Merge pull request #47 from jdha/PyNEMO3

Py nemo3

DESCRIPTION.rst

+PyNEMO Description
+===================
\ No newline at end of file

inputs/namelist_local.bdy

@@ -40,7 +40,7 @@
 !------------------------------------------------------------------------------
 !  I/O 
 !------------------------------------------------------------------------------
-   sn_src_dir = '/Users/jdha/Projects/GitHub/PyNEMO/inputs/src_data.ncml' ! src_files/'
+   sn_src_dir = '/Users/jdha/Projects/GitHub/PyNEMO3/inputs/src_data_local.ncml' ! src_files/'
    sn_dst_dir = './outputs'
    sn_fn      = 'NNA_R12'             ! prefix for output files
    nn_fv      = -1e20                 !  set fill value for output files

pynemo/gui/nemo_bdy_input_window.py

@@ -6,13 +6,13 @@ Created on 21 Jan 2015
 # pylint: disable=E1103
 # pylint: disable=no-name-in-module
 # pylint: disable=E1002
-from PyQt4 import QtGui
+from PyQt5 import QtGui, QtWidgets
 from .nemo_bdy_namelist_edit import NameListEditor
 from .nemo_bdy_mask_gui import MatplotlibWidget
-from PyQt4.QtGui import QSizePolicy
-from PyQt4.Qt import Qt
+from PyQt5.QtWidgets import QSizePolicy
+from PyQt5.Qt import Qt
 
-class InputWindow(QtGui.QDialog):
+class InputWindow(QtWidgets.QDialog):
     '''
     Input Window for editing pyNEMO settings
     '''
@@ -43,15 +43,15 @@ class InputWindow(QtGui.QDialog):
 
         self.mpl_widget.set_mask_settings(float(setup.settings['mask_max_depth']), float(setup.settings['mask_shelfbreak_dist']))
 
-        splitter = QtGui.QSplitter(Qt.Horizontal)
+        splitter = QtWidgets.QSplitter(Qt.Horizontal)
         splitter.addWidget(self.nl_editor)
         splitter.addWidget(self.mpl_widget)
 
-        hbox = QtGui.QHBoxLayout()
+        hbox = QtWidgets.QHBoxLayout()
         hbox.addWidget(splitter)
         self.setLayout(hbox)
         #set the Dialog title
         self.setWindowTitle("PyNEMO Settings Editor")
-        QtGui.QApplication.setStyle(QtGui.QStyleFactory.create('Cleanlooks'))        
+        QtWidgets.QApplication.setStyle(QtWidgets.QStyleFactory.create('Cleanlooks'))        
         #show the window
         self.show()

pynemo/gui/nemo_bdy_mask.py

@@ -12,8 +12,8 @@ import logging
 from scipy import ndimage
 import matplotlib.pyplot as plt
 from pynemo.utils import gcoms_break_depth
-from PyQt4.QtGui import QMessageBox
-from PyQt4 import QtCore
+from PyQt5.QtWidgets import QMessageBox
+from PyQt5 import QtCore
 
 class Mask(object):
     """This is a Mask holder. which reads from a netCDF bathymetry file and
@@ -199,7 +199,7 @@ class Mask(object):
         mask_data[index] = self.data[index]        
         #connected components
         label_mask, num_labels = ndimage.label(mask_data)
-        mean_values = ndimage.sum(np.ones(self.data.shape),label_mask,range(1, num_labels+1))
+        mean_values = ndimage.sum(np.ones(self.data.shape),label_mask,list(range(1, num_labels+1)))
         max_area_mask = None
         if mean_values.size != 0:
             max_area_index = np.argmax(mean_values)+1
@@ -228,7 +228,7 @@ class Mask(object):
         label_mask, num_labels = ndimage.label(mask_data)
         if num_labels == 0: #if mask is empty/clear
             return
-        mean_values = ndimage.sum(np.ones(self.data.shape),label_mask,range(1, num_labels+1))
+        mean_values = ndimage.sum(np.ones(self.data.shape),label_mask,list(range(1, num_labels+1)))
         max_area_mask = None
         if mean_values.size != 0:
             max_area_index = np.argmax(mean_values)+1

pynemo/gui/nemo_bdy_mask_gui.py

@@ -10,15 +10,15 @@ from mpl_toolkits.basemap import Basemap, cm
 import numpy as np
 from .selection_editor import PolygonEditor, BoxEditor
 import os.path
-from PyQt4.QtCore import pyqtSignal, pyqtSlot, Qt
-from nemo_bdy_mask import Mask
+from PyQt5.QtCore import pyqtSignal, pyqtSlot, Qt
+from .nemo_bdy_mask import Mask
 import logging
-from PyQt4.QtGui import QSizePolicy
+from PyQt5.QtWidgets import QSizePolicy
 from matplotlib.colors import Normalize
 
 mask_alpha = 0.3
 
-from PyQt4 import QtGui
+from PyQt5 import QtGui, QtWidgets
 import matplotlib.pyplot as plt
 from matplotlib.figure import Figure
 from matplotlib.path import Path
@@ -26,7 +26,7 @@ from matplotlib.transforms import Bbox
 from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
 # pylint: disable=E1002
-class MatplotlibWidget(QtGui.QWidget):
+class MatplotlibWidget(QtWidgets.QWidget):
     """This class is a QWidget for pyNEMO mask plot"""
     min_depth = 200.0
     shelfbreak_dist = 200.0
@@ -34,7 +34,7 @@ class MatplotlibWidget(QtGui.QWidget):
     def __init__(self, parent=None, mask=None, min_depth = 200.0, shelfbreak_dist = 200.0,*args, **kwargs):
         """ Initialises the mask, matplot and the navigation toolbar """
         super(MatplotlibWidget, self).__init__(parent)
-        #QtGui.QWidget.__init__(self, parent)
+        #QtWidgets.QWidget.__init__(self, parent)
         self.figure = Figure(*args, **kwargs)
         self.canvas = FigureCanvas(self.figure)
         self.mask = mask
@@ -51,7 +51,7 @@ class MatplotlibWidget(QtGui.QWidget):
         self.toolbar.drawing_tool.connect(self.drawing_tool_callback)
         self.axes = self.figure.add_subplot(111)
         self.cbar = None
-        layout = QtGui.QVBoxLayout()
+        layout = QtWidgets.QVBoxLayout()
         layout.addWidget(self.toolbar)
         layout.addWidget(self.canvas)
         self.setLayout(layout)
@@ -126,7 +126,7 @@ class MatplotlibWidget(QtGui.QWidget):
                 x = np.arange(0, self.mask.lon.shape[0])
                 y = np.arange(0, self.mask.lon.shape[1])
                 x_vals, y_vals = np.meshgrid(y, x)
-                grid = zip(x_vals.ravel(), y_vals.ravel())
+                grid = list(zip(x_vals.ravel(), y_vals.ravel()))
                 
                 self._drawing_tool.polygon.set_linewidth(1.0)
                 p_path = Path(self._drawing_tool.polygon.xy)
@@ -146,7 +146,7 @@ class MatplotlibWidget(QtGui.QWidget):
                 x = np.arange(0, self.mask.lon.shape[0])
                 y = np.arange(0, self.mask.lon.shape[1])
                 x_vals, y_vals = np.meshgrid(y, x)
-                grid = zip(x_vals.ravel(), y_vals.ravel()) #check for the index
+                grid = list(zip(x_vals.ravel(), y_vals.ravel())) #check for the index
 
                 self._drawing_tool.polygon.set_linewidth(1.0)
                 p_path = Path(self._drawing_tool.polygon.xy)

pynemo/gui/nemo_bdy_mask_gui.py.interactive_cbar

@@ -10,10 +10,10 @@ from mpl_toolkits.basemap import Basemap, cm
 import numpy as np
 from .selection_editor import PolygonEditor, BoxEditor
 import os.path
-from PyQt4.QtCore import pyqtSignal, pyqtSlot, Qt
+from PyQt5.QtCore import pyqtSignal, pyqtSlot, Qt
 from nemo_bdy_mask import Mask
 import logging
-from PyQt4.QtGui import QSizePolicy
+from PyQt5.QtGui import QSizePolicy
 
 mask_alpha = 0.3
 

pynemo/gui/nemo_bdy_namelist_edit.py

@@ -6,13 +6,14 @@ Editor for namelist.bdy file
 # pylint: disable=E1103
 # pylint: disable=no-name-in-module
 # pylint: disable=E1002
-from PyQt4 import QtGui, QtCore
-from PyQt4.QtCore import pyqtSignal, Qt, QRect, QPoint
+from PyQt5 import QtGui, QtCore, QtWidgets
+from PyQt5.QtCore import pyqtSignal, Qt, QRect, QPoint
 
 import ast
-from PyQt4.QtGui import QMessageBox, QRegion, QIcon, QToolTip, QCursor
+from PyQt5.QtGui import QRegion, QIcon, QCursor
+from PyQt5.QtWidgets import QMessageBox, QToolTip
 
-class NameListEditor(QtGui.QWidget):
+class NameListEditor(QtWidgets.QWidget):
     '''
     This class creates a gui for the Namelist file options
     '''
@@ -34,25 +35,25 @@ class NameListEditor(QtGui.QWidget):
         '''
         Initialises the UI components of the GUI
         '''
-        client = QtGui.QWidget(self)
+        client = QtWidgets.QWidget(self)
         # Create the Layout to Grid
-        grid = QtGui.QGridLayout()
+        grid = QtWidgets.QGridLayout()
 
         # Loop through the settings and create widgets for each setting
         index = 0
         for setting in self.settings:
             # initialises setting Widget
-            label = QtGui.QLabel(setting)
-            qlabel = QtGui.QPushButton("")
-            qlabel.setIcon(self.style().standardIcon(QtGui.QStyle.SP_MessageBoxQuestion))
+            label = QtWidgets.QLabel(setting)
+            qlabel = QtWidgets.QPushButton("")
+            qlabel.setIcon(self.style().standardIcon(QtWidgets.QStyle.SP_MessageBoxQuestion))
             if type(self.settings[setting]).__name__ in ['str', 'float', 'double',
                                                          'int', 'time', 'dict']:
-                text = QtGui.QLineEdit(self)
+                text = QtWidgets.QLineEdit(self)
                 text.setText(str(self.settings[setting]))
                 text.textChanged.connect(lambda value=setting,\
                                          var_name=setting: self.label_changed(value, var_name))
-                if self.bool_settings.has_key(setting):
-                    chkbox = QtGui.QCheckBox(self)
+                if setting in self.bool_settings:
+                    chkbox = QtWidgets.QCheckBox(self)
                     chkbox.setChecked(self.bool_settings[setting])
                     chkbox.stateChanged.connect(lambda value=setting,\
                                                 var_name=setting:\
@@ -60,7 +61,7 @@ class NameListEditor(QtGui.QWidget):
                     grid.addWidget(chkbox, index, 0)
 
             elif type(self.settings[setting]).__name__ == 'bool':
-                text = QtGui.QComboBox(self)
+                text = QtWidgets.QComboBox(self)
                 text.insertItem(0, 'True')
                 text.insertItem(1, 'False')
                 if self.settings[setting]:
@@ -83,22 +84,22 @@ class NameListEditor(QtGui.QWidget):
 
         client.setLayout(grid)
         #scrollbars
-        scroll_area = QtGui.QScrollArea(self)
+        scroll_area = QtWidgets.QScrollArea(self)
         #scroll_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
         scroll_area.setWidget(client)
 
         #save cancel buttons
-        btn_widget = QtGui.QWidget(self)
-        hbox_layout = QtGui.QHBoxLayout(self)      
-        btn_save = QtGui.QPushButton('Save')
+        btn_widget = QtWidgets.QWidget(self)
+        hbox_layout = QtWidgets.QHBoxLayout(self)      
+        btn_save = QtWidgets.QPushButton('Save')
         btn_save.clicked.connect(self._btn_save_callback)
-        self.btn_cancel = QtGui.QPushButton('Close')
+        self.btn_cancel = QtWidgets.QPushButton('Close')
         self.btn_cancel.clicked.connect(self._btn_cancel_callback)
         hbox_layout.addWidget(btn_save)
         hbox_layout.addWidget(self.btn_cancel)
         btn_widget.setLayout(hbox_layout)
 
-        box_layout = QtGui.QVBoxLayout(self)
+        box_layout = QtWidgets.QVBoxLayout(self)
         box_layout.addWidget(scroll_area)
         box_layout.addWidget(btn_widget)
         btn_widget.setMaximumWidth(400)
@@ -109,7 +110,7 @@ class NameListEditor(QtGui.QWidget):
 
     def label_changed(self, value, name):
         """ callback when the text is changed in the text box"""
-        self.new_settings[name] = unicode(value).encode('utf_8')
+        self.new_settings[name] = str(value).encode('utf_8')
 
     def combo_index_changed(self, value, name):
         """ callback when the True/False drop down for the settings which has boolean value
@@ -153,7 +154,7 @@ class NameListEditor(QtGui.QWidget):
         try:
             self.mask_settings_update.emit(float(self.settings['mask_max_depth']), float(self.settings['mask_shelfbreak_dist']))
         except KeyError:
-            print 'Set the mask setting mask_max_depth and mask_shelfbreak_dist'
+            print('Set the mask setting mask_max_depth and mask_shelfbreak_dist')
             
         if self.bool_settings['mask_file']:
             self.bathymetry_update.emit(self.settings['bathy'],self.settings['mask_file'])

pynemo/gui/nemo_ncml_generator.py

@@ -6,13 +6,13 @@ Created on 6 Aug 2015
 import logging
 import os
 import xml.etree.ElementTree as ET
-from PyQt4 import QtGui
-from PyQt4 import QtCore
-from PyQt4.QtCore import pyqtSlot
-import nemo_ncml_tab_widget
+from PyQt5 import QtGui, QtWidgets
+from PyQt5 import QtCore
+from PyQt5.QtCore import pyqtSlot
+from . import nemo_ncml_tab_widget
 from thredds_crawler.crawl import Crawl
 
-class Ncml_generator(QtGui.QDialog):
+class Ncml_generator(QtWidgets.QDialog):
     '''
     Gui editor to capture user input for the purpose of generating NCML representation of pynemo source datasets.
     '''
@@ -30,35 +30,35 @@ class Ncml_generator(QtGui.QDialog):
             self.baseFile = os.path.join(testpath,'base.ncml')
         else:
             self.baseFile = basefile
-            print 'ncml baseFile : ', str(self.baseFile)
+            print('ncml baseFile : ', str(self.baseFile))
         
         self.filename = None # store the output file pointer      
         self.initUI()
         
         
     def initUI(self):
-        QtGui.QToolTip.setFont(QtGui.QFont('SansSerif', 11))
+        QtWidgets.QToolTip.setFont(QtGui.QFont('SansSerif', 11))
         '''
         vbox is the top container
         '''
         #the 
-        vbox = QtGui.QVBoxLayout(self)
+        vbox = QtWidgets.QVBoxLayout(self)
         vbox.setSpacing(10)
         vbox.setContentsMargins(10, 10, 5, 5)
         
         '''
         top panel for output file
         '''
-        top_outfile_label = QtGui.QLabel(unicode('Output filename').encode('utf-8'))
-        self.top_outfile_name = QtGui.QLineEdit()    #location is pre-defined
-        self.top_outfile_name.setToolTip(unicode('Define output file').encode('utf-8'))
+        top_outfile_label = QtWidgets.QLabel('Output filename')
+        self.top_outfile_name = QtWidgets.QLineEdit()    #location is pre-defined
+        self.top_outfile_name.setToolTip('Define output file')
         self.top_outfile_name.returnPressed.connect(self.get_fname_input)
         
-        top_outfile_button = QtGui.QPushButton(unicode('Select file').encode('utf-8'))
+        top_outfile_button = QtWidgets.QPushButton('Select file')
         top_outfile_button.clicked.connect(self.get_fname)
         
-        top_grpBox = QtGui.QGroupBox(unicode('Define output file').encode('utf-8'), None)
-        top_grid = QtGui.QGridLayout(top_grpBox)
+        top_grpBox = QtWidgets.QGroupBox('Define output file', None)
+        top_grid = QtWidgets.QGridLayout(top_grpBox)
         top_grid.setVerticalSpacing(5)
         top_grid.setHorizontalSpacing(10)
         top_grid.addWidget(top_outfile_label, 1, 0)
@@ -68,23 +68,23 @@ class Ncml_generator(QtGui.QDialog):
         '''
         middle panel for tab folder
         '''
-        self.tabWidget = QtGui.QTabWidget()
-        self.tracer_tab = nemo_ncml_tab_widget.Ncml_tab(unicode("Tracer").encode('utf-8'))
+        self.tabWidget = QtWidgets.QTabWidget()
+        self.tracer_tab = nemo_ncml_tab_widget.Ncml_tab("Tracer")
         self.tracer_tab.setEnabled(False)
-        self.dynamic_tab = nemo_ncml_tab_widget.Ncml_tab(unicode("Dynamics").encode('utf-8'))
+        self.dynamic_tab = nemo_ncml_tab_widget.Ncml_tab("Dynamics")
         self.dynamic_tab.setEnabled(False)
-        self.ice_tab = nemo_ncml_tab_widget.Ncml_tab(unicode("Ice").encode('utf-8'))
+        self.ice_tab = nemo_ncml_tab_widget.Ncml_tab("Ice")
         self.ice_tab.setEnabled(False)
-        self.ecosys_tab = nemo_ncml_tab_widget.Ncml_tab(unicode("Ecosystem").encode('utf-8'))
+        self.ecosys_tab = nemo_ncml_tab_widget.Ncml_tab("Ecosystem")
         self.ecosys_tab.setEnabled(False)
-        self.grid_tab = nemo_ncml_tab_widget.Ncml_tab(unicode("Grid").encode('utf-8'))
+        self.grid_tab = nemo_ncml_tab_widget.Ncml_tab("Grid")
         self.grid_tab.setEnabled(False)
                 
-        self.tabWidget.addTab(self.tracer_tab, unicode("Tracer").encode('utf-8'))
-        self.tabWidget.addTab(self.dynamic_tab, unicode("Dynamics").encode('utf-8'))
-        self.tabWidget.addTab(self.ice_tab, unicode("Ice").encode('utf-8'))
-        self.tabWidget.addTab(self.ecosys_tab, unicode("Ecosystem").encode('utf-8')) # should be disabled
-        self.tabWidget.addTab(self.grid_tab, unicode("Grid").encode('utf-8')) # should be disabled
+        self.tabWidget.addTab(self.tracer_tab, "Tracer")
+        self.tabWidget.addTab(self.dynamic_tab, "Dynamics")
+        self.tabWidget.addTab(self.ice_tab, "Ice")
+        self.tabWidget.addTab(self.ecosys_tab, "Ecosystem") # should be disabled
+        self.tabWidget.addTab(self.grid_tab, "Grid") # should be disabled
         self.tabWidget.setMovable(False)
 #        if self.tabWidget.widget(self.tabWidget.currentIndex()).isEnabled() is True:
         
@@ -93,13 +93,13 @@ class Ncml_generator(QtGui.QDialog):
         '''
         button bar
         '''
-        go_btn = QtGui.QPushButton(unicode('Generate').encode('utf-8'))
-        go_btn.setToolTip(unicode('Add all variable definitions before generating NcML file.').encode('utf-8'))
-        cancel_btn = QtGui.QPushButton(unicode('Cancel').encode('utf-8'))
-        enable_btn = QtGui.QPushButton(unicode('Enable Tab').encode('utf-8'))
+        go_btn = QtWidgets.QPushButton('Generate')
+        go_btn.setToolTip('Add all variable definitions before generating NcML file.')
+        cancel_btn = QtWidgets.QPushButton('Cancel')
+        enable_btn = QtWidgets.QPushButton('Enable Tab')
         #layout button bar        
-        btn_hBox = QtGui.QHBoxLayout(None)
-        btn_hBox.setMargin(5)
+        btn_hBox = QtWidgets.QHBoxLayout(None)
+        btn_hBox.setContentsMargins(5, 5, 5, 5)
         btn_hBox.setSpacing(10)
         btn_hBox.setAlignment(QtCore.Qt.AlignRight)
         btn_hBox.addWidget(enable_btn)
@@ -120,7 +120,7 @@ class Ncml_generator(QtGui.QDialog):
         
         #self.setLayout(grp_box)        
         self.setWindowIcon(QtGui.QIcon('/Users/jdha/anaconda/lib/python2.7/site-packages/pynemo-0.2-py2.7.egg/pynemo/gui/nemo_icon.png'))    #doesn't work       
-        self.setWindowTitle(unicode("PyNEMO NcML Generator").encode('utf-8'))
+        self.setWindowTitle("PyNEMO NcML Generator")
         self.resize(650,300)
         
         #has to change the default focus to stop the output file QTextedit to trigger the widget in focus when enter is pressed.  Not sure why this happens???
@@ -137,7 +137,7 @@ class Ncml_generator(QtGui.QDialog):
         # When you call getOpenFileName, a file picker dialog is created
         # and if the user selects a file, it's path is returned, and if not
         # (ie, the user cancels the operation) None is returned
-        fname = QtGui.QFileDialog.getSaveFileName(self, 'Select output file', '', selectedFilter='*.ncml')
+        fname = QtWidgets.QFileDialog.getSaveFileName(self, 'Select output file', '', selectedFilter='*.ncml')
         if fname:
             self.filename = fname #returns a QString
             self.top_outfile_name.setText(str(fname))
@@ -155,9 +155,9 @@ class Ncml_generator(QtGui.QDialog):
     @pyqtSlot()
     def enable_btn_update(self, enable_btn):
         if self.tabWidget.widget(self.tabWidget.currentIndex()).isEnabled() is True:
-            enable_btn.setText(unicode('Disable Tab').encode('utf-8'))
+            enable_btn.setText('Disable Tab')
         else:
-            enable_btn.setText(unicode('Enable Tab').encode('utf-8'))
+            enable_btn.setText('Enable Tab')
     '''
     call back to handle the generate button pressed
     '''
@@ -167,10 +167,10 @@ class Ncml_generator(QtGui.QDialog):
         #validate output file
         if self.tabWidget.widget(self.tabWidget.currentIndex()).isEnabled() is True:
             self.tabWidget.widget(self.tabWidget.currentIndex()).setEnabled(False)
-            enable_btn.setText(unicode('Enable Tab').encode('utf-8'))
+            enable_btn.setText('Enable Tab')
         else:
             self.tabWidget.widget(self.tabWidget.currentIndex()).setEnabled(True)
-            enable_btn.setText(unicode('Disable Tab').encode('utf-8'))
+            enable_btn.setText('Disable Tab')
 
     '''
     call back to handle the generate button pressed
@@ -180,14 +180,14 @@ class Ncml_generator(QtGui.QDialog):
         #validate output file
         if self.filename is None or self.filename == "":
             if self.top_outfile_name.text() is None or self.top_outfile_name.text() == "":
-                QtGui.QMessageBox.critical(self, unicode('Something is wrong').encode('utf-8'), unicode('No output file specified!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                QtWidgets.QMessageBox.critical(self, 'Something is wrong', 'No output file specified!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                 return
             else:
                 self.filename = self.top_outfile_name.text()
             
         if(os.path.exists(os.path.dirname(str(self.filename)))) == False:
             #if os.path.dirname(os.path.dirname(os.path.exists(os.path.normpath(str(self.filename))))) == False:
-            QtGui.QMessageBox.critical(self, unicode('Something is wrong').encode('utf-8'), unicode('Invalid output directory!  Cannot generate file!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+            QtWidgets.QMessageBox.critical(self, 'Something is wrong', 'Invalid output directory!  Cannot generate file!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
             #print 'invalid target directory!  Cannot generate.'
             return
             
@@ -201,7 +201,7 @@ class Ncml_generator(QtGui.QDialog):
                self.tracer_tab.vosaline.src != "" :
                 tabsList.extend([self.tracer_tab.votemper, self.tracer_tab.vosaline])
             else:
-                QtGui.QMessageBox.information(self, unicode('Something is wrong').encode('utf-8'), unicode('Not all the variables under the tracer tab have been defined!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                QtWidgets.QMessageBox.information(self, 'Something is wrong', 'Not all the variables under the tracer tab have been defined!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
 
 
         if self.ice_tab.isEnabled() is True:
@@ -210,7 +210,7 @@ class Ncml_generator(QtGui.QDialog):
                self.ice_tab.isnowthi.src != "" :
                 tabsList.extend([self.ice_tab.iicethic, self.ice_tab.ileadfra, self.ice_tab.isnowthi])
             else:
-                QtGui.QMessageBox.information(self, unicode('Something is wrong').encode('utf-8'), unicode('Not all the variables under the ice tab have been defined!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                QtWidgets.QMessageBox.information(self, 'Something is wrong', 'Not all the variables under the ice tab have been defined!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
 
         if self.dynamic_tab.isEnabled() is True:
             if self.dynamic_tab.vozocrtx.src != ""  and \
@@ -218,7 +218,7 @@ class Ncml_generator(QtGui.QDialog):
                self.dynamic_tab.sossheig.src != "" :
                 tabsList.extend([self.dynamic_tab.vozocrtx, self.dynamic_tab.vomecrty, self.dynamic_tab.sossheig])
             else:
-                QtGui.QMessageBox.information(self, unicode('Something is wrong').encode('utf-8'), unicode('Not all the variables under the dynamics tab have been defined!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                QtWidgets.QMessageBox.information(self, 'Something is wrong', 'Not all the variables under the dynamics tab have been defined!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
 
         if self.grid_tab.isEnabled() is True:
             if self.grid_tab.gdept.src != ""    and \
@@ -229,14 +229,14 @@ class Ncml_generator(QtGui.QDialog):
                self.grid_tab.e3v.src != "" :
                 tabsList.extend([self.grid_tab.gdept, self.grid_tab.gdepw, self.grid_tab.mbathy, self.grid_tab.e3t, self.grid_tab.e3u, self.grid_tab.e3v])
             else:
-                QtGui.QMessageBox.information(self, unicode('Something is wrong').encode('utf-8'), unicode('Not all the variables under the grid tab have been defined!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                QtWidgets.QMessageBox.information(self, 'Something is wrong', 'Not all the variables under the grid tab have been defined!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
 
         try:
             self.generateNcML(tabsList) #go ahead and do it
         except:
             raise
 
-        QtGui.QMessageBox.information(self, unicode('Success.').encode('utf-8'), unicode('NcML file generated.').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+        QtWidgets.QMessageBox.information(self, 'Success.', 'NcML file generated.', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
 
     '''
     Function to generates the NcML text and write it to the user defined output file
@@ -248,68 +248,68 @@ class Ncml_generator(QtGui.QDialog):
         self.root = self.tree.getroot()
         #create a netcdf element for each tab variable
         for tab in tabsList:
-            netcdfE = ET.Element(ns+unicode('netcdf').encode('utf-8')) #src directory is converted to the correct format when added/
+            netcdfE = ET.Element(ns+'netcdf') #src directory is converted to the correct format when added/
             if str(tab.src).startswith("http:") or str(tab.src).startswith("https:"):
                 #Its url so use thredds crawler to get the urls
                 urls = self.url_trawler(tab.src,str(tab.regex))
-                aggE = ET.Element(ns+unicode('aggregation').encode('utf-8'), name=unicode(str(tab.name)).encode('utf-8'), type=unicode('joinExisting').encode('utf-8'), dimName=unicode('time_counter').encode('utf-8')) #tab.name already encoded                
+                aggE = ET.Element(ns+'aggregation', name=str(tab.name), type='joinExisting', dimName='time_counter') #tab.name already encoded                
                 for nc_url in urls:
-                    tcNetcdf = ET.Element(ns+unicode('netcdf').encode('utf-8'), location=unicode(str(nc_url)).encode('utf-8'))
+                    tcNetcdf = ET.Element(ns+'netcdf', location=str(nc_url))
                     aggE.append(tcNetcdf)
                 netcdfE.append(aggE)
             else:
-                scanE = ET.Element(ns+unicode('scan').encode('utf-8'), location=unicode(str(tab.src)).encode('utf-8'), regExp=unicode(str(tab.regex)).encode('utf-8'))
+                scanE = ET.Element(ns+'scan', location=str(tab.src), regExp=str(tab.regex))
                 if tab.subdirs == True:
-                    scanE.set(unicode('subdirs').encode('utf-8'), unicode('true').encode('utf-8'))
-                aggE = ET.Element(ns+unicode('aggregation').encode('utf-8'), name=unicode(str(tab.name)).encode('utf-8'), type=unicode('joinExisting').encode('utf-8'), dimName=unicode('time_counter').encode('utf-8')) #tab.name already encoded
+                    scanE.set('subdirs', 'true')
+                aggE = ET.Element(ns+'aggregation', name=str(tab.name), type='joinExisting', dimName='time_counter') #tab.name already encoded
                 aggE.append(scanE)
                 netcdfE.append(aggE)
             self.root[0].append(netcdfE)    #add the new netcdf element to the top aggregation 
             
             #deal with variable name change TODO put this into a loop?
             if tab.old_name is not None and tab.old_name != "":
-                vname = unicode('variable').encode('utf-8')
+                vname = 'variable'
                 #v is None          
-                if tab.name == unicode('temperature').encode('utf-8') and tab.old_name != unicode('votemper').encode('utf-8'):
+                if tab.name == 'temperature' and tab.old_name != 'votemper':
                     v = ET.Element(ns+vname, name='votemper', orgName = str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('salinity').encode('utf-8') and tab.old_name != unicode('vosaline').encode('utf-8'):
+                elif tab.name == 'salinity' and tab.old_name != 'vosaline':
                     v = ET.Element(ns+vname, name='vosaline', orgName =  str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('ice_thickness').encode('utf-8') and tab.old_name != unicode('iicethic').encode('utf-8'):
+                elif tab.name == 'ice_thickness' and tab.old_name != 'iicethic':
                     v = ET.Element(ns+vname, name='iicethic', orgName =  str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('leads_fraction').encode('utf-8') and tab.old_name != unicode('ileadfra').encode('utf-8'):
+                elif tab.name == 'leads_fraction' and tab.old_name != 'ileadfra':
                     v = ET.Element(ns+vname, name='ileadfra', orgName =  str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('snow_thickness').encode('utf-8') and tab.old_name != unicode('isnowthi').encode('utf-8'):
+                elif tab.name == 'snow_thickness' and tab.old_name != 'isnowthi':
                     v = ET.Element(ns+vname, name='isnowthi', orgName =  str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('zonal_velocity').encode('utf-8') and tab.old_name != unicode('vozocrtx').encode('utf-8'):
+                elif tab.name == 'zonal_velocity' and tab.old_name != 'vozocrtx':
                     v = ET.Element(ns+vname, name='vozocrtx', orgName =  str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('meridian_velocity').encode('utf-8') and tab.old_name != unicode('vomecrty').encode('utf-8'):
+                elif tab.name == 'meridian_velocity' and tab.old_name != 'vomecrty':
                     v = ET.Element(ns+vname, name='vomecrty', orgName =  str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('sea_surface_height').encode('utf-8') and tab.old_name != unicode('sossheig').encode('utf-8'):
+                elif tab.name == 'sea_surface_height' and tab.old_name != 'sossheig':
                     v = ET.Element(ns+vname, name='sossheig', orgName =  str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('depth_at_t_points').encode('utf-8') and tab.old_name != unicode('gdept').encode('utf-8'):
+                elif tab.name == 'depth_at_t_points' and tab.old_name != 'gdept':
                     v = ET.Element(ns+vname, name='gdept', orgName =  str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('depth_at_w_points').encode('utf-8') and tab.old_name != unicode('gdepw').encode('utf-8'):
+                elif tab.name == 'depth_at_w_points' and tab.old_name != 'gdepw':
                     v = ET.Element(ns+vname, name='gdepw', orgName =  str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('number_of_wet_levels').encode('utf-8') and tab.old_name != unicode('mbathy').encode('utf-8'):
+                elif tab.name == 'number_of_wet_levels' and tab.old_name != 'mbathy':
                     v = ET.Element(ns+vname, name='mbathy', orgName =  str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('vertical_scale_factors_at_t_points').encode('utf-8') and tab.old_name != unicode('e3t').encode('utf-8'):
+                elif tab.name == 'vertical_scale_factors_at_t_points' and tab.old_name != 'e3t':
                     v = ET.Element(ns+vname, name='e3t', orgName =  str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('vertical_scale_factors_at_u_points').encode('utf-8') and tab.old_name != unicode('e3u').encode('utf-8'):
+                elif tab.name == 'vertical_scale_factors_at_u_points' and tab.old_name != 'e3u':
                     v = ET.Element(ns+vname, name='e3u', orgName =  str(tab.old_name))
                     self.root.append(v)
-                elif tab.name == unicode('vertical_scale_factors_at_v_points').encode('utf-8') and tab.old_name != unicode('e3v').encode('utf-8'):
+                elif tab.name == 'vertical_scale_factors_at_v_points' and tab.old_name != 'e3v':
                     v = ET.Element(ns+vname, name='e3v', orgName =  str(tab.old_name))
                     self.root.append(v)
                    
@@ -317,7 +317,8 @@ class Ncml_generator(QtGui.QDialog):
         try:
             self.indent(self.root, 0)   #24Aug15 format the xml for pretty printing
             self.tree.write(self.filename, encoding='utf-8')
-        except IOError as (errno, strerror):
+        except IOError as xxx_todo_changeme:
+            (errno, strerror) = xxx_todo_changeme.args
             self.logger.error("I/O error({0}): {1}".format(errno, strerror))
         except:
             self.logger.error('Error generating ncml file')
@@ -331,9 +332,9 @@ class Ncml_generator(QtGui.QDialog):
             parser = ET.XMLParser(encoding="utf-8")
             tree = ET.parse(self.baseFile, parser=parser)
             return tree
-        except ET.ParseError, v:
+        except ET.ParseError as v:
                 row, column = v.position
-                print "error on row", row, "column", column, ":", v
+                print("error on row", row, "column", column, ":", v)
                 
     '''
     Function to format xml.  Based on code provided by http://effbot.org/zone/element-lib

pynemo/gui/nemo_ncml_tab_widget.py

@@ -5,11 +5,11 @@ Created on 2 Jul 2015
 '''
 import logging
 import os
-from PyQt4 import QtGui
-from PyQt4 import QtCore
-from PyQt4.QtCore import pyqtSlot
+from PyQt5 import QtGui, QtWidgets
+from PyQt5 import QtCore
+from PyQt5.QtCore import pyqtSlot
 
-class Ncml_tab(QtGui.QWidget):
+class Ncml_tab(QtWidgets.QWidget):
     '''
     tab contents to define child aggregation
     '''
@@ -28,49 +28,49 @@ class Ncml_tab(QtGui.QWidget):
         
         
     def initUI(self):  
-        QtGui.QToolTip.setFont(QtGui.QFont('SansSerif', 11))
-        self.varStackedWidget = QtGui.QStackedWidget()                   
+        QtWidgets.QToolTip.setFont(QtGui.QFont('SansSerif', 11))
+        self.varStackedWidget = QtWidgets.QStackedWidget()                   
         #variable chooser combobox
         combo_vars = []
-        if(self.var == unicode("Tracer").encode('utf-8')):
-            combo_vars = [unicode('temperature').encode('utf-8'),unicode('salinity').encode('utf-8')] #votemper, vosaline
-            self.votemper = ncml_variable(unicode('temperature').encode('utf-8'),'votemper')
-            self.vosaline = ncml_variable(unicode('salinity').encode('utf-8'),'vosaline')
+        if(self.var == "Tracer"):
+            combo_vars = ['temperature','salinity'] #votemper, vosaline
+            self.votemper = ncml_variable('temperature','votemper')
+            self.vosaline = ncml_variable('salinity','vosaline')
             self.varStackedWidget.addWidget(self._addStackWidget("votemper"))
             self.varStackedWidget.addWidget(self._addStackWidget("vosaline"))
             #debug
 #            print 'Tracer has ' + str(self.varStackedWidget.count())
-        elif(self.var == unicode("Ice").encode('utf-8')):
-            combo_vars = [unicode('ice thickness').encode('utf-8'),unicode('leads fraction').encode('utf-8'),unicode('snow thickness').encode('utf-8')] #'iicethic,ileadfra,isnowthi
-            self.iicethic = ncml_variable(unicode('ice_thickness').encode('utf-8'),'iicethic')
-            self.ileadfra = ncml_variable(unicode('leads_fraction').encode('utf-8'),'ileadfra')
-            self.isnowthi = ncml_variable(unicode('snow_thickness').encode('utf-8'),'isnowthi')
+        elif(self.var == "Ice"):
+            combo_vars = ['ice thickness','leads fraction','snow thickness'] #'iicethic,ileadfra,isnowthi
+            self.iicethic = ncml_variable('ice_thickness','iicethic')
+            self.ileadfra = ncml_variable('leads_fraction','ileadfra')
+            self.isnowthi = ncml_variable('snow_thickness','isnowthi')
             self.varStackedWidget.addWidget(self._addStackWidget("iicethic"))
             self.varStackedWidget.addWidget(self._addStackWidget("ileadfra"))
             self.varStackedWidget.addWidget(self._addStackWidget("isnowthi"))
 #            print 'Ice has ' + str(self.varStackedWidget.count())
-        elif(self.var == unicode("Dynamics").encode('utf-8')):
-            combo_vars = [unicode('zonal velocity').encode('utf-8'), unicode('meridian velocity').encode('utf-8'), unicode('sea surface height').encode('utf-8')] #vozocrtx, vomecrty, sossheig
-            self.vozocrtx = ncml_variable(unicode('zonal_velocity').encode('utf-8'),'vozocrtx')
-            self.vomecrty = ncml_variable(unicode('meridian_velocity').encode('utf-8'),'vomecrty')
-            self.sossheig = ncml_variable(unicode('sea_surface_height').encode('utf-8'),'sossheig')
+        elif(self.var == "Dynamics"):
+            combo_vars = ['zonal velocity', 'meridian velocity', 'sea surface height'] #vozocrtx, vomecrty, sossheig
+            self.vozocrtx = ncml_variable('zonal_velocity','vozocrtx')
+            self.vomecrty = ncml_variable('meridian_velocity','vomecrty')
+            self.sossheig = ncml_variable('sea_surface_height','sossheig')
             self.varStackedWidget.addWidget(self._addStackWidget("vozocrtx"))
             self.varStackedWidget.addWidget(self._addStackWidget("vomecrty"))
             self.varStackedWidget.addWidget(self._addStackWidget("sossheig"))
 #            print 'Dynamics has ' + str(self.varStackedWidget.count())
-        elif(self.var == unicode("Grid").encode('utf-8')):
-            combo_vars = [unicode('depth at T points').encode('utf-8'), 
-                          unicode('depth at W points').encode('utf-8'), 
-                          unicode('number of wet levels').encode('utf-8'), 
-                          unicode('vertical scale factor at T points').encode('utf-8'), 
-                          unicode('vertical scale factor at U points').encode('utf-8'), 
-                          unicode('vertical scale factor at V points').encode('utf-8')] #gdept,gdepw,mbathy
-            self.gdept = ncml_variable(unicode('depth_at_t_points').encode('utf-8'),'gdept')
-            self.gdepw = ncml_variable(unicode('depth_at_w_points').encode('utf-8'),'gdepw')
-            self.mbathy = ncml_variable(unicode('number_of_wet_levels').encode('utf-8'),'mbathy')
-            self.e3t = ncml_variable(unicode('vertical_scale_factors_at_t_points').encode('utf-8'),'e3t')
-            self.e3u = ncml_variable(unicode('vertical_scale_factors_at_u_points').encode('utf-8'),'e3u')
-            self.e3v = ncml_variable(unicode('vertical_scale_factors_at_v_points').encode('utf-8'),'e3v')
+        elif(self.var == "Grid"):
+            combo_vars = ['depth at T points', 
+                          'depth at W points', 
+                          'number of wet levels', 
+                          'vertical scale factor at T points', 
+                          'vertical scale factor at U points', 
+                          'vertical scale factor at V points'] #gdept,gdepw,mbathy
+            self.gdept = ncml_variable('depth_at_t_points','gdept')
+            self.gdepw = ncml_variable('depth_at_w_points','gdepw')
+            self.mbathy = ncml_variable('number_of_wet_levels','mbathy')
+            self.e3t = ncml_variable('vertical_scale_factors_at_t_points','e3t')
+            self.e3u = ncml_variable('vertical_scale_factors_at_u_points','e3u')
+            self.e3v = ncml_variable('vertical_scale_factors_at_v_points','e3v')
             self.varStackedWidget.addWidget(self._addStackWidget("gdept"))
             self.varStackedWidget.addWidget(self._addStackWidget("gdepw"))
             self.varStackedWidget.addWidget(self._addStackWidget("mbathy"))
@@ -82,7 +82,7 @@ class Ncml_tab(QtGui.QWidget):
             vars = ['nitrate','silicate'] #nitrate, silicate
         self.varStackedWidget.setCurrentIndex(0)  #we rely on the stacked tab index to be the same as the combo box 
         #combo box     
-        self.var_combo = QtGui.QComboBox()
+        self.var_combo = QtWidgets.QComboBox()
         self.var_combo.addItems(combo_vars)
         self.var_combo.setEditable(False)
         self.var_combo.setCurrentIndex(0)
@@ -90,20 +90,20 @@ class Ncml_tab(QtGui.QWidget):
         self.var_combo.currentIndexChanged.connect(lambda var_name = self.var : self.src_combo_changed(var_name))
         self.var_combo.currentIndexChanged.connect(self.setWidgetStack)
         #label
-        var_label = QtGui.QLabel(unicode('Variable').encode('utf-8'))
+        var_label = QtWidgets.QLabel('Variable')
         #set layout
-        stacked_hBox = QtGui.QHBoxLayout()
-        stacked_hBox.setMargin(5)
+        stacked_hBox = QtWidgets.QHBoxLayout()
+        stacked_hBox.setContentsMargins(5, 5, 5, 5)
         stacked_hBox.setSpacing(50) # spacing between items
         stacked_hBox.setAlignment(QtCore.Qt.AlignLeft)
         stacked_hBox.addWidget(var_label)
         stacked_hBox.addWidget(self.var_combo)
         #
-        vBoxLayout = QtGui.QVBoxLayout()        
+        vBoxLayout = QtWidgets.QVBoxLayout()        
         vBoxLayout.addLayout(stacked_hBox)
         vBoxLayout.addWidget(self.varStackedWidget)
         #
-        grp_box = QtGui.QGroupBox(None)
+        grp_box = QtWidgets.QGroupBox(None)
         grp_box.setLayout(vBoxLayout)
                         
         '''
@@ -115,24 +115,24 @@ class Ncml_tab(QtGui.QWidget):
         button bar
         '''
         # reset button
-        reset_btn = QtGui.QPushButton(unicode('Reset').encode('utf-8'))
-        reset_btn.setToolTip(unicode('Reset fields to previously saved values').encode('utf-8'))
-        add_btn = QtGui.QPushButton(unicode('Add').encode('utf-8')) 
+        reset_btn = QtWidgets.QPushButton('Reset')
+        reset_btn.setToolTip('Reset fields to previously saved values')
+        add_btn = QtWidgets.QPushButton('Add') 
         add_btn.setDefault(True)
-        add_btn.setToolTip(unicode('Add the current definition to the NcML').encode('utf-8'))
+        add_btn.setToolTip('Add the current definition to the NcML')
         #connect up with events
         reset_btn.clicked.connect(self.reset_tab)
         add_btn.clicked.connect(self.add_tab)
        
-        btn_hBox = QtGui.QHBoxLayout(None)
-        btn_hBox.setMargin(5)
+        btn_hBox = QtWidgets.QHBoxLayout(None)
+        btn_hBox.setContentsMargins(5, 5, 5, 5)
         btn_hBox.setSpacing(10)
         btn_hBox.setAlignment(QtCore.Qt.AlignCenter)
         btn_hBox.addWidget(reset_btn)
         btn_hBox.addWidget(add_btn)
         
         #build the contents         
-        vbox = QtGui.QVBoxLayout(self)
+        vbox = QtWidgets.QVBoxLayout(self)
         vbox.setSpacing(10)
         vbox.setContentsMargins(10, 10, 5, 5)
         vbox.addWidget(grp_box)
@@ -141,30 +141,30 @@ class Ncml_tab(QtGui.QWidget):
     create the stacked widget for each nemo variable
     '''    
     def _addStackWidget(self, old_name=""):
-        self.varWidget = QtGui.QWidget()
+        self.varWidget = QtWidgets.QWidget()
         #self.varWidget.setObjectName(objName)
-        varLayout = QtGui.QGridLayout()
+        varLayout = QtWidgets.QGridLayout()
         varLayout.setSpacing(20)
                
         #labels
-        src_label = QtGui.QLabel(unicode('Source directory*').encode('utf-8'))  
-        cbox_label = QtGui.QLabel(unicode('Includes subdirs').encode('utf-8'))
-        regex_label = QtGui.QLabel(unicode('Regular expression').encode('utf-8'))
-        old_name_label = QtGui.QLabel(unicode('Existing variable name*').encode('utf-8'))        
+        src_label = QtWidgets.QLabel('Source directory*')  
+        cbox_label = QtWidgets.QLabel('Includes subdirs')
+        regex_label = QtWidgets.QLabel('Regular expression')
+        old_name_label = QtWidgets.QLabel('Existing variable name*')        
         #input textboxs
-        self.varWidget.src_tedit = QtGui.QLineEdit()       # input widgets need to be attached to the stacked widget itself 
-        self.varWidget.src_tedit.setToolTip(unicode('either remote OPeNDAP server or local file absolute path').encode('utf-8'))
+        self.varWidget.src_tedit = QtWidgets.QLineEdit()       # input widgets need to be attached to the stacked widget itself 
+        self.varWidget.src_tedit.setToolTip('either remote OPeNDAP server or local file absolute path')
         self.varWidget.src_tedit.returnPressed.connect(self.src_tedit_edited)
         
         
-        self.varWidget.cbox = QtGui.QCheckBox()
+        self.varWidget.cbox = QtWidgets.QCheckBox()
         self.varWidget.cbox.setCheckable(True)
         self.varWidget.cbox.setChecked(False)
-        self.varWidget.cbox.setToolTip(unicode('includes subdirectories').encode('utf-8'))
-        self.varWidget.regex_tedit = QtGui.QLineEdit()
-        self.varWidget.regex_tedit.setToolTip(unicode('see http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/ncml/AnnotatedSchema4.html#regexp').encode('utf-8'))                
-        self.varWidget.old_name_tedit = QtGui.QLineEdit()
-        self.varWidget.old_name_tedit.setToolTip(unicode('variable name in data file').encode('utf-8'))
+        self.varWidget.cbox.setToolTip('includes subdirectories')
+        self.varWidget.regex_tedit = QtWidgets.QLineEdit()
+        self.varWidget.regex_tedit.setToolTip('see http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/ncml/AnnotatedSchema4.html#regexp')
+        self.varWidget.old_name_tedit = QtWidgets.QLineEdit()
+        self.varWidget.old_name_tedit.setToolTip('variable name in data file')
         self.varWidget.old_name_tedit.setText(old_name)
         
         varLayout.addWidget(src_label, 1, 0, 1, 1)
@@ -201,10 +201,10 @@ class Ncml_tab(QtGui.QWidget):
         #validate the input now
         if not str(src_tedit_input).startswith('http'): 
             if not os.path.isabs(src_tedit_input): #assumes local file
-                QtGui.QMessageBox.critical(self, unicode('Something is wrong').encode('utf-8'), unicode('source directory must be an absolute path!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                QtWidgets.QMessageBox.critical(self, 'Something is wrong', 'source directory must be an absolute path!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                 self.varStackedWidget.currentWidget().src_tedit.clear()
             if not os.path.exists(src_tedit_input) :
-                QtGui.QMessageBox.critical(self, unicode('Something is wrong').encode('utf-8'), unicode('source directory does not exist!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                QtWidgets.QMessageBox.critical(self, 'Something is wrong', 'source directory does not exist!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                 self.varStackedWidget.currentWidget().src_tedit.clear()   
     '''
     reset button pushed callback.  The widgets are reset to default values
@@ -213,34 +213,34 @@ class Ncml_tab(QtGui.QWidget):
     def reset_tab(self):        
         #current screen value is not saved until the add button is pressed
         #reset only reset the screen values, not the cached values        
-        if self.var_combo.currentText() == unicode("temperature").encode('utf-8'):
+        if self.var_combo.currentText() == "temperature":
 #            print 'reset button is pushed, temperature ....'
             self.resetValues(self.votemper)
-        elif self.var_combo.currentText() == unicode("salinity").encode('utf-8'):
+        elif self.var_combo.currentText() == "salinity":
             self.resetValues(self.vosaline)
-        elif self.var_combo.currentText() == unicode("ice thickness").encode('utf-8'):
+        elif self.var_combo.currentText() == "ice thickness":
             self.resetValues(self.iicethic)
-        elif self.var_combo.currentText() == unicode("leads fraction").encode('utf-8'):
+        elif self.var_combo.currentText() == "leads fraction":
             self.resetValues(self.ileadfra)
-        elif self.var_combo.currentText() == unicode("snow thickness").encode('utf-8'):
+        elif self.var_combo.currentText() == "snow thickness":
             self.resetValues(self.isnowthi)
-        elif self.var_combo.currentText() == unicode("zonal velocity").encode('utf-8'):
+        elif self.var_combo.currentText() == "zonal velocity":
             self.resetValues(self.vozocrtx) 
-        elif self.var_combo.currentText() == unicode("meridian velocity").encode('utf-8'):
+        elif self.var_combo.currentText() == "meridian velocity":
             self.resetValues(self.vomecrty)
-        elif self.var_combo.currentText() == unicode("sea surface height").encode('utf-8'):
-            self.resetValues(self.sossheig)   
-        elif self.var_combo.currentText() == unicode("depth at T points").encode('utf-8'):
+        elif self.var_combo.currentText() == "sea surface height":
+            self.resetValues(self.sossheig)  
+        elif self.var_combo.currentText() == "depth at T points":
             self.resetValues(self.gdept)   
-        elif self.var_combo.currentText() == unicode("depth at W points").encode('utf-8'):
+        elif self.var_combo.currentText() == "depth at W points":
             self.resetValues(self.gdepw)   
-        elif self.var_combo.currentText() == unicode("number of wet levels").encode('utf-8'):
+        elif self.var_combo.currentText() == "number of wet levels":
             self.resetValues(self.mbathy)   
-        elif self.var_combo.currentText() == unicode("vertical scale factor at T points").encode('utf-8'):
+        elif self.var_combo.currentText() == "vertical scale factor at T points":
             self.resetValues(self.e3t)   
-        elif self.var_combo.currentText() == unicode("vertical scale factor at U points").encode('utf-8'):
+        elif self.var_combo.currentText() == "vertical scale factor at U points":
             self.resetValues(self.e3u)   
-        elif self.var_combo.currentText() == unicode("vertical scale factor at V points").encode('utf-8'):
+        elif self.var_combo.currentText() == "vertical scale factor at V points":
             self.resetValues(self.e3v)   
             
     '''
@@ -270,7 +270,7 @@ class Ncml_tab(QtGui.QWidget):
         #first validate the src tab is not null
         if(self.varStackedWidget.currentWidget().src_tedit.text() is None or self.varStackedWidget.currentWidget().src_tedit.text() == '' or               
            self.varStackedWidget.currentWidget().old_name_tedit.text() is None or self.varStackedWidget.currentWidget().old_name_tedit.text() == ''):
-                QtGui.QMessageBox.critical(self, unicode('Something is wrong').encode('utf-8'), unicode('source directory and existing variable name cannot be blank!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                QtWidgets.QMessageBox.critical(self, 'Something is wrong', 'source directory and existing variable name cannot be blank!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
         else:
             '''        
             if not str(target).startsWith(unicode('http').encode('utf-8')):
@@ -283,10 +283,10 @@ class Ncml_tab(QtGui.QWidget):
             # be in the same directory.
 
 
-            if(self.var == unicode("Tracer").encode('utf-8')):                
-                if (self.var_combo.currentText() == unicode("temperature").encode('utf-8')):            
+            if(self.var == "Tracer"):                
+                if (self.var_combo.currentText() == "temperature"):            
                     if(self._sameValues(self.votemper)):
-                        QtGui.QMessageBox.information(self, 'For information', 'No changes have been made!', QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else:   
                         self.votemper.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.votemper.old_name = self.varStackedWidget.currentWidget().old_name_tedit.text()
@@ -297,7 +297,7 @@ class Ncml_tab(QtGui.QWidget):
                             self.votemper.regex = ''    #blank it over    
                 else: # can only be salinity
                     if(self._sameValues(self.vosaline)):
-                        QtGui.QMessageBox.information(self, 'For information', 'No changes have been made!', QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else:
                         self.vosaline.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.vosaline.old_name = self.varStackedWidget.currentWidget().old_name_tedit.text()
@@ -312,10 +312,10 @@ class Ncml_tab(QtGui.QWidget):
                 if self.vosaline.src == '':
                     self.vosaline.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                     self.varStackedWidget.widget(1).src_tedit.setText(self.varStackedWidget.currentWidget().src_tedit.text())
-            elif(self.var == unicode('Ice').encode('utf-8')): #iicethic,ileadfra,isnowthi
-                if (self.var_combo.currentText() == unicode("ice thickness").encode('utf-8')):            
+            elif(self.var == 'Ice'): #iicethic,ileadfra,isnowthi
+                if (self.var_combo.currentText() == "ice thickness"):            
                     if(self._sameValues(self.iicethic)):
-                        QtGui.QMessageBox.information(self, 'For information', 'No changes have been made!', QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else:
                         self.iicethic.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.iicethic.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
@@ -324,9 +324,9 @@ class Ncml_tab(QtGui.QWidget):
                             self.iicethic.regex = self.varStackedWidget.currentWidget().regex_tedit.text() 
                         else:
                             self.iicethic.regex = ''                       
-                elif(self.var_combo.currentText() == unicode("leads fraction").encode('utf-8')): 
+                elif(self.var_combo.currentText() == "leads fraction"): 
                     if(self._sameValues(self.ileadfra)):
-                        QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else:
                         self.ileadfra.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.ileadfra.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
@@ -337,7 +337,7 @@ class Ncml_tab(QtGui.QWidget):
                             self.ileadfra.regex = ''
                 else:
                     if(self._sameValues(self.isnowthi)): #snow thickness
-                        QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else:
                         self.isnowthi.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.isnowthi.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
@@ -355,10 +355,10 @@ class Ncml_tab(QtGui.QWidget):
                 if self.isnowthi.src == '':
                     self.isnowthi.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                     self.varStackedWidget.widget(2).src_tedit.setText(self.varStackedWidget.currentWidget().src_tedit.text())
-            elif(self.var == unicode("Dynamics").encode('utf-8')):
-                if (self.var_combo.currentText() == unicode("zonal velocity").encode('utf-8')):            
+            elif(self.var == "Dynamics"):
+                if (self.var_combo.currentText() == "zonal velocity"):            
                     if(self._sameValues(self.vozocrtx)):
-                        QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else:
                         self.vozocrtx.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.vozocrtx.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
@@ -367,9 +367,9 @@ class Ncml_tab(QtGui.QWidget):
                             self.vozocrtx.regex = self.varStackedWidget.currentWidget().regex_tedit.text()
                         else:
                             self.vozocrtx.regex = ''
-                elif(self.var_combo.currentText() == unicode('meridian velocity').encode('utf-8')): 
+                elif(self.var_combo.currentText() == 'meridian velocity'): 
                     if(self._sameValues(self.vomecrty)):
-                        QtGui.QMessageBox.information(self, 'For information', 'No changes have been made!', QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else: 
                         self.vomecrty.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.vomecrty.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
@@ -378,9 +378,9 @@ class Ncml_tab(QtGui.QWidget):
                             self.vomecrty.regex = self.varStackedWidget.currentWidget().regex_tedit.text()
                         else:
                             self.vomecrty.regex = ''
-                elif(self.var_combo.currentText() == unicode('sea surface height').encode('utf-8')):      
+                elif(self.var_combo.currentText() == 'sea surface height'):      
                     if(self._sameValues(self.sossheig)): #sea surface height
-                        QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else:
                         self.sossheig.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.sossheig.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
@@ -398,10 +398,10 @@ class Ncml_tab(QtGui.QWidget):
                 if self.sossheig.src == '':
                     self.sossheig.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                     self.varStackedWidget.widget(2).src_tedit.setText(self.varStackedWidget.currentWidget().src_tedit.text())
-            elif(self.var == unicode("Grid").encode('utf-8')):
-                if (self.var_combo.currentText() == unicode("depth at T points").encode('utf-8')):            
+            elif(self.var == "Grid"):
+                if (self.var_combo.currentText() == "depth at T points"):            
                     if(self._sameValues(self.gdept)):
-                        QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else:
                         self.gdept.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.gdept.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
@@ -410,9 +410,9 @@ class Ncml_tab(QtGui.QWidget):
                             self.gdept.regex = self.varStackedWidget.currentWidget().regex_tedit.text()
                         else:
                             self.gdept.regex = ''
-                elif(self.var_combo.currentText() == unicode('depth at W points').encode('utf-8')): 
+                elif(self.var_combo.currentText() == 'depth at W points'): 
                     if(self._sameValues(self.gdepw)):
-                        QtGui.QMessageBox.information(self, 'For information', 'No changes have been made!', QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else: 
                         self.gdepw.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.gdepw.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
@@ -421,9 +421,9 @@ class Ncml_tab(QtGui.QWidget):
                             self.gdepw.regex = self.varStackedWidget.currentWidget().regex_tedit.text()
                         else:
                             self.gdepw.regex = ''
-                elif(self.var_combo.currentText() == unicode('number of wet levels').encode('utf-8')):      
+                elif(self.var_combo.currentText() == 'number of wet levels'):      
                     if(self._sameValues(self.mbathy)): #sea surface height
-                        QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else:
                         self.mbathy.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.mbathy.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
@@ -432,9 +432,9 @@ class Ncml_tab(QtGui.QWidget):
                             self.mbathy.regex = self.varStackedWidget.currentWidget().regex_tedit.text()  
                         else:
                             self.mbathy.regex = ''
-                elif(self.var_combo.currentText() == unicode('vertical scale factor at T points').encode('utf-8')):      
+                elif(self.var_combo.currentText() == 'vertical scale factor at T points'):      
                     if(self._sameValues(self.e3t)): #sea surface height
-                        QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else:
                         self.e3t.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.e3t.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
@@ -443,9 +443,9 @@ class Ncml_tab(QtGui.QWidget):
                             self.e3t.regex = self.varStackedWidget.currentWidget().regex_tedit.text()  
                         else:
                             self.e3t.regex = ''
-                elif(self.var_combo.currentText() == unicode('vertical scale factor at U points').encode('utf-8')):      
+                elif(self.var_combo.currentText() == 'vertical scale factor at U points'):      
                     if(self._sameValues(self.e3u)): #sea surface height
-                        QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else:
                         self.e3u.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.e3u.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
@@ -454,9 +454,9 @@ class Ncml_tab(QtGui.QWidget):
                             self.e3u.regex = self.varStackedWidget.currentWidget().regex_tedit.text()  
                         else:
                             self.e3u.regex = ''
-                elif(self.var_combo.currentText() == unicode('vertical scale factor at V points').encode('utf-8')):      
+                elif(self.var_combo.currentText() == 'vertical scale factor at V points'):      
                     if(self._sameValues(self.e3v)): #sea surface height
-                        QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+                        QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
                     else:
                         self.e3v.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
                         self.e3v.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
@@ -497,10 +497,10 @@ class Ncml_tab(QtGui.QWidget):
         elif fpath.startswith('file:/'):
             temp = os.path.normpath(fpath[6:])
 #            print 'normal path : ', temp
-            target =  unicode('file:/' + str(os.path.abspath(temp)).replace("\\", "/")).encode('utf-8') 
+            target =  str('file:/' + str(os.path.abspath(temp)).replace("\\", "/")).encode('utf-8') 
         else: #should be local file but not prefixed by file:/  we still check for absolute path
 #            print 'normal path : ', os.path.normpath(fpath)
-            target = unicode('file:/' + str(os.path.abspath(fpath)).replace("\\", "/")).encode('utf-8')
+            target = str('file:/' + str(os.path.abspath(fpath)).replace("\\", "/")).encode('utf-8')
         
  #       if not str(target).endswith('/'):
  #           target = target + '/'

pynemo/gui/selection_editor.py

@@ -9,7 +9,7 @@ import numpy as np
 from matplotlib.lines import Line2D
 from matplotlib.patches import Polygon
 from matplotlib.artist import Artist
-from matplotlib.mlab import dist_point_to_segment
+from pynemo.utils.nemo_bdy_lib import dist_point_to_segment
 from matplotlib.widgets import RectangleSelector
 
 
@@ -58,12 +58,12 @@ class PolygonEditor(object):
             self.reset_line()
             self.reset_polygon()
         elif self.xy_values.shape[0] <= 2: # point or line for 1 or 2 points
-            xval, yval = zip(*self.xy_values)
+            xval, yval = list(zip(*self.xy_values))
             if self.line == None:
                 self.line = Line2D(xval, yval, marker='o', markerfacecolor='r', animated=True)
                 self.axis.add_line(self.line)
             else:
-                self.line.set_data(zip(*self.xy_values))
+                self.line.set_data(list(zip(*self.xy_values)))
             self.reset_polygon()
         else: # more than 2 points if polygon is not created then creates one and draws
             if self.polygon == None:
@@ -72,7 +72,7 @@ class PolygonEditor(object):
                 self.axis.add_patch(self.polygon)
             else:
                 self.polygon.xy = self.xy_values
-            self.line.set_data(zip(*self.xy_values))
+            self.line.set_data(list(zip(*self.xy_values)))
         self.draw_callback(None)
         self.canvas.draw()
 

pynemo/nemo_bdy_extr_tm3.py

@@ -38,12 +38,12 @@ import numpy as np
 import scipy.spatial as sp
 from calendar import monthrange, isleap
 from scipy.interpolate import interp1d
-from netcdftime import datetime, utime
+from cftime import datetime, utime
 from pynemo import nemo_bdy_ncgen as ncgen
 from pynemo import nemo_bdy_ncpop as ncpop
 
 # Local Imports
-import nemo_bdy_grid_angle as ga
+from . import nemo_bdy_grid_angle as ga
 from pynemo.reader.factory import GetFile
 from pynemo.utils.nemo_bdy_lib import rot_rep, sub2ind
 
@@ -233,12 +233,12 @@ class Extract:
         # Ann Query substitute
         source_tree = None
         try:
-            source_tree = sp.cKDTree(zip(SC.lon.ravel(order='F'),
-                                     SC.lat.ravel(order='F')), balanced_tree=False,compact_nodes=False)
+            source_tree = sp.cKDTree(list(zip(SC.lon.ravel(order='F'),
+                                     SC.lat.ravel(order='F'))), balanced_tree=False,compact_nodes=False)
         except TypeError: #added this fix to make it compatible with scipy 0.16.0
-            source_tree = sp.cKDTree(zip(SC.lon.ravel(order='F'),
-                                     SC.lat.ravel(order='F')))            
-        dst_pts = zip(dst_lon[:].ravel(order='F'), dst_lat[:].ravel(order='F'))
+            source_tree = sp.cKDTree(list(zip(SC.lon.ravel(order='F'),
+                                     SC.lat.ravel(order='F'))))            
+        dst_pts = list(zip(dst_lon[:].ravel(order='F'), dst_lat[:].ravel(order='F')))
         nn_dist, nn_id = source_tree.query(dst_pts, k=1)
 
         # Find surrounding points
@@ -280,8 +280,8 @@ class Extract:
             ind[p, :] = ind[p, dist_ind[p, :]]
 
         if self.key_vec:
-            self.gcos = self.gcos.flatten(1)[ind].reshape(ind.shape, order='F')
-            self.gsin = self.gsin.flatten(1)[ind].reshape(ind.shape, order='F')
+            self.gcos = self.gcos.flatten('F')[ind].reshape(ind.shape, order='F')
+            self.gsin = self.gsin.flatten('F')[ind].reshape(ind.shape, order='F')
 
         sc_ind = {}
         sc_ind['ind'] = ind
@@ -301,14 +301,14 @@ class Extract:
             tmp_lat[r_id] = -9999
             source_tree = None
             try:
-                source_tree = sp.cKDTree(zip(tmp_lon.ravel(order='F'),
-                                         tmp_lat.ravel(order='F')), balanced_tree=False,compact_nodes=False)
+                source_tree = sp.cKDTree(list(zip(tmp_lon.ravel(order='F'),
+                                         tmp_lat.ravel(order='F'))), balanced_tree=False,compact_nodes=False)
             except TypeError: #fix for scipy 0.16.0
-                source_tree = sp.cKDTree(zip(tmp_lon.ravel(order='F'),
-                                         tmp_lat.ravel(order='F')))
+                source_tree = sp.cKDTree(list(zip(tmp_lon.ravel(order='F'),
+                                         tmp_lat.ravel(order='F'))))
                 
-            dst_pts = zip(dst_lon[rr_id].ravel(order='F'),
-                          dst_lat[rr_id].ravel(order='F'))
+            dst_pts = list(zip(dst_lon[rr_id].ravel(order='F'),
+                          dst_lat[rr_id].ravel(order='F')))
             junk, an_id = source_tree.query(dst_pts, k=3,
                                             distance_upper_bound=fr)
             id_121[rr_id, :] = an_id
@@ -347,11 +347,11 @@ class Extract:
             z_ind = np.zeros((num_bdy * dst_len_z, 2), dtype=np.int64)
             source_tree = None
             try:
-                source_tree = sp.cKDTree(zip(sc_z.ravel(order='F')), balanced_tree=False,compact_nodes=False)
+                source_tree = sp.cKDTree(list(zip(sc_z.ravel(order='F'))), balanced_tree=False,compact_nodes=False)
             except TypeError: #fix for scipy 0.16.0
-                source_tree = sp.cKDTree(zip(sc_z.ravel(order='F')))
+                source_tree = sp.cKDTree(list(zip(sc_z.ravel(order='F'))))
 
-            junk, nn_id = source_tree.query(zip(dst_dep_rv), k=1)
+            junk, nn_id = source_tree.query(list(zip(dst_dep_rv)), k=1)
 
             # WORKAROUND: the tree query returns out of range val when
             # dst_dep point is NaN, causing ref problems later.
@@ -453,7 +453,7 @@ class Extract:
         # Get first and last date within range, init to cover entire range
         first_date = 0
         last_date = len(sc_time.time_counter) - 1 
-        rev_seq = range(len(sc_time.time_counter))
+        rev_seq = list(range(len(sc_time.time_counter)))
         rev_seq.reverse()
         for date in rev_seq:
             if src_date_seconds[date] < dst_start:
@@ -571,11 +571,11 @@ class Extract:
                 for dep in range(sc_z_len):
                     tmp_arr = [None, None]
                     # Consider squeezing
-                    tmp_arr[0] = sc_array[0][0,dep,:,:].flatten(1) #[:,:,dep]
+                    tmp_arr[0] = sc_array[0][0,dep,:,:].flatten('F') #[:,:,dep]
                     if not self.key_vec:
                         sc_bdy[vn, dep, :, :] = self._flat_ref(tmp_arr[0], ind)
                     else:
-                        tmp_arr[1] = sc_array[1][0,dep,:,:].flatten(1) #[:,:,dep]
+                        tmp_arr[1] = sc_array[1][0,dep,:,:].flatten('F') #[:,:,dep]
                         # Include in the collapse the rotation from the
                         # grid to real zonal direction, ie ij -> e
                         sc_bdy[vn, dep, :] = (tmp_arr[0][ind[:]] * self.gcos -
@@ -669,11 +669,11 @@ class Extract:
                 # Apply 1-2-1 filter along bdy pts using NN ind self.id_121
                 if self.first:
                     tmp_valid = np.invert(np.isnan(
-                                            dst_bdy.flatten(1)[self.id_121]))
+                                            dst_bdy.flatten('F')[self.id_121]))
                     # Finished first run operations
                     self.first = False
 
-                dst_bdy = (np.nansum(dst_bdy.flatten(1)[self.id_121] * 
+                dst_bdy = (np.nansum(dst_bdy.flatten('F')[self.id_121] * 
                            self.tmp_filt, 2) / np.sum(self.tmp_filt *
                            tmp_valid, 2))
                 # Set land pts to zero
@@ -688,7 +688,7 @@ class Extract:
                 # If we have depth dimension
                 if not self.isslab:
                     # If all else fails fill down using deepest pt
-                    dst_bdy = dst_bdy.flatten(1)
+                    dst_bdy = dst_bdy.flatten('F')
                     dst_bdy += ((dst_bdy == 0) *
                                 dst_bdy[data_ind].repeat(sc_z_len))
                     # Weighted averaged on new vertical grid
@@ -732,7 +732,7 @@ class Extract:
         alpha -- input array
         beta -- index array 
         """
-        return alpha.flatten(1)[beta.flatten(1)].reshape(
+        return alpha.flatten('F')[beta.flatten('F')].reshape(
                                                    beta.shape, order='F')
 
     # Convert numeric date from source to dest
@@ -752,7 +752,7 @@ class Extract:
         """
         vals = {'gregorian': 365. + isleap(year), 'noleap': 
                 365., '360_day': 360.}
-        if source not in vals.keys():
+        if source not in list(vals.keys()):
             raise ValueError('Unknown source calendar type: %s' %source)
         # Get month length
         if dest == '360_day':

pynemo/nemo_bdy_gen_c.py

@@ -13,7 +13,7 @@ import numpy as np
 import logging
 
 #Local Imports
-from utils.nemo_bdy_lib import sub2ind
+from .utils.nemo_bdy_lib import sub2ind
 
 class Boundary:
     # Bearings for overlays
@@ -102,8 +102,8 @@ class Boundary:
         bdy_i = np.transpose(bdy_i, (1, 2, 0))
         bdy_i = np.reshape(bdy_i, 
                  (bdy_i.shape[0],bdy_i.shape[1]*bdy_i.shape[2]))
-        bdy_r = bdy_r.flatten(1)
-
+        bdy_r = bdy_r.flatten('F')
+        
         ##   Remove duplicate and open sea points  ##
         
         bdy_i, bdy_r = self._remove_duplicate_points(bdy_i, bdy_r)
@@ -210,11 +210,11 @@ class Boundary:
         t -- input 2D array
         """ 
         sh = np.shape(t)
-	if (len(sh)> 2) or (sh[0] ==0) or (sh[1] == 0):
-	    print 'Warning: Shape of expected 2D array:', sh
+        if (len(sh)> 2) or (sh[0] ==0) or (sh[1] == 0):
+           print('Warning: Shape of expected 2D array:', sh)
         tlist = t.tolist()
         sortt = []
-        indx = zip(*sorted([(val, i) for i,val in enumerate(tlist)]))[1]
+        indx = list(zip(*sorted([(val, i) for i,val in enumerate(tlist)])))[1]
         indx = np.array(indx)
         for i in indx:
             sortt.append(tlist[i])
@@ -224,7 +224,7 @@ class Boundary:
                 indx[i] = -1
         # all the rows are identical, set the first as the unique row
         if sortt[0] == sortt[-1]:
-	    indx[0] = 0
+            indx[0] = 0
 			        
         return indx[indx != -1]
 

pynemo/nemo_bdy_grid_angle.py

@@ -13,7 +13,7 @@
 # cd_type: define the nature of pt2d grid points
 
 import numpy as np
-from reader.factory import GetFile
+from .reader.factory import GetFile
 import logging
 #     pylint: disable=E1101
 

pynemo/nemo_bdy_ncpop.py

@@ -23,13 +23,13 @@ def write_data_to_file(filename, variable_name, data):
 
     if variable_name in three_dim_variables:
         if len(count) == 3:
-            count += (1L, )
+            count += (1, )
         ncid.variables[variable_name][:, :, :, :] = np.reshape(data, count)[:, :, :, :]
     elif variable_name in two_dim_variables:
         if len(count) == 2:
-            count += (1L, )
+            count += (1, )
         elif len(count) == 1:
-            count += (1L, 1L, )
+            count += (1, 1, )
         ncid.variables[variable_name][:, :, :] = np.reshape(data, count)[:, :, :]
     elif variable_name == 'time_counter':
         ncid.variables[variable_name][:] = data[:]

pynemo/nemo_bdy_setup.py

@@ -204,11 +204,11 @@ def _get_val(vars_dictionary, bool_vars_dictionary, line):
 
     if name_prefix == 'ln':
         if value.find('true') is not -1:
-            if vars_dictionary.has_key(name) != True:
+            if (name in vars_dictionary) != True:
                 vars_dictionary[name] = True
             bool_vars_dictionary[name] = True
         elif value.find('false') is not -1:
-            if vars_dictionary.has_key(name) != True:
+            if (name in vars_dictionary) != True:
                 vars_dictionary[name] = False
             bool_vars_dictionary[name] = False
         else:

pynemo/nemo_bdy_src_time.py

@@ -29,7 +29,7 @@ class SourceTime:
 
         dir_list.sort()
             
-        return filter(None, dir_list)
+        return [_f for _f in dir_list if _f]
     
     # Returns list of dicts of date/time info
     # I assume there is only one date per file

pynemo/nemo_bdy_zgrv2.py

@@ -14,12 +14,12 @@ Initialise with bdy t, u and v grid attributes (Grid.bdy_i)
 and settings dictionary 
 """
 
-from reader.factory import GetFile
+from .reader.factory import GetFile
 import numpy as np
 import logging
 
-from utils.nemo_bdy_lib import sub2ind
-from utils.e3_to_depth import e3_to_depth
+from .utils.nemo_bdy_lib import sub2ind
+from .utils.e3_to_depth import e3_to_depth
 #     pylint: disable=E1101
 # Query name
 class Depth:
@@ -52,6 +52,7 @@ class Depth:
 
         # Check inputs
         # FIX ME? Errors for wrong obj arg len. probably better to work around
+        print(settings)
         if settings['sco']:
             # hc = ... FIX ME??
             # Depth of water column at t-point
@@ -68,7 +69,7 @@ class Depth:
         v_ind = sub2ind(mbathy.shape, bdy_v[:,0], bdy_v[:,1])
         v_ind2 = sub2ind(mbathy.shape, bdy_v[:,0], bdy_v[:,1] + 1) 
    
-    	[tmp_zt, tmp_zw] = e3_to_depth(np.squeeze(nc['e3t'][:,:,:,:]), np.squeeze(nc['e3w'][:,:,:,:]), nz)
+        [tmp_zt, tmp_zw] = e3_to_depth(np.squeeze(nc['e3t'][:,:,:,:]), np.squeeze(nc['e3w'][:,:,:,:]), nz)
         # This is very slow
         self.logger.debug( 'starting nc reads loop' )
         for k in range(nz):
@@ -95,12 +96,12 @@ class Depth:
 
             # Set u and v grid point depths
             zshapes = {}
-            for p in self.zpoints.keys():
+            for p in list(self.zpoints.keys()):
                 zshapes[p] = self.zpoints[p].shape
             wshapes = []
             wshapes.append(wrk1.shape)
             wshapes.append(wrk2.shape)
-            wrk1, wrk2 = wrk1.flatten(1), wrk2.flatten(1)
+            wrk1, wrk2 = wrk1.flatten('F'), wrk2.flatten('F')
 
             self.zpoints['t'][k,:]  = wrk1[t_ind]
             self.zpoints['wt'][k,:] = wrk2[t_ind]
@@ -111,7 +112,7 @@ class Depth:
             self.zpoints['v'][k,:]  = 0.5 * (wrk1[v_ind] + wrk1[v_ind2])
             self.zpoints['wv'][k,:] = 0.5 * (wrk2[v_ind] + wrk2[v_ind2])
 
-            for p in self.zpoints.keys():
+            for p in list(self.zpoints.keys()):
                 self.zpoints[p] = self.zpoints[p].reshape(zshapes[p])
             
         self.logger.debug( 'Done loop, zpoints: %s ', self.zpoints['t'].shape)

pynemo/nemo_bogadons_gauntlet.py

-#
-# The loop from nemo_bdy_extr_tm3
-#
-# 
-#
-
-from calendar import monthrange
-from datetime import datetime
-
-from netCDF4 import Dataset, netcdftime
-
-
-class Enter:
-
-    def __init__(self, settings, sc_time, dir_list, dst_cal_type, year, month):
-
-        var_nam = ['votemper', 'vosaline']
-        sc_fields = source_fields
-
-        #self.setup = settings # dict
-        # define src/dst cals
-        sf, ed = cal_trans(sc_time, dst_cal_type, year, month)
-        # W
-        DstCal = utime('seconds since %d-1-1' %year, dst_cal_type)
-        dst_start = DstCal.date2num(datetime(year, month, 1))
-        dst_end = DstCal.date2num(datetime(year, month, ed, 23, 59, 59))
-
-        self.S_cal = utime(sc_time[0]['units'], sc_time[0]['calendar'])
-        self.D_cal = utime('seconds since %d-1-1' %settings['year_000'], 
-                           settings['dst_calendar'])
-
-        for date in sc_time:
-            date['date_num'] = DstCal.date2num(date['date']) * sf
-
-        # Get first and last date within range
-        first_date, last_date = None, None
-        rev_seq = range(len_sc_time)
-        rev_seq.reverse()
-        # Multiple values.. might be broken.. 
-        for date in rev_seq:
-            if sc_time[date]['date_num'] < dst_start:
-                first_date = date #number..
-                break
-        for date in range(len_sc_time):
-            if sc_time[date]['date_num'] > dst_end:
-                last_date = date
-                break
-
-        for date in range(first_date, last_date + 1):
-            nc = Dataset(sc_time[date], 'r')
-            if key_vec:
-                pass
-                #nc_2 = Dataset
-                # FIX ME
-
-            # We shouldnt have to worry about counters
-            sc_bdy = np.zeros(nvar, sc_z_len, source_ind['ind'].shape[0],
-                                  source_ind['ind'].shape[1])
-            ind_vec = {}
-            # distinctive variable name since it gets lost in the huge loop
-            for shoggoth in range(nvar):
-                varid = nc.variables[var_nam[shoggoth]]
-                i, ii = source_ind['imin'], source_ind['imax']
-                j, jj = source_ind['jmin'], source_ind['jmax']
-                sc_arrays = []
-                col_sc_arrays = []
-                if key_vec:
-                    varid_2 = nc_2.variables[var_nam[shoggoth + 1]]
-                if not isslab and not key_vec:
-                    # NOTE: 0 v 1 indexing may problemate
-                    sc_arrays.append(varid[i-1:ii, j-1:jj, :sc_z_len, :1])
-                elif key_vec:
-                    sc_arrays.append(varid[i-2:ii, j-1:jj, :sc_z_len, :1])
-                    sc_arrays.append(varid_2[i-1:ii, j-2:jj, :sc_z_len, :1])
-                    for x in 0,1:
-                        # tidy up src array - replace missing val
-                        for y in 'mv', 'fv':
-                            if not np.isnan(sc_fields[y][x]):
-                                ind_vec[y] = sc_arrays[x] == sc_fields[y][x]
-                                sc_arrays[x][ind_vec[y]] = 0
-                            else:
-                                sc_arrays[x][np.isnan(scarr)] = 0
-                        # Adjust for scaling or offsets
-                        if not np.isnan(sc_fields['sf'][x]):
-                            sc_arrays[x] *= sc_fields['sf'][x]
-                        if not np.isnan(sc_fields['os'][x]):
-                            sc_arrays[x] += sc_fields['os'][x]
-                
-                        # Colocate velocity points on T grid prior to rotation
-                        axis = [1, None]
-                        col = 0.5 * (sc_arrays[x][:-axis[0],:-axis[1],:] + 
-                                     sc_arrays[x][axis[0]:,axis[1]:,:])
-                        col[col == 0] = np.NaN
-                        col_sc_arrays.append(col)
-                        axis.reverse()
-                
-                # This is a slab
-                else:
-                    sc_arrays.append(varid[i-1:ii, j-1:jj, :1])
-                    #query var names
-                    if msk and first and shoggoth==0:
-                        pass
-                        # Open another magic file and do stuff
-                        nc3 = Dataset(source_mask, 'r')
-                        varid_3 = nc3.variables['tmaskutil']
-                        msk_array = varid_3[i-1:ii, j-1:jj, :1]
-                    if msk: #must be true for msk array ??...
-                        sc_arrays[0][msk_array == 0] = np.NaN
-
-        
-            # Finished reading Source data
-
-            #for depth_val in range(sc_z_len):
-            #    tmp_arrays = []
-            #    if not key_vec:
-            #        tmp_arrays.append(sc_arrays[0][:,:depth_val]
-
-
-    def _fv_mv_to_zero(self, scarr, indvec, sc_fields, pos):
-        
-        for x in 'mv', 'fv':
-            if not np.isnan(sc_fields[x][pos]):
-                ind_vec[x] = scarr == sc_fields[x][pos]
-                scarr[ind_vec[x]] = 0
-            else:
-                scarr[np.isnan(scarr)] = 0
-        return scarr, indvec
-
-    # Convert numeric date from source to dest
-    def convert_date(self, date):
-        
-        val = self.S_cal.num2date(date)
-        return self.D_cal.date2num(val)
-
-    def cal_trans(self, source, dest, year, month):
-        vals = {'gregorian': [monthrange(year, month)[1], 31], 'noleap': 
-                [365., 31],'360_day': [360., 30]}
-        if source not in vals.keys():
-            raise ValueError('Unknown calendar type: %s' %source)
-        
-        sf = val[source][0] / val[dest][0]
-        
-        return sf, vals[dest][1]
-
-
-
-
-

pynemo/nemo_coord_gen_pop.py

@@ -28,7 +28,7 @@ class Coord:
         self.logger = logging.getLogger(__name__)
         self.logger.debug( fname )
         if not fname:
-            print 'need some error handling in here or is this redundant?' # TODO
+            print('need some error handling in here or is this redundant?') # TODO
          
         # Enter define mode
         self.ncid = Dataset(fname, 'w', clobber=True, format='NETCDF4')

pynemo/profile.py

@@ -34,7 +34,7 @@ $Last commit on:$
 import time
 import logging
 import numpy as np
-from PyQt4.QtGui import QMessageBox
+from PyQt5.QtWidgets import QMessageBox
 
 #Local imports
 from pynemo import pynemo_settings_editor
@@ -245,13 +245,13 @@ def process_bdy(setup_filepath=0, mask_gui=False):
                       'values in input bdy file')
         return
     
-    yrs = range(yr_000, yr_end+1)
+    yrs = list(range(yr_000, yr_end+1))
     
     if yr_end - yr_000 >= 1:
-        if range(mn_000, mn_end+1) < 12:
+        if list(range(mn_000, mn_end+1)) < 12:
             logger.info('Warning: All months will be extracted as the number '+
                         'of years is greater than 1')
-        mns = range(1,13)
+        mns = list(range(1,13))
     else:
         mn_000 = settings['month_000']
         mn_end = settings['month_end']
@@ -259,7 +259,7 @@ def process_bdy(setup_filepath=0, mask_gui=False):
             logging.error('Please check the nn_month_000 and nn_month_end '+
                           'values in input bdy file')
             return
-        mns = range(mn_000, mn_end+1)
+        mns = list(range(mn_000, mn_end+1))
     
     # Enter the loop for each year and month extraction
     
@@ -312,7 +312,7 @@ def process_bdy(setup_filepath=0, mask_gui=False):
     
     # Initialise the mapping indices for each grid 
     
-    for key, val in emap.items():
+    for key, val in list(emap.items()):
         
         extract_obj[key] = extract.Extract(Setup.settings, 
                                            SourceCoord, DstCoord,
@@ -325,7 +325,7 @@ def process_bdy(setup_filepath=0, mask_gui=False):
         
     for year in yrs:
         for month in mns:
-            for key, val in emap.items():
+            for key, val in list(emap.items()):
                 
                 # Extract the data for a given month and year
                 
@@ -380,7 +380,7 @@ def write_tidal_data(setup_var, dst_coord_var, grid, tide_cons, cons):
         const_name = setup_var.settings['clname'][tide_con]
         const_name = const_name.replace("'", "").upper()
 
-        for key,val in tmap.items():
+        for key,val in list(tmap.items()):
             
             fout_tide = setup_var.settings['dst_dir']+             \
                         setup_var.settings['fn']+                  \