lamindb_setup 1.0a1__tar.gz → 1.0a5__tar.gz

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.0a1
+Version: 1.0a5
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.9

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/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-1.0a5}/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-1.0a5}/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-1.0a5}/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-1.0a5}/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-1.0a5}/lamindb_setup/__init__.py

@@ -33,7 +33,7 @@ Modules & settings:
 
 """
 
-__version__ = "1.0a1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "1.0a5"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 import sys as _sys

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/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-1.0a5}/lamindb_setup/_connect_instance.py

@@ -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,

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/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-1.0a5}/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-1.0a5}/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-1.0a5}/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
         }

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/lamindb_setup/core/_deprecated.py

@@ -30,23 +30,30 @@ from functools import wraps
 def deprecated(new_name: str):
     """Deprecated.
 
-    This is a decorator which can be used to mark functions
+    This is a decorator which can be used to mark functions, methods and properties
     as deprecated. It will result in a warning being emitted
     when the function is used.
+
+    It will also hide the function from the docs.
+
+    Example::
+
+        @property
+        @deprecated("n_files")
+        def n_objects(self) -> int:
+            return self.n_files
+
     """
 
     def decorator(func):
         @wraps(func)
         def new_func(*args, **kwargs):
-            # turn off filter
-            warnings.simplefilter("always", DeprecationWarning)
             warnings.warn(
                 f"Use {new_name} instead of {func.__name__}, "
                 f"{func.__name__} will be removed in the future.",
-                category=DeprecationWarning,
+                category=FutureWarning,
                 stacklevel=2,
             )
-            warnings.simplefilter("default", DeprecationWarning)  # reset filter
             return func(*args, **kwargs)
 
         setattr(new_func, "__deprecated", True)

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/lamindb_setup/core/_hub_utils.py

@@ -7,15 +7,6 @@ from pydantic import BaseModel, Field, GetCoreSchemaHandler
 from pydantic_core import CoreSchema, core_schema
 
 
-def validate_schema_arg(schema: str | None = None) -> str:
-    if schema is None or schema == "":
-        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 schema.split(",")]
-    return ",".join(to_be_validated)
-
-
 def validate_db_arg(db: str | None) -> None:
     if db is not None:
         LaminDsnModel(db=db)

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/lamindb_setup/core/_settings_instance.py

@@ -8,6 +8,7 @@ from typing import TYPE_CHECKING, Literal
 from django.db.utils import ProgrammingError
 from lamin_utils import logger
 
+from ._deprecated import deprecated
 from ._hub_client import call_with_fallback
 from ._hub_crud import select_account_handle_name_by_lnid
 from ._hub_utils import LaminDsn, LaminDsnModel
@@ -53,7 +54,7 @@ class InstanceSettings:
         keep_artifacts_local: bool = False,  # default to local storage
         uid: str | None = None,  # instance uid/lnid
         db: str | None = None,  # DB URI
-        schema: str | None = None,  # comma-separated string of schema names
+        modules: str | None = None,  # comma-separated string of module names
         git_repo: str | None = None,  # a git repo URL
         is_on_hub: bool | None = None,  # initialized from hub
         api_url: str | None = None,
@@ -69,7 +70,7 @@ class InstanceSettings:
         self._storage: StorageSettings = storage
         validate_db_arg(db)
         self._db: str | None = db
-        self._schema_str: str | None = schema
+        self._schema_str: str | None = modules
         self._git_repo = None if git_repo is None else sanitize_git_repo_url(git_repo)
         # local storage
         self._keep_artifacts_local = keep_artifacts_local
@@ -84,7 +85,7 @@ class InstanceSettings:
     def __repr__(self):
         """Rich string representation."""
         representation = f"Current instance: {self.slug}"
-        attrs = ["owner", "name", "storage", "db", "schema", "git_repo"]
+        attrs = ["owner", "name", "storage", "db", "modules", "git_repo"]
         for attr in attrs:
             value = getattr(self, attr)
             if attr == "storage":
@@ -271,12 +272,20 @@ class InstanceSettings:
         return hash_and_encode_as_b62(self._id.hex)[:12]
 
     @property
-    def schema(self) -> set[str]:
-        """Schema modules in addition to core schema."""
+    def modules(self) -> set[str]:
+        """The set of modules that defines the database schema.
+
+        The core schema contained in lamindb is not included in this set.
+        """
         if self._schema_str is None:
             return {}  # type: ignore
         else:
-            return {schema for schema in self._schema_str.split(",") if schema != ""}
+            return {module for module in self._schema_str.split(",") if module != ""}
+
+    @property
+    @deprecated("modules")
+    def schema(self) -> set[str]:
+        return self.modules
 
     @property
     def _sqlite_file(self) -> UPath:

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/lamindb_setup/core/_settings_load.py

@@ -98,7 +98,7 @@ def setup_instance_from_store(store: InstanceSettingsStore) -> InstanceSettings:
         name=store.name,
         storage=ssettings,
         db=_null_to_value(store.db),
-        schema=_null_to_value(store.schema_str),
+        modules=_null_to_value(store.schema_str),
         git_repo=_null_to_value(store.git_repo),
         keep_artifacts_local=store.keep_artifacts_local,  # type: ignore
     )

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/lamindb_setup/core/_setup_bionty_sources.py

@@ -17,7 +17,7 @@ RENAME = {"name": "source", "description": "source_name"}
 
 def write_bionty_sources(isettings: InstanceSettings) -> None:
     """Write bionty sources to Source table."""
-    if "bionty" not in isettings.schema:
+    if "bionty" not in isettings.modules:
         return None
     import shutil
 
@@ -79,7 +79,7 @@ def load_bionty_sources(isettings: InstanceSettings | None = None):
             # not setting up bionty sources
             return None
     if isettings is not None:
-        if "bionty" not in isettings.schema:
+        if "bionty" not in isettings.modules:
             # no need to setup anything
             return None
 
@@ -96,7 +96,7 @@ def load_bionty_sources(isettings: InstanceSettings | None = None):
         for kwargs in active_records:
             for db_field, base_col in RENAME.items():
                 kwargs[base_col] = kwargs.pop(db_field)
-            # TODO: non-bionty schema?
+            # TODO: non-bionty modules?
             kwargs["entity"] = kwargs["entity"].replace("bionty.", "")
         write_yaml(
             parse_currently_used_sources(active_records),

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/lamindb_setup/core/django.py

@@ -52,14 +52,14 @@ def setup_django(
         }
         from .._init_instance import get_schema_module_name
 
-        schema_names = ["core"] + list(isettings.schema)
+        module_names = ["core"] + list(isettings.modules)
         raise_import_error = True if init else False
         installed_apps = [
             package_name
-            for n in schema_names
+            for name in module_names
             if (
                 package_name := get_schema_module_name(
-                    n, raise_import_error=raise_import_error
+                    name, raise_import_error=raise_import_error
                 )
             )
             is not None
@@ -113,7 +113,9 @@ def setup_django(
     elif init:
         global IS_MIGRATING
         IS_MIGRATING = True
-        call_command("migrate", verbosity=0)
+        call_command(
+            "migrate", verbosity=2
+        )  # may change back to verbosity 0 in the future
         IS_MIGRATING = False
 
     global IS_SETUP

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/noxfile.py

@@ -27,24 +27,26 @@ 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/lamindb@migrate git+https://github.com/laminlabs/wetlab@lamindbv1 git+https://github.com/laminlabs/lamin-cli@migrate"
-    schema_deps = f"""uv pip install --system git+https://github.com/laminlabs/bionty@lamindbv1
+    no_deps_packages = "git+https://github.com/laminlabs/lamindb git+https://github.com/laminlabs/wetlab git+https://github.com/laminlabs/lamin-cli"
+    modules_deps = f"""uv pip install --system git+https://github.com/laminlabs/bionty
 uv pip install --system --no-deps {no_deps_packages}
 """
     if group == "hub-cloud":
-        cmds = schema_deps + "uv pip install --system ./laminhub/rest-hub line_profiler"
+        cmds = (
+            modules_deps + "uv pip install --system ./laminhub/rest-hub line_profiler"
+        )
     elif group == "docs":
-        cmds = """uv pip install --system git+https://github.com/laminlabs/lamindb@migrate"""
+        cmds = """uv pip install --system git+https://github.com/laminlabs/lamindb"""
     elif group == "storage":
-        cmds = schema_deps + "uv pip install --system gcsfs huggingface_hub"
+        cmds = modules_deps + "uv pip install --system gcsfs huggingface_hub"
     elif group == "hub-prod":
         # cmds = "git clone --depth 1 https://github.com/django/django\n"
         # cmds += "uv pip install --system -e ./django\n"
         cmds = ""
-        cmds += schema_deps.strip()
+        cmds += modules_deps.strip()
         cmds += """\nuv pip install --system huggingface_hub"""
     elif group == "hub-local":
-        cmds = schema_deps.strip()
+        cmds = modules_deps.strip()
     # current package
     cmds += """\nuv pip install --system -e '.[aws,dev]'"""
 

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/tests/hub-cloud/test_init_instance.py

@@ -199,7 +199,7 @@ def test_init_invalid_name():
 # #     with pytest.raises(RuntimeError):
 # #         ln_setup.init(
 # #             storage="s3://lamindb-ci",
-# #             schema="retro, bionty",
+# #             modules="retro, bionty",
 # #             db="postgresql://batman:robin@35.222.187.204:5432/retro",
 # #         )
 
@@ -211,6 +211,6 @@ def test_init_invalid_name():
 # #     ln_setup.init(storage="s3://lamindb-ci")
 
 
-# def test_value_error_schema():
+# def test_value_error_modules():
 #     with pytest.raises(ModuleNotFoundError):
-#         ln_setup.init(storage="tmpstorage1", schema="bionty, xyz1")
+#         ln_setup.init(storage="tmpstorage1", modules="bionty, xyz1")

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/tests/hub-local/test_update_schema_in_hub.py

@@ -7,20 +7,20 @@ from lamindb_setup._schema_metadata import _dict_to_uuid, update_schema_in_hub
 def setup_instance():
     ln_setup.init(
         storage="./test_storage",
-        schema="bionty,wetlab",
+        modules="bionty,wetlab",
         db="postgresql://postgres:postgres@127.0.0.1:54322/postgres",
-        name="test-update-schema",
+        name="test-update-modules",
     )
     ln_setup.register()
     yield
-    ln_setup.delete("test-update-schema", force=True)
+    ln_setup.delete("test-update-modules", force=True)
 
 
 def test_update_schema_in_hub(setup_instance):
     is_new, schema_uuid, schema = update_schema_in_hub()
 
     # TODO: construct a test in which is_new is true
-    # currently it's false because the schema is already registered
+    # currently it's false because the modules is already registered
     # via `lamin register` earlier in the test
     assert not is_new
     assert _dict_to_uuid(schema["schema_json"]) == schema_uuid

{lamindb_setup-1.0a1 → lamindb_setup-1.0a5}/tests/hub-prod/conftest.py

@@ -12,7 +12,7 @@ def pytest_sessionstart(session: pytest.Session):
     assert lamindb_setup.settings.user.handle == "testuser2"
     lamindb_setup.init(
         storage="./default_storage",
-        schema="bionty",
+        modules="bionty",
         name="lamindb-setup-unit-tests",
     )
     assert lamindb_setup.settings.instance._id == lamindb_instance_id