chore: Remove unused settings

Remove dead code:
- filepath_checksum_size_limit (never used)
- enable_python_native_blobs (never used)
- cache (only query_cache is used)
- init_function/init_command (database init command)

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

Author: dimitri-yatsenko

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)
             - charset: Character set (default from kwargs)
@@ -85,7 +84,6 @@ 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)
@@ -99,7 +97,6 @@ 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",
             "charset": charset,

src/datajoint/connection.py

@@ -55,7 +55,6 @@ 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:
@@ -73,8 +72,6 @@ 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
@@ -103,9 +100,8 @@ 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
 
 
@@ -150,8 +146,6 @@ 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.
 
@@ -169,7 +163,6 @@ def __init__(
         user: str,
         password: str,
         port: int | None = None,
-        init_fun: str | None = None,
         use_tls: bool | dict | None = None,
     ) -> None:
         if ":" in host:
@@ -190,7 +183,6 @@ 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
@@ -227,7 +219,6 @@ def connect(self) -> None:
                     port=self.conn_info["port"],
                     user=self.conn_info["user"],
                     password=self.conn_info["passwd"],
-                    init_command=self.init_fun,
                     charset=config["connection.charset"],
                     use_tls=self.conn_info.get("ssl"),
                 )
@@ -244,7 +235,6 @@ def connect(self) -> None:
                         port=self.conn_info["port"],
                         user=self.conn_info["user"],
                         password=self.conn_info["passwd"],
-                        init_command=self.init_fun,
                         charset=config["connection.charset"],
                         use_tls=False,  # Explicitly disable SSL for fallback
                     )

src/datajoint/settings.py

@@ -224,7 +224,6 @@ class ConnectionSettings(BaseSettings):
 
     model_config = SettingsConfigDict(extra="forbid", validate_assignment=True)
 
-    init_function: str | None = None
     charset: str = ""  # pymysql uses '' as default
 
 
@@ -341,11 +340,8 @@ class Config(BaseSettings):
     # Top-level settings
     loglevel: Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"] = Field(default="INFO", validation_alias="DJ_LOG_LEVEL")
     safemode: bool = True
-    enable_python_native_blobs: bool = True
-    filepath_checksum_size_limit: int | None = None
 
-    # Cache paths
-    cache: Path | None = None
+    # Cache path for query results
     query_cache: Path | None = None
 
     # Download path for attachments and filepaths
@@ -362,7 +358,7 @@ def set_logger_level(cls, v: str) -> str:
         logger.setLevel(v)
         return v
 
-    @field_validator("cache", "query_cache", mode="before")
+    @field_validator("query_cache", mode="before")
     @classmethod
     def convert_path(cls, v: Any) -> Path | None:
         """Convert string paths to Path objects."""
@@ -819,7 +815,6 @@ def save_template(
                     "use_tls": None,
                 },
                 "connection": {
-                    "init_function": None,
                     "charset": "",
                 },
                 "display": {
@@ -844,8 +839,6 @@ def save_template(
                 },
                 "loglevel": "INFO",
                 "safemode": True,
-                "enable_python_native_blobs": True,
-                "cache": None,
                 "query_cache": None,
                 "download_path": ".",
             }

tests/integration/test_jobs.py

@@ -108,10 +108,9 @@ def test_sigterm(clean_jobs, schema_any):
 
 
 def test_suppress_dj_errors(clean_jobs, schema_any):
-    """Test that DataJoint errors are suppressible without native py blobs."""
+    """Test that DataJoint errors are suppressible."""
     error_class = schema.ErrorClass()
-    with dj.config.override(enable_python_native_blobs=False):
-        error_class.populate(reserve_jobs=True, suppress_errors=True)
+    error_class.populate(reserve_jobs=True, suppress_errors=True)
     assert len(schema.DjExceptionName()) == len(error_class.jobs.errors) > 0
 
 

tests/unit/test_settings.py

@@ -504,23 +504,23 @@ def test_display_limit(self):
 class TestCachePaths:
     """Test cache path settings."""
 
-    def test_cache_path_string(self):
-        """Test setting cache path as string."""
-        original = dj.config.cache
+    def test_query_cache_path_string(self):
+        """Test setting query_cache path as string."""
+        original = dj.config.query_cache
         try:
-            dj.config.cache = "/tmp/cache"
-            assert dj.config.cache == Path("/tmp/cache")
+            dj.config.query_cache = "/tmp/cache"
+            assert dj.config.query_cache == Path("/tmp/cache")
         finally:
-            dj.config.cache = original
+            dj.config.query_cache = original
 
-    def test_cache_path_none(self):
-        """Test cache path can be None."""
-        original = dj.config.cache
+    def test_query_cache_path_none(self):
+        """Test query_cache path can be None."""
+        original = dj.config.query_cache
         try:
-            dj.config.cache = None
-            assert dj.config.cache is None
+            dj.config.query_cache = None
+            assert dj.config.query_cache is None
         finally:
-            dj.config.cache = original
+            dj.config.query_cache = original
 
 
 class TestSaveTemplate: