindb_version"])
         else:
             if hub_result != "anonymous-user":
                 message = INSTANCE_NOT_FOUND_MESSAGE.format(
@@ -263,7 +260,7 @@ def connect(slug: str, **kwargs) -> str | tuple | None:
                 logger.warning(
                     "SQLite file does not exist in the cloud, but exists locally:"
                     f" {isettings._sqlite_file_local}\nTo push the file to the cloud,"
-                    " call: lamin load --unload"
+                    " call: lamin disconnect"
                 )
             elif _raise_not_found_error:
                 raise SystemExit(msg)
@@ -313,6 +310,7 @@ 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-0.78.0}/lamindb_setup/_delete.py

@@ -24,7 +24,7 @@ def delete_cache(isettings: InstanceSettings):
     # avoid init of root
     root = isettings.storage._root_init
     if not isinstance(root, LocalPathClasses):
-        cache_dir = isettings.storage.cache_dir / root
+        cache_dir = settings.cache_dir / root.path
         if cache_dir.exists():
             shutil.rmtree(cache_dir)
 

{lamindb_setup-0.77.5 → lamindb_setup-0.78.0}/lamindb_setup/_django.py

@@ -1,7 +1,5 @@
 from __future__ import annotations
 
-from typing import Optional
-
 from .core._settings import settings
 from .core.django import setup_django
 

{lamindb_setup-0.77.5 → lamindb_setup-0.78.0}/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
 """
 
 
@@ -314,7 +309,7 @@ def init(
             isettings._cloud_sqlite_locker.lock()
             logger.warning(
                 "locked instance (to unlock and push changes to the cloud SQLite file,"
-                " call: lamin load --unload)"
+                " call: lamin disconnect)"
             )
         if register_on_hub and isettings.dialect != "sqlite":
             from ._schema_metadata import update_schema_in_hub
@@ -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-0.78.0}/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-0.78.0}/lamindb_setup/_setup_user.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 import os
-from typing import TYPE_CHECKING, Optional, Union
+from typing import TYPE_CHECKING
 
 from lamin_utils import logger
 

{lamindb_setup-0.77.5 → lamindb_setup-0.78.0}/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"]