Replace ConnectionPlus with a subclass of sqlite Connection

docs/changes/newsfragments/6942.breaking

@@ -0,0 +1,4 @@
+The QCoDeS dataset sqlite connection class `ConnectionPlus` has been deprecated and replace with `AtomicConnection`.
+Unlike `ConnectionPlus` `AtomicConnection` is a direct subclass of `sqlite3.Connection` which enables better type checking
+and will allow QCoDeS to drop the dependency on `wrapt`. The function `make_connection_plus_from` is also deprecated and
+it is no longer supported to convert a connection from a sqlite3 connection to a QCoDeS specific connection.

pyproject.toml

@@ -239,7 +239,9 @@ filterwarnings = [
     'ignore:open_binary is deprecated:DeprecationWarning', # pyvisa-sim
     'ignore:Jupyter is migrating its paths to use standard platformdirs:DeprecationWarning', # jupyter
     'ignore:Parsing dates involving a day of month without a year specified is ambiguious:DeprecationWarning', # ipykernel 3.13+
-    'ignore:unclosed database in:ResourceWarning' # internal should be fixed
+    'ignore:unclosed database in:ResourceWarning', # internal should be fixed
+    'ignore:ConnectionPlus is deprecated:qcodes.utils.deprecate.QCoDeSDeprecationWarning',  # remove once deprecated ConnectionPlus has been removed
+    'ignore:make_connection_plus_from is deprecated:qcodes.utils.deprecate.QCoDeSDeprecationWarning',  # remove once deprecated ConnectionPlus has been removed
 ]
 
 [tool.ruff]

src/qcodes/dataset/__init__.py

@@ -44,7 +44,10 @@
 )
 from .measurements import Measurement
 from .plotting import plot_by_id, plot_dataset
-from .sqlite.connection import ConnectionPlus
+from .sqlite.connection import (
+    AtomicConnection,
+    ConnectionPlus,  # pyright: ignore[reportDeprecated]
+)
 from .sqlite.database import (
     connect,
     initialise_database,
@@ -61,6 +64,7 @@
 __all__ = [
     "AbstractSweep",
     "ArraySweep",
+    "AtomicConnection",
     "BreakConditionInterrupt",
     "ConnectionPlus",
     "DataSetDefinition",

src/qcodes/dataset/data_set.py

@@ -35,7 +35,11 @@
 )
 from qcodes.dataset.guids import filter_guids_by_parts, generate_guid, parse_guid
 from qcodes.dataset.linked_datasets.links import Link, links_to_str, str_to_links
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic, atomic_transaction
+from qcodes.dataset.sqlite.connection import (
+    AtomicConnection,
+    atomic,
+    atomic_transaction,
+)
 from qcodes.dataset.sqlite.database import (
     conn_from_dbpath_or_conn,
     connect,
@@ -128,7 +132,7 @@
     Write the results from the DataSet's dataqueue in a new thread
     """
 
-    def __init__(self, queue: Queue[Any], conn: ConnectionPlus):
+    def __init__(self, queue: Queue[Any], conn: AtomicConnection):
         super().__init__(daemon=True)
         self.queue = queue
         self.path = conn.path_to_dbfile
@@ -206,7 +210,7 @@
         self,
         path_to_db: str | None = None,
         run_id: int | None = None,
-        conn: ConnectionPlus | None = None,
+        conn: AtomicConnection | None = None,
         exp_id: int | None = None,
         name: str | None = None,
         specs: SpecsOrInterDeps | None = None,
@@ -1556,7 +1560,7 @@
     sample_id: int | None = None,
     location: int | None = None,
     work_station: int | None = None,
-    conn: ConnectionPlus | None = None,
+    conn: AtomicConnection | None = None,
 ) -> DataSetProtocol:
     """
     Load a run from one or more pieces of runs specification. All
@@ -1635,7 +1639,7 @@
     sample_id: int | None = None,
     location: int | None = None,
     work_station: int | None = None,
-    conn: ConnectionPlus | None = None,
+    conn: AtomicConnection | None = None,
 ) -> list[str]:
     """
     Get a list of matching guids from one or more pieces of runs specification. All
@@ -1677,7 +1681,7 @@
     return matched_guids
 
 
-def load_by_id(run_id: int, conn: ConnectionPlus | None = None) -> DataSetProtocol:
+def load_by_id(run_id: int, conn: AtomicConnection | None = None) -> DataSetProtocol:
     """
     Load a dataset by run id
 
@@ -1723,7 +1727,7 @@
     return d
 
 
-def load_by_guid(guid: str, conn: ConnectionPlus | None = None) -> DataSetProtocol:
+def load_by_guid(guid: str, conn: AtomicConnection | None = None) -> DataSetProtocol:
     """
     Load a dataset by its GUID
 
@@ -1763,7 +1767,7 @@
 
 
 def load_by_counter(
-    counter: int, exp_id: int, conn: ConnectionPlus | None = None
+    counter: int, exp_id: int, conn: AtomicConnection | None = None
 ) -> DataSetProtocol:
     """
     Load a dataset given its counter in a given experiment
@@ -1807,7 +1811,9 @@
     return d
 
 
-def _get_datasetprotocol_from_guid(guid: str, conn: ConnectionPlus) -> DataSetProtocol:
+def _get_datasetprotocol_from_guid(
+    guid: str, conn: AtomicConnection
+) -> DataSetProtocol:
     run_id = get_runid_from_guid(conn, guid)
     if run_id is None:
         raise NameError(
@@ -1840,7 +1846,7 @@
     return d
 
 
-def _get_datasetprotocol_export_info(run_id: int, conn: ConnectionPlus) -> ExportInfo:
+def _get_datasetprotocol_export_info(run_id: int, conn: AtomicConnection) -> ExportInfo:
     metadata = get_metadata_from_run_id(conn=conn, run_id=run_id)
     export_info_str = metadata.get("export_info", "")
     export_info = ExportInfo.from_str(export_info_str)
@@ -1853,7 +1859,7 @@
     specs: SPECS | None = None,
     values: VALUES | None = None,
     metadata: Any | None = None,
-    conn: ConnectionPlus | None = None,
+    conn: AtomicConnection | None = None,
     in_memory_cache: bool = True,
 ) -> DataSet:
     """
@@ -1894,15 +1900,15 @@
 
 
 def generate_dataset_table(
-    guids: Sequence[str], conn: ConnectionPlus | None = None
+    guids: Sequence[str], conn: AtomicConnection | None = None
 ) -> str:
     """
     Generate an ASCII art table of information about the runs attached to the
     supplied guids.
 
     Args:
         guids: Sequence of one or more guids
-        conn: A ConnectionPlus object with a connection to the database.
+        conn: An AtomicConnection object with a connection to the database.
 
     Returns: ASCII art table of information about the supplied guids.
 

src/qcodes/dataset/data_set_cache.py

@@ -25,7 +25,7 @@
     import xarray as xr
 
     from qcodes.dataset.descriptions.rundescriber import RunDescriber
-    from qcodes.dataset.sqlite.connection import ConnectionPlus
+    from qcodes.dataset.sqlite.connection import AtomicConnection
 
     # used in forward refs that cannot be detected
     from .data_set import DataSet  # noqa F401
@@ -201,7 +201,7 @@ def to_xarray_dataset(
 
 
 def load_new_data_from_db_and_append(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     table_name: str,
     rundescriber: RunDescriber,
     write_status: Mapping[str, int | None],

src/qcodes/dataset/data_set_in_memory.py

@@ -23,7 +23,7 @@
 from qcodes.dataset.export_config import DataExportType
 from qcodes.dataset.guids import generate_guid
 from qcodes.dataset.linked_datasets.links import Link, links_to_str
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic
+from qcodes.dataset.sqlite.connection import AtomicConnection, atomic
 from qcodes.dataset.sqlite.database import conn_from_dbpath_or_conn
 from qcodes.dataset.sqlite.queries import (
     RUNS_TABLE_COLUMNS,
@@ -302,7 +302,7 @@
         return ds
 
     @classmethod
-    def _load_from_db(cls, conn: ConnectionPlus, guid: str) -> DataSetInMem:
+    def _load_from_db(cls, conn: AtomicConnection, guid: str) -> DataSetInMem:
         run_attributes = get_raw_run_attributes(conn, guid)
         if run_attributes is None:
             raise RuntimeError(

src/qcodes/dataset/data_set_info.py

@@ -16,7 +16,7 @@
 
 if TYPE_CHECKING:
     from qcodes.dataset.descriptions.rundescriber import RunDescriber
-    from qcodes.dataset.sqlite.connection import ConnectionPlus
+    from qcodes.dataset.sqlite.connection import AtomicConnection
 
 
 class RunAttributesDict(TypedDict):
@@ -34,7 +34,7 @@ class RunAttributesDict(TypedDict):
     snapshot: dict[str, Any] | None
 
 
-def get_run_attributes(conn: ConnectionPlus, guid: str) -> RunAttributesDict | None:
+def get_run_attributes(conn: AtomicConnection, guid: str) -> RunAttributesDict | None:
     """
     Look up all information and metadata about a given dataset captured
     in the database.

src/qcodes/dataset/database_extract_runs.py

@@ -9,7 +9,7 @@
 from qcodes.dataset.data_set import DataSet
 from qcodes.dataset.dataset_helpers import _add_run_to_runs_table
 from qcodes.dataset.experiment_container import _create_exp_if_needed
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic
+from qcodes.dataset.sqlite.connection import AtomicConnection, atomic
 from qcodes.dataset.sqlite.database import (
     connect,
     get_db_version_and_newest_available_version,
@@ -128,7 +128,7 @@
 
 
 def _extract_single_dataset_into_db(
-    dataset: DataSet, target_conn: ConnectionPlus, target_exp_id: int
+    dataset: DataSet, target_conn: AtomicConnection, target_exp_id: int
 ) -> None:
     """
     NB: This function should only be called from within

src/qcodes/dataset/database_fix_functions.py

@@ -15,7 +15,11 @@
 from qcodes.dataset.descriptions.rundescriber import RunDescriber
 from qcodes.dataset.descriptions.versioning import v0
 from qcodes.dataset.descriptions.versioning.converters import old_to_new
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic, atomic_transaction
+from qcodes.dataset.sqlite.connection import (
+    AtomicConnection,
+    atomic,
+    atomic_transaction,
+)
 from qcodes.dataset.sqlite.db_upgrades.version import get_user_version
 from qcodes.dataset.sqlite.queries import (
     _get_parameters,
@@ -35,7 +39,7 @@
 log = logging.getLogger(__name__)
 
 
-def fix_version_4a_run_description_bug(conn: ConnectionPlus) -> dict[str, int]:
+def fix_version_4a_run_description_bug(conn: AtomicConnection) -> dict[str, int]:
     """
     Fix function to fix a bug where the RunDescriber accidentally wrote itself
     to string using the (new) InterDependencies_ object instead of the (old)
@@ -124,7 +128,7 @@ def _convert_run_describer_v1_like_dict_to_v0_like_dict(
     return old_desc_dict
 
 
-def fix_wrong_run_descriptions(conn: ConnectionPlus, run_ids: Sequence[int]) -> None:
+def fix_wrong_run_descriptions(conn: AtomicConnection, run_ids: Sequence[int]) -> None:
     """
     NB: This is a FIX function. Do not use it unless your database has been
     diagnosed with the problem that this function fixes.

src/qcodes/dataset/dataset_helpers.py

@@ -11,12 +11,12 @@
 
 if TYPE_CHECKING:
     from qcodes.dataset.data_set_protocol import DataSetProtocol
-    from qcodes.dataset.sqlite.connection import ConnectionPlus
+    from qcodes.dataset.sqlite.connection import AtomicConnection
 
 
 def _add_run_to_runs_table(
     dataset: DataSetProtocol,
-    target_conn: ConnectionPlus,
+    target_conn: AtomicConnection,
     target_exp_id: int,
     create_run_table: bool = True,
 ) -> tuple[int, int, str | None]:

src/qcodes/dataset/experiment_container.py

@@ -7,7 +7,7 @@
 
 from qcodes.dataset.data_set import DataSet, load_by_id, new_data_set
 from qcodes.dataset.experiment_settings import _set_default_experiment_id
-from qcodes.dataset.sqlite.connection import ConnectionPlus, path_to_dbfile
+from qcodes.dataset.sqlite.connection import AtomicConnection, path_to_dbfile
 from qcodes.dataset.sqlite.database import (
     conn_from_dbpath_or_conn,
     connect,
@@ -42,7 +42,7 @@
         name: str | None = None,
         sample_name: str | None = None,
         format_string: str = "{}-{}-{}",
-        conn: ConnectionPlus | None = None,
+        conn: AtomicConnection | None = None,
     ) -> None:
         """
         Create or load an experiment. If exp_id is None, a new experiment is
@@ -207,7 +207,7 @@
 # public api
 
 
-def experiments(conn: ConnectionPlus | None = None) -> list[Experiment]:
+def experiments(conn: AtomicConnection | None = None) -> list[Experiment]:
     """
     List all the experiments in the container (database file from config)
 
@@ -228,7 +228,7 @@
     name: str,
     sample_name: str | None,
     format_string: str = "{}-{}-{}",
-    conn: ConnectionPlus | None = None,
+    conn: AtomicConnection | None = None,
 ) -> Experiment:
     """
     Create a new experiment (in the database file from config)
@@ -259,7 +259,7 @@
     return experiment
 
 
-def load_experiment(exp_id: int, conn: ConnectionPlus | None = None) -> Experiment:
+def load_experiment(exp_id: int, conn: AtomicConnection | None = None) -> Experiment:
     """
     Load experiment with the specified id (from database file from config)
 
@@ -304,7 +304,7 @@
 def load_experiment_by_name(
     name: str,
     sample: str | None = None,
-    conn: ConnectionPlus | None = None,
+    conn: AtomicConnection | None = None,
     load_last_duplicate: bool = False,
 ) -> Experiment:
     """
@@ -365,7 +365,7 @@
 def load_or_create_experiment(
     experiment_name: str,
     sample_name: str | None = None,
-    conn: ConnectionPlus | None = None,
+    conn: AtomicConnection | None = None,
     load_last_duplicate: bool = False,
 ) -> Experiment:
     """
@@ -405,7 +405,7 @@
 
 
 def _create_exp_if_needed(
-    target_conn: ConnectionPlus,
+    target_conn: AtomicConnection,
     exp_name: str,
     sample_name: str,
     fmt_str: str,

src/qcodes/dataset/experiment_settings.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from qcodes.dataset.sqlite.connection import ConnectionPlus, path_to_dbfile
+from qcodes.dataset.sqlite.connection import AtomicConnection, path_to_dbfile
 from qcodes.dataset.sqlite.queries import get_last_experiment
 
 _default_experiment: dict[str, int | None] = {}
@@ -38,7 +38,7 @@
     return _default_experiment.get(db_path, None)
 
 
-def reset_default_experiment_id(conn: ConnectionPlus | None = None) -> None:
+def reset_default_experiment_id(conn: AtomicConnection | None = None) -> None:
     """
     Resets the default experiment id to to the last experiment in the db.
     """
@@ -50,7 +50,7 @@
         _default_experiment[db_path] = None
 
 
-def get_default_experiment_id(conn: ConnectionPlus) -> int:
+def get_default_experiment_id(conn: AtomicConnection) -> int:
     """
     Returns the latest created/ loaded experiment's exp_id as the default
     experiment. If it is not set the maximum exp_id returned as the default.

src/qcodes/dataset/measurements.py

@@ -59,7 +59,7 @@
 
     from qcodes.dataset.descriptions.versioning.rundescribertypes import Shapes
     from qcodes.dataset.experiment_container import Experiment
-    from qcodes.dataset.sqlite.connection import ConnectionPlus
+    from qcodes.dataset.sqlite.connection import AtomicConnection
     from qcodes.dataset.sqlite.query_helpers import VALUE
 
 log = logging.getLogger(__name__)
@@ -631,7 +631,7 @@ def __enter__(self) -> DataSaver:
         if self.experiment is not None:
             exp_id: int | None = self.experiment.exp_id
             path_to_db: str | None = self.experiment.path_to_db
-            conn: ConnectionPlus | None = self.experiment.conn
+            conn: AtomicConnection | None = self.experiment.conn
         else:
             exp_id = None
             path_to_db = None