Merge master into pre/v2.1

Author: dimitri-yatsenko

README.md

@@ -10,7 +10,7 @@ DataJoint is a framework for scientific data pipelines based on the **Relational
 **Documentation:** https://docs.datajoint.com
 
 > **📘 Upgrading from legacy DataJoint (pre-2.0)?**
-> See the **[Migration Guide](https://docs.datajoint.com/how-to/migrate-from-0x/)** for a step-by-step upgrade path.
+> See the **[Migration Guide](https://docs.datajoint.com/how-to/migrate-to-v20/)** for a step-by-step upgrade path.
 
 <table>
 <tr>
@@ -78,8 +78,8 @@ conda install -c conda-forge datajoint
 - **[Documentation](https://docs.datajoint.com)** — Complete guides and reference
   - [Tutorials](https://docs.datajoint.com/tutorials/) — Learn by example
   - [How-To Guides](https://docs.datajoint.com/how-to/) — Task-oriented guides
-  - [API Reference](https://docs.datajoint.com/reference/api/) — Complete API documentation
-  - [Migration Guide](https://docs.datajoint.com/how-to/migrate-from-0x/) — Upgrade from legacy versions
+  - [API Reference](https://docs.datajoint.com/api/) — Complete API documentation
+  - [Migration Guide](https://docs.datajoint.com/how-to/migrate-to-v20/) — Upgrade from legacy versions
 - **[DataJoint Elements](https://datajoint.com/docs/elements/)** — Example pipelines for neuroscience
 - **[GitHub Discussions](https://github.com/datajoint/datajoint-python/discussions)** — Community support
 

src/datajoint/__init__.py

@@ -39,7 +39,6 @@
     "Top",
     "U",
     "Diagram",
-    "kill",
     "MatCell",
     "MatStruct",
     # Codec API
@@ -94,8 +93,6 @@
     # Diagram imports networkx and matplotlib
     "Diagram": (".diagram", "Diagram"),
     "diagram": (".diagram", None),  # Return the module itself
-    # kill imports pymysql via connection
-    "kill": (".admin", "kill"),
     # cli imports click
     "cli": (".cli", "cli"),
 }

src/datajoint/admin.py

@@ -11,7 +11,6 @@
 import re
 import warnings
 from contextlib import contextmanager
-from getpass import getpass
 from typing import Callable
 
 from . import errors
@@ -71,9 +70,9 @@ def conn(
     host : str, optional
         Database hostname.
     user : str, optional
-        MySQL username.
+        Database username. Required if not set in config.
     password : str, optional
-        MySQL password. Prompts if not provided.
+        Database password. Required if not set in config.
     init_fun : callable, optional
         Initialization function called after connection.
     reset : bool, optional
@@ -86,15 +85,24 @@ def conn(
     -------
     Connection
         Persistent database connection.
+
+    Raises
+    ------
+    DataJointError
+        If user or password is not provided and not set in config.
     """
     if not hasattr(conn, "connection") or reset:
         host = host if host is not None else config["database.host"]
         user = user if user is not None else config["database.user"]
         password = password if password is not None else config["database.password"]
         if user is None:
-            user = input("Please enter DataJoint username: ")
+            raise errors.DataJointError(
+                "Database user not configured. Set datajoint.config['database.user'] or pass user= argument."
+            )
         if password is None:
-            password = getpass(prompt="Please enter DataJoint password: ")
+            raise errors.DataJointError(
+                "Database password not configured. Set datajoint.config['database.password'] or pass password= argument."
+            )
         init_fun = init_fun if init_fun is not None else config["connection.init_function"]
         use_tls = use_tls if use_tls is not None else config["database.use_tls"]
         conn.connection = Connection(host, user, password, None, init_fun, use_tls)

src/datajoint/connection.py

@@ -72,7 +72,8 @@ class Schema:
     create_schema : bool, optional
         If False, raise error if schema doesn't exist. Default True.
     create_tables : bool, optional
-        If False, raise error when accessing missing tables. Default True.
+        If False, raise error when accessing missing tables.
+        Default from ``dj.config.database.create_tables`` (True unless configured).
     add_objects : dict, optional
         Additional objects for the declaration context.
 
@@ -93,7 +94,7 @@ def __init__(
         *,
         connection: Connection | None = None,
         create_schema: bool = True,
-        create_tables: bool = True,
+        create_tables: bool | None = None,
         add_objects: dict[str, Any] | None = None,
     ) -> None:
         """
@@ -110,15 +111,16 @@ def __init__(
         create_schema : bool, optional
             If False, raise error if schema doesn't exist. Default True.
         create_tables : bool, optional
-            If False, raise error when accessing missing tables. Default True.
+            If False, raise error when accessing missing tables.
+            Default from ``dj.config.database.create_tables`` (True unless configured).
         add_objects : dict, optional
             Additional objects for the declaration context.
         """
         self.connection = connection
         self.database = None
         self.context = context
         self.create_schema = create_schema
-        self.create_tables = create_tables
+        self.create_tables = create_tables if create_tables is not None else config.database.create_tables
         self.add_objects = add_objects
         self.declare_list = []
         if schema_name:

src/datajoint/schemas.py

@@ -65,6 +65,8 @@
     "database.password": "DJ_PASS",
     "database.backend": "DJ_BACKEND",
     "database.port": "DJ_PORT",
+    "database.schema_prefix": "DJ_SCHEMA_PREFIX",
+    "database.create_tables": "DJ_CREATE_TABLES",
     "loglevel": "DJ_LOG_LEVEL",
     "display.diagram_direction": "DJ_DIAGRAM_DIRECTION",
 }
@@ -196,6 +198,18 @@ class DatabaseSettings(BaseSettings):
     port: int | None = Field(default=None, validation_alias="DJ_PORT")
     reconnect: bool = True
     use_tls: bool | None = Field(default=None, validation_alias="DJ_USE_TLS")
+    schema_prefix: str = Field(
+        default="",
+        validation_alias="DJ_SCHEMA_PREFIX",
+        description="Project-specific prefix for schema names. "
+        "Not automatically applied; use dj.config.database.schema_prefix when creating schemas.",
+    )
+    create_tables: bool = Field(
+        default=True,
+        validation_alias="DJ_CREATE_TABLES",
+        description="Default for Schema create_tables parameter. "
+        "Set to False for production mode to prevent automatic table creation.",
+    )
 
     @model_validator(mode="after")
     def set_default_port_from_backend(self) -> "DatabaseSettings":

src/datajoint/settings.py

@@ -27,25 +27,6 @@ def test_lazy_diagram_import():
     assert Diagram.__name__ == "Diagram"
 
 
-def test_lazy_admin_import():
-    """Admin module should not be loaded until dj.kill is accessed."""
-    # Remove datajoint from sys.modules to get fresh import
-    modules_to_remove = [key for key in sys.modules if key.startswith("datajoint")]
-    for mod in modules_to_remove:
-        del sys.modules[mod]
-
-    # Import datajoint
-    import datajoint as dj
-
-    # Admin module should not be loaded yet
-    assert "datajoint.admin" not in sys.modules, "admin module loaded eagerly"
-
-    # Access kill - should trigger lazy load
-    kill = dj.kill
-    assert "datajoint.admin" in sys.modules, "admin module not loaded after access"
-    assert callable(kill)
-
-
 def test_lazy_cli_import():
     """CLI module should not be loaded until dj.cli is accessed."""
     # Remove datajoint from sys.modules to get fresh import
@@ -103,5 +84,4 @@ def test_core_imports_available():
 
     # Heavy modules should still not be loaded
     assert "datajoint.diagram" not in sys.modules
-    assert "datajoint.admin" not in sys.modules
     assert "datajoint.cli" not in sys.modules