more default channels, fixed README.rst link for pypi

README.rst

@@ -11,7 +11,7 @@ A comprehensive data acquisition and analysis tool for Electrospray Ion-Beam Dep
    :target: https://badge.fury.io/py/esibd-explorer
    :alt: ESIBD Explorer on PyPI
 
-.. figure:: https://github.com/ioneater/ESIBD-Explorer/blob/main/docs/pages/2023-10_ESIBD_GUI_plain.png
+.. figure:: https://github.com/ioneater/ESIBD-Explorer/blob/main/docs/pages/2023-10_ESIBD_GUI_plain.png?raw=true
 
    **ESIBD Explorer user interface.** The ESIBD Explorer controls all aspects of an Electrospray Ion-Beam Deposition (ESIBD) experiment, 
    including optimization and characterization of the ion-beam energy, beam intensity, and beam size, as well as monitoring of the deposition. 

build.bat

@@ -56,7 +56,7 @@ twine upload -r testpypi dist/*
 REM conda create -n "estest" python=3.11
 REM conda activate estest
 REM pip install -i https://test.pypi.org/simple/ esibd-explorer
-REM pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ esibd-explorer==0.6.11 # use pypi dependencies that are not present on testpypi 
+REM pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ esibd-explorer==0.6.12 # use pypi dependencies that are not present on testpypi 
 
 REM only upload on real pypi after testing!
 REM twine upload dist/*
@@ -66,9 +66,10 @@ REM pyinstaller
 :::::::::::::::
 
 call rmdir /q /s build
+call rmdir /q /s pyinstaller_dist
 conda create -n "esibdtest" python=3.11
 conda activate esibdtest
-pip install -i https://pypi.org/simple/ esibd-explorer
+pip install esibd-explorer --upgrade
 pip install pyinstaller
 
 REM Run the following line to create initial spec file

esibd/core.py

@@ -185,7 +185,6 @@ def loading(self, loading):
             self._loading +=1
         else:
             self._loading -= 1
-        # print('pluginManager', self._loading)
 
     def loadPlugins(self, reload=False):
         """Loads all enabled plugins."""
@@ -1551,7 +1550,7 @@ def initGUI(self, item):
                 self.getParameterByName(name).value = item[name]
             else:
                 self.getParameterByName(name).value = default[self.VALUE]
-                if not name in self.tempParameters() and not item == {}: # item == {} -> generating default file
+                if not name in self.tempParameters() and not len(item) < 2: # len(item) < 2 -> generating default file
                     self.print(f'Added missing parameter {name} to channel {self.name} using default value {default[self.VALUE]}.')
 
         line = self.getParameterByName(self.EQUATION).line
@@ -1690,7 +1689,6 @@ class FloatValidator(QValidator):
 
         def valid_float_string(self, string):
             match = self._float_re.search(string)
-            # print(string, match.groups()[0], match.groups()[0] == string, match)
             return match.groups()[0] == string if match else False
 
         def validate(self, string, position): # -> typing.Tuple[State, str, int]:
@@ -1939,7 +1937,6 @@ def __init__(self, plugin):
 
     def toggleTitleBar(self):
         """Updates titlebar as dock is changing from floating to docked states."""
-        # print('toggleTitleBar', self.plugin.name, self.isFloating())
         if self.isFloating(): # dock is floating on its own
             # self.setWindowFlags(Qt.WindowType.Window)
             if self.plugin.titleBarLabel is not None:
@@ -2476,7 +2473,6 @@ def __init__(self, parent=None, background='default', plotItem=None, **kargs):
     def mouseMoveEvent(self, ev):
         pos = QPointF(ev.pos())
         if self.getPlotItem().getViewBox().geometry().contains(pos): # add offset
-            # print(ev.pos(), self.getPlotItem().getViewBox().mapSceneToView(pos))
             pos = self.getPlotItem().getViewBox().mapSceneToView(pos)
             try:
                 if self.getPlotItem().ctrl.logYCheck.isChecked():
@@ -2506,7 +2502,6 @@ class SciAxisItem(pg.AxisItem):
 
     def logTickStrings(self, values, scale, spacing):
         estrings = [f'{x:.0e}' for x in 10 ** np.array(values).astype(float) * np.array(scale)]
-        # print(estrings, values, scale)
         convdict = {"0": "⁰",
                     "1": "¹",
                     "2": "²",

esibd/plugins.py

@@ -159,7 +159,6 @@ def loading(self, loading):
             self._loading +=1
         else:
             self._loading -= 1
-        # print(self.name, self._loading)
 
     def test(self):
         """Runs :meth:`~esibd.plugins.Plugin.runTestParallel` in parallel thread."""
@@ -1049,7 +1048,6 @@ def updateLivePlot(self):
             return
         # otherwise toogle visibility is sufficient
         for channel in self.device.channels:
-            # print(channel.name, channel.display)
             if channel.display:
                 channel.plotCurve.setPen(pg.mkPen(QColor(channel.color), width=int(channel.linewidth)))
                 channel.plotCurve.opts['name'] = channel.name
@@ -1475,7 +1473,8 @@ def loadConfiguration(self, file=None, default=False):
                 else: # Generate default settings file if file was not found.
                     # To update files with new parameters, simply delete the old file and the new one will be generated.
                     self.print(f'Generating default config file {file}')
-                    self.addChannel(item={})
+                    for i in range(9):
+                        self.addChannel(item={Parameter.NAME : f'{self.name}{i+1}'})
                     self.exportConfiguration(file, default=True)
             else: # file.suffix == EsibdCore.FILE_H5:
                 with h5py.File(name=file, mode='r', track_order=True) as f:
@@ -1827,7 +1826,6 @@ def updateValues(self, N=2, apply=False):
         if self.updating or self.pluginManager.closing:
             return
         self.updating = True # prevent recursive call caused by changing values from here
-        # print(self.name,'updateValues rand:', np.random.rand())
         channels = self.pluginManager.DeviceManager.channels(inout=INOUT.IN) if self.inout == INOUT.IN else self.pluginManager.DeviceManager.channels(inout=INOUT.BOTH)
         for _ in range(N): # go through parsing N times, in case the dependencies are not ordered
             for channel in [c for c in self.channels if not c.active and c.equation != '']: # ignore if no equation defined
@@ -3702,13 +3700,11 @@ def stop(self):
         self.recording = False
         for d in self.getDevices():
             d.stop()
-            print(f'stopped {d.name}')
         self.stopScans()
 
     def stopScans(self):
         for s in self.pluginManager.getPluginsByType(PluginManager.TYPE.SCAN):
             s.recording = False # stop all running scans
-            print(f'stopped {s.name}')
 
     def exportOutputData(self, file=None):
         self.pluginManager.Settings.measurementNumber += 1

esibd/plugins_internal/displays/Displays.py

@@ -183,12 +183,9 @@ def downsample(self, ax):
             xdata = self.origXData[mask]
             ydata = self.origYData[mask]
             cutoff = abs(0.0001*(ymax-ymin))
-            # print('xdata before ', len(xdata),'cutoff: ', cutoff)
             while [abs(ydata[i] - ydata[i-1]) > cutoff for i in range(len(ydata))].count(True) > self.max_points:
                 cutoff *= 4
-                # print([abs(ydata[i] - ydata[i-1]) > cutoff for i, v in enumerate(ydata)].count(True), self.max_points, cutoff)
             mask = [abs(ydata[i] - ydata[i-1]) > cutoff for i in range(len(ydata))]
-            # print('xdata cleaned ', len(xdata[mask]),'cutoff', cutoff)
             return xdata[mask], ydata[mask]
 
         def update(self, ax):
@@ -420,7 +417,6 @@ def loadData(self, file, _show=True):
         self.raiseDock(_show)
 
     def mapSliderToData(self, slider, data):
-        # print(slider.value(), data.min(), data.max(), data.min() + slider.value()/100*(data.max() - data.min()))
         return data.min() + slider.value()/100*(data.max() - data.min())
 
     def drawSurface(self, angle=True):

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "esibd-explorer" # package name can include hyphens, module names should be lower case without hyphens.
 requires-python = ">=3.11"
-version = "0.6.12"
+version = "0.6.14"
 description = "A comprehensive data acquisition and analysis tool for Electrospray Ion-Beam Deposition experiments and beyond."
 license = {file = "LICENSE"}
 readme = "README.rst"