Merge pull request #8 from phenomecentre/pyqt6

Pyqt6

.gitignore

@@ -0,0 +1,8 @@
+*.pdf
+*.html
+.ipynb_checkpoints/
+.DS_Store
+Example Data/
+.idea/
+.idea/other.xml
+**/__pycache__/

README.md

@@ -1,6 +1,6 @@
 # ISTOCSY
 
-* Version 2.0.0
+* Version 3.0.0
 
 ISTOCSY is a python library for interactively exploring the correlations between features in metabolomics datasets
 
@@ -19,19 +19,20 @@ Exports:
  - Interactive html plots (plotly)
 
 ## Installation
+
+Download and unzip ISTOCSY code from Git:
+https://github.com/phenomecentre/ISTOCSY/archive/refs/heads/pyqt6.zip
+
+### Windows
+
+
+In a PowerShell terminal window, cd to the unzipped directory and run the batch file
+called install_and_run_istocsy.bat
+
+### Mac
+
+
+In a terminal window, cd to the unzipped directory and run the batch file
+called install_and_run_istocsy.sh
 
-Download or clone ISTOCSY repo, then from inside Python run:
 
-    import sys
-	sys.path.append('path to saved ISTOCSY code')
-	import runISTOCSY
-	runISTOCSY.main()
-
-## Documentation
-
-See 'Example input data' files for examples of required format.
-Documentation in progress - watch this space!
-
-## Testing
-
-Unit testing code in progress - watch this space!

install_and_run_istocsy.bat

@@ -0,0 +1,22 @@
+@echo off
+REM First download and unzip ISTOCSY code from Git:
+
+REM https://github.com/phenomecentre/ISTOCSY/archive/refs/heads/pyqt6.zip
+REM then in a PowerShell terminal window, cd to the unzipped directory and run this batch file.
+
+echo "=== Making Python3 environment ==="
+python3 "-m" "venv" "istocsy-env"
+call istocsy-env\Scripts\activate.bat
+
+echo "=== Installing ISTOCSY Python libraries ==="
+pip "install" "-r" "requirements.txt"
+echo "=== Launching app ==="
+python "pyIstocsy\runISTOCSY.py"
+
+REM using Conda:
+REM conda create -n istocsy python=3.7.1 ipykernel # this creates istocsy environment
+REM conda activate istocsy # this activates the environment
+REM navigate to the folder which contains requirements.txt file and use cd to change directories, then run line 4
+REM pip install -r requirements.txt
+REM Once everything’s downloaded then navigate to the folder which contains runISTOCSY.py file and use cd to change directories, then run line 6
+REM python runISTOCSY.py # Runs ISTOCSY

install_and_run_istocsy.sh

@@ -0,0 +1,14 @@
+#!/bin/sh -e
+
+echo "=== Making Python3 environment ==="
+python3 -m venv istocsy-env
+source istocsy-env/bin/activate
+echo "=== Upgrading pip ==="
+python3 -m pip install --upgrade pip
+echo "=== Installing ISTOCSY Python libraries ==="
+pip install -r requirements.txt
+
+echo "=== Launching app ==="
+python pyIstocsy/runISTOCSY.py
+
+

pyIstocsy/_annotationsDialog.py

@@ -6,9 +6,10 @@
 @author: cs401
 """
 
-import sip
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QLabel, QDialog, QFileDialog
+from PyQt6 import sip
+from PyQt6.QtCore import Qt
+from PyQt6.QtWidgets import QInputDialog, QWidget, QApplication, QPushButton, QGridLayout
+from PyQt6.QtWidgets import QLabel, QDialog, QFileDialog
 import pyqtgraph as pg
 pg.setConfigOption('background', 'w')
 pg.setConfigOption('foreground', 'k')
@@ -46,29 +47,29 @@ def init_ui(self):
 			self.setWindowTitle('Load/match Annotations')
 			self.setGeometry(10, 10, 500, 300)
 
-		self.hbox = QtGui.QGridLayout()
+		self.hbox = QGridLayout()
 		self.setLayout(self.hbox)
 
 		# Display annotations file
 		self.annotationFileText = QLabel('Annotations file location: ' + str(self.Attributes['annotationFilePath']))
 		self.hbox.addWidget(self.annotationFileText, 1, 0)
 
 		# Update annotations file
-		self.annotationFileButton = QtGui.QPushButton("Load new annotations file")
-		self.annotationFileButton.setFocusPolicy(QtCore.Qt.NoFocus)
+		self.annotationFileButton = QPushButton("Load new annotations file")
+		self.annotationFileButton.setFocusPolicy(Qt.FocusPolicy.NoFocus)
 		self.annotationFileButton.clicked.connect(self.on_annotationFileButton_clicked)
 		self.hbox.addWidget(self.annotationFileButton, 1, 1)
 
 		# Match annotations file to dataset
-		self.closeButton = QtGui.QPushButton("Match to ISTOCSY dataset (if available) and close")
+		self.closeButton = QPushButton("Match to ISTOCSY dataset (if available) and close")
 		self.closeButton.clicked.connect(self.on_closeButton_clicked)
 		self.hbox.addWidget(self.closeButton, 2, 1)
 
 
 	def getResults(self):
 		""" Return results """
 
-		if self.exec_() == QDialog.Accepted:
+		if self.exec() == QDialog.DialogCode.Accepted:
 
 			return self.Attributes
 

pyIstocsy/_batchDialog.py

@@ -7,9 +7,10 @@
 """
 
 
-import sip
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QLabel, QDialog, QFileDialog
+from PyQt6 import sip
+from PyQt6.QtCore import Qt
+from PyQt6.QtWidgets import QInputDialog, QWidget, QApplication, QPushButton, QGridLayout
+from PyQt6.QtWidgets import QLabel, QDialog, QFileDialog
 import pyqtgraph as pg
 pg.setConfigOption('background', 'w')
 pg.setConfigOption('foreground', 'k')
@@ -47,29 +48,29 @@ def init_ui(self):
 			self.setWindowTitle('Load/run Batch file')
 			self.setGeometry(10, 10, 500, 300)
 
-		self.hbox = QtGui.QGridLayout()
+		self.hbox = QGridLayout()
 		self.setLayout(self.hbox)
 
 		# Display batch file
 		self.batchFileText = QLabel('Batch file location: ' + str(self.Attributes['batchFilePath']))
 		self.hbox.addWidget(self.batchFileText, 1, 0)
 
 		# Update annotations file
-		self.batchFileButton = QtGui.QPushButton("Load new batch file")
-		self.batchFileButton.setFocusPolicy(QtCore.Qt.NoFocus)
+		self.batchFileButton = QPushButton("Load new batch file")
+		self.batchFileButton.setFocusPolicy(Qt.FocusPolicy.NoFocus)
 		self.batchFileButton.clicked.connect(self.on_batchFileButton_clicked)
 		self.hbox.addWidget(self.batchFileButton, 1, 1)
 
 		# Match annotations file to dataset
-		self.closeButton = QtGui.QPushButton("Run ISTOCSY from batch file (if dataset loaded) and close")
+		self.closeButton = QPushButton("Run ISTOCSY from batch file (if dataset loaded) and close")
 		self.closeButton.clicked.connect(self.on_closeButton_clicked)
 		self.hbox.addWidget(self.closeButton, 2, 1)
 
 
 	def getResults(self):
 		""" Return results """
 
-		if self.exec_() == QDialog.Accepted:
+		if self.exec() == QDialog.DialogCode.Accepted:
 
 			return self.Attributes