tcltk macosfix and new binaries

Author: reslp

README.md

@@ -9,14 +9,21 @@ Description
 
 iqtreeGUI is a graphical front-end for [IQ-TREE](http://www.iqtree.org). The goal is to implement all features of IQ-TREE 1.6.*. It is under active development and therefore several features are still missing (eg. a GUI for likelihood mapping, topology tests). iqtreeGUI is written in Python3 and executables are available for Windows, Linux and MacOS.
 
-**Note:** In the MacOS version on MacOS 10.14 of iqtreeGUI at start some buttons and menus will not display text correctly. This is due to a bug in Tcl/Tk framework. Till the bug in Tcl/Tk gets removed, simply resize the window slightly and everythingh should look fine.
 
 ![Screenshot of iqtreeGUI](screenshot.png)
 *Figure: iqtreeGUi running on MacOS High Sierra*
 
 A work in progress
 ==============
-One of the great things about IQ-TREE is that is has lots of possibilities to combine different parameters and analyses. While iqtreeGUI aims to provide a graphical way to access all these features, it is almost impossible to test every possible combination of parameters IQ-TREE allows. At the moment iqtreeGUI is still under active developement. Therefore there may still be a large number of bugs. I am greatful for every bug report I receive. Reporting bugs will help to improve iqtreeGUI.
+One of the great things about IQ-TREE is that is has lots of possibilities to combine different parameters and analyses. While iqtreeGUI aims to provide a graphical way to access all these features, it is almost impossible to test every possible combination of parameters IQ-TREE allows. At the moment iqtreeGUI is still under active development. Therefore there may still be a large number of bugs. I am greatful for every bug report I receive. Reporting bugs will help to improve iqtreeGUI.
+
+Changelog:
+========
+
+Nov.13 2019 v(13112019): New version with many bug fixes:
+	- The pyinstaller executable for MacOS should now work properly again.
+	- The code is now better organized which removed occasional strange behavior in older versions
+	- A problem with tkinter on newer versions of MacOS caused different rendering problems. This should now be fixed as well (tested on MacOS 10.14)
 
 Features
 ===========
@@ -39,7 +46,7 @@ Currently implemented features:
 
 Obtaining and configuring iqtreeGUI
 ================
-Executables are available for Linux, MacOS and Windows. The Windows and Linux versions were built using a combination of Docker and pyinstaller. 
+Executables are available for Linux, MacOS and Windows. The Windows and Linux versions were built using a combination of Docker and [pyinstaller] (https://pyinstaller.readthedocs.io). 
 
 For iqtreeGUI to work you will also need to download and install [IQ-TREE](http://www.iqtree.org). Once you have started iqtreeGUI you will have to set the correct path to the IQ-TREE executable. Click on iqtreeGUI -> GUI settings and select the iqtree executable.
 

build_all.sh

@@ -1,10 +1,12 @@
-#!/bin/bash
-# This script builds the Linux and Windows Versions of iqtreeGUI using Docker
+#!/bin/zsh
+# This script builds Linux, Windows and MacOS Versions of iqtreeGUI using cdrx/pyinstallers Docker containers.
 
 
 #Windows build: requires Docker
-docker run -v "$(pwd):/src/" cdrx/pyinstaller-windows:python3
+docker run -t --rm -v "$(pwd):/src/" cdrx/pyinstaller-windows:python3 "apt-get update -y && apt-get install -y python3-tk && pyinstaller --clean -y --dist ./dist/windows --workpath /tmp *.spec"
 
 #Linux Build: requires Docker with custom command
-docker run -v "$(pwd):/src/" cdrx/pyinstaller-linux:python3 "apt-get update -y && apt-get install -y python3-tk && pyinstaller --clean -y --dist ./dist/linux --workpath /tmp *.spec"
+docker run --rm  -v "$(pwd):/src/" cdrx/pyinstaller-linux:python3 "apt-get update -y && apt-get install -y python3-tk && pyinstaller --clean -y --dist ./dist/linux --workpath /tmp *.spec"
 
+pyinstaller iqtreegui_mac.spec
+cp -r tcltk_lib/lib dist/iqtreeGUI.app/Contents/

config.txt

@@ -0,0 +1,4 @@
+[Settings]
+iqtree = iqtree111
+version = 12112019
+

dist/iqtrGUI_v13112019.zip

@@ -0,0 +1,52 @@
+#! /usr/bin/env python
+# add credits...
+import sys
+from tkinter import *
+from tkinter.ttk import *
+
+class ScrollableFrame(Frame):
+	"""
+	Consider me a regular frame with a vertical scrollbar 
+	on the right, after adding/removing widgets to/from me 
+	call my method update() to refresh the scrollable area. 
+	Don't pack() me, nor place() nor grid(). 
+	I work best when I am alone in the parent frame.
+	"""
+	def __init__(self, parent, *args, **kw):
+
+		# scrollbar on right in parent 
+		yscrollbar = Scrollbar(parent)#, width=15)
+		yscrollbar.pack(side=RIGHT, fill=Y, expand=False)
+
+		# canvas on left in parent
+		#plain_can_style = Style()
+		#plain_can_style.configure("plain_canvas.TCanvas", foreground="green", background="red")
+		self.canvas = Canvas(parent, yscrollcommand=yscrollbar.set, bd=0, highlightthickness=0, relief='ridge', background="#ECECEC")
+		#self.canvas.config(bg="gray85")
+		self.canvas.pack(side=LEFT, fill=BOTH, expand=True)
+
+		def fill_canvas(event):
+			"enlarge the windows item to the canvas width"
+			canvas_width = event.width
+			self.canvas.itemconfig(self.windows_item, width = canvas_width)
+
+		self.canvas.bind('<Configure>', fill_canvas)
+
+		yscrollbar.config(command=self.canvas.yview)    
+		
+		#plain_style = Style()
+		#plain_style.configure("plain_st.TFrame", foreground="black", background="#F0F0F0")
+		
+		#self.configure(style="plain_style")
+		
+		# create the scrollable frame and assign it to the windows item of the canvas
+		Frame.__init__(self, parent, *args, **kw)
+		self.windows_item = self.canvas.create_window(-1,-1, window=self, anchor=NW)
+
+	def update(self):
+		"""
+		Update changes to the canvas before the program gets
+		back the mainloop, then update the scrollregion
+		"""
+		self.update_idletasks()
+		self.canvas.config(scrollregion=self.canvas.bbox(self.windows_item))

iqtgui_modules/ScrollableFrame.py

@@ -0,0 +1,15 @@
+from . import model_select
+from . import partition
+from . import ScrollableFrame
+from . import iqtree_out
+from . import settings
+from . import bootstrap_settings
+from . import data_types_settings
+from . import iqtree_settings
+from . import treesearch_settings
+from . import modelselect_settings
+#from iqtgui_modules.special import consensustree
+#from iqtgui_modules.special import robinsonfoulds
+#from iqtgui_modules.special import randomtree
+from iqtgui_modules import special
+from . import alignment

iqtgui_modules/__init__.py

@@ -0,0 +1,64 @@
+#! /usr/bin/env python
+# tkinter Frame for importing multiple alignments
+# written by Philipp Resl
+from iqtgui_modules import alignment_view
+from tkinter import *
+from tkinter.ttk import *
+
+class Alignment(Frame):
+	alignment_id = ""
+	alignment_path = ""
+	window = ""
+	def show_alignment(self):
+		self.window = Toplevel()
+		self.al_window = alignment_view.AlignmentView(self.window, alignment=self.alignment_id, filename=self.alignment_path)
+		self.master.wait_window(self.al_window)
+		
+	
+	def remove_alignment(self):
+		#print("Length of alignment list before: %s" % len(self.al_list))
+		for no in range(0,len(self.al_list)):
+			self.al_list[no].grid_forget()
+		
+		del self.al_list[self.alignment_no-1]
+		#print("Length of alignment list after: %s" % len(self.al_list))
+		for no in range(0,len(self.al_list)):
+			#self.al_list[no].grid_forget()
+			#print("Alignment %s is now %s" % (str(self.al_list[no].alignment_no), str(no+1)))
+			self.al_list[no].alignment_no = no + 1
+			self.al_list[no].alignment_label.configure(text="Alignment "+str(no+1)+": ")
+			self.al_list[no].alignment_label.configure(font=("TkTextFont", 12, "bold"))
+			self.al_list[no].grid(sticky=W)
+			self.al_list[no].update()
+		#kill the alignment window if present, need to find a better way of doing this
+		if isinstance(self.window,str) == False and Toplevel.winfo_exists(self.window)==1: 
+			self.window.destroy()
+		self.info_lab.config(text="Alignments: %s Alignment(s) loaded" % str(len(self.al_list)))
+		
+		self.destroy()
+		
+	def create_widgets(self):
+		self.alignment_label = Label(self, text=self.alignment_id)
+		self.alignment_label.grid(row=0,column=3)
+		self.alignment_label.configure(font=("TkTextFont", 12, "bold"))
+		
+		self.alignment_path_label = Label(self, text=self.alignment_path)
+		self.alignment_path_label.grid(row=0,column=4, sticky=E)
+
+		
+		self.view_button = Button(self, text="View", command=self.show_alignment)
+		self.view_button.grid(row=0,column=1)
+		
+		self.remove_button = Button(self, text="Remove", command=self.remove_alignment)
+		self.remove_button.grid(row=0,column=2)
+		print("Alignment created: %s" % self.alignment_no)
+			
+	def __init__(self, master, align_id, path, number, alignment_list, info_label):
+		Frame.__init__(self, master)
+		self.info_lab = info_label
+		self.al_list = alignment_list
+		self.master = master
+		self.alignment_id = align_id
+		self.alignment_path = path
+		self.alignment_no = number
+		self.create_widgets()

iqtgui_modules/__pycache__/ScrollableFrame.cpython-36.pyc

@@ -0,0 +1,29 @@
+#! /usr/bin/env python
+# tkinter window for settings
+# written by Philipp Resl
+import os
+from tkinter import *
+from tkinter.scrolledtext import ScrolledText
+from tkinter.ttk import *
+
+
+#import ttk
+#import tkFileDialog, tkMessageBox
+
+class AlignmentView():
+	def __init__(self, master, alignment, filename):
+		self.master = master
+		self.master.title(alignment)
+		self.master.grid_columnconfigure(0,weight=1)
+		self.master.grid_rowconfigure(0,weight=1)
+		#self.master.geometry("500x400")		
+		self.alignment_text = ScrolledText(self.master)
+		self.alignment_text.grid(row=0,column=0,sticky=N+S+W+E)
+		file = open(filename, "U")
+		sequence = ""
+		for line in file.readlines():
+			sequence += line
+		file.close()
+		self.alignment_text.insert(END, sequence)
+		
+		

iqtgui_modules/__pycache__/__init__.cpython-36.pyc

@@ -0,0 +1,109 @@
+#! /usr/bin/env python
+# tkinter window for settings
+# written by Philipp Resl
+import os
+from tkinter import *
+from tkinter.ttk import *
+import tkinter.filedialog, tkinter.messagebox
+
+class AdvancedBSWindow():
+	wbtvar = 0
+	wbtlvar = 0
+	def __init__(self, master, data):
+		self.master = master
+		self.master.title("Advanced Bootstrap settings")
+		self.settings_frame = Frame(self.master)
+		#create an empty margin so that the widgets wont stick to the very edges
+		self.settings_frame.rowconfigure(0, minsize=30)
+		self.settings_frame.rowconfigure(20, minsize=30)
+		self.settings_frame.columnconfigure(0, minsize=30)
+		self.settings_frame.columnconfigure(20, minsize=30)
+		
+		self.description = Label(self.settings_frame,text="Here you can configure advanced options of the\nbootstraping functionality of iqtree", justify=LEFT)
+		self.description.configure(font="Helvetica 14 bold")
+		self.description.grid(row=1,column=1, sticky=W, columnspan=5)
+
+		self.settings_frame.rowconfigure(2, minsize=20)
+		
+		self.bcor_label= Label(self.settings_frame,text="Minimum correlation coefficient for UFBoot: ")
+		self.bcor_label.grid(row=3, column=1, sticky=W)
+		self.bcor_entry = Entry(self.settings_frame)
+		self.bcor_entry.insert(END,data.bcor)
+		self.bcor_entry.grid(row=3, column=2, sticky=W)
+		
+		self.beps_label= Label(self.settings_frame,text="Epsilon to break tie in RELL: ")
+		self.beps_label.grid(row=4, column=1, sticky=W)
+		self.beps_entry = Entry(self.settings_frame)
+		self.beps_entry.insert(END,data.beps)
+		self.beps_entry.grid(row=4, column=2, sticky=W)
+		
+		self.nm_label= Label(self.settings_frame,text="Maximum number of iterations to stop: ")
+		self.nm_label.grid(row=5, column=1, sticky=W)
+		self.nm_entry = Entry(self.settings_frame)
+		self.nm_entry.insert(END,data.nm)
+		self.nm_entry.grid(row=5, column=2, sticky=W)
+		
+		self.nstep_label= Label(self.settings_frame,text="Iteration interval to check for\nUFBoot convergence: ")
+		self.nstep_label.grid(row=6, column=1, sticky=W)
+		self.nstep_entry = Entry(self.settings_frame)
+		self.nstep_entry.insert(END,data.nstep)
+		self.nstep_entry.grid(row=6, column=2, sticky=W)
+		
+		self.settings_frame.rowconfigure(8, minsize=20)
+		
+		self.bbnivar = IntVar()
+		self.bbnivar.set(data.bnni)
+		
+		def bbni():
+			self.bbnivar.set(1)
+		
+		
+		self.bbni = Checkbutton(self.settings_frame, text="reduce model violation (-bnni)", command=bbni, variable=self.bbnivar)
+		self.bbni.grid(row=9, column=1, sticky=W)
+
+		
+		self.wbtvar = IntVar()
+		self.wbtlvar = IntVar()
+		
+		self.wbtvar.set(data.wbt)
+		self.wbtlvar.set(data.wbtl)
+		
+		def wbt():
+			if self.wbtlvar.get() == 1:
+				self.wbtlvar.set(0)
+			print() #change!!
+			
+		self.wbt = Checkbutton(self.settings_frame, text="Write bootstrap trees to .ufboot file. (-wbt)", command=wbt, variable=self.wbtvar)
+		self.wbt.grid(row=10, column=1, sticky=W)
+		
+		
+		def wbtl():
+			if self.wbtvar.get() == 1:
+				self.wbtvar.set(0)
+			print() #change!!
+		
+		
+		self.wbtl = Checkbutton(self.settings_frame, text="Write bootstrap trees to .ufboot file\nincluding branch lengths. (-wbtl)", command=wbtl, variable=self.wbtlvar)
+		self.wbtl.grid(row=11, column=1, sticky=W)
+		
+		def apply():
+			try:
+				data.bnni = self.bbnivar.get()
+				data.beps = float(self.beps_entry.get())
+				data.bcor = float(self.bcor_entry.get())
+				data.nm = int(self.nm_entry.get())
+				data.nstep = int(self.nstep_entry.get())
+				data.wbt = self.wbtvar.get()
+				data.wbtl = self.wbtlvar.get()
+				self.master.destroy()
+				
+			except ValueError:
+				tkinter.messagebox.showinfo("Error", "Some of the entered values are incorrect")
+		
+		self.apply_button = Button(self.settings_frame, text="Apply & Close", command=apply)
+		self.apply_button.grid(row=11, column=12, sticky=W)
+		self.cancel_button = Button(self.settings_frame, text="Cancel", command=self.master.destroy)
+		self.cancel_button.grid(row=11, column=11, sticky=W)
+		self.settings_frame.grid()
+		
+