Merge pull request #4818 from jenshnielsen/ds_path_support

Consistently allow pathlib.Path in all relevant public dataset methods

docs/changes/newsfragments/4818.improved

@@ -0,0 +1,2 @@
+All public methods avilable in ``qcodes.dataset`` that takes a
+path to a db or data file now accepts a ``pathlib.Path`` object in addition to a ``str``.

qcodes/dataset/database_extract_runs.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import os
+from pathlib import Path
 from warnings import warn
 
 import numpy as np
@@ -22,10 +23,13 @@
 )
 
 
-def extract_runs_into_db(source_db_path: str,
-                         target_db_path: str, *run_ids: int,
-                         upgrade_source_db: bool = False,
-                         upgrade_target_db: bool = False) -> None:
+def extract_runs_into_db(
+    source_db_path: str | Path,
+    target_db_path: str | Path,
+    *run_ids: int,
+    upgrade_source_db: bool = False,
+    upgrade_target_db: bool = False,
+) -> None:
     """
     Extract a selection of runs into another DB file. All runs must come from
     the same experiment. They will be added to an experiment with the same name

qcodes/dataset/legacy_import.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import json
+from pathlib import Path
 
 import numpy as np
 
@@ -77,7 +78,7 @@ def store_array_to_database_alt(meas: Measurement, array: DataArray) -> int:
     return datasaver.run_id
 
 
-def import_dat_file(location: str, exp: Experiment | None = None) -> list[int]:
+def import_dat_file(location: str | Path, exp: Experiment | None = None) -> list[int]:
     """
     This imports a QCoDeS legacy :class:`qcodes.data.data_set.DataSet`
     into the database.
@@ -90,7 +91,7 @@ def import_dat_file(location: str, exp: Experiment | None = None) -> list[int]:
     """
 
 
-    loaded_data = load_data(location)
+    loaded_data = load_data(str(location))
     meas = setup_measurement(loaded_data,
                              exp=exp)
     run_ids = []

qcodes/dataset/sqlite/database.py

@@ -170,7 +170,9 @@ def connect(name: str | Path, debug: bool = False, version: int = -1) -> Connect
     return conn
 
 
-def get_db_version_and_newest_available_version(path_to_db: str) -> tuple[int, int]:
+def get_db_version_and_newest_available_version(
+    path_to_db: str | Path,
+) -> tuple[int, int]:
     """
     Connect to a DB without performing any upgrades and get the version of
     that database file along with the newest available version (the one that
@@ -240,7 +242,7 @@ def set_journal_mode(conn: ConnectionPlus, journal_mode: JournalMode) -> None:
 
 
 def initialise_or_create_database_at(
-    db_file_with_abs_path: str, journal_mode: JournalMode | None = "WAL"
+    db_file_with_abs_path: str | Path, journal_mode: JournalMode | None = "WAL"
 ) -> None:
     """
     This function sets up QCoDeS to refer to the given database file. If the
@@ -254,12 +256,12 @@ def initialise_or_create_database_at(
             Options are DELETE, TRUNCATE, PERSIST, MEMORY, WAL and OFF. If set to None
             no changes are made.
     """
-    qcodes.config.core.db_location = db_file_with_abs_path
+    qcodes.config.core.db_location = str(db_file_with_abs_path)
     initialise_database(journal_mode)
 
 
 @contextmanager
-def initialised_database_at(db_file_with_abs_path: str) -> Iterator[None]:
+def initialised_database_at(db_file_with_abs_path: str | Path) -> Iterator[None]:
     """
     Initializes or creates a database and restores the 'db_location' afterwards.
 
@@ -277,7 +279,7 @@ def initialised_database_at(db_file_with_abs_path: str) -> Iterator[None]:
 
 
 def conn_from_dbpath_or_conn(
-    conn: ConnectionPlus | None, path_to_db: str | None
+    conn: ConnectionPlus | None, path_to_db: str | Path | None
 ) -> ConnectionPlus:
     """
     A small helper function to abstract the logic needed for functions

qcodes/tests/dataset/measurement/test_load_legacy_data.py

@@ -77,3 +77,39 @@ def test_load_legacy_files_1d():
         "loop",
         "station",
     ]
+
+
+@pytest.mark.usefixtures("experiment")
+def test_load_legacy_files_1d_pathlib_path():
+    full_location = (
+        Path(__file__).parent.parent
+        / "fixtures"
+        / "data_2018_01_17"
+        / "data_001_testsweep_15_42_57"
+    )
+    run_ids = import_dat_file(full_location)
+    run_id = run_ids[0]
+    data = load_by_id(run_id)
+    assert isinstance(data, DataSet)
+    assert data.parameters == "dac_ch1_set,dmm_voltage"
+    assert data.number_of_results == 201
+    expected_names = ["dac_ch1_set", "dmm_voltage"]
+    expected_labels = ["Gate ch1", "Gate voltage"]
+    expected_units = ["V", "V"]
+    expected_depends_on = ["", "dac_ch1_set"]
+    for i, parameter in enumerate(data.get_parameters()):
+        assert parameter.name == expected_names[i]
+        assert parameter.label == expected_labels[i]
+        assert parameter.unit == expected_units[i]
+        assert parameter.depends_on == expected_depends_on[i]
+        assert parameter.type == "numeric"
+    snapshot = json.loads(data.get_metadata("snapshot"))
+    assert sorted(list(snapshot.keys())) == [
+        "__class__",
+        "arrays",
+        "formatter",
+        "io",
+        "location",
+        "loop",
+        "station",
+    ]

qcodes/tests/dataset/test_database_creation_and_upgrading.py

@@ -110,6 +110,16 @@ def test_initialise_database_at_for_nonexisting_db(tmp_path):
     assert qc.config["core"]["db_location"] == db_location
 
 
+def test_initialise_database_at_for_nonexisting_db_pathlib_path(tmp_path):
+    db_location = tmp_path / "temp.db"
+    assert not db_location.exists()
+
+    initialise_or_create_database_at(db_location)
+
+    assert db_location.exists()
+    assert qc.config["core"]["db_location"] == str(db_location)
+
+
 def test_initialise_database_at_for_existing_db(tmp_path):
     # Define DB location
     db_location = str(tmp_path / 'temp.db')

qcodes/tests/dataset/test_database_extract_runs.py

@@ -209,6 +209,32 @@ def test_real_dataset_1d(two_empty_temp_db_connections, inst):
         assert_array_equal(source_data, target_data)
 
 
+def test_real_dataset_1d_pathlib_path(two_empty_temp_db_connections, inst):
+    source_conn, target_conn = two_empty_temp_db_connections
+
+    source_path = Path(path_to_dbfile(source_conn))
+    target_path = Path(path_to_dbfile(target_conn))
+
+    source_exp = load_or_create_experiment(experiment_name="myexp", conn=source_conn)
+
+    source_dataset, _, _ = do1d(inst.back, 0, 1, 10, 0, inst.plunger, exp=source_exp)
+
+    extract_runs_into_db(source_path, target_path, source_dataset.run_id)
+
+    target_dataset = load_by_guid(source_dataset.guid, conn=target_conn)
+
+    assert source_dataset.the_same_dataset_as(target_dataset)
+    # explicit regression  test for https://github.com/QCoDeS/Qcodes/issues/3953
+    assert source_dataset.description.shapes == {"extract_run_inst_plunger": (10,)}
+    assert source_dataset.description.shapes == target_dataset.description.shapes
+
+    source_data = source_dataset.get_parameter_data()["extract_run_inst_plunger"]
+    target_data = target_dataset.get_parameter_data()["extract_run_inst_plunger"]
+
+    for source_data, target_data in zip(source_data.values(), target_data.values()):
+        assert_array_equal(source_data, target_data)
+
+
 def test_real_dataset_2d(two_empty_temp_db_connections, inst):
     source_conn, target_conn = two_empty_temp_db_connections