fix: Make conn() with credentials update singleton connection

- conn(host, user, password) now updates the singleton connection
  instead of creating a separate connection
- Remove irrelevant safemode=False from spec examples
- thread_safe is set via DJ_THREAD_SAFE env var or config file

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: dimitri-yatsenko

docs/design/thread-safe-mode.md

@@ -18,7 +18,6 @@ import datajoint as dj
 # Configure credentials (no connection yet)
 dj.config.database.user = "user"
 dj.config.database.password = "password"
-dj.config.safemode = False
 
 # First call to conn() or Schema() creates the singleton connection
 dj.conn()  # Creates connection using dj.config credentials
@@ -29,6 +28,11 @@ class Mouse(dj.Manual):
     definition = "..."
 ```
 
+Alternatively, pass credentials directly to `conn()`:
+```python
+dj.conn(host="localhost", user="user", password="password")
+```
+
 Internally:
 - `dj.config` → delegates to `_global_config` (with thread-safety check)
 - `dj.conn()` → returns `_singleton_connection` (created lazily)
@@ -45,7 +49,6 @@ inst = dj.Instance(
     user="user",
     password="password",
 )
-inst.config.safemode = False
 schema = inst.Schema("my_schema")
 
 @schema
@@ -107,7 +110,6 @@ dj.conn()               # ThreadSafetyError
 dj.Schema("name")       # ThreadSafetyError
 
 inst = dj.Instance(host="h", user="u", password="p")  # OK
-inst.config.safemode = False  # OK
 inst.Schema("name")           # OK
 ```
 
@@ -147,10 +149,6 @@ inst = dj.Instance(
     password="password",
 )
 
-# Configure
-inst.config.safemode = False
-inst.config.stores = {"raw": {"protocol": "file", "location": "/data"}}
-
 # Create schema
 schema = inst.Schema("my_schema")
 
@@ -162,7 +160,7 @@ class Mouse(dj.Manual):
 
 # Use tables
 Mouse().insert1({"mouse_id": 1})
-Mouse().delete()  # Uses inst.config.safemode
+Mouse().fetch()
 ```
 
 ## Implementation

src/datajoint/__init__.py

@@ -103,17 +103,18 @@ def conn(
     """
     Return a persistent connection object.
 
-    When called without arguments, returns the singleton connection.
-    When connection parameters are provided, creates a new Connection.
+    When called without arguments, returns the singleton connection using
+    credentials from dj.config. When connection parameters are provided,
+    updates the singleton connection with the new credentials.
 
     Parameters
     ----------
     host : str, optional
-        Database hostname.
+        Database hostname. If provided, updates singleton.
     user : str, optional
-        Database username.
+        Database username. If provided, updates singleton.
     password : str, optional
-        Database password.
+        Database password. If provided, updates singleton.
     reset : bool, optional
         If True, reset existing connection. Default False.
     use_tls : bool or dict, optional
@@ -127,15 +128,38 @@ def conn(
     Raises
     ------
     ThreadSafetyError
-        If thread_safe mode is enabled and using singleton.
+        If thread_safe mode is enabled.
     """
-    # If any connection params provided, use legacy behavior
-    if host is not None or user is not None or password is not None or reset:
-        from .connection import conn as _legacy_conn
+    from .instance import _singleton_connection, _check_thread_safe, _global_config
+    import datajoint.instance as instance_module
 
-        return _legacy_conn(host, user, password, reset=reset, use_tls=use_tls)
+    _check_thread_safe()
+
+    # If credentials provided or reset requested, (re)create the singleton
+    if host is not None or user is not None or password is not None or reset:
+        # Use provided values or fall back to config
+        host = host if host is not None else _global_config.database.host
+        user = user if user is not None else _global_config.database.user
+        password = password if password is not None else _global_config.database.password
+        if password is not None and hasattr(password, 'get_secret_value'):
+            password = password.get_secret_value()
+        port = _global_config.database.port
+        use_tls = use_tls if use_tls is not None else _global_config.database.use_tls
+
+        if user is None:
+            from .errors import DataJointError
+            raise DataJointError(
+                "Database user not configured. Set dj.config['database.user'] or pass user= argument."
+            )
+        if password is None:
+            from .errors import DataJointError
+            raise DataJointError(
+                "Database password not configured. Set dj.config['database.password'] or pass password= argument."
+            )
+
+        instance_module._singleton_connection = Connection(host, user, password, port, use_tls)
+        instance_module._singleton_connection._config = _global_config
 
-    # Otherwise use singleton connection
     return _get_singleton_connection()