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
@@ -50,37 +50,40 @@ 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)
+                             constrained_layout=True)
         super().__init__(self.figure)
         self.ds = []
         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):
@@ -89,18 +92,19 @@ 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)\
-                          and not os.path.isdir(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.ds, augCanvas.chrom['timesarg'],
+                    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"))]
+                 for i in load_raw(filename, settings.value("tmp_location"))]
             except rawprasslib.ParsingException as pex:
                 errormsg.append("Opening of the file has failed!")
                 errormsg.append(
@@ -109,14 +113,14 @@ 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]
+                                for subset in augCanvas.ds]
                     indicies = [sum(segments[:i+1])
-                            for i in range(len(segments))]
+                                for i in range(len(segments))]
                     augCanvas.ms['headers'] = np.split(
                             rawheaders, indicies)[:-1]
                 except Exception as pex:
@@ -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)
@@ -145,70 +149,71 @@ 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):
     if event.mimeData().hasUrls() and event.mimeData().urls()[0]\
-        .toLocalFile().lower().endswith('.raw'):
+            .toLocalFile().lower().endswith('.raw'):
         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):
@@ -221,8 +226,8 @@ def key_pressed(event, augCanvas, config):
             else:
                 imgt.clip_spect_img(augCanvas.ms, augCanvas.spectplot,
                                     augCanvas.filename)
-        if event.modifiers().__int__() == QtCore.Qt.ControlModifier+\
-                                          QtCore.Qt.ShiftModifier:
+        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):
         gt.shift_times(event, augCanvas)
@@ -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)
@@ -269,16 +274,16 @@ 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")
+                               "view/acqparvisible")
     update.signal.connect(lambda: gt.update_paramstable(augCanvas))
     paramsdock.setWidget(augCanvas.paramstable)
 
@@ -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)
 
@@ -53,7 +53,7 @@ def posvarconf(label, value, config, num="int"):
     textfield.editingFinished.connect(lambda: config.setValue(
         value, textfield.text()))
     validator = QtGui.QIntValidator() if num == "int"\
-            else QtGui.QDoubleValidator()
+        else QtGui.QDoubleValidator()
     validator.setBottom(0)
     textfield.setValidator(validator)
     layout = QtWidgets.QHBoxLayout()
@@ -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

@@ -27,8 +27,9 @@ 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\
-                i < len(line.get_xdata()) else delim for line in lines]
+        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)
     strdata = "".join(strdata)
@@ -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