Merge branch 'main' into trlemon/refactor-keithley2600-driver-fastsweep

Author: trlemon

.github/workflows/codeql-analysis.yml

@@ -39,12 +39,12 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@b1bff81932f5cdfc8695c7752dcee935dcd061c8 # v3.29.5
+      uses: github/codeql-action/init@38697555549f1db7851b81482ff19f1fa5c4fedc # v3.29.5
       with:
         languages: ${{ matrix.language }}
 
     - name: Autobuild
-      uses: github/codeql-action/autobuild@b1bff81932f5cdfc8695c7752dcee935dcd061c8 # v3.29.5
+      uses: github/codeql-action/autobuild@38697555549f1db7851b81482ff19f1fa5c4fedc # v3.29.5
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@b1bff81932f5cdfc8695c7752dcee935dcd061c8 # v3.29.5
+      uses: github/codeql-action/analyze@38697555549f1db7851b81482ff19f1fa5c4fedc # v3.29.5

.github/workflows/scorecards.yml

@@ -71,6 +71,6 @@ jobs:
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@b1bff81932f5cdfc8695c7752dcee935dcd061c8 # v3.29.5
+        uses: github/codeql-action/upload-sarif@38697555549f1db7851b81482ff19f1fa5c4fedc # v3.29.5
         with:
           sarif_file: results.sarif

docs/changes/newsfragments/7960.improved

@@ -0,0 +1,7 @@
+Fixed ``to_xarray_dataset`` failing with a ``MergeError`` when exporting
+incomplete measurements where a shared setpoint parameter was treated as a
+coordinate in some sub-datasets and a data variable in others. This could
+happen when the actual data shape did not match the declared shape (e.g. a
+measurement that was interrupted before completion) and one of the sweep axes
+had non-unique values, causing different export code paths to disagree on the
+role of the shared setpoint.

docs/changes/newsfragments/7967.improved

@@ -0,0 +1,7 @@
+``initialise_database``, ``initialise_or_create_database_at``, and ``initialised_database_at``
+now accept more consistent arguments:
+
+- ``initialise_database`` accepts a new ``db_path`` parameter to specify the database file
+  location directly, instead of always reading from the config.
+- ``initialised_database_at`` accepts a new ``journal_mode`` parameter, consistent with
+  ``initialise_database`` and ``initialise_or_create_database_at``.

requirements.txt

@@ -137,7 +137,7 @@ jinja2==3.1.6
     #   nbsphinx
     #   sphinx
     #   towncrier
-jsonpointer==3.0.0
+jsonpointer==3.1.1
     # via sphinx-jsonschema
 jsonref==1.1.0
     # via zhinst-toolkit
@@ -317,7 +317,7 @@ pytest==9.0.2
     #   pytest-xdist
 pytest-asyncio==1.3.0
     # via qcodes (pyproject.toml)
-pytest-cov==7.0.0
+pytest-cov==7.1.0
     # via qcodes (pyproject.toml)
 pytest-mock==3.15.1
     # via qcodes (pyproject.toml)
@@ -454,13 +454,13 @@ traitlets==5.14.3
     #   nbconvert
     #   nbformat
     #   nbsphinx
-types-jsonschema==4.26.0.20260202
+types-jsonschema==4.26.0.20260324
     # via qcodes (pyproject.toml)
-types-networkx==3.6.1.20260303
+types-networkx==3.6.1.20260321
     # via qcodes (pyproject.toml)
-types-pywin32==311.0.0.20260317
+types-pywin32==311.0.0.20260323
     # via qcodes (pyproject.toml)
-types-requests==2.32.4.20260107
+types-requests==2.32.4.20260324
     # via
     #   qcodes (pyproject.toml)
     #   types-tqdm

src/qcodes/dataset/exporters/export_to_xarray.py

@@ -286,6 +286,25 @@ def load_to_xarray_dataset(
         dataset, data, use_multi_index=use_multi_index
     )
 
+    # When shapes are inconsistent (e.g. incomplete measurements), different
+    # code paths may represent the same setpoint parameter as a coordinate in
+    # some sub-datasets and a data variable in others.  xr.merge refuses to
+    # combine them when the role is ambiguous, so we normalise first by
+    # promoting any such variable to a coordinate everywhere.
+    all_coords: set[Hashable] = set()
+    all_data_vars: set[Hashable] = set()
+    for xr_ds in xr_dataset_dict.values():
+        all_coords.update(xr_ds.coords)
+        all_data_vars.update(xr_ds.data_vars)
+    conflicting = all_coords & all_data_vars
+    if conflicting:
+        for key in xr_dataset_dict:
+            vars_to_promote = [
+                v for v in conflicting if v in xr_dataset_dict[key].data_vars
+            ]
+            if vars_to_promote:
+                xr_dataset_dict[key] = xr_dataset_dict[key].set_coords(vars_to_promote)
+
     xr_dataset = xr.merge(xr_dataset_dict.values(), compat="equals", join="outer")
 
     _add_param_spec_to_xarray_coords(dataset, xr_dataset)

src/qcodes/dataset/sqlite/database.py

@@ -220,7 +220,10 @@ def get_DB_debug() -> bool:
     return bool(qcodes.config["core"]["db_debug"])
 
 
-def initialise_database(journal_mode: JournalMode | None = "WAL") -> None:
+def initialise_database(
+    journal_mode: JournalMode | None = "WAL",
+    db_path: str | Path | None = None,
+) -> None:
     """
     Initialise a database in the location specified by the config object
     and set ``atomic commit and rollback mode`` of the db. The db is created
@@ -232,45 +235,28 @@ def initialise_database(journal_mode: JournalMode | None = "WAL") -> None:
         journal_mode: Which `journal_mode` should be used for atomic commit and rollback.
             Options are DELETE, TRUNCATE, PERSIST, MEMORY, WAL and OFF. If set to None
             no changes are made.
+        db_path: Path to database file. If None, the path specified in the config object is used.
 
     """
     # calling connect performs all the needed actions to create and upgrade
     # the db to the latest version.
-    conn = connect(get_DB_location(), get_DB_debug())
+    if db_path is None:
+        db_path = get_DB_location()
+    conn = connect(db_path, get_DB_debug())
     reset_default_experiment_id(conn)
     if journal_mode is not None:
         set_journal_mode(conn, journal_mode)
     conn.close()
     del conn
 
 
-def set_journal_mode(conn: AtomicConnection, journal_mode: JournalMode) -> None:
-    """
-    Set the ``atomic commit and rollback mode`` of the sqlite database.
-    See https://www.sqlite.org/pragma.html#pragma_journal_mode for details.
-
-    Args:
-        conn: Connection to the database.
-        journal_mode: Which `journal_mode` should be used for atomic commit and rollback.
-            Options are DELETE, TRUNCATE, PERSIST, MEMORY, WAL and OFF.
-
-    """
-    valid_journal_modes = ["DELETE", "TRUNCATE", "PERSIST", "MEMORY", "WAL", "OFF"]
-    if journal_mode not in valid_journal_modes:
-        raise RuntimeError(
-            f"Invalid journal_mode {journal_mode} Valid modes are {valid_journal_modes}"
-        )
-    query = f"PRAGMA journal_mode={journal_mode};"
-    cursor = conn.cursor()
-    cursor.execute(query)
-
-
 def initialise_or_create_database_at(
     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
-    database file does not exist, it will be initiated.
+    Initialises or creates a database at the specified location and configures QCoDeS to use
+    this as the default database for the duration of the session.
+
 
     Args:
         db_file_with_abs_path: Database file name with absolute path, for example
@@ -285,23 +271,52 @@ def initialise_or_create_database_at(
 
 
 @contextmanager
-def initialised_database_at(db_file_with_abs_path: str | Path) -> Iterator[None]:
+def initialised_database_at(
+    db_file_with_abs_path: str | Path, *, journal_mode: JournalMode | None = "WAL"
+) -> Iterator[None]:
     """
-    Initializes or creates a database and restores the 'db_location' afterwards.
+    Initialises or creates a database at the specified location, configures QCoDeS to use this as the
+    default database for the duration of the context, and restores the 'db_location' afterwards.
 
     Args:
         db_file_with_abs_path: Database file name with absolute path, for example
             ``C:\\mydata\\majorana_experiments.db``
+        journal_mode: Which `journal_mode` should be used for atomic commit and rollback.
+            Options are DELETE, TRUNCATE, PERSIST, MEMORY, WAL and OFF. If set to None
+            no changes are made.
 
     """
     db_location = qcodes.config["core"]["db_location"]
     try:
-        initialise_or_create_database_at(db_file_with_abs_path)
+        initialise_or_create_database_at(
+            db_file_with_abs_path, journal_mode=journal_mode
+        )
         yield
     finally:
         qcodes.config["core"]["db_location"] = db_location
 
 
+def set_journal_mode(conn: AtomicConnection, journal_mode: JournalMode) -> None:
+    """
+    Set the ``atomic commit and rollback mode`` of the sqlite database.
+    See https://www.sqlite.org/pragma.html#pragma_journal_mode for details.
+
+    Args:
+        conn: Connection to the database.
+        journal_mode: Which `journal_mode` should be used for atomic commit and rollback.
+            Options are DELETE, TRUNCATE, PERSIST, MEMORY, WAL and OFF.
+
+    """
+    valid_journal_modes = ["DELETE", "TRUNCATE", "PERSIST", "MEMORY", "WAL", "OFF"]
+    if journal_mode not in valid_journal_modes:
+        raise RuntimeError(
+            f"Invalid journal_mode {journal_mode} Valid modes are {valid_journal_modes}"
+        )
+    query = f"PRAGMA journal_mode={journal_mode};"
+    cursor = conn.cursor()
+    cursor.execute(query)
+
+
 def conn_from_dbpath_or_conn(
     conn: AtomicConnection | None,
     path_to_db: str | Path | None,