Merge branch 'master' into Tektronix_5014_performance

.github/static/environment_forge_full.yml

@@ -27,6 +27,7 @@ dependencies:
  - packaging>=20.0
  - ipywidgets>=7.5.0
  - broadbean>=0.9.1
+ - uncertainties>=3.0.2
  # test requirements from setup.cfg
  - deepdiff>=5.0.2
  - hypothesis>=5.49.0

.github/workflows/docs.yaml

@@ -42,7 +42,7 @@ jobs:
       run: sudo apt install pandoc
       if: runner.os == 'Linux'
     - name: Install pandoc on windows
-      uses: crazy-max/ghaction-chocolatey@v1.4.1
+      uses: crazy-max/ghaction-chocolatey@v1.4.2
       with:
         args: install pandoc
       if: runner.os == 'Windows'

docs/changes/0.25.0.rst

@@ -10,6 +10,8 @@ Breaking Changes:
 - `get_data_by_id` no longer returns data for standalone parameters
   if there are no dependent parameters in the dataset. For the same reason
   `plot_by_id` and `plot_dataset` will no longer plot these standalone parameters.
+- `xarray` exported data no longer exports extra metadata columns under the `extra_metadata` tag
+  since the extra dictionary level prevents exporting to `netcdf`
 
 
 ------------

docs_requirements.txt

@@ -15,7 +15,7 @@ docutils==0.16
 entrypoints==0.3
 idna==2.10
 imagesize==1.2.0
-importlib-metadata==3.10.0;python_version<'3.8'
+importlib-metadata==4.0.0;python_version<'3.8'
 ipykernel==5.5.3
 ipython==7.22.0
 ipython-genutils==0.2.0

qcodes/dataset/exporters/export_to_xarray.py

@@ -73,11 +73,9 @@ def _add_metadata_to_xarray(
     if dataset.completed_timestamp_raw is not None:
         xrdataset.attrs[
             "completed_timestamp_raw"] = dataset.completed_timestamp_raw
-    if len(dataset._metadata) > 0:
-        xrdataset.attrs['extra_metadata'] = {}
-
-        for metadata_tag, metadata in dataset._metadata.items():
-            xrdataset.attrs['extra_metadata'][metadata_tag] = metadata
+    if len(dataset.metadata) > 0:
+        for metadata_tag, metadata in dataset.metadata.items():
+            xrdataset.attrs[metadata_tag] = metadata
 
 
 def load_to_xarray_dataset(dataset: DataSet, data: ParameterData) -> xr.Dataset:

qcodes/instrument_drivers/Keysight/Keysight_34411A_submodules.py

@@ -0,0 +1,11 @@
+from typing import Any
+from .private.Keysight_344xxA_submodules import _Keysight_344xxA
+
+
+class Keysight_34411A(_Keysight_344xxA):
+    """
+    This is the qcodes driver for the Keysight 34411A Multimeter
+    """
+    def __init__(self, name: str, address: str, silent: bool = False,
+                 **kwargs: Any):
+        super().__init__(name, address, silent, **kwargs)

qcodes/instrument_drivers/Keysight/private/Keysight_344xxA_submodules.py

@@ -86,7 +86,7 @@ def __init__(self, parent: '_Keysight_344xxA', name: str, **kwargs: Any):
                            get_cmd='TRIGger:SLOPe?',
                            vals=vals.Enum('POS', 'NEG'))
 
-        if self.parent.is_34465A_34470A and self.parent.has_DIG:
+        if self.parent.has_DIG or (self.parent.model == '34411A'):
             self.add_parameter('level',
                                label='Trigger Level',
                                unit='V',
@@ -122,7 +122,7 @@ def __init__(self, parent: '_Keysight_344xxA', name: str, **kwargs: Any):
                 it buffers one trigger.""")
         _trigger_source_vals = vals.Enum('IMM', 'EXT', 'BUS')
 
-        if self.parent.has_DIG:
+        if self.parent.has_DIG or (self.parent.model == '34411A'):
             _trigger_source_vals = vals.Enum('IMM', 'EXT', 'BUS', 'INT')
             # extra empty lines are needed for readability of the docstring
             _trigger_source_docstring += textwrap.dedent("""\
@@ -170,12 +170,18 @@ def __init__(self, parent: '_Keysight_344xxA', name: str, **kwargs: Any):
             Specifies the number of measurements (samples) the instrument
             takes per trigger.
 
-            MAX selects 1 billion readings. However, when pretrigger is
-            selected, the maximum is 50,000 readings (without the MEM
-            option) or 2,000,000 readings (with the MEM option)"""))
-
-        if self.parent.has_DIG:
-            if self.parent.has_MEM:
+            For the models 34460A and above, MAX selects 1 billion readings.
+            However, when pretrigger is selected, the maximum is 50,000
+            readings (without the MEM option) or 2,000,000 readings (with the
+            MEM option).
+            For the model 34410A the maximum is 50,000 readings, and for the
+            model 34411A the maximum is 1,000,000 readings. The latter does
+            not depend on the pretrigger count."""))
+
+        if self.parent.has_DIG or (self.parent.model == '34411A'):
+            if self.parent.model == '34411A':
+                _max_pretrig_count = int(1e6) - 1
+            elif self.parent.has_MEM:
                 _max_pretrig_count = int(2e6) - 1
             else:
                 _max_pretrig_count = int(5e4) - 1
@@ -199,7 +205,7 @@ def __init__(self, parent: '_Keysight_344xxA', name: str, **kwargs: Any):
                 ``sample.count`` parameter for information on the maximum
                 number of sample counts."""))
 
-        if self.parent.is_34465A_34470A:
+        if self.parent.is_34465A_34470A or self.parent.is_34410A_34411A:
             self.add_parameter('source',
                                label='Sample Timing Source',
                                set_cmd='SAMPle:SOURce {}',
@@ -418,8 +424,8 @@ def get_raw(self) -> np.ndarray:  # pylint: disable=method-hidden
 
 class _Keysight_344xxA(KeysightErrorQueueMixin, VisaInstrument):
     """
-    Instrument class for Keysight 34460A, 34461A, 34465A and 34470A
-    multimeters.
+    Instrument class for Keysight 34410A, 34411A, 34460A, 34461A, 34465A and
+    34470A multimeters.
 
     The driver currently only supports using the instrument as a voltmeter
     for DC measurements.
@@ -451,6 +457,7 @@ def __init__(self, name: str, address: str, silent: bool = False,
         self.model = idn['model']
 
         self.is_34465A_34470A = self.model in ['34465A', '34470A']
+        self.is_34410A_34411A = self.model in ['34410A', '34411A']
 
         ####################################
         # Instrument specifications
@@ -466,6 +473,7 @@ def __init__(self, name: str, address: str, silent: bool = False,
         self.has_MEM = self.is_34465A_34470A and 'MEM' in options
 
         PLCs = {'34410A': [0.006, 0.02, 0.06, 0.2, 1, 2, 10, 100],
+                '34411A': [0.001, 0.002, 0.006, 0.02, 0.06, 0.2, 1, 2, 10, 100],
                 '34460A': [0.02, 0.2, 1, 10, 100],
                 '34461A': [0.02, 0.2, 1, 10, 100],
                 '34465A': [0.02, 0.06, 0.2, 1, 10, 100],
@@ -475,15 +483,10 @@ def __init__(self, name: str, address: str, silent: bool = False,
             PLCs['34465A'] = [0.001, 0.002, 0.006] + PLCs['34465A']
             PLCs['34470A'] = [0.001, 0.002, 0.006] + PLCs['34470A']
 
-        ranges = {'34410A': [10**n for n in range(3, 10)],  # 100 to 1 G
-                  '34460A': [10**n for n in range(-3, 9)],  # 1 m to 100 M
-                  '34461A': [10**n for n in range(-3, 9)],  # 1 m to 100 M
-                  '34465A': [10**n for n in range(-3, 10)],  # 1 m to 1 G
-                  '34470A': [10**n for n in range(-3, 10)],  # 1 m to 1 G
-                  }
-
         # The resolution factor order matches the order of PLCs
-        res_factors = {'34410A': [30e-6, 15e-5, 6e-6, 3e-6, 1.5e-6, 0.7e-6,
+        res_factors = {'34410A': [6e-6, 3e-6, 1.5e-6, 0.7e-6,
+                                  0.3e-6, 0.2e-6, 0.1e-6, 0.03e-6],
+                       '34411A': [30e-6, 15e-5, 6e-6, 3e-6, 1.5e-6, 0.7e-6,
                                   0.3e-6, 0.2e-6, 0.1e-6, 0.03e-6],
                        '34460A': [300e-6, 100e-6, 30e-6, 10e-6, 3e-6],
                        '34461A': [100e-6, 10e-6, 3e-6, 1e-6, 0.3e-6],
@@ -497,7 +500,7 @@ def __init__(self, name: str, address: str, silent: bool = False,
             res_factors['34470A'] = [30e-6, 10e-6, 3e-6] + res_factors['34470A']
 
         self._resolution_factors = res_factors[self.model]
-        self.ranges = ranges[self.model]
+        self.ranges = [10**n for n in range(-1, 4)] # 100 m to 1 k
         self.NPLC_list = PLCs[self.model]
 
         ####################################
@@ -616,14 +619,21 @@ def __init__(self, name: str, address: str, silent: bool = False,
         ####################################
         # Aperture parameters
 
-        if self.is_34465A_34470A:
-            # Define the extreme aperture time values for the 34465A and 34470A
+        if self.is_34465A_34470A or self.is_34410A_34411A:
+            # Define the extreme aperture time values for the 34410A, 34411A,
+            # 34465A and 34470A. The upper limits for 34410A and 34411A in the
+            # case of a 60Hz line frequency are just calculated by multiplying
+            # the respective limit with 50/60.
             utility_freq = self.line_frequency()
             if utility_freq == 50:
-                apt_times = {'34465A': [0.3e-3, 2],
+                apt_times = {'34410A': [100e-6, 1],
+                            '34411A': [20e-6, 1],
+                            '34465A': [0.3e-3, 2],
                             '34470A': [0.3e-3, 2]}
             elif utility_freq == 60:
-                apt_times = {'34465A': [0.3e-3, 1.67],
+                apt_times = {'34410A': [100e-6, 0.83],
+                            '34411A': [20e-6, 0.83],
+                            '34465A': [0.3e-3, 1.67],
                             '34470A': [0.3e-3, 1.67]}
             if self.has_DIG:
                 apt_times['34465A'][0] = 20e-6
@@ -781,10 +791,11 @@ def abort_measurement(self) -> None:
 
     def _licenses(self) -> Sequence[str]:
         """
-        Return extra licenses purchased with the DMM. The 34410A does not have
-        optional modules, hence always returns an empty tuple.
+        Return extra licenses purchased with the DMM. The 34410A and 34411A
+        models do not have optional modules, hence always returns an empty
+        tuple.
         """
-        if self.model != '34410A':
+        if not self.is_34410A_34411A:
             licenses_raw = self.ask('SYST:LIC:CAT?')
             licenses_list = [x.strip('"') for x in licenses_raw.split(',')]
             return licenses_list
@@ -793,14 +804,14 @@ def _licenses(self) -> Sequence[str]:
     def _options(self) -> Tuple[str, ...]:
         """
         Return enabled options of the DMM returned by ``*OPT?`` command.
-        The 34410A model does not have options, hence always returns
+        The 34410A and 34411A models do not have options, hence always returns
         an empty tuple.
 
         Note that for firmware version 3.0, output of ```*OPT?`` will contain
         the ``DIG`` option only if it has been purchased before, although
         the option itself is enabled by default in the firmware version 3.0.
         """
-        if self.model != '34410A':
+        if not self.is_34410A_34411A:
             options_raw = self.ask('*OPT?')
             options_list = [opt for opt in options_raw.split(',') if opt != '0']
             return tuple(options_list)

qcodes/tests/dataset/test_dataset_export.py

@@ -4,6 +4,7 @@
 import pytest
 import xarray as xr
 
+import qcodes
 from qcodes import new_data_set
 from qcodes.dataset.descriptions.dependencies import InterDependencies_
 from qcodes.dataset.descriptions.param_spec import ParamSpecBase
@@ -230,6 +231,34 @@ def test_export_to_xarray_ds_dict_extra_metadata(mock_dataset):
         _assert_xarray_metadata_is_as_expected(datarray, mock_dataset)
 
 
+def test_export_to_xarray_extra_metadate_can_be_stored(mock_dataset, tmp_path):
+
+    nt_metadata = {
+        "foo": {
+            "bar": {
+                "baz": "test"
+            },
+            "spam": [1, 2, 3],
+        }
+    }
+    mock_dataset.add_metadata("foo_metadata", json.dumps(nt_metadata))
+    mock_dataset.export(export_type="netcdf", path=str(tmp_path))
+    data_as_xarray = mock_dataset.to_xarray_dataset()
+
+    loaded_data = xr.load_dataset(
+        tmp_path/f"{qcodes.config.dataset.export_prefix}{mock_dataset.run_id}.nc"
+    )
+
+    # check that the metadata in the qcodes dataset is roundtripped to the loaded
+    # dataset
+    for key in mock_dataset.metadata.keys():
+        assert mock_dataset.metadata[key] == loaded_data.attrs[key]
+    # check that the added metadata roundtrip correctly
+    assert loaded_data.attrs["foo_metadata"] == json.dumps(nt_metadata)
+    # check that all attrs roundtrip correctly within the xarray ds
+    assert loaded_data.attrs == data_as_xarray.attrs
+
+
 def _assert_xarray_metadata_is_as_expected(xarray_ds, qc_dataset):
 
     assert xarray_ds.ds_name == qc_dataset.name

qcodes/tests/drivers/test_keysight_34465a.py

@@ -108,15 +108,15 @@ def test_set_get_autorange(driver):
 
 
 def test_increase_decrease_range(driver):
-    driver_range_user = driver.ranges[4]
+    driver_range_user = driver.ranges[2]
     driver.increase_range(driver_range_user)
-    assert driver.range.get() == driver.ranges[5]
+    assert driver.range() == driver.ranges[3]
     driver.increase_range(driver_range_user, 2)
-    assert driver.range() == driver.ranges[6]
+    assert driver.range() == driver.ranges[4]
     driver.decrease_range(driver_range_user)
-    assert driver.range() == driver.ranges[3]
+    assert driver.range() == driver.ranges[1]
     driver.decrease_range(driver_range_user, -2)
-    assert driver.range() == driver.ranges[2]
+    assert driver.range() == driver.ranges[0]
     driver_range_user = driver.ranges[3]
     driver.decrease_range(driver_range_user, -2)
     assert driver.range() == driver.ranges[1]

qcodes/tests/helpers/test_json_encoder.py

@@ -2,6 +2,7 @@
 import json
 
 import numpy as np
+import uncertainties
 import pytest
 from qcodes.utils.helpers import NumpyJSONEncoder
 from qcodes.utils.types import numpy_ints, numpy_floats, numpy_complex
@@ -35,6 +36,10 @@ def test_complex_types():
         assert e.encode(complex_type(complex(1, 2))) == \
                '{"__dtype__": "complex", "re": 1.0, "im": 2.0}'
 
+def test_UFloat_type():
+    e = NumpyJSONEncoder()
+    assert e.encode(uncertainties.ufloat(1.0, 2.0)) == \
+           '{"__dtype__": "UFloat", "nominal_value": 1.0, "std_dev": 2.0}'
 
 def test_numpy_int_types():
     e = NumpyJSONEncoder()

qcodes/tests/helpers/test_waitsecs.py

@@ -13,19 +13,6 @@ def test_bad_calls():
             wait_secs(arg)
 
 
-def test_good_calls():
-    for secs in [0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1]:
-        finish_clock = time.perf_counter() + secs
-        secs_out = wait_secs(finish_clock)
-        assert secs_out > secs - 3e-4
-        # add a tiny offset as this test may fail if
-        # otherwise if the two calls to perf_counter are close
-        # enough to return the same result as a + b - a cannot
-        # in general be assumed to be <= b in floating point
-        # math (here a is perf_counter() and b is the wait time
-        assert secs_out <= secs + 1e-14
-
-
 def test_warning():
     with LogCapture() as logs:
         secs_out = wait_secs(time.perf_counter() - 1)

qcodes/utils/helpers.py

@@ -4,6 +4,7 @@
 import logging
 import math
 import numbers
+import uncertainties
 import os
 import time
 from asyncio import iscoroutinefunction
@@ -51,6 +52,10 @@ def default(self, obj: Any) -> Any:
         converted to a dictionary with fields ``re`` and ``im`` containing floating
         numbers for the real and imaginary parts respectively, and a field
         ``__dtype__`` containing value ``complex``.
+        * Numbers with uncertainties  (numbers that conforms to ``uncertainties.UFloat``) get
+        converted to a dictionary with fields ``nominal_value`` and ``std_dev`` containing floating
+        numbers for the nominal and uncertainty parts respectively, and a field
+        ``__dtype__`` containing value ``UFloat``.
         * Object with a ``_JSONEncoder`` method get converted the return value of
         that method.
         * Objects which support the pickle protocol get converted using the
@@ -72,6 +77,12 @@ def default(self, obj: Any) -> Any:
                 're': float(obj.real),
                 'im': float(obj.imag)
             }
+        elif isinstance(obj, uncertainties.UFloat):
+            return {
+                '__dtype__': 'UFloat',
+                'nominal_value': float(obj.nominal_value),
+                'std_dev': float(obj.std_dev)
+            }
         elif hasattr(obj, '_JSONEncoder'):
             # Use object's custom JSON encoder
             jsosencode = getattr(obj, "_JSONEncoder")

requirements.txt

@@ -15,11 +15,11 @@ decorator~=4.4.2
 defusedxml~=0.7.1
 entrypoints~=0.3
 google-api-core~=1.26.3
-google-auth~=1.28.1
+google-auth~=1.29.0
 googleapis-common-protos~=1.53.0
 h5py~=3.2.1
 idna~=2.10
-importlib-metadata==3.10.0;python_version<'3.8'
+importlib-metadata==4.0.0;python_version<'3.8'
 ipykernel~=5.5.3
 ipython~=7.22.0
 ipython-genutils~=0.2.0
@@ -74,14 +74,15 @@ ruamel.yaml.clib~=0.2.2
 schema~=0.7.4
 Send2Trash~=1.5.0
 six~=1.15.0
-slack-sdk~=3.4.2
+slack-sdk~=3.5.0
 tabulate~=0.8.9
 terminado~=0.9.4
 testpath~=0.4.4
 tornado~=6.1
 tqdm~=4.60.0
 traitlets~=5.0.5
 typing-extensions~=3.7.4.3
+uncertainties>=3.0.2
 urllib3~=1.26.4
 wcwidth~=0.2.5
 webencodings~=0.5.1

science_requirements.txt

@@ -1 +1 @@
-spyder==5.0.0
+spyder==5.0.1