Pep8 fix, more fixes after uniting of spect vars

* spectrum variables were implemented into update_spectrum
* flake8 check of the whole project

prasopes/__main__.py

 #!/usr/bin/env python3
 
-from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt5agg import\
+    FigureCanvasQTAgg as FigureCanvas
 from matplotlib.figure import Figure
 from matplotlib.widgets import SpanSelector
-from matplotlib.gridspec import GridSpec
 from PyQt5 import QtCore
 from PyQt5 import QtWidgets
 from PyQt5 import QtGui
@@ -14,7 +14,7 @@ from prasopes.predictmz import predict as getmzpattern
 try:
     from rawautoparams import load_params
     autoparams = True
-except:
+except ImportError:
     autoparams = False
 import numpy as np
 import prasopes.config as cf
@@ -50,7 +50,7 @@ class QStatusBarLogger(logging.Handler):
 
 
 class AugFigureCanvas(FigureCanvas):
-    #TODO: move the widget into graphtools when I'm done
+    # TODO: move the widget into graphtools when I'm done
     def __init__(self):
         self.figure = Figure(figsize=(5, 4), dpi=100, facecolor="None",
                              constrained_layout=True)
@@ -59,28 +59,31 @@ class AugFigureCanvas(FigureCanvas):
         self.ms = dict(annotation=[], name="Spectrum", xlabel="m/z",
                        ylabel="ion count", xtics=20, predict=None,
                        params=[], headers=[], texts=[])
-        self.chrom = dict(x=[0], y=[0], t_start=None, t_end=None, machtype=None,
-                          name="Chromatogram", xlabel="time(min)",
-                          ylabel="total ion count", timesarg=[])
+        self.chrom = dict(
+            x=[0], y=[0], t_start=None, t_end=None, machtype=None,
+            name="Chromatogram", xlabel="time(min)", ylabel="total ion count",
+            timesarg=[])
         self.filename = None
         self.drlcache = [None, None]
         grid = self.figure.add_gridspec(2, 1)
-        self.chromplot = self.figure.add_subplot(grid[0,0], facecolor=(1, 1, 1, 0.8))
-        self.spectplot = self.figure.add_subplot(grid[1,0], facecolor=(1, 1, 1, 0.8))
+        self.chromplot = self.figure.add_subplot(grid[0, 0],
+                                                 facecolor=(1, 1, 1, 0.8))
+        self.spectplot = self.figure.add_subplot(grid[1, 0],
+                                                 facecolor=(1, 1, 1, 0.8))
         self.setStyleSheet("background-color:transparent;")
         self.setAutoFillBackground(False)
-        self.paramstable = dt.table(["","name","value"], 100)
+        self.paramstable = dt.table(["", "name", "value"], 100)
         gt.pan_factory(self.chromplot)
         gt.zoom_factory(self.chromplot, 1.15)
         gt.pan_factory(self.spectplot, self.ms)
         gt.zoom_factory(self.spectplot, 1.15, self.ms)
         gt.textedit_factory(self.spectplot, self.ms)
         self.mass_selector = gt.AugSpanSelector(self.spectplot, self.ms)
-        #TODO: rewrite timeSelector to better shape when I'm done
-        self.time_selector = SpanSelector(self.chromplot, lambda x_min, x_max:
-                gt.pick_times(x_min, x_max, self), 'horizontal',
-                useblit=True, rectprops=dict(alpha=0.15, facecolor='purple'),
-                button=3)
+        # TODO: rewrite timeSelector to better shape when I'm done
+        self.time_selector = SpanSelector(
+                self.chromplot, lambda x_min, x_max: gt.pick_times(
+                    x_min, x_max, self), 'horizontal', useblit=True,
+                rectprops=dict(alpha=0.15, facecolor='purple'), button=3)
 
 
 def load_file(parent, augCanvas, update, settings, loadthread, filename=None):
@@ -89,15 +92,16 @@ def load_file(parent, augCanvas, update, settings, loadthread, filename=None):
     filename = filename or QtWidgets.QFileDialog.getOpenFileName(
             caption="Open spectrum", directory=directory,
             filter="Finnigan RAW files (*.raw, *.RAW)")[0]
-    if filename is not '' and os.path.isfile(filename)\
+    if filename != '' and os.path.isfile(filename)\
             and not os.path.isdir(filename):
         error = update_signal()
         errormsg = []
+
         def runfnc():
             try:
                 [i.clear() for i in (
                     augCanvas.ds, augCanvas.chrom['timesarg'],
-                    augCanvas.ms['params'],augCanvas.ms['headers'])]
+                    augCanvas.ms['params'], augCanvas.ms['headers'])]
                 [augCanvas.ds.append(dict(
                     chrom_dat=i[0], masses=i[1], matrix=i[2]))
                  for i in load_raw(filename, settings.value("tmp_location"))]
@@ -109,10 +113,10 @@ def load_file(parent, augCanvas, update, settings, loadthread, filename=None):
                     "Error message:\n{}".format(pex.args[0]))
                 error.signal.emit()
                 return
-            if autoparams == True:
+            if autoparams:
                 try:
-                    (augCanvas.ms['params'], rawheaders
-                        , augCanvas.chrom['machtype']) = load_params(filename)
+                    (augCanvas.ms['params'], rawheaders,
+                        augCanvas.chrom['machtype']) = load_params(filename)
                     segments = [len(subset['chrom_dat'][0])
                                 for subset in augCanvas.ds]
                     indicies = [sum(segments[:i+1])
@@ -131,13 +135,13 @@ def load_file(parent, augCanvas, update, settings, loadthread, filename=None):
             parent.setWindowTitle("Prasopes - {}".format(
                 os.path.basename(filename)))
             update.signal.emit()
-        error.signal.connect(lambda:
-            QtWidgets.QMessageBox.critical(parent, errormsg[0], errormsg[1]))
+        error.signal.connect(lambda: QtWidgets.QMessageBox.critical(
+            parent, errormsg[0], errormsg[1]))
         loadthread.run = runfnc
         loadthread.start()
 
 
-def print_graph(data_set, mass_spec, chrom_spec, spect, fn, table):
+def print_graph(augCanvas):
     def printimage(printdevice, img):
         printer.setResolution(600)
         painter = QtGui.QPainter(printdevice)
@@ -145,45 +149,46 @@ def print_graph(data_set, mass_spec, chrom_spec, spect, fn, table):
         linesize = printer.resolution()/15
         font.setPixelSize(linesize)
         painter.setFont(font)
-        painter.drawImage(0,0,img)
+        painter.drawImage(0, 0, img)
         offset = img.size().height()
         line = 1
         spacing = 1.5
-        for row in range(table.rowCount()):
-            if table.cellWidget(row,0).checkState() == 2:
-                text = table.item(row,1).text() + table.item(row,2).text()
-                painter.drawText(300,int(offset+line*linesize*spacing), text)
+        for row in range(augCanvas.paramstable.rowCount()):
+            if augCanvas.paramstable.cellWidget(row, 0).checkState() == 2:
+                text = augCanvas.paramstable.item(row, 1).text() +\
+                       augCanvas.paramstable.item(row, 2).text()
+                painter.drawText(300, int(offset+line*linesize*spacing), text)
                 line += 1
         painter.end()
-    #TODO: substitute the QPrintPreviewDialog with QPrintPreviewWidget
+    # TODO: substitute the QPrintPreviewDialog with QPrintPreviewWidget
     printPreview = QtPrintSupport.QPrintPreviewDialog()
     printer = printPreview.printer()
     printer.setPageSize(printer.A5)
     printer.setDuplex(printer.DuplexNone)
-    image = imgt.paint_image(mass_spec, spect, printer)
+    image = imgt.paint_image(augCanvas.ms, augCanvas.spectplot,
+                             augCanvas.filename, printer)
     printPreview.paintRequested.connect(lambda:
                                         printimage(printer, image))
     printPreview.exec()
 
 
-def update_spectrum(chromatogram, spect, ds, ms, fn, chrom, config):
-    if fn[0] is not None:
-        slims = [spect.get_xlim(), spect.get_ylim()]
-        ds.clear()
-        [ds.append(dict(chrom_dat=i[0], masses=i[1], matrix=i[2])) for i
-                in load_raw(fn[0], config.value("tmp_location"))]
-        gt.populate(chromatogram, spect, ds, ms, chrom)
-        spect.set_xlim(slims[0])
-        spect.set_ylim(slims[1])
-        gt.ann_spec(spect, ms)
-        spect.get_figure().canvas.draw()
+def update_spectrum(augCanvas, config):
+    if augCanvas.filename:
+        slims = [augCanvas.spectplot.get_xlim(),
+                 augCanvas.spectplot.get_ylim()]
+        augCanvas.ds.clear()
+        [augCanvas.ds.append(dict(chrom_dat=i[0], masses=i[1], matrix=i[2]))
+         for i in load_raw(augCanvas.filename, config.value("tmp_location"))]
+        gt.populate(augCanvas)
+        augCanvas.spectplot.set_xlim(slims[0])
+        augCanvas.spectplot.set_ylim(slims[1])
+        gt.ann_spec(augCanvas.spectplot, augCanvas.ms)
+        augCanvas.draw()
 
 
-def dropped(event, parent, chromatogram, spectrum, ds, ms, filename,
-            chrom, update, config, loadthread):
+def dropped(event, parent, augCanvas, update, config, loadthread):
     dropurl = event.mimeData().urls()[0].toLocalFile()
-    load_file(parent, chromatogram, spectrum, ds, ms, filename,
-              chrom, update, config, loadthread, filename=dropurl)
+    load_file(parent, augCanvas, update, config, loadthread, filename=dropurl)
 
 
 def drag_entered(event):
@@ -192,23 +197,23 @@ def drag_entered(event):
         event.accept()
 
 
-def predictmz(form, chromatogram, spect, ds, ms, chrom):
+def predictmz(form, augCanvas):
     text = form.text()
     if text == "":
-        ms["predict"] = None
+        augCanvas.ms["predict"] = None
         return
-    slims = [spect.get_xlim(), spect.get_ylim()]
-    ms["predict"] = getmzpattern(text)
-    gt.populate(chromatogram, spect, ds, ms, chrom)
-    spect.set_xlim(slims[0])
-    spect.set_ylim(slims[1])
-    spect.get_figure().canvas.draw()
+    slims = [augCanvas.spectplot.get_xlim(),
+             augCanvas.spectplot.get_ylim()]
+    augCanvas.ms["predict"] = getmzpattern(text)
+    gt.populate(augCanvas)
+    augCanvas.spectplot.set_xlim(slims[0])
+    augCanvas.spectplot.set_ylim(slims[1])
+    augCanvas.draw()
 
 
-def oddeven_changed(chromatogram, spectrum, ds, ms, filename, chrom, config,
-        oddevenact):
+def oddeven_changed(augCanvas, config, oddevenact):
     config.setValue("view/oddeven", oddevenact.isChecked())
-    update_spectrum(chromatogram, spectrum, ds, ms, filename, chrom, config)
+    update_spectrum(augCanvas, config)
 
 
 def key_pressed(event, augCanvas, config):
@@ -221,7 +226,7 @@ def key_pressed(event, augCanvas, config):
             else:
                 imgt.clip_spect_img(augCanvas.ms, augCanvas.spectplot,
                                     augCanvas.filename)
-        if event.modifiers().__int__() == QtCore.Qt.ControlModifier+\
+        if event.modifiers().__int__() == QtCore.Qt.ControlModifier + \
                 QtCore.Qt.ShiftModifier:
             dt.clip_spectstr(augCanvas)
     if event.key() in (QtCore.Qt.Key_Left, QtCore.Qt.Key_Right):
@@ -246,22 +251,22 @@ def main():
     config = cf.settings()
 
     barHandler = QStatusBarLogger()
-    barHandler.trigger.signal.connect(lambda:
-            barHandler.statusBar.showMessage(barHandler.msg))
+    barHandler.trigger.signal.connect(
+        lambda: barHandler.statusBar.showMessage(barHandler.msg))
 
     p_logger = logging.getLogger('parseLogger')
     params_logger = logging.getLogger('acqLogLogger')
     drl_logger = logging.getLogger('drlLogger')
     zce_logger = logging.getLogger('zceLogger')
-    #mpl_logger = logging.getLogger('matplotlib')
-    #mpl_logger.setLevel("DEBUG")
+    # mpl_logger = logging.getLogger('matplotlib')
+    # mpl_logger.setLevel("DEBUG")
     logging.basicConfig()
-    #p_logger.setLevel("WARN")
-    #p_logger.setLevel("DEBUG")
-    #drl_logger.setLevel("INFO")
+    # p_logger.setLevel("WARN")
+    # p_logger.setLevel("DEBUG")
+    # drl_logger.setLevel("INFO")
     drl_logger.setLevel("DEBUG")
     zce_logger.setLevel("DEBUG")
-    #params_logger.setLevel("DEBUG")
+    # params_logger.setLevel("DEBUG")
     p_logger.addHandler(barHandler)
     zce_logger.addHandler(barHandler)
     params_logger.addHandler(barHandler)
@@ -269,14 +274,14 @@ def main():
 
     main_window = QtWidgets.QMainWindow(windowTitle="Prasopes")
 
-    if QtGui.QIcon.themeName() is "":
+    if QtGui.QIcon.themeName() == "":
         QtGui.QIcon.setThemeName("TangoMFK")
 
     consoledock = docks.consoleDockWidget(
             locals(), "&Console", "view/consolevisible")
     treedock = docks.treeDockWidget(
-            "&File browser", "view/filebrowservisible", update, load_file, main_window,
-            augCanvas, config, loadthread)
+            "&File browser", "view/filebrowservisible", update, load_file,
+            main_window, augCanvas, config, loadthread)
     paramsdock = docks.augDock("Acquisition parameters", "&Acq parameters",
                                "view/acqparvisible")
     update.signal.connect(lambda: gt.update_paramstable(augCanvas))
@@ -321,18 +326,19 @@ def main():
     autozoomy.triggered.connect(lambda: config.setValue(
                                 "view/autozoomy", autozoomy.isChecked()))
     autozoomy.triggered.connect(lambda: gt.autozoomy(augCanvas.spectrum))
-    intensitiesact = QtWidgets.QAction("&Show intensities", None,
-            checkable=True, checked=config.value("view/intensities",
-                type=bool))
+    intensitiesact = QtWidgets.QAction(
+        "&Show intensities", None, checkable=True, checked=config.value(
+            "view/intensities", type=bool))
     intensitiesact.triggered.connect(lambda: config.setValue(
         "view/intensities", intensitiesact.isChecked()))
     intensitiesact.triggered.connect(lambda: gt.ann_spec(
         augCanvas.spectplot, augCanvas.ms))
     intensitiesact.triggered.connect(lambda: augCanvas.draw())
-    oddevenact = QtWidgets.QAction("&Odd / even", None, checkable=True,
-            checked=config.value("view/oddeven", type=bool))
-    oddevenact.triggered.connect(lambda:
-        oddeven_changed(augCanvas, config, oddevenact))
+    oddevenact = QtWidgets.QAction(
+        "&Odd / even", None, checkable=True, checked=config.value(
+            "view/oddeven", type=bool))
+    oddevenact.triggered.connect(
+        lambda: oddeven_changed(augCanvas, config, oddevenact))
 
     predictform = QtWidgets.QLineEdit(maximumWidth=150)
     predictform.editingFinished.connect(lambda: predictmz(
@@ -354,7 +360,8 @@ def main():
     tools_menu.addAction(drlact)
     tools_menu.addSeparator()
     view_menu = QtWidgets.QMenu('&View', main_window)
-    [view_menu.addAction(i.action) for i in (treedock, paramsdock, consoledock)]
+    [view_menu.addAction(i.action) for i in
+     (treedock, paramsdock, consoledock)]
     [view_menu.addAction(i) for i in (autozoomy, intensitiesact)]
     view_menu.addSeparator()
     view_menu.addAction(oddevenact)
@@ -384,7 +391,7 @@ def main():
 
     main_window.dragEnterEvent = lambda event: drag_entered(event)
     main_window.dropEvent = lambda event: dropped(
-        event, main_window, augCanvas, update, config)
+        event, main_window, augCanvas, update, config, loadthread)
     main_window.setAcceptDrops(True)
     main_window.keyPressEvent = lambda event: key_pressed(
             event, augCanvas, config)

prasopes/config.py

@@ -2,11 +2,10 @@
 from PyQt5 import QtCore
 from PyQt5 import QtWidgets
 from PyQt5 import QtGui
-from PyQt5 import QtPrintSupport
 
 
 def settings():
-    settings = QtCore.QSettings("Yansoft","Prasopes")
+    settings = QtCore.QSettings("Yansoft", "Prasopes")
     defvals = {("view/autozoomy", True),
                ("view/filebrowservisible", True),
                ("view/consolevisible", True),
@@ -21,13 +20,14 @@ def settings():
                ("imggen/yinch", 4),
                ("imggen/dpi", 300),
                ("imggen/xtics", 5)}
-    [settings.setValue(i[0], i[1]) for i in defvals if settings.value(i[0]) == None]
+    [settings.setValue(i[0], i[1])
+     for i in defvals if not settings.value(i[0])]
     return settings
 
 
 def pathsearch(text, value, config):
     filename = QtWidgets.QFileDialog.getExistingDirectory()
-    if filename is not '':
+    if filename != '':
         text.setText(filename)
         config.setValue(value, filename)
 
@@ -67,7 +67,7 @@ def dial(parent):
     """constructs a dialog window"""
     dialog = QtWidgets.QDialog(
         parent, windowTitle='Settings')
-    dialog.resize(600,-1)
+    dialog.resize(600, -1)
 
     config = settings()
 

prasopes/datatools.py

@@ -27,7 +27,8 @@ def specttostr(augCanvas, delim=" "):
 
     strdata = []
     for i in range(np.max([len(line.get_xdata()) for line in lines])):
-        pairs = [("{}"+delim+"{}").format(line.get_xdata()[i], line.get_ydata()[i]) if\
+        pairs = [("{}"+delim+"{}").format(
+                 line.get_xdata()[i], line.get_ydata()[i]) if
                  i < len(line.get_xdata()) else delim for line in lines]
         strline = delim.join(pairs)+"\n"
         strdata.append(strline)
@@ -37,7 +38,7 @@ def specttostr(augCanvas, delim=" "):
 
 def clip_spectstr(augCanvas):
     string = specttostr(augCanvas, delim="\t")
-    QApplication.clipboard().clear()
+    QtWidgets.QApplication.clipboard().clear()
     [QtWidgets.QApplication.clipboard().setText(string, i) for i in range(2)]
 
 
@@ -47,7 +48,7 @@ def clip_tablestr(augCanvas):
              for row in range(augCanvas.paramstable.rowCount())
              if augCanvas.paramstable.cellWidget(row, 0).checkState()]
     text = ", ".join(pairs)
-    QApplication.clipboard().clear()
+    QtWidgets.QApplication.clipboard().clear()
     [QtWidgets.QApplication.clipboard().setText(text, i) for i in range(2)]
 
 

prasopes/docks.py

@@ -5,7 +5,6 @@ from code import InteractiveConsole
 from io import StringIO
 from os import path
 import contextlib
-import numpy as np
 import prasopes.config as cf
 
 
@@ -19,11 +18,13 @@ class augDock(QtWidgets.QDockWidget):
         self.action = QtWidgets.QAction(
                 actionname, None, checkable=True,
                 checked=config.value(cfval, type=bool))
-        self.action.triggered.connect(lambda: self.show() if\
-                self.action.isChecked() == True else self.hide())
+        self.action.triggered.connect(
+            lambda: self.show() if self.action.isChecked()
+            else self.hide())
         self.closeEvent = lambda event: self.closeOverride(event)
         if not config.value(cfval, type=bool):
             self.hide()
+
     def closeOverride(self, event):
         self.action.setChecked(False)
         self.hide()
@@ -42,8 +43,9 @@ def consoleDockWidget(localvars, actionname, cfval):
             outtext = stream.getvalue()
             if outtext == "":
                 with contextlib.redirect_stderr(StringIO()):
-                    #If anybody knows better sanitization feel free to let me know
-                    console.runcode("""print(eval('{}'.format(str('"""+text+"""'))))""")
+                    # Brief sanitization
+                    console.runcode("""print(eval('{}'.format(str('""" +
+                                    text + """'))))""")
                 outtext = stream.getvalue()
             if outtext != "":
                 outp.append(outtext[:-1])
@@ -71,9 +73,15 @@ def treeDockWidget(actionname, cfval, update, loadfnc, parent,
     dirview.setModel(fileModel)
     dock = augDock("Folder View", actionname, cfval)
     [dock.layout.addWidget(i) for i in (treeview, dirview)]
+
     def scrolltoonce():
         fileModel.layoutChanged.disconnect(scrolltoonce)
         treeview.scrollTo(fileModel.index(config.value("open_folder")), 1)
+
+    def clickload(index):
+        loadfnc(parent, augCanvas, update, config, loadthread,
+                filename=fileModel.filePath(index))
+
     fileModel.directoryLoaded.connect(
             lambda: treeview.resizeColumnToContents(0))
     update.signal.connect(lambda: treeview.setCurrentIndex(fileModel.index(
@@ -81,8 +89,7 @@ def treeDockWidget(actionname, cfval, update, loadfnc, parent,
     update.signal.connect(lambda: dirview.setRootIndex(fileModel.index(
             path.dirname(path.realpath(augCanvas.filename)))))
     fileModel.layoutChanged.connect(scrolltoonce)
-    clickload = lambda index: loadfnc(parent, augCanvas, update, config,
-            loadthread, filename=fileModel.filePath(index))
+
     for i in [treeview.doubleClicked, dirview.doubleClicked, dirview.clicked]:
         i.connect(clickload)
     return dock

prasopes/drltools.py

 #!/usr/bin/env python3
-from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt5agg import\
+        FigureCanvasQTAgg as FigureCanvas
 from matplotlib.figure import Figure
 from PyQt5 import QtCore
 from PyQt5 import QtWidgets
@@ -25,22 +26,20 @@ class StretchWidget(QtWidgets.QWidget):
     def __init__(self):
         super(StretchWidget, self).__init__()
         self._main = QtWidgets.QWidget()
-        self.setSizePolicy(QtWidgets.QSizePolicy.Expanding
-                          ,QtWidgets.QSizePolicy.Preferred)
+        self.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
+                           QtWidgets.QSizePolicy.Preferred)
 
 
 def floatize(table, row, column, nonneg=True):
     """grabs the tableWidgetItem and transforms its text safely to
     float, if the text is not acceptable as float, returns zero"""
-    imptext = table.item(row, column).text().replace(",",".")
+    imptext = table.item(row, column).text().replace(",", ".")
     validator = QtGui.QDoubleValidator()
-    if nonneg == True:
+    if nonneg:
         validator.setBottom(0)
     status = validator.validate(imptext, 0)[0]
-    if status == QtGui.QValidator.Acceptable:
-        outfloat = float(imptext)
-    else:
-        outfloat = 0
+    outfloat = float(imptext) if status == QtGui.QValidator.Acceptable\
+        else 0
     return outfloat
 
 
@@ -60,27 +59,27 @@ def update_profile(pt, row, dataset):
     spectrum = pt.cellWidget(row, 3).figure.get_axes()[0]
     spectrum.clear()
     limits = []
-    for i,subset in enumerate(dataset):
+    for i, subset in enumerate(dataset):
         masses = subset['masses']
         massargs = get_massargs(pt, row, subset)
         yshape = np.mean(subset['matrix'], axis=0)
         spectrum.plot(masses, yshape, ':', color='gray')
-        spectrum.plot(masses[massargs], yshape[massargs], color=
-                gt.colors[i % len(gt.colors)]/255)
-        limits.append((masses[massargs[[0,-1]]],max(yshape[massargs])))
+        spectrum.plot(masses[massargs], yshape[massargs], color=gt.colors[
+            i % len(gt.colors)]/255)
+        limits.append((masses[massargs[[0, -1]]], max(yshape[massargs])))
     widest = np.argmax([abs(lim[0][1]-lim[0][0]) for lim in limits])
     xmin, xmax = limits[widest][0]
-    xex = max((xmax-xmin)*0.25,0.20)
+    xex = max((xmax-xmin)*0.25, 0.20)
     spectrum.set_xlim(xmin-xex, xmax+xex)
-    ymax = max(*[lim[1] for lim in limits],1)
+    ymax = max(*[lim[1] for lim in limits], 1)
     spectrum.set_ylim(ymax*-0.1, ymax*1.2)
     spectrum.figure.canvas.draw()
 
 
 def get_intensity(row, ds, drls):
-    #prevent division by 0
+    # prevent division by 0
     intensity = np.concatenate([np.divide(np.sum(subset['matrix'].T[
-        get_massargs(drls['pt'],row,subset)].T, axis=1),
+        get_massargs(drls['pt'], row, subset)].T, axis=1),
         np.clip(subset['chrom_dat'][1], np.finfo(np.float32).eps, None))
         for subset in ds])
     return intensity
@@ -90,7 +89,8 @@ def get_daughterset(ds, drls):
     """Fuction to acquire the curves of the daugher ions"""
     logger.info("getting set of the daughter ions")
     names = []
-    times = np.concatenate([sub['chrom_dat'][0, :] - drls['tshift'].value() for sub in ds])
+    times = np.concatenate([sub['chrom_dat'][0, :] - drls['tshift'].value()
+                            for sub in ds])
     intensities = []
     for row in range(drls['dt'].rowCount()):
         if drls['dt'].cellWidget(row, 0).checkState() == 2:
@@ -103,8 +103,8 @@ def get_daughterset(ds, drls):
                     correction = get_intensity(cor, ds, drls) * factor
                     intensity = intensity - correction
                     corlist.append("{} * {}".format(
-                        drls['dt'].item(row,2+i*2).text(),
-                        drls['dt'].cellWidget(row,1+i*2).currentText()))
+                        drls['dt'].item(row, 2+i*2).text(),
+                        drls['dt'].cellWidget(row, 1+i*2).currentText()))
             cortext = " + ".join(corlist)
             intensities.append(intensity)
             names.append("{} - ({})".format(
@@ -159,7 +159,7 @@ def update_drlspectrum(ds, drls, drlspectrum):
             label = " {}".format(drls['pt'].item(row, 0).text())
             intensity = intensities[i]
             if drls['rel'].checkState() == 2:
-                #Do not divide by 0
+                # Do not divide by 0
                 intensity = np.divide(intensity, np.clip(np.sum(
                     intensities, 0), np.finfo(np.float32).eps, None),
                     dtype=np.float64)
@@ -255,16 +255,14 @@ def corcount_changed(ds, drls, drlspectrum):
         for col in range(drls['dt'].columnCount() - (diff * 2),
                          drls['dt'].columnCount(), 2):
             for row in range(drls['dt'].rowCount()):
-                    drls['dt'].setCellWidget(
-                        row, col, QtWidgets.QComboBox())
+                drls['dt'].setCellWidget(row, col, QtWidgets.QComboBox())
                 drls['dt'].cellWidget(row, col).setFrame(False)
                 drls['dt'].cellWidget(row, col).setFocusPolicy(
                         QtCore.Qt.NoFocus)
-                    drls['dt'].setItem(
-                        row, col+1, QtWidgets.QTableWidgetItem())
+                drls['dt'].setItem(row, col+1, QtWidgets.QTableWidgetItem())
                 newcors.append(drls['dt'].cellWidget(row, col))
-        list(map(lambda x: x.currentIndexChanged.connect(lambda:
-            corr_changed(x, ds, drls, drlspectrum)), newcors))
+        list(map(lambda x: x.currentIndexChanged.connect(
+            lambda: corr_changed(x, ds, drls, drlspectrum)), newcors))
         update_corrfors(drls)
         dcolums = ["Name"]
         for i in range(drls['cors'].value()):
@@ -281,12 +279,12 @@ def corcount_changed(ds, drls, drlspectrum):
 
 def remove_rows(ds, drls, drlspectrum, rows=None):
     logger.info("remowing rows")
-    if rows == None:
+    if not rows:
         rows = reversed(list(set(
             map(lambda x: x.row(), drls['pt'].selectedIndexes()))))
     cors = []
     for row in rows:
-        drls['dt'].cellWidget(row,0).setCheckState(0)
+        drls['dt'].cellWidget(row, 0).setCheckState(0)
         drls['dt'].removeRow(row)
         drls['pt'].removeRow(row)
         for i in range(drls['dt'].rowCount()):
@@ -305,8 +303,8 @@ def remove_rows(ds, drls, drlspectrum, rows=None):
                     corfor.setCurrentIndex<