Update CI

.travis.yml

@@ -4,8 +4,8 @@ cache: pip
 
 matrix:
   include:
-  - name: Minimal installation 3.8
-    python: 3.8
+  - name: Minimal installation 3.9
+    python: 3.9
     sudo: true
     dist: xenial
     env: QT_QPA_PLATFORM=offscreen
@@ -20,6 +20,7 @@ matrix:
     - xvfb
 
 install:
+  - sudo apt-get install libhdf5-dev
   - pip install coveralls
   - pip install --upgrade pip
   - pip install -e .

CHANGELOG.md

@@ -12,11 +12,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add method to combine legends of multiple matplotlib axes (#782)
 - Functionality plot onto a matplotlib Axes object (#785)
 - Context manager 'restore_at_exit' in the 'VirtualDAC' object (#792)
+- Added python 3.9 support (#773)
 
 ### Changed
 
 - Improve sine fitting (#762)
 - The 'dataset_labels' method can handle both DataSet's DataArray's (#771)
+- Hickle is now optional for installation (#773)
 
 ### Removed
 

docs/notebooks/qtt_example.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """ Example script to show QTT capabilities
 
 The script should be executed from an interactive environment such as Spyder.
@@ -8,23 +7,24 @@
 """
 
 # %% Load packages
-import numpy as np
-import matplotlib.pyplot as plt
+
 import tempfile
+import time
 from collections import OrderedDict
-import pyqtgraph
 
+import matplotlib.pyplot as plt
+import numpy as np
+import pyqtgraph
 import qcodes
 from qcodes.data.data_set import DataSet
+
 import qtt
-from qtt.gui.parameterviewer import createParameterWidget
-from qtt.algorithms.gatesweep import analyseGateSweep
-from qtt.measurements.scans import scanjob_t
-from qtt.instrument_drivers.virtual_gates import VirtualGates
-from qtt import save_state
 import qtt.measurements.videomode
-
 import qtt.simulation.virtual_dot_array
+from qtt.algorithms.gatesweep import analyseGateSweep
+from qtt.gui.parameterviewer import createParameterWidget
+from qtt.instrument_drivers.virtual_gates import VirtualGates
+from qtt.measurements.scans import scanjob_t
 
 _ = pyqtgraph.mkQApp()
 datadir = tempfile.mkdtemp(prefix='qtt_example')
@@ -47,8 +47,7 @@
 
 # %% Setup measurement windows
 
-
-mwindows = qtt.gui.live_plotting.setupMeasurementWindows(station, create_parameter_widget=False)
+mwindows = qtt.gui.live_plotting.setupMeasurementWindows(station, create_parameter_widget=False, qtplot_remote=False)
 pv = createParameterWidget([gates, ])
 
 logviewer = qtt.gui.dataviewer.DataViewer()
@@ -64,17 +63,14 @@
 param_left = station.model.bottomgates[0]
 param_right = station.model.bottomgates[-1]
 scanjob = scanjob_t({'sweepdata': dict({'param': param_right, 'start': -500, 'end': 0,
-                                        'step': .8, 'wait_time': 3e-3}), 'minstrument': ['keithley3.amplitude']})
+                                        'step': .8, 'wait_time': 2.2e-3}), 'minstrument': ['keithley3.amplitude']})
 data1d = qtt.measurements.scans.scan1D(station, scanjob, location=None, verbose=1)
 
 
-# %% Save the current state of the system to disk
-
-save_state(station)
-
 # %% Print the scanned data
 
-print(data1d.default_parameter_name())
+print(data1d)
+print(f'default parameter name in dataset: {data1d.default_parameter_name()}')
 
 # %% Make a 2D scan
 start = -500
@@ -158,12 +154,16 @@
 
 # %% Close all GUI elements
 if not qtt.utilities.tools.is_spyder_environment():
-    print('close all GUI elements')
+    print('closing all GUI elements')
+    time.sleep(.5)
     vm.close()
     vm_virtual.close()
     plt.close('all')
     pv.close()
     logviewer.close()
 
     qtt.gui.live_plotting.liveplotwindow.win.close()
-    print('close all GUI elements: done')
+    pyqtgraph.mkQApp().processEvents()
+
+    print('closed all GUI elements: done')
+    time.sleep(.5)

setup.py

@@ -35,7 +35,7 @@ def get_package_data(root_dir):
 tests_require = ['coverage', 'jupyter', 'mypy', 'types-redis', 'types-python-dateutil', 'pytest']
 
 install_requires = [
-    'apscheduler', 'attrs', 'dulwich', 'h5py<3.0', 'hickle', 'IPython>=0.1', 'jupyter', 'lmfit', 'matplotlib>=3.0',
+    'apscheduler', 'attrs', 'dulwich', 'h5py', 'IPython>=0.1', 'jupyter', 'lmfit', 'matplotlib>=3.0',
     'numdifftools', 'numpy>=1.15', 'opencv-python', 'pandas', 'PyQt5', 'pyqtgraph', 'pyvisa', 'pyzmqrpc', 'qcodes>=0.23.0',
     'qcodes-contrib-drivers', 'qilib', 'qtpy', 'qupulse', 'redis', 'scipy', 'scikit-image',
     'shapely', 'sympy', 'imageio'
@@ -67,6 +67,7 @@ def get_package_data(root_dir):
           'Programming Language :: Python :: 3',
           'Programming Language :: Python :: 3.7',
           'Programming Language :: Python :: 3.8',
+          'Programming Language :: Python :: 3.9',
           'Topic :: Scientific/Engineering'
       ],
       license='MIT',

src/qtt/data.py

@@ -30,7 +30,7 @@ def load_example_dataset(filename: str, verbose: int = 0) -> Optional[DataSet]:
     Returns:
         Example dataset or None of no dataset can be found
     """
-    exampledatadir = os.path.join(qtt.__path__[0], 'exampledata') # type: ignore # mypy issue #1422
+    exampledatadir = os.path.join(qtt.__path__[0], 'exampledata')  # type: ignore # mypy issue #1422
 
     dataset = qtt.data.load_dataset(os.path.join(exampledatadir, filename), verbose=verbose)
     return dataset
@@ -165,8 +165,12 @@ def load_dataset(location, io=None, verbose=0):
     formatters = [DataSet.default_formatter]
 
     from qcodes.data.hdf5_format import HDF5FormatMetadata
-    from qcodes.data.hdf5_format_hickle import HDF5FormatHickle
-    formatters += [HDF5FormatHickle(), HDF5FormatMetadata()]
+    formatters += [HDF5FormatMetadata()]
+    try:
+        from qcodes.data.hdf5_format_hickle import HDF5FormatHickle
+        formatters += [HDF5FormatHickle()]
+    except ImportError as ex:
+        logging.info(f'HDF5FormatHickle not available {ex}')
 
     from qcodes.data.hdf5_format import HDF5Format
     formatters += [HDF5Format()]
@@ -912,7 +916,6 @@ def _data_extension():
 
 def load_data(mfile: str):
     """ Load data from specified file """
-    # return hickle.load(mfile)
     ext = _data_extension()
     if ext is not None:
         if not mfile.endswith(ext):

src/qtt/gui/live_plotting.py

@@ -1,18 +1,20 @@
 # %% Load packages
-import time
 import logging
-import numpy as np
+import time
 from functools import partial
-import qtpy.QtWidgets as QtWidgets
-import qtpy.QtCore as QtCore
-from qtpy.QtCore import Signal
-import pyqtgraph as pg
+
+import numpy as np
 import pyqtgraph
+import pyqtgraph as pg
 import pyqtgraph.multiprocess as mp
 import qcodes
+import qtpy.QtCore as QtCore
+import qtpy.QtWidgets as QtWidgets
+from qtpy.QtCore import Signal
+
 import qtt
-from qtt import pgeometry
 import qtt.algorithms.generic
+from qtt import pgeometry
 
 # %% Static variables
 
@@ -247,21 +249,22 @@ def start_measurement_control(doexec=False):
 
 
 try:
-    import qtt.gui.parameterviewer
-    import qtt.gui
-    from qtt.utilities.tools import monitorSizes
     from qcodes.plots.pyqtgraph import QtPlot
 
+    import qtt.gui
+    import qtt.gui.parameterviewer
+    from qtt.utilities.tools import monitorSizes
 
     def setupMeasurementWindows(station=None, create_parameter_widget=True,
-                                ilist=None):
+                                ilist=None, qtplot_remote=True):
         """
         Create liveplot window and parameter widget (optional)
 
         Args:
             station (QCoDeS station): station with instruments
             create_parameter_widget (bool): if True create ParameterWidget
             ilist (None or list): list of instruments to add to ParameterWidget
+            qtplot_remote (bool): If True, then use remote plotting
         Returns:
             dict: created gui objects
         """
@@ -277,7 +280,7 @@ def setupMeasurementWindows(station=None, create_parameter_widget=True,
             w.setGeometry(vv[0] + vv[2] - 400 - 300, vv[1], 300, 600)
             windows['parameterviewer'] = w
 
-        plotQ = QtPlot(window_title='Live plot', interval=.5)
+        plotQ = QtPlot(window_title='Live plot', interval=.5, remote=qtplot_remote)
         plotQ.setGeometry(vv[0] + vv[2] - 600, vv[1] + vv[3] - 400, 600, 400)
         plotQ.update()
 
@@ -430,7 +433,7 @@ def __init__(
         self.fps = pgeometry.fps_t(nn=6)
         self.datafunction = datafunction
         self.datafunction_result = None
-        self.plot_dimension=plot_dimension
+        self.plot_dimension = plot_dimension
         self.alpha = alpha
         if is1dscan is None:
             is1dscan = (
@@ -691,7 +694,7 @@ def startreadout(self, callback=None, rate=30, maxidx=None):
             self.maxidx = maxidx
         if callback is not None:
             self.datafunction = callback
-        self.timer.start( int(1000 * (1. / rate)) )
+        self.timer.start(int(1000 * (1. / rate)))
         if self.verbose:
             print('live_plotting: start readout: rate %.1f Hz' % rate)
 
@@ -722,6 +725,3 @@ def __call__(self):
         lt.semiLine(data_reshaped, [self.nx / 2, self.nx / 2],
                     np.deg2rad(self.q()), w=2, l=self.nx / 4, H=3)
         return data_reshaped
-
-
-