python3: revert some of the changes by toubol and try not to break pr…

…evious workflows

.gitignore

@@ -79,3 +79,5 @@ tests/data
 .cache
 .eggs
 .env
+
+.pytest_cache

.travis/linux_install.sh

@@ -5,6 +5,9 @@ sudo apt-get update -qq
 # Fixes the error:
 # - ImportError: No module named _tkinter, please install the python-tk package
 sudo apt-get install -qq python-pip python-tk
+# requirements for building wxPython4 on Ubuntu 17.10
+# see https://github.com/wxWidgets/Phoenix/blob/master/README.rst
+#sudo apt-get install -qq libgtk2.0 libgtk2.0-dev libwebkitgtk-dev dpkg-dev build-essential python3.6-dev libjpeg-dev libtiff-dev libsdl1.2-dev libnotify-dev freeglut3 freeglut3-dev libsm-dev libgtk-3-dev libwebkit2gtk-4.0-dev libxtst-dev libgstreamer-plugins-base1.0-dev
 sudo pip install virtualenv
 # use separate virtual environment
 virtualenv --system-site-packages ~/env

ChangeLog.txt

@@ -1,9 +1,8 @@
 2.0.0
 - BREAKING CHANGE: Move to Python3
 - GUI:
-  - mice don't change the parameter box automatically
-  - close the tools after use
-  - add shortcuts:
+  - Add option in Preferences to automatically close tools after usage
+  - Add keybord shortcuts:
     - Load data:        Ctrl + O
     - Load session:     Ctrl + Shift + O
     - Clear Session:    Alt + C

pycorrfit/__init__.py

@@ -4,14 +4,6 @@
 PyCorrFit is a tool to fit fluorescence correlation spectroscopy
 data on a logarithmic scale.
 """
-
-from os import walk
-import sys
-
-for path, _, _ in walk('..'):
-    sys.path.append(path)
-
-
 from . import meta
 from . import models
 from . import openfile

pycorrfit/correlation.py

@@ -318,7 +318,7 @@ def fit_model(self):
     def fit_model(self, value):
         """set the fit model
         """
-        if isinstance(value, (int, float)):
+        if isinstance(value, int):
             newmodel = mdls.modeldict[value]
         elif isinstance(value, mdls.Model):
             newmodel = value

pycorrfit/fit.py

@@ -49,7 +49,7 @@ def parameters(self):
         """
         Returns list of dict for each parameter.
         """
-        parms = [ it for it in self.constraint if isinstance(it, (int, float))]
+        parms = [ it for it in self.constraint if isinstance(it, int)]
         id2 = self.constraint.index(parms[1])
 
         p1 = {"id": parms[0],
@@ -68,7 +68,7 @@ def parameters(self):
 
     @property
     def operator(self):
-        strval = [ it for it in self.constraint if not isinstance(it, (int, float))]
+        strval = [ it for it in self.constraint if not isinstance(it, int)]
         return strval[0]
 
     @property
@@ -672,8 +672,8 @@ def compute_weights(correlation, verbose=0, uselatex=False):
             elif weights.shape[0] == x_full.shape[0]:
                 dataweights = weights[ival[0]:ival[1]]
             else:
-                raise ValueError("`weights` must have length of full \
-or cropped array.")
+                msg = "`weights` must have length of full or cropped array."
+                raise ValueError(msg)
 
         return dataweights
 
@@ -803,8 +803,10 @@ def lmfitparm2array(parms, parmid="parm", attribute="value"):
         """
         if isinstance(parms, lmfit.parameter.Parameters):
             items = parms.items()
-            # items.sort(key=lambda x: x[0])
-            parr = [getattr(p[1], attribute) for p in sorted(items, key=lambda x: x[0]) if p[0].startswith(parmid)]
+            parr = []
+            for p in sorted(items, key=lambda x: x[0]):
+                if p[0].startswith(parmid):
+                    parr.append(getattr(p[1], attribute))
         else:
             parr = parms
 

pycorrfit/gui/frontend.py

@@ -5,19 +5,19 @@
 The frontend displays the GUI (Graphic User Interface). All necessary
 functions and modules are called from here.
 """
-
-from distutils.version import LooseVersion # For version checking
+from distutils.version import LooseVersion  # For version checking
 import os
-import webbrowser
-import wx
-import wx.lib.agw.flatnotebook as fnb
-import wx.py.shell
-import wx.adv
-import numpy as np
+import pathlib
 import platform
 import sys
 import traceback
 import warnings
+import webbrowser
+
+import numpy as np
+import wx.adv
+import wx.lib.agw.flatnotebook as fnb
+import wx.py.shell
 
 from pycorrfit import models as mdls
 from pycorrfit import openfile as opf
@@ -90,9 +90,8 @@ def __init__(self, parent, anid, version):
         ## Set initial variables that make sense
         self.version = version
 
-        ##Init of the superClass
-        # super(MyFrame, self).__init__(parent, anid, "PyCorrFit " + self.version)
-        wx.Frame.__init__(self, parent, anid, "PyCorrFit " + self.version)
+        ## Init of the superClass
+        super(MyFrame, self).__init__(parent, anid, "PyCorrFit " + self.version)
 
         self.CreateStatusBar() # A Statusbar in the bottom of the window
         self.StatusBar.SetStatusText("Find help and updates online:"+
@@ -305,6 +304,9 @@ def MakeMenu(self):
                            "Enables/Disables displaying weights of fit.",
                             kind=wx.ITEM_CHECK)
         self.MenuShowWeights.Check()
+        self.MenuAutocloseTools = prefmenu.Append(wx.ID_ANY, "Autoclose tools",
+                            "Automatically close tools after usage.",
+                            kind=wx.ITEM_CHECK)
         # toolmenu
         toolkeys = list(tools.ToolDict.keys())
         toolkeys.sort()
@@ -607,7 +609,7 @@ def OnCommSession(self,e=None):
             self.EditCommentDlg = tools.EditComment(self)
             self.EditCommentDlg.Bind(wx.EVT_CLOSE, self.EditCommentDlg.OnClose)
             self.filemenu.Check(self.menuComm.GetId(), True)
-        except RuntimeError as rte:
+        except RuntimeError:
             del self.EditCommentDlg
             self.OnCommSession()
         else:
@@ -634,23 +636,23 @@ def OnDeletePage(self, event=None):
 
     def OnDocumentation(self, e=None):
         """ Get the documentation and view it with browser"""
-        filename = doc.GetLocationOfDocumentation()
-        if filename is None:
+        path = doc.GetLocationOfDocumentation()
+        if path is None:
             # Now we have to tell the user that there is no documentation
             self.StatusBar.SetStatusText("...documentation not found.")
         else:
-            self.StatusBar.SetStatusText("...documentation: "+filename)
+            path = pathlib.Path(path)
+            self.StatusBar.SetStatusText("...documentation: {}".format(path))
             if platform.system().lower() == 'windows':
-                path = '\\'.join(filename.split('\\')[:-1])
-                file = filename.split('\\')[-1]
-                os.system("start /d \"{}\" {}".format(path, file))
+                cmd = 'start /d "{}" {}'.format(path.parent, path.name)
             elif platform.system().lower() == 'linux':
-                os.system("xdg-open "+filename+" &")
+                cmd = 'xdg-open "{}" &'.format(path)
             elif platform.system().lower() == 'darwin':
-                os.system("open "+filename+" &")
+                cmd = 'open "{}" &'.format(path)
             else:
                 # defaults to linux style:
-                os.system("xdg-open "+filename+" &")
+                cmd = 'xdg-open "{}" &'.format(path)
+            os.system(cmd)
 
 
     def OnExit(self,e=None):

pycorrfit/gui/page.py

@@ -106,7 +106,7 @@ def __init__(self, parent, counter, modelid, active_parms, tau=None):
         self.canvascorr.SetSize((canvasx, cupsizey))
         # Lower Plot for plotting of the residuals
         self.canvaserr = plot.PlotCanvas(self.spcanvas)
-        self.canvaserr.logScale =(True, False)
+        self.canvaserr.logScale = (True, False)
         self.canvaserr.enableZoom = True
         self.canvaserr.SetSize((canvasx, size[1]-cupsizey))
         self.spcanvas.SplitHorizontally(self.canvascorr, self.canvaserr,

pycorrfit/gui/tools/average.py

@@ -335,8 +335,9 @@ def OnAverage(self, evt=None):
             self.AvgPage.apply_parameters()
             self.AvgPage.corr.set_weights(listname,  standarddev)
         self.AvgPage.PlotAll()
-        # Keep the average tool open.
-        self.OnClose()
+        if self.parent.MenuAutocloseTools.IsChecked():
+            # Autoclose
+            self.OnClose()
 
     def SetPageNumbers(self, pagestring):
         self.WXTextPages.SetValue(pagestring)

pycorrfit/gui/tools/batchcontrol.py

@@ -126,7 +126,11 @@ def OnFit(self, event):
                 fit_page_list.append(pageii)
 
         FitProgressDlg(self, fit_page_list, trigger="fit_batch")
-        self.OnClose()
+
+        if self.parent.MenuAutocloseTools.IsChecked():
+            # Autoclose
+            self.OnClose()
+
 
     def OnPageChanged(self, Page=None, trigger=None):
         """

pycorrfit/gui/tools/globalfit.py

@@ -118,7 +118,10 @@ def OnFit(self, e=None):
             if int(j) in global_pages:
                 Page.apply_parameters_reverse()
                 Page.PlotAll()
-        self.OnClose()
+        if self.parent.MenuAutocloseTools.IsChecked():
+            # Autoclose
+            self.OnClose()
+
 
     def OnPageChanged(self, page, trigger=None):
         """

pycorrfit/gui/tools/parmrange.py

@@ -159,5 +159,6 @@ def OnSetParmRange(self, e):
         parm1 = mdls.GetInternalFromHumanReadableParm(corr.fit_model.id,
                                                      self.parameter_range[:,1])[1]
         corr.fit_parameters_range = np.dstack((parm0, parm1))[0]
-        #self.Page.PlotAll()
-        self.OnClose()
+        if self.parent.MenuAutocloseTools.IsChecked():
+            # Autoclose
+            self.OnClose()

pycorrfit/gui/wxutils.py

@@ -114,8 +114,8 @@ class PCFFloatTextCtrl(wx.TextCtrl):
     def __init__(self, *args, **kwargs):
         wx.TextCtrl.__init__(self, *args, validator=PCFFloatValidator(), size=(110,-1),
                              style=wx.TE_PROCESS_ENTER, **kwargs)
-        # self.Bind(wx.EVT_ENTER_WINDOW, self.OnMouseEnter)
-        # self.Bind(wx.EVT_LEAVE_WINDOW, self.OnMouseLeave)
+        self.Bind(wx.EVT_ENTER_WINDOW, self.OnMouseEnter)
+        self.Bind(wx.EVT_LEAVE_WINDOW, self.OnMouseLeave)
         self._PCFvalue = 0.0
 
     def OnMouseEnter(self, e):

pycorrfit/models/classes.py

@@ -1,8 +1,9 @@
-# -*- coding: utf-8 -*-
 import copy
-import numpy as np
+import numbers
 import warnings
 
+import numpy as np
+
 
 class Model(object):
     """General class for handling FCS fitting models"""
@@ -27,7 +28,11 @@ def __init__(self, datadict):
             # larger than the last.
             newcc = []
             for cc in datadict["Constraints"]:
-                if cc[0] < cc[2]:
+                # check for integral numbers to avoid comparison to strings
+                # in e.g. confocal t_3d_3d_3d model.
+                if (isinstance(cc[0], numbers.Integral) and
+                    isinstance(cc[2], numbers.Integral) and
+                    cc[0] < cc[2]):
                     if cc[1] == ">":
                         cc = [cc[2], "<", cc[0]]
                     elif cc[1] == "<":

pycorrfit/models/model_confocal_t_3d_3d_2d.py

@@ -155,7 +155,7 @@ def supplements(parms, countrate=None):
                        False, True, False, False,
                        False, False, True, False],
              par_boundaries=boundaries,
-             par_constraints=[[2, ">", 1], [3, ">", 2], [9, "<", 1]],  # , [5, 4, "<", "1"]],
+             par_constraints=[[2, ">", 1], [3, ">", 2], [9, "<", 1], [5, 4, "<", "1"]],
              par_hr_labels=[
                             u"n",
                             u"τ"+u"\u2081"+" [ms]",

pycorrfit/models/model_confocal_t_3d_3d_3d.py

@@ -156,7 +156,7 @@ def supplements(parms, countrate=None):
                        False, True, False, False,
                        False, False, True, False],
              par_boundaries=boundaries,
-             par_constraints=[[2, ">", 1], [3, ">", 2], [9, "<", 1]],  # [5, 4, "<", "1"]],
+             par_constraints=[[2, ">", 1], [3, ">", 2], [9, "<", 1], [5, 4, "<", "1"]],
              par_hr_labels=[
                             u"n",
                             u"τ"+u"\u2081"+" [ms]",