Merge branch 'qkitgroup:master' into master

.gitignore

@@ -15,3 +15,9 @@ dist/
 
 # Legacy qkit folder logs
 qkit/logs
+
+# Data folders
+
+qkit/data/*
+data/*
+src/qkit/data/*

src/qkit/core/instrument_tools.py

@@ -25,7 +25,6 @@
 import qkit.core.instrument_base as instrument
 
 import importlib
-from imp import reload  # this is needed for py3
 
 
 from qkit.core.lib.misc import get_traceback
@@ -39,7 +38,7 @@ def _get_driver_module(name, do_reload=False):
     try:
         mod = importlib.import_module(name)
         if do_reload:
-            reload(mod)
+            importlib.reload(mod)
     except ImportError as e:
         fields = str(e).split(' ')
         if len(fields) > 0 and fields[-1] == name:
@@ -233,7 +232,7 @@ def create(self, name, instype, **kwargs):
         if module is None:
             return self._create_invalid_ins(name, instype, **kwargs)
 
-        reload(module)
+        importlib.reload(module)
 
         insclass = getattr(module, instype, None)
         if insclass is None:
@@ -323,7 +322,7 @@ def auto_load(self, driver):
         module = _get_driver_module(driver)
         if module is None:
             return False
-        reload(module)
+        importlib.reload(module)
 
         if not hasattr(module, 'detect_instruments'):
             logging.warning('Driver does not support instrument detection')

src/qkit/measure/transport/transport.py

@@ -293,7 +293,8 @@ def _numerical_derivative(self, x, y):
         # TODO: catch error, if len(dataset) < window_length in case of SavGol filter
         try:
             return self._numder_func(y, *self._numder_args, **self._numder_kwargs)/self._numder_func(x, *self._numder_args, **self._numder_kwargs)
-        except:
+        except Exception as e:
+            logging.warning("Can't calculate numerical derivative, possibly insufficient data points. %s", e)
             return np.zeros(len(y))*np.nan
 
     def set_x_dt(self, x_dt):

src/qkit/storage/hdf_file.py

@@ -279,12 +279,10 @@ def append(self,ds,data, next_matrix=False, reset=False, pointwise=False):
             if dim0 == 1:
                 fill[0] = 1
                 dim1 += 1
-            if reset:
-                ds[fill[0]-1,fill[1]-2] = data  # reset overwrites last data series
-            else:  # standard reset = False
-                ds.resize((dim0,dim1,len(data)))
-                fill[1] += 1
-                ds[fill[0]-1,fill[1]-1] = data
+            if not reset:  # standard reset = False
+                ds.resize((dim0,dim1,len(data))) # Update array size
+                fill[1] += 1 # Update write position
+            ds[fill[0]-1,fill[1]-1] = data # Our indices start with one.
             ds.attrs.modify("fill", fill)
 
         self.flush()