Commit e778a669 authored by Andreas Tille's avatar Andreas Tille
Browse files

First attempt to port to PyQt5 (not finished yet)

parent c456bd2a

debian/changelog

+7 −0
Original line number Diff line number Diff line 
microbegps (1.0.0-5) UNRELEASED; urgency=medium



  * Port to PyQt5

    Closes: #935345



 -- Andreas Tille <tille@debian.org>  Fri, 06 Sep 2019 10:26:15 +0200



microbegps (1.0.0-4) unstable; urgency=medium



  * Use 2to3 to port to Python3

debian/control

+2 −2
Original line number Diff line number Diff line
@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 12), 
               dh-python,

               python3,

               python3-setuptools,

               python3-pyqt4

               python3-pyqt5

Standards-Version: 4.4.0

Vcs-Browser: https://salsa.debian.org/med-team/microbegps

Vcs-Git: https://salsa.debian.org/med-team/microbegps.git
@@ -18,7 +18,7 @@ Architecture: all 
Depends: ${misc:Depends},

         ${python3:Depends},

         python3-matplotlib-venn,

         python3-pyqt4

         python3-pyqt5

Description: explorative taxonomic profiling tool for metagenomic data

 MicrobeGPS is a bioinformatics tool for the analysis of metagenomic

 sequencing data. The goal is to profile the composition of metagenomic

debian/patches/PyQt5.patch

0 → 100644
+242 −0
Original line number Diff line number Diff line 
Description: Port to PyQt5

Bug-Debian: https://bugs.debian.org/935345

Author: Andreas Tille <tille@debian.org>

Last-Update: Fri, 06 Sep 2019 10:26:15 +0200



--- a/setup.py

+++ b/setup.py

@@ -1,9 +1,9 @@

 """ MicrobeGPS setup.py script. Allows direct installation of the tool or creating Python eggs. """

 

 try:

-	import PyQt4

+	import PyQt5

 except ImportError:

-	print('PyQt4 is not installed on your system! Please install PyQt4 first. You can download PyQt4 from http://www.riverbankcomputing.co.uk/software/pyqt/download or use your package manager to install the library.')

+	print('PyQt5 is not installed on your system!')

 	import sys

 	sys.exit()

 

--- a/microbegps/gui.py

+++ b/microbegps/gui.py

@@ -9,7 +9,7 @@ import pkg_resources

 import threading

 import pickle

 

-from PyQt4 import QtGui, QtCore

+from PyQt5 import QtGui, QtCore, QtWidgets

 

 import matplotlib.pyplot as plt

 from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas

@@ -79,7 +79,7 @@ First, a subset of reads is selected tha

 ]

 

 

-class Pipeline(QtGui.QWidget):

+class Pipeline(QtWidgets.QWidget):

 	def __init__(self,mainWindow):

 		super(Pipeline, self).__init__()

 		self.mainWindow = mainWindow

@@ -126,13 +126,13 @@ class Pipeline(QtGui.QWidget):

 		sublayout = QtGui.QHBoxLayout()

 		sublayout.addWidget(self.fileNameEdit,stretch=4)

 		sublayout.addWidget(selectButton,stretch=1)

-		subwidget = QtGui.QWidget()

+		subwidget = QtWidgets.QWidget()

 		subwidget.setLayout(sublayout)

 		layout = QtGui.QGridLayout()

 		layout.setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)

 		layout.addWidget(QtGui.QLabel('Input Directory'),0,0)

 		layout.addWidget(subwidget,0,1)

-		loadDataWidget = QtGui.QWidget()

+		loadDataWidget = QtWidgets.QWidget()

 		loadDataWidget.setLayout(layout)

 		self.settingsBox.addWidget(loadDataWidget)

 

@@ -167,7 +167,7 @@ class Pipeline(QtGui.QWidget):

 		layout.addRow(QtGui.QLabel('Max. Read Matches'),self.maxMatchesBox)

 		layout.addRow(QtGui.QLabel('Max. Read Mapping Error'),self.maxMappingError)

 		layout.addRow(QtGui.QLabel('Mapping Error Quantile'),self.mappingErrorQuantile)

-		rawFilterWidget = QtGui.QWidget()

+		rawFilterWidget = QtWidgets.QWidget()

 		rawFilterWidget.setLayout(layout)

 		self.settingsBox.addWidget(rawFilterWidget)

 		

@@ -191,12 +191,12 @@ class Pipeline(QtGui.QWidget):

 		sublayout1 = QtGui.QHBoxLayout()

 		sublayout1.addWidget(self.mappingFileEdit,stretch=4)

 		sublayout1.addWidget(selectButton1,stretch=1)

-		subwidget1 = QtGui.QWidget()

+		subwidget1 = QtWidgets.QWidget()

 		subwidget1.setLayout(sublayout1)

 		sublayout2 = QtGui.QHBoxLayout()

 		sublayout2.addWidget(self.NCBICatalogPath,stretch=4)

 		sublayout2.addWidget(selectButton2,stretch=1)

-		subwidget2 = QtGui.QWidget()

+		subwidget2 = QtWidgets.QWidget()

 		subwidget2.setLayout(sublayout2)

 		layout = QtGui.QGridLayout()

 		layout.setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)

@@ -205,7 +205,7 @@ class Pipeline(QtGui.QWidget):

 		layout.addWidget(subwidget1,1,1)

 		layout.addWidget(self.useNCBIFiles,2,0)

 		layout.addWidget(subwidget2,2,1)

-		referenceTableWidget = QtGui.QWidget()

+		referenceTableWidget = QtWidgets.QWidget()

 		referenceTableWidget.setLayout(layout)

 		self.settingsBox.addWidget(referenceTableWidget)

 		

@@ -228,7 +228,7 @@ class Pipeline(QtGui.QWidget):

 		layout.addRow(QtGui.QLabel('Min. Number Unique Reads'),self.minAbsoluteUnique)

 		layout.addRow(QtGui.QLabel('Max. Homogeneity'),self.maxHomogeneity)

 

-		qualFilterWidget = QtGui.QWidget()

+		qualFilterWidget = QtWidgets.QWidget()

 		qualFilterWidget.setLayout(layout)

 		self.settingsBox.addWidget(qualFilterWidget)

 		

@@ -266,7 +266,7 @@ class Pipeline(QtGui.QWidget):

 		layout.addRow(QtGui.QLabel('Coverage Similarity'),self.coverageSimilarity)

 		layout.addRow(QtGui.QLabel('Fraction Shared USR'),self.sharedFractionUSR)

 		layout.addRow(QtGui.QLabel('Fraction Shared Reads'),self.sharedFractionAll)

-		extractUSRWidget = QtGui.QWidget()

+		extractUSRWidget = QtWidgets.QWidget()

 		extractUSRWidget.setLayout(layout)

 		self.settingsBox.addWidget(extractUSRWidget)

 		

@@ -274,7 +274,7 @@ class Pipeline(QtGui.QWidget):

 		self.closeOnFinish = QtGui.QCheckBox('Close this window after visualizing results')

 		layout = QtGui.QVBoxLayout()

 		layout.addWidget(self.closeOnFinish)

-		visualizeWidget = QtGui.QWidget()

+		visualizeWidget = QtWidgets.QWidget()

 		visualizeWidget.setLayout(layout)

 		self.settingsBox.addWidget(visualizeWidget)		

 		

@@ -294,7 +294,7 @@ class Pipeline(QtGui.QWidget):

 		consoleLayout = QtGui.QVBoxLayout()

 		consoleLayout.addWidget(self.progress)

 		consoleLayout.addWidget(self.consoleText)

-		consoleWidget = QtGui.QWidget()

+		consoleWidget = QtWidgets.QWidget()

 		consoleWidget.setLayout(consoleLayout)

 

 		self.runStepBtn = QtGui.QPushButton("Run Step")

@@ -304,7 +304,7 @@ class Pipeline(QtGui.QWidget):

 		buttonLayout = QtGui.QHBoxLayout()

 		buttonLayout.addWidget(self.runStepBtn)

 		buttonLayout.addWidget(self.runPipelineBtn)

-		buttonBar = QtGui.QWidget()

+		buttonBar = QtWidgets.QWidget()

 		buttonBar.setLayout(buttonLayout)

 		

 		gridLayout = QtGui.QGridLayout()

@@ -871,7 +871,7 @@ class Pipeline(QtGui.QWidget):

 		self.sharedFractionAll.setValue(settings.get('fraction_shared_all',0.8))

 

 

-class GPSAnalyzer(QtGui.QMainWindow):

+class GPSAnalyzer(QtWidgets.QMainWindow):

 	def __init__(self):

 		super(GPSAnalyzer, self).__init__()

 		self.initUI()

@@ -901,19 +901,19 @@ class GPSAnalyzer(QtGui.QMainWindow):

 		self.graphicDock = QtGui.QDockWidget('Graphic',self)

 		self.graphicDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)

 		self.graphicDock.setMinimumSize(450,300)

-		self.graphicDock.setTitleBarWidget(QtGui.QWidget())

+		self.graphicDock.setTitleBarWidget(QtWidgets.QWidget())

 		

 		self.toolsDock = QtGui.QDockWidget('Tools',self)

 		self.toolsDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)

 		self.toolsDock.setMinimumHeight(150)

 		self.toolsDock.setMaximumHeight(250)

-		self.toolsDock.setTitleBarWidget(QtGui.QWidget())

+		self.toolsDock.setTitleBarWidget(QtWidgets.QWidget())

 

 		self.consoleDock = QtGui.QDockWidget('Console',self)

 		self.consoleDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)

 		self.consoleDock.setMinimumHeight(150)

 		self.consoleDock.setMaximumHeight(450)

-		self.consoleDock.setTitleBarWidget(QtGui.QWidget())

+		self.consoleDock.setTitleBarWidget(QtWidgets.QWidget())

 		

 		self.addDockWidget(QtCore.Qt.RightDockWidgetArea,self.graphicDock)

 		self.addDockWidget(QtCore.Qt.RightDockWidgetArea,self.toolsDock)

@@ -966,7 +966,7 @@ class GPSAnalyzer(QtGui.QMainWindow):

 		toolsGrid.addWidget(self.exportFigureQuality,1,1)

 		toolsGrid.addWidget(showPipelineBtn,2,0)

 

-		toolsWidget = QtGui.QWidget()

+		toolsWidget = QtWidgets.QWidget()

 		toolsWidget.setLayout(toolsGrid)

 		

 		self.toolsTab = QtGui.QTabWidget()

@@ -1734,7 +1734,7 @@ the LICENSE file shipped with this softw

 		self.treeView.scrollToItem(sel)

 		

 def main():

-	app = QtGui.QApplication(sys.argv)

+	app = QtWidgets.QApplication(sys.argv)

 	GPSAnalyzer() 

 	app.exec_()	

 

--- a/microbegps/modules/composition_analysis.py

+++ b/microbegps/modules/composition_analysis.py

@@ -1,4 +1,4 @@

-from PyQt4 import QtGui

+from PyQt5 import QtGui, QtWidgets

 import matplotlib.pyplot as plt

 

 class GPSModule:

@@ -56,7 +56,7 @@ class GPSModule:

 		tabGrid.addWidget(self.getFromTree, 3,1)

 		tabGrid.addWidget(self.taxSelectedText,4,0)

 		tabGrid.addWidget(self.showComposition,4,1)

-		tabWidget = QtGui.QWidget()

+		tabWidget = QtWidgets.QWidget()

 		tabWidget.setLayout(tabGrid)

 		tabWidget.helpText = self.helpText

 		

--- a/microbegps/modules/export_table.py

+++ b/microbegps/modules/export_table.py

@@ -1,4 +1,4 @@

-from PyQt4 import QtGui

+from PyQt5 import QtGui, QtWidgets

 from os import linesep

 from microbegps import taxonomy

 

@@ -57,7 +57,7 @@ class GPSModule:

 		tabGrid.addWidget(self.genomeValidity,4,1)

 		tabGrid.addWidget(self.homogeneity,5,0)

 		tabGrid.addWidget(self.mappingError,5,1)

-		tabWidget = QtGui.QWidget()

+		tabWidget = QtWidgets.QWidget()

 		tabWidget.setLayout(tabGrid)

 		tabWidget.helpText = self.helpText

 		

--- a/microbegps/modules/search_tab.py

+++ b/microbegps/modules/search_tab.py

@@ -1,5 +1,5 @@

 # -*- coding: utf-8 -*-

-from PyQt4 import QtGui

+from PyQt5 import QtGui, QtWidgets

 

 class GPSModule:

 	""" This GPS Module implements a search tab, that allows the user to

@@ -24,7 +24,7 @@ class GPSModule:

 		searchGrid.addWidget(self.searchBtn, 0,1)

 		searchGrid.addWidget(self.searchRes, 1,0,1,2)

 		

-		searchWidget = QtGui.QWidget()

+		searchWidget = QtWidgets.QWidget()

 		searchWidget.setLayout(searchGrid)

 		

 		GPS.toolsTab.addTab(searchWidget,"Search")

@@ -54,4 +54,4 @@ class GPSModule:

 		self.GPS.treeView.setCurrentItem(sel)

 		self.GPS.treeView.expand(self.GPS.treeView.currentIndex())

 		self.GPS.treeView.scrollToItem(self.GPS.treeView.currentItem())

-		self.GPS.tree_item_clicked_handler(self.GPS.treeView.currentItem(),0)

\ No newline at end of file

+		self.GPS.tree_item_clicked_handler(self.GPS.treeView.currentItem(),0)

debian/patches/series

+1 −0
Original line number Diff line number Diff line 
2to3.patch

PyQt5.patch