fix: Remove unused init_fun/init_function setting

Removed init_function from ConnectionSettings and all connection
code paths. This was dead code - a pass-through to PyMySQL's
init_command that was never used by DataJoint.

Removed from:
- ConnectionSettings class (now removed entirely)
- Config.connection field
- Template generation
- dj.conn() function
- Connection.__init__
- Connection.from_config
- MySQL adapter
- Thread-safe mode spec

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

Author: dimitri-yatsenko

docs/design/thread-safe-mode.md

@@ -69,7 +69,6 @@ Connection parameters (set at creation, read-only after):
 | `password` | str | *required* | Database password |
 | `backend` | str | "mysql" | Database backend |
 | `use_tls` | bool/dict | None | TLS configuration |
-| `init_function` | str | None | SQL init command |
 
 ---
 
@@ -375,7 +374,7 @@ class Config(BaseSettings):
 
 ```python
 class Connection:
-    def __init__(self, host, user, password, port=None, init_fun=None,
+    def __init__(self, host, user, password, port=None,
                  use_tls=None, backend=None, *, _config=None):
         # ... existing connection setup ...
 
@@ -387,8 +386,7 @@ class Connection:
     def from_config(cls, cfg=None, *, host=None, user=None, password=None,
                     port=None, backend=None, safemode=None, stores=None,
                     database_prefix=None, cache=None, query_cache=None,
-                    reconnect=None, init_fun=None,
-                    use_tls=None) -> "Connection":
+                    reconnect=None, use_tls=None) -> "Connection":
         """
         Create connection with explicit configuration.
 
@@ -413,7 +411,6 @@ class Connection:
             user=effective_user,
             password=effective_password,
             port=effective_port,
-            init_fun=effective_init_fun,
             use_tls=effective_use_tls,
             backend=effective_backend,
             _config=conn_config,

src/datajoint/adapters/mysql.py

@@ -75,7 +75,6 @@ def connect(
             Password for authentication.
         **kwargs : Any
             Additional MySQL-specific parameters:
-            - init_command: SQL initialization command
             - ssl: TLS/SSL configuration dict (deprecated, use use_tls)
             - use_tls: bool or dict - DataJoint's SSL parameter (preferred)
 
@@ -84,7 +83,6 @@ def connect(
         pymysql.Connection
             MySQL connection object.
         """
-        init_command = kwargs.get("init_command")
         # Handle both ssl (old) and use_tls (new) parameter names
         ssl_config = kwargs.get("use_tls", kwargs.get("ssl"))
         # Convert boolean True to dict for PyMySQL (PyMySQL expects dict or SSLContext)
@@ -97,7 +95,6 @@ def connect(
             "port": port,
             "user": user,
             "passwd": password,
-            "init_command": init_command,
             "sql_mode": "NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,"
             "STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY",
             "autocommit": True,  # DataJoint manages transactions explicitly

src/datajoint/connection.py

@@ -250,7 +250,6 @@ def conn(
     user: str | None = None,
     password: str | None = None,
     *,
-    init_fun: Callable | None = None,
     reset: bool = False,
     use_tls: bool | dict | None = None,
 ) -> "Connection":
@@ -275,8 +274,6 @@ def conn(
         Database username. Required if not set in config.
     password : str, optional
         Database password. Required if not set in config.
-    init_fun : callable, optional
-        Initialization function called after connection.
     reset : bool, optional
         If True, reset existing connection. Default False.
     use_tls : bool or dict, optional
@@ -317,9 +314,8 @@ def conn(
             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)
+        conn.connection = Connection(host, user, password, None, use_tls)
     return conn.connection
 
 
@@ -364,8 +360,6 @@ class Connection:
         Database password.
     port : int, optional
         Port number. Overridden if specified in host.
-    init_fun : str, optional
-        SQL initialization command.
     use_tls : bool or dict, optional
         TLS encryption option.
     backend : str, optional
@@ -388,7 +382,6 @@ def __init__(
         user: str,
         password: str,
         port: int | None = None,
-        init_fun: str | None = None,
         use_tls: bool | dict | None = None,
         backend: str | None = None,
         *,
@@ -417,7 +410,6 @@ def __init__(
                 # use_tls=True: enable SSL with default settings
                 self.conn_info["ssl"] = True
         self.conn_info["ssl_input"] = use_tls
-        self.init_fun = init_fun
         self._conn = None
         self._query_cache = None
         self._is_closed = True  # Mark as closed until connect() succeeds
@@ -454,7 +446,6 @@ def from_config(
         password: str | None = None,
         port: int | None = None,
         backend: str | None = None,
-        init_fun: str | None = None,
         use_tls: bool | dict | None = None,
         # Connection-scoped settings
         safemode: bool | None = None,
@@ -494,8 +485,6 @@ def from_config(
         backend : str, optional
             Database backend ('mysql' or 'postgresql'). Overrides cfg['backend'].
             Default: 'mysql'.
-        init_fun : str, optional
-            SQL initialization command. Overrides cfg['init_function'].
         use_tls : bool or dict, optional
             TLS encryption option. Overrides cfg['use_tls'].
         safemode : bool, optional
@@ -565,7 +554,6 @@ def from_config(
         effective_password = None
         effective_port = None  # Will be set based on backend
         effective_backend = "mysql"
-        effective_init_fun = None
         effective_use_tls = None
 
         # Connection-scoped settings (will be passed to ConnectionConfig)
@@ -584,8 +572,6 @@ def from_config(
                 effective_port = cfg["port"]
             if "backend" in cfg:
                 effective_backend = cfg["backend"]
-            if "init_function" in cfg:
-                effective_init_fun = cfg["init_function"]
             if "use_tls" in cfg:
                 effective_use_tls = cfg["use_tls"]
 
@@ -624,8 +610,6 @@ def from_config(
             effective_port = port
         if backend is not None:
             effective_backend = backend
-        if init_fun is not None:
-            effective_init_fun = init_fun
         if use_tls is not None:
             effective_use_tls = use_tls
 
@@ -679,7 +663,6 @@ def from_config(
             user=effective_user,
             password=effective_password,
             port=effective_port,
-            init_fun=effective_init_fun,
             use_tls=effective_use_tls,
             backend=effective_backend,
             _config=conn_config,
@@ -705,7 +688,6 @@ def connect(self) -> None:
                     port=self.conn_info["port"],
                     user=self.conn_info["user"],
                     password=self.conn_info["passwd"],
-                    init_command=self.init_fun,
                     use_tls=self.conn_info.get("ssl"),
                 )
             except Exception as ssl_error:
@@ -721,7 +703,6 @@ def connect(self) -> None:
                         port=self.conn_info["port"],
                         user=self.conn_info["user"],
                         password=self.conn_info["passwd"],
-                        init_command=self.init_fun,
                         use_tls=False,  # Explicitly disable SSL for fallback
                     )
                 else:

src/datajoint/settings.py

@@ -219,14 +219,6 @@ def set_default_port_from_backend(self) -> "DatabaseSettings":
         return self
 
 
-class ConnectionSettings(BaseSettings):
-    """Connection behavior settings."""
-
-    model_config = SettingsConfigDict(extra="forbid", validate_assignment=True)
-
-    init_function: str | None = None
-
-
 class DisplaySettings(BaseSettings):
     """Display and preview settings."""
 
@@ -325,7 +317,6 @@ class Config(BaseSettings):
 
     # Nested settings groups
     database: DatabaseSettings = Field(default_factory=DatabaseSettings)
-    connection: ConnectionSettings = Field(default_factory=ConnectionSettings)
     display: DisplaySettings = Field(default_factory=DisplaySettings)
     jobs: JobsSettings = Field(default_factory=JobsSettings)
 
@@ -827,9 +818,6 @@ def save_template(
                     "reconnect": True,
                     "use_tls": None,
                 },
-                "connection": {
-                    "init_function": None,
-                },
                 "display": {
                     "limit": 12,
                     "width": 14,

tests/unit/test_settings.py

@@ -561,7 +561,6 @@ def test_save_full_template(self, tmp_path):
 
         # Full template should have all settings groups
         assert "database" in content
-        assert "connection" in content
         assert "display" in content
         assert "stores" in content
         assert "loglevel" in content

tests/unit/test_thread_safe.py

@@ -128,7 +128,7 @@ def test_from_config_with_explicit_params(self):
 
         captured_args = {}
 
-        def mock_init(self, host, user, password, port=None, init_fun=None, use_tls=None, backend=None, *, _config=None):
+        def mock_init(self, host, user, password, port=None, use_tls=None, backend=None, *, _config=None):
             captured_args["host"] = host
             captured_args["user"] = user
             captured_args["port"] = port
@@ -158,7 +158,7 @@ def test_from_config_with_dict(self):
 
         captured_args = {}
 
-        def mock_init(self, host, user, password, port=None, init_fun=None, use_tls=None, backend=None, *, _config=None):
+        def mock_init(self, host, user, password, port=None, use_tls=None, backend=None, *, _config=None):
             captured_args["host"] = host
             captured_args["port"] = port
 
@@ -175,7 +175,7 @@ def test_from_config_kwargs_override_dict(self):
         cfg = {"host": "dicthost", "user": "dictuser", "password": "dictpass"}
         captured_args = {}
 
-        def mock_init(self, host, user, password, port=None, init_fun=None, use_tls=None, backend=None, *, _config=None):
+        def mock_init(self, host, user, password, port=None, use_tls=None, backend=None, *, _config=None):
             captured_args["host"] = host
             captured_args["user"] = user
 
@@ -193,7 +193,7 @@ def test_from_config_works_in_thread_safe_mode(self):
 
         captured_args = {}
 
-        def mock_init(self, host, user, password, port=None, init_fun=None, use_tls=None, backend=None, *, _config=None):
+        def mock_init(self, host, user, password, port=None, use_tls=None, backend=None, *, _config=None):
             captured_args["host"] = host
 
         with patch.object(dj.Connection, "__init__", mock_init):
@@ -212,7 +212,7 @@ def test_from_config_default_port_mysql(self):
 
         captured_args = {}
 
-        def mock_init(self, host, user, password, port=None, init_fun=None, use_tls=None, backend=None, *, _config=None):
+        def mock_init(self, host, user, password, port=None, use_tls=None, backend=None, *, _config=None):
             captured_args["port"] = port
             captured_args["backend"] = backend
 
@@ -228,7 +228,7 @@ def test_from_config_default_port_postgresql(self):
 
         captured_args = {}
 
-        def mock_init(self, host, user, password, port=None, init_fun=None, use_tls=None, backend=None, *, _config=None):
+        def mock_init(self, host, user, password, port=None, use_tls=None, backend=None, *, _config=None):
             captured_args["port"] = port
 
         with patch.object(dj.Connection, "__init__", mock_init):
@@ -401,7 +401,7 @@ def test_from_config_creates_connection_config(self):
 
         captured_config = {}
 
-        def mock_init(self, host, user, password, port=None, init_fun=None, use_tls=None, backend=None, *, _config=None):
+        def mock_init(self, host, user, password, port=None, use_tls=None, backend=None, *, _config=None):
             captured_config["config"] = _config
 
         with patch.object(dj.Connection, "__init__", mock_init):
@@ -417,7 +417,7 @@ def test_from_config_passes_all_settings(self):
 
         captured_config = {}
 
-        def mock_init(self, host, user, password, port=None, init_fun=None, use_tls=None, backend=None, *, _config=None):
+        def mock_init(self, host, user, password, port=None, use_tls=None, backend=None, *, _config=None):
             captured_config["config"] = _config
 
         with patch.object(dj.Connection, "__init__", mock_init):
@@ -443,7 +443,7 @@ def test_from_config_extracts_settings_from_dict(self):
 
         captured_config = {}
 
-        def mock_init(self, host, user, password, port=None, init_fun=None, use_tls=None, backend=None, *, _config=None):
+        def mock_init(self, host, user, password, port=None, use_tls=None, backend=None, *, _config=None):
             captured_config["config"] = _config
 
         cfg_dict = {
@@ -471,7 +471,7 @@ def test_from_config_does_not_use_global_fallback(self):
 
         captured_config = {}
 
-        def mock_init(self, host, user, password, port=None, init_fun=None, use_tls=None, backend=None, *, _config=None):
+        def mock_init(self, host, user, password, port=None, use_tls=None, backend=None, *, _config=None):
             captured_config["config"] = _config
 
         try: