From 0efcaf0c2a7b87c664a6f78a9a25b53a4260aecd Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 05 Jan 2017 16:22:24 +0000
Subject: [PATCH] Removed the python scripts to separate project.

---
 /dev/null |  105 ----------------------------------------------------
 build.sh  |    6 +-
 2 files changed, 3 insertions(+), 108 deletions(-)

diff --git a/build.sh b/build.sh
index a587e47..241f00c 100755
--- a/build.sh
+++ b/build.sh
@@ -8,6 +8,6 @@
 make clean
 make
 sudo make install
-cd python
-sudo python3 setup.py install
-cd ..
+echo "Warning!"
+echo "Python scripts for running the trisurf-ng have been moved to separate package"
+
diff --git a/python/MANIFEST.in b/python/MANIFEST.in
deleted file mode 100644
index 73b9b6d..0000000
--- a/python/MANIFEST.in
+++ /dev/null
@@ -1 +0,0 @@
-recursive-include trisurf *.py
diff --git a/python/myTestConfig.py b/python/myTestConfig.py
deleted file mode 100755
index aa307f4..0000000
--- a/python/myTestConfig.py
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/python3
-from trisurf import tsmgr
-from trisurf import trisurf
-from trisurf import statistics
-
-
-print("Running trisurf version "+ tsmgr.getTrisurfVersion())
-
-#Simple example how to start simulation from a previos snapshot
-run1=trisurf.Runner(snapshot='snapshot.vtu')
-run1.setMaindir(("N","k","V","Np","Nm"),("nshell","xk0","constvolswitch","npoly","nmono"))
-run1.setSubdir("run0")
-
-
-#Example how to start simulation from tape. Extra argument in runArgs will be passed to trisurf executable (meaning that simulation will always start from the beginning (bipyramid) ignoring the fact that some states may have been calculated already)
-run2=trisurf.Runner(tape='tape', runArgs=['--force-from-tape'])
-run2.setMaindir(("N","k","V","Np","Nm"),("nshell","xk0","constvolswitch","npoly","nmono"))
-run2.setSubdir("run1")
-
-#Example of programatical setup of 4 runs
-pRun=[]
-for i in range(0,4): #0,1,2,3
-	tpRun=trisurf.Runner(tape='tape')
-	tpRun.setMaindir(("N","k","V","Np","Nm"),("nshell","xk0","constvolswitch","npoly","nmono"))
-	tpRun.setSubdir("programatical_"+str(i))
-	pRun.append(tpRun)
-
-
-#obligatory final configuration step: combine all runs
-Runs=[run1,run2]+pRun
-#start manager with configured runs
-tsmgr.start(Runs)
-#statistics.combine([run1,run2])
diff --git a/python/networkedExample.py b/python/networkedExample.py
deleted file mode 100755
index b444447..0000000
--- a/python/networkedExample.py
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/python3
-from trisurf import trisurf
-from trisurf import tsmgr
-
-
-
-
-#Ok... Configure your keys:
-#ssh-keygen
-#and copy them to all the remote hosts
-#ssh-copy-id -i ./ssh/id_rsa.pub username@remotehost
-
-run2=trisurf.Runner(tape='tape')
-run2.setMaindir(("N","k","V","Np","Nm"),("nshell","xk0","constvolswitch","npoly","nmono"))
-run2.setSubdir("run1")
-
-run3=trisurf.Runner(tape='tape')
-run3.setMaindir(("N","k","V","Np","Nm"),("nshell","xk0","constvolswitch","npoly","nmono"))
-run3.setSubdir("run2")
-
-
-
-Runs=[run2, run3]
-
-hosts=({'name':'Hestia','address':'kabinet.penic.eu', 'runs':Runs, 'username':'samo'},
-	{'name':'altea','address':'127.0.0.1', 'runs':Runs, 'username':'samo'})
-
-tsmgr.start(hosts)
diff --git a/python/parse_vtu.py b/python/parse_vtu.py
deleted file mode 100755
index 3f864c3..0000000
--- a/python/parse_vtu.py
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/python3
-import xml.etree.ElementTree as ET
-import base64
-import zlib
-
-tree = ET.parse('../src/timestep_000000.vtu')
-root = tree.getroot()
-trisurf=root.find('trisurf')
-version=root.find('trisurfversion')
-print(version.text);
-print(trisurf.items())
-
-#xml=zlib.decompress(base64.b64decode(trisurf.text))
-#xml=trisurf.text
-#print(xml)
-
-#tree2=ET.ElementTree(ET.fromstring(str(xml))
-#tree2=ET.ElementTree(ET.fromstring("<root>"+str(xml)[0:-1]+"</root>"))
diff --git a/python/pythonvtk.py b/python/pythonvtk.py
deleted file mode 100644
index b50ff7c..0000000
--- a/python/pythonvtk.py
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# by Panos Mavrogiorgos, email: pmav99 <> gmail
- 
-from vtk import *
- 
-# The source file
-#file_name = "uGridEx.vtk"
-file_name="timestep.vtu"
-# Read the source file.
-#reader = vtkUnstructuredGridReader()
-reader=vtkXMLUnstructuredGridReader()
-reader.SetFileName(file_name)
-reader.Update() # Needed because of GetScalarRange
-output = reader.GetOutput()
-scalar_range = output.GetScalarRange()
- 
-# Create the mapper that corresponds the objects of the vtk file
-# into graphics elements
-mapper = vtkDataSetMapper()
-mapper.SetInput(output)
-mapper.SetScalarRange(scalar_range)
- 
-# Create the Actor
-actor = vtkActor()
-actor.SetMapper(mapper)
- 
-# Create the Renderer
-renderer = vtkRenderer()
-renderer.AddActor(actor)
-renderer.SetBackground(0, 0, 0) # Set background to white
- 
-# Create the RendererWindow
-renderer_window = vtkRenderWindow()
-renderer_window.AddRenderer(renderer)
- 
-# Create the RendererWindowInteractor and display the vtk_file
-interactor = vtkRenderWindowInteractor()
-interactor.SetRenderWindow(renderer_window)
-interactor.Initialize()
-interactor.Start()
diff --git a/python/setup.py b/python/setup.py
deleted file mode 100644
index fb98073..0000000
--- a/python/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-from distutils.core import setup
-
-setup(name="trisurf", version="0.1a",
-description="Python trisurf-ng managing scripts for organized multiple runs of simultations",
-author="Samo Penic",
-author_email="samo.penic@gmail.com",
-url="",
-packages=["trisurf"]
-)
diff --git a/python/tape b/python/tape
deleted file mode 100644
index 35b52e6..0000000
--- a/python/tape
+++ /dev/null
@@ -1,80 +0,0 @@
-####### Vesicle definitions ###########
-# nshell is a number of divisions of dipyramid
-nshell=10
-# dmax is the max. bond length (in units l_min)
-dmax=1.7
-# dmin_interspecies in the min. dist. between different vertex species (in units l_min)
-dmin_interspecies=1.2
-# bending rigidity of the membrane (in units kT)
-xk0=10.0
-# max step size (in units l_min)
-stepsize=0.15
-
-# Pressure calculations
-# (pswitch=1: calc. p*dV energy contribution)
-pswitch = 0
-# pressure difference: p_inside - p_outside (in units kT/l_min^3):
-pressure=0.0
-
-#Constant volume constraint (0 disable constant volume, 1 enable wiht additional vertex move, 2 enable with epsvol)
-constvolswitch=0
-constvolprecision=1e-14
-
-#Constant area constraint (0 disable constant area, 2 enable constant area with epsarea)
-constareaswitch=0
-
-####### Polymer (brush) definitions ###########
-# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=60
-# nmono is a number of monomers in each polymer
-nmono=10
-# Spring constant between monomers of the polymer
-k_spring=800
-
-####### Filament (inside the vesicle) definitions ###########
-# nfil is a number of filaments inside the vesicle
-nfil=0
-# nfono is a number of monomers in each filament
-nfono=300
-# Persistence lenght of the filaments (in units l_min)
-xi=0
-
-####### Nucleus (inside the vesicle) ###########
-# Radius of an impenetrable hard sphere inside the vesicle
-R_nucleus=0
-
-#######  Cell definitions ############
-nxmax=60
-nymax=60
-nzmax=60
-
-
-####### Program Control ############
-#how many MC sweeps between subsequent records of states to disk
-#200000
-mcsweeps=200
-#how many initial mcsweeps*inititer MC sweeps before recording to disk?
-#2
-inititer=10
-#how many records do you want on the disk iteration are there in a run?
-#10000
-iterations=100
-
-
-###### Spherical harmonics ###########
-# If 0 then spherical harmonics are not calculated at all.
-spherical_harmonics_coefficients=0
-
-#shut up if we are using cluster!!!
-quiet=false
-
-#what type of multiprocessing? (*none, smp, cluster, distributed, cuda, auto)
-#currently only none makes sense.
-multiprocessing=none
-#how many cores are allowed to process in SMP?
-smp_cores=2
-#how many nodes in cluster?
-cluster_nodes=50
-#max number of processes in distributed (voluntary) environment
-distributed_processes=50
-#cuda options???
diff --git a/python/trisurf/Remote.py b/python/trisurf/Remote.py
deleted file mode 100644
index 8da08be..0000000
--- a/python/trisurf/Remote.py
+++ /dev/null
@@ -1,73 +0,0 @@
-import paramiko
-
-
-
-class Connection:
-	def __init__(self, hostname, port=22, username=None, password=None):
-		self.hostname=hostname
-		self.port=port
-		if(username!=None):
-			self.username=username
-		else:
-			self.username=''
-		if(password!=None):
-			self.password=password
-		else:
-			self.password=''
-		self.ssh=paramiko.SSHClient()
-		self.ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
-		self.connected=False
-		return
-	
-	def connect(self, Timeout=5):
-		if(not self.connected):
-			try:
-				print("Trying to connect to: "+self.username+"@"+self.hostname+":"+str(self.port)+".")
-				self.ssh.connect(self.hostname, username=self.username, password=self.password, port=self.port, timeout=Timeout)
-				self.connected=True
-			except:
-				print("Error establishing connection with "+self.username+"@"+self.hostname+":"+str(self.port)+".")
-				exit(1)
-		else:
-			print("Already connected!")
-		return
-
-	def disconnect(self):
-		if(self.connected):
-			try:
-				self.ssh.close()
-			except:
-				print("Cannot disconect. Unknown error.")
-		else:
-			print("Cannot disconect. Already disconnected.")
-		self.connected=False
-
-	def execute(self,command):
-		if(self.connected):
-			try:
-				stdin,stdout,stderr=self.ssh.exec_command(command)
-				output=stdout.readlines()
-				errors=stderr.readlines()
-			#	print(errors)
-				return(output)
-			except:
-				print("Cannot execute remote commands")
-		else:
-			print("Cannot execute remote commands. Connect first.")
-
-	def send_file(self, local, remote):
-		sftp=self.ssh.open_sftp()
-		sftp.put(local,remote)
-		sftp.close()
-
-	def receive_file(self,remote,local):
-		sftp=self.ssh.open_sftp()
-		sftp.get(remote,local)
-		sftp.close()
-
-	def mkdir_remote(self,directory):
-		sftp=self.ssh.open_sftp()
-		sftp.mkdir(directory)
-		sftp.close()
-
-	
diff --git a/python/trisurf/VTKRendering.py b/python/trisurf/VTKRendering.py
deleted file mode 100644
index 76ff9e7..0000000
--- a/python/trisurf/VTKRendering.py
+++ /dev/null
@@ -1,155 +0,0 @@
-import os,sys
-from . import trisurf
-if sys.version_info<(3,0):
-	from vtk import *
-
-
-
-class MultiRender:
-	def __init__(self,args,host):
-		target_runs=getRargetRunIdxList(args)
-		if target_runs==None:
-			target_runs=list(range(1,len(host['runs'])+1))
-		nruns=len(target_runs)
-		#prepare rendering window
-		self.renderer_window = vtkRenderWindow()
-		self.renderer_window.AddRenderer(self.renderer)
-		self.renderer_window.SetSize(1200,600)
-		interactor = vtkRenderWindowInteractor()
-		interactor.SetRenderWindow(self.renderer_window)
-		interactor.Initialize()
-		interactor.AddObserver("TimerEvent", self.RenderUpdate)
-		timerIDR = interactor.CreateRepeatingTimer(1000)
-		self.filename=[]
-		self.renderer=[]
-		i=0
-		for run in target_runs:	
-			#for each target run calculate renderer location
-			r.vtkRenderer()
-			r.SetBackground(0,0,0)
-			p=1.0/float(nruns)
-			x1=i*p
-			x2=(i+1)*p
-			r.SetViewport(x1,0.0,x2,1.0)
-			self.renderer.Append(r)
-			self.renderer_window.AddRenderer(r)
-			i=i+1
-		#call Renderer object with Run, renderer
-		#start endless loop of interactor
-		interactor.Start()
-
-	def lastVTU(self,run):
-		Dir=trisurf.Directory(maindir=run.maindir,simdir=run.subdir)
-		filename=os.path.join("./",Dir.fullpath(),run.getLastVTU())
-		return filename
-
-	def lastActorForRun(self,run):
-		filename=self.lastVTU(run)
-		reader=vtkXMLUnstructuredGridReader()
-		reader.SetFileName(self.filename)
-		reader.Update() # Needed because of GetScalarRange
-		output = reader.GetOutput()
-		scalar_range = output.GetScalarRange()
-		mapper = vtkDataSetMapper()
-		mapper.SetInput(output)
-		mapper.SetScalarRange(scalar_range)
-
-		# Create the Actor
-		actor = vtkActor()
-		actor.SetMapper(mapper)
-		return actor
-
-
-
-	def RenderUpdate(self, obj, event):
-		i=0
-		for run in runs:
-			if(self.lastVTU(run)!=self.filename[i]):
-				#print("updejt")
-				self.renderer.RemoveActor(self.actor)
-				self.renderer.RemoveActor(self.textactor)
-				self.actor=self.lastActor()
-				self.textactor=self.textActor()
-				self.renderer.AddActor(self.actor)
-				self.renderer.AddActor(self.textactor)
-				self.renderer_window.Render()
-			#self.render.RemoveActor(self.actor)
-			i=i+1	
-		return
-
-
-class Renderer:
-	def __init__(self,args,host):
-		self.host=host
-		self.args=args
-		self.renderer = vtkRenderer()
-		self.actor=self.lastActor()
-		self.textactor=self.textActor()
-		self.renderer.AddActor(self.actor)
-		self.renderer.AddActor(self.textactor)
-		self.renderer.SetBackground(0, 0, 0) # Set background to white
-		# Create the RendererWindow
-		self.renderer_window = vtkRenderWindow()
-		self.renderer_window.AddRenderer(self.renderer)
-		self.renderer_window.SetSize(1200,600)
-	
-		self.renderer.SetViewport(0.0,0.0,0.5,1.0)
-		rend=vtk.vtkRenderer()
-		rend.AddActor(self.actor)
-		rend.SetViewport(0.5,0.0,1.0,1.0)
-		self.renderer_window.AddRenderer(rend)	
-# Set up a check for aborting rendering.
-		# Create the RendererWindowInteractor and display the vtk_file
-		interactor = vtkRenderWindowInteractor()
-		interactor.SetRenderWindow(self.renderer_window)
-		interactor.Initialize()
- 		interactor.AddObserver("TimerEvent", self.RenderUpdate)
-		timerIDR = interactor.CreateRepeatingTimer(1000)
-		interactor.Start()
-
-		return
-
-	def lastVTU(self):
-		Dir=trisurf.Directory(maindir=self.host['runs'][0].maindir,simdir=self.host['runs'][0].subdir)
-		filename=os.path.join("./",Dir.fullpath(),self.host['runs'][0].getLastVTU())
-		return filename
-
-	def textActor(self):
-		textactor=vtkTextActor()
-		textactor.SetInput(self.filename)
-		tp=textactor.GetTextProperty()
-		tp.SetColor(1,1,1)
-		tp.SetFontSize(11)
-		textactor.SetDisplayPosition(20,30)
-		return textactor
-
-	def lastActor(self):
-		self.filename=self.lastVTU()
-		reader=vtkXMLUnstructuredGridReader()
-		reader.SetFileName(self.filename)
-		reader.Update() # Needed because of GetScalarRange
-		output = reader.GetOutput()
-		scalar_range = output.GetScalarRange()
-		mapper = vtkDataSetMapper()
-		mapper.SetInput(output)
-		mapper.SetScalarRange(scalar_range)
-
-		# Create the Actor
-		actor = vtkActor()
-		actor.SetMapper(mapper)
-		return actor
-
-
-	def RenderUpdate(self, obj, event):
-		if(self.lastVTU()!=self.filename):
-			#print("updejt")
-			self.renderer.RemoveActor(self.actor)
-			self.renderer.RemoveActor(self.textactor)
-			self.actor=self.lastActor()
-			self.textactor=self.textActor()
-			self.renderer.AddActor(self.actor)
-			self.renderer.AddActor(self.textactor)
-			self.renderer_window.Render()
-		#self.render.RemoveActor(self.actor)
-		
-		return
diff --git a/python/trisurf/WebTrisurf.py b/python/trisurf/WebTrisurf.py
deleted file mode 100644
index 4b36ec9..0000000
--- a/python/trisurf/WebTrisurf.py
+++ /dev/null
@@ -1,59 +0,0 @@
-import subprocess
-import sys, os
-if sys.version_info>=(3,0):
-	from urllib.parse import urlparse
-else:
-	from urlparse import urlparse
-import http.server
-import socketserver
-
-#Web server
-class TsWEB(http.server.BaseHTTPRequestHandler):
-	def do_GET(self):
-		parsed_path=urlparse(self.path)
-		"""	message_parts = [
-                'CLIENT VALUES:',
-                'client_address=%s (%s)' % (self.client_address, self.address_string()),
-                'command=%s' % self.command,
-                'path=%s' % self.path,
-                'real path=%s' % parsed_path.path,
-                'query=%s' % parsed_path.query,
-                'request_version=%s' % self.request_version,
-                '',
-                'SERVER VALUES:',
-                'server_version=%s' % self.server_version,
-                'sys_version=%s' % self.sys_version,
-                'protocol_version=%s' % self.protocol_version,
-                '',
-                'HEADERS RECEIVED:',
-                ]
-		for name, value in sorted(self.headers.items()):
-			message_parts.append('%s=%s' % (name, value.rstrip()))
-		message_parts.append('')
-		message = '<br>'.join(message_parts) """
-		self.send_response(200)
-		self.end_headers()
-		self.wfile.write(b"<h1>Trisurf-ng manager web interface</h1><hr>")
-		oldstdout=sys.stdout
-		process=subprocess.Popen (['/usr/bin/python3', sys.argv[0], '-s', '--html'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-		stdout, stderr= process.communicate()
-		output=stdout.decode('ascii')
-		output=output.replace('\n','<BR>')
-		output=bytearray(output,'ascii')
-		self.wfile.write(output)
-
-
-
-
-class WebServer():
-	def __init__(self, port=8000):
-		http_server = socketserver.TCPServer(('', port), TsWEB)
-		try:
-			http_server.serve_forever()
-		except KeyboardInterrupt:
-			print('^C received, shutting down the web server')
-			http_server.socket.close()
-
-
-
-
diff --git a/python/trisurf/__init__.py b/python/trisurf/__init__.py
deleted file mode 100644
index e69de29..0000000
--- a/python/trisurf/__init__.py
+++ /dev/null
diff --git a/python/trisurf/__module__.py b/python/trisurf/__module__.py
deleted file mode 100644
index e69de29..0000000
--- a/python/trisurf/__module__.py
+++ /dev/null
diff --git a/python/trisurf/statistics.py b/python/trisurf/statistics.py
deleted file mode 100644
index 016e24c..0000000
--- a/python/trisurf/statistics.py
+++ /dev/null
@@ -1,20 +0,0 @@
-from trisurf import trisurf
-import os
-
-def combine(Runs,filename="statistics.csv",output="combinedStatistics.csv"):
-	"""Runs are those runs of which statistics are to be combined"""
-	data=[]
-	for run in Runs:
-		dir=trisurf.Directory(maindir=run.maindir,simdir=run.subdir)
-		statfile=os.path.join(dir.fullpath(),filename)
-		with open (statfile,"r") as myfile:
-			#lines = [line.rstrip('\n') for line in myfile]
-			data=data+myfile.readlines()[1:]
-
-	with open (output,"w") as output:
-		output.write("Header line placer... Not yet implemented\n")
-		for line in data:
-			output.write(line)
-
-	
-
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
deleted file mode 100644
index 92b138b..0000000
--- a/python/trisurf/trisurf.py
+++ /dev/null
@@ -1,522 +0,0 @@
-import configobj
-import xml.etree.ElementTree as ET
-import base64
-import zlib
-import sys,io
-import os
-from itertools import islice
-import mmap
-import shlex
-import psutil
-import time
-import datetime
-import subprocess
-import shutil
-
-# Process status
-TS_NOLOCK=0 # lock file does not exist
-TS_NONEXISTANT=0 # process is not in the list of processes
-TS_STOPPED=1 # the process is listed, but is in stopped state
-TS_RUNNING=2 # process is running
-TS_COMPLETED=3 #simulation is completed
-
-class FileContent:
-	'''
-	Class is helpful for reading and writting the specific files.
-	'''
-	def __init__(self,filename):
-		''' The instance is done by calling constructor FileContent(filename)
-
-		The object then reads filename if it exists, otherwise the data is empty string.
-		User may force to reread file by calling the readline() method of the class.
-
-		Filename is stored in local variable for future file operations.
-		'''
-
-		self.filename=filename
-		self.readfile()
-
-	def readfile(self):
-		'''Force reread of the file and setting the data'''
-		self.data=""
-		try:
-			with open (self.filename, "r") as myfile:
-				self.data=myfile.read().replace('\n', '') #read the file and remove newline from the text
-		except:
-			pass # does nothing if error occurs
-
-
-	def writefile(self, data, mode='w'):
-		'''File may be updated by completely rewritting the file contents or appending the data to the end of the file.
-		this is achieved by calling writefile(data, mode) method, where data is the string data to be written and
-		mode can be 'a' for append and 'w' for writting the file anew.
-		'''
-		with open (self.filename, mode) as myfile:
-			myfile.write(data)
-
-	def getText(self):
-		'''
-		Method getText() or calling the object itself returns string of data
-		'''
-		return self.data
-
-	def __str__(self):
-		'''
-		Method getText() or calling the object itself returns string of data
-		'''
-		return self.getText()
-
-class Tape:
-	'''
-	Special class that manages configuration of trisurf (commonly named tape). It can read and parse configuration from disk or parse it from string.
-	'''
-
-	def __init__(self):
-		'''The object is instatiated by calling Tape() constructor without parameters'''
-		return
-
-	def readTape(self, tape='tape'):
-		'''
-		Tape is read and parsed by calling the readTape() method with optional tape parameter, which is full path to filename where the configuration is stored.
-		If the tape cannot be read, it prints error and exits.
-		'''
-		try:
-			self.config=configobj.ConfigObj(tape)
-			with open (tape, "r") as myfile:
-				self.rawText=myfile.read() #read the file
-
-		except:
-			print("Error reading or parsing tape file!\n")
-			exit(1)
-
-	def setTape(self, string):
-		'''Method setTape(string) parses the string in memory that hold the tape contents.'''
-		self.config=configobj.ConfigObj(io.StringIO(string))
-		self.rawText=string
-		return
-
-	def getValue(self,key):
-		'''Method getValue(key) returns value of a single parsed setting named "key".'''
-
-		return self.config[key]
-
-	def __str__(self):
-		'''Calling the object itself, it recreates the tape contents from parsed values in form of key=value.'''
-		retval=""
-		for key,val in self.config.iteritems():
-			retval=retval+str(key)+" = "+str(val)+"\n"
-		return retval
-
-
-
-class Directory:
-	'''
-	Class deals with the paths where the simulation is run and data is stored.
-	'''
-	def __init__(self, maindir=".", simdir=""):
-		'''Initialization Directory() takes two optional parameters, namely maindir and simdir. Defaults to current directory. It sets local variables maindir and simdir accordingly.'''
-		self.maindir=maindir
-		self.simdir=simdir
-		return
-
-	def fullpath(self):
-		'''
-		Method returns string of path where the data is stored. It combines values of maindir and simdir as maindir/simdir on Unix.
-		'''
-		return os.path.join(self.maindir,self.simdir)
-
-	def exists(self):
-		''' Method checks whether the directory  specified by fullpath() exists. It return True/False on completion.'''
-		path=self.fullpath()
-		if(os.path.exists(path)):
-			return True
-		else:
-			return False
-
-	def make(self):
-		''' Method make() creates directory. If it fails it exits the program with error message.'''
-		try:
-			os.makedirs(self.fullpath())
-		except:
-			print("Cannot make directory "+self.fullpath()+"\n")
-			exit(1)
-		return
-
-	def makeifnotexist(self):
-		'''Method makeifnotexist() creates directory if it does not exist.'''
-		if(self.exists()==0):
-			self.make()
-			return True
-		else:
-			return False
-
-	def remove(self):
-		'''Method remove() removes directory recursively. WARNING! No questions asked.'''
-		if(self.exists()):
-			try:
-				os.rmdir(self.fullpath())
-			except:
-				print("Cannot remove directory "+self.fullpath()+ "\n")
-				exit(1)
-		return
-
-	def goto(self):
-		'''
-		Method goto() moves current directory to the one specified by fullpath(). WARNING: when using the relative paths, do not call this function multiple times.
-		'''
-		try:
-			os.chdir(self.fullpath())
-		except:
-			print("Cannot go to directory "+self.fullpath()+"\n")
-		return
-
-
-class Statistics:
-	'''
-	Class that deals with the statistics file from the simulations.
-	File is generally large and not all data is needed, so it is dealt with in a specific way.
-	'''
-
-	def __init__(self,path,filename="statistics.csv"):
-		'''
-		At the initialization call it receives optional filename parameter specifying the path and filename of the statistics file.
-
-		The local variables path, filename, fullname (joined path and filename) and private check if the file exists are stored.
-		'''
-		self.path=path
-		self.filename=filename
-		self.fullname=os.path.join(path,filename)
-		self.fileOK=self.read()
-		return
-
-	def exists(self):
-		'''Method check if the statistics file exists.'''
-		if(os.path.isfile(self.fullname)):
-			return True
-		else:
-			return False
-
-	def mapcount(self):
-		'''
-		Internal method for determining the number of the lines in the most efficient way. Is it really the most efficient?
-		'''
-		f = open(self.fullname, "r+")
-		try:
-			buf = mmap.mmap(f.fileno(), 0)
-			lines = 0
-			readline = buf.readline
-			while readline():
-				lines += 1
-			f.close()
-		except:
-			lines=0
-			f.close()
-		return lines
-
-	def tail(self,filename,n=2):
-		with open(filename,'r') as myfile:
-			lines=myfile.readlines()
-		return [lines[len(lines)-2].replace('\n',''),lines[len(lines)-1].replace('\n','')]
-
-	def read(self):
-		try:
-			lines=self.tail(self.fullname)
-		except:
-			return(False)
-		if len(lines)<2:
-			return(False)
-		#print (line)
-		fields=shlex.split(lines[0])
-		epoch1=fields[0]
-		n1=fields[1]
-		
-		fields=shlex.split(lines[1])
-		epoch2=fields[0]
-		n2=fields[1]
-		try:
-			self.dT=int(epoch2)-int(epoch1)
-			self.last=n2
-			#print(epoch1)
-			#print(epoch2)
-			#print(self.dT)
-			#print(self.last)
-			self.startDate=os.path.getmtime(os.path.join(self.path,'.lock'))
-		except:
-			return(False)
-		return(True)
-
-	def readText(self):
-		with open(self.fullname, 'r+') as fin:
-			cont=fin.read()
-		return cont
-
-	def read_old(self):
-		'''
-		Method read() reads the statistics if it exists. It sets local variable dT storing the time differential between two intervals of simulation (outer loops). It also stores last simulation loop and the start of the run.
-		'''
-		if(self.exists()):
-		#	epoch1=0
-		#	epoch2=0
-		#	n1=0
-		#	n2=0
-			nlines=self.mapcount()
-			if nlines<2:
-				return(False)
-			try:
-				with open(self.fullname, "r+") as fin:
-					i=0;
-					for line in fin:
-						if(i==1):
-							#print (line)
-							fields=shlex.split(line)
-							epoch1=fields[0]
-							n1=fields[1]
-						if(i==nlines-1):
-							fields=shlex.split(line)
-							epoch2=fields[0]
-							n2=fields[1]
-						i=i+1
-			except:
-				#print("Cannot read statistics file in "+self.fullname+"\n")
-				return(False)
-		else:
-			#print("File "+self.fullname+" does not exists.\n")
-			return(False)
-		try:
-			self.dT=(int(epoch2)-int(epoch1))/(int(n2)-int(n1))
-		except:
-			self.dT=0
-		self.last=n2
-		self.startDate=epoch1
-		return(True)
-
-	def __str__(self):
-		'''
-		Prints the full path with filename of the statistics.csv file
-		'''
-		return(str(self.fullname))
-
-
-
-class Runner:
-	'''
-	Class Runner consists of a single running or terminated instance of the trisurf. It manages starting, stopping, verifying the running process and printing the reports of the configured instances.
-	'''
-
-	@property
-	def Dir(self):
-		return Directory(maindir=self.maindir,simdir=self.subdir)
-
-
-	@property
-	def Statistics(self):
-		return Statistics(self.Dir.fullpath(), "statistics.csv")
-
-	def __init__(self, subdir='run0', tape=None, snapshot=None, runArgs=[]):
-		self.subdir=subdir
-		self.runArgs=runArgs
-		self.isFromSnapshot=False
-		if(tape!=None):
-			self.initFromTape(tape)
-		if(snapshot!=None):
-			self.initFromSnapshot(snapshot)
-		return
-
-
-	def initFromTape(self, tape):
-		self.Tape=Tape()
-		self.Tape.readTape(tape)
-		self.tapeFilename=tape
-
-	def initFromSnapshot(self, snapshotfile):
-		try:
-			tree = ET.parse(snapshotfile)
-		except:
-			print("Error reading snapshot file")
-			exit(1)
-		self.isFromSnapshot=True
-		self.snapshotFile=snapshotfile
-		root = tree.getroot()
-		tapetxt=root.find('tape')
-		version=root.find('trisurfversion')
-		self.Tape=Tape()
-		self.Tape.setTape(tapetxt.text)
-
-	def getPID(self):
-		try:
-			fp = open(os.path.join(self.Dir.fullpath(),'.lock'))
-		except IOError as e:
-			return 0 #file probably does not exist. e==2??
-		pid=fp.readline()
-		fp.close()
-		return int(pid)
-
-	def getLastIteration(self):
-		try:
-			fp = open(os.path.join(self.Dir.fullpath(),'.status'))
-		except IOError as e:
-			return -1 #file probably does not exist. e==2??
-		status=fp.readline()
-		fp.close()
-		return int(status)
-
-	def isCompleted(self):
-		if int(self.Tape.getValue("iterations"))+int(self.Tape.getValue("inititer"))==self.getLastIteration()+1:
-			return True
-		else:
-			return False
-
-	def getStatus(self):
-		pid=self.getPID()
-		if(self.isCompleted()):
-			return TS_COMPLETED
-		if(pid==0):
-			return TS_NOLOCK
-		if(psutil.pid_exists(int(pid))):
-			proc= psutil.Process(int(pid))
-			#psutil.__version__ == '3.4.2' requires name() and status(), some older versions reguire name, status
-			if(psutil.__version__>='2.0.0'):
-				procname=proc.name()
-				procstat=proc.status()
-			else:
-				procname=proc.name
-				procstat=proc.status
-			if procname=="trisurf":
-				if procstat=="stopped":
-					return TS_STOPPED
-				else:
-					return TS_RUNNING
-			else:
-				return TS_NONEXISTANT
-		else:
-			return TS_NONEXISTANT
-
-	def start(self):
-		if(self.getStatus()==0 or self.getStatus()==TS_COMPLETED):
-			#check if executable exists
-			if(shutil.which('trisurf')==None):
-				print("Error. Trisurf executable not found in PATH. Please install trisurf prior to running trisurf manager.")
-				exit(1)
-#Symlinks tape file to the directory or create tape file from snapshot in the direcory...
-			if(self.Dir.makeifnotexist()):
-				if(self.isFromSnapshot==False):
-					try:
-						os.symlink(os.path.abspath(self.tapeFilename), self.Dir.fullpath()+"/tape")
-					except:
-						print("Error while symlinking "+os.path.abspath(self.tapeFilename)+" to "+self.Dir.fullpath()+"/tape")
-						exit(1)
-				else:
-					try:
-						with open (os.path.join(self.Dir.fullpath(),"tape"), "w") as myfile:
-							#myfile.write("#This is automatically generated tape file from snapshot")
-							myfile.write(str(self.Tape.rawText))
-					except:
-						print("Error -- cannot make tapefile  "+ os.path.join(self.Dir.fullpath(),"tape")+" from the snapshot in the running directory")
-						exit(1)
-					try:
-						os.symlink(os.path.abspath(self.snapshotFile), os.path.join(self.Dir.fullpath(),"initial_snapshot.vtu"))
-					except:
-						print("Error while symlinking "+os.path.abspath(self.snapshotFile)+" to "+os.path.join(self.Dir.fullpath(),self.snapshotFile))
-		
-			#check if the simulation has been completed. in this case notify user and stop executing.
-			if(self.isCompleted() and ("--force-from-tape" not in self.runArgs) and ("--reset-iteration-count" not in self.runArgs)):
-				print("The simulation was completed. Not starting executable in "+self.Dir.fullpath())
-				return
-
-			cwd=Directory(maindir=os.getcwd())
-			lastVTU=self.getLastVTU() #we get last VTU file in case we need to continue the simulation from last snapshot. Need to be done before the Dir.goto() call.
-			self.Dir.goto()
-			print("Starting trisurf-ng executable in "+self.Dir.fullpath())
-			if(self.isFromSnapshot==True):
-				#here we try to determine whether we should continue the simulation or start from last known VTU snapshot.
-				if(lastVTU==None):
-					initSnap="initial_snapshot.vtu"
-				else:
-					initSnap=lastVTU
-					print("WARNING: Not using initial snapshot as starting point, but selecting "+initSnap+" as a starting vesicle")
-				params=["trisurf", "--restore-from-vtk",initSnap]+self.runArgs
-				print("InitSnap is: "+initSnap)
-			else:
-				#veify if dump exists. If not it is a first run and shoud be run with --force-from-tape
-				if(os.path.isfile("dump.bin")==False):
-					self.runArgs.append("--force-from-tape")
-				params=["trisurf"]+self.runArgs
-			subprocess.Popen (params, stdout=subprocess.DEVNULL)
-			cwd.goto()
-		else:
-			print("Process in "+self.Dir.fullpath()+" already running. Not starting.")
-		return
-
-
-	def setMaindir(self,prefix,variables):
-		maindir=""
-		for p,v in zip(prefix,variables):
-			if(v=="xk0"):
-				tv=str(round(float(self.Tape.config[v])))
-				if sys.version_info<(3,0):
-					tv=str(int(float(self.Tape.config[v])))
-			else:
-				tv=self.Tape.config[v]
-			maindir=maindir+p+tv
-		self.maindir=maindir
-		return
-
-	def setSubdir(self, subdir="run0"):
-		self.subdir=subdir
-		return
-
-	def getStatistics(self, statfile="statistics.csv"):
-		self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment"))
-		pid=self.getPID()
-		status=self.getStatus()
-		if(self.Statistics.fileOK):
-			ETA=str(datetime.timedelta(microseconds=(int(self.Tape.config['iterations'])-int(self.Statistics.last))*self.Statistics.dT)*1000000)
-		if(status==TS_NONEXISTANT or status==TS_NOLOCK):
-			statustxt="Not running"
-			pid=""
-			ETA=""
-		elif status==TS_STOPPED:
-			statustxt="Stopped"
-			ETA="N/A"
-		elif status==TS_COMPLETED:
-			statustxt="Completed"
-			pid=""
-			ETA=""
-		else:
-			statustxt="Running"
-
-		if(self.Statistics.fileOK):
-			report=[time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(int(self.Statistics.startDate))),ETA, statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
-		else:
-			report=["N/A","N/A",statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
-		return report
-
-
-	def stop(self):
-		try:
-			p=psutil.Process(self.getPID())
-			p.kill()
-		except:
-			print("Could not stop the process. Is the process running? Do you have sufficient privileges?")
-
-
-	def writeComment(self, data, mode='w'):
-		self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment"))
-		self.Comment.writefile(data,mode=mode)
-
-
-	def getLastVTU(self):
-		vtuidx=self.getLastIteration()-int(self.Tape.getValue("inititer"))
-		if vtuidx<0:
-			return None
-		else:
-			return  'timestep_{:06d}.vtu'.format(vtuidx)
-
-	def __str__(self):
-		if(self.getStatus()==0):
-			str=" not running."
-		else:
-			str=" running."
-		return(self.Dir.fullpath()+str)
-
-
diff --git a/python/trisurf/tsmgr.py b/python/trisurf/tsmgr.py
deleted file mode 100644
index d973360..0000000
--- a/python/trisurf/tsmgr.py
+++ /dev/null
@@ -1,270 +0,0 @@
-import argparse
-import paramiko
-from . import Remote
-from . import trisurf
-import socket
-import os,sys
-import tabulate
-import subprocess,re
-import psutil
-#import http.server
-#import socketserver
-if sys.version_info>=(3,0):
-	from urllib.parse import urlparse
-	from . import WebTrisurf
-else:
-	from urlparse import urlparse
-	from vtk import *
-	from . import VTKRendering
-#import io
-
-
-
-#Color definitions for terminal
-class bcolors:
-    HEADER = '\033[95m'
-    OKBLUE = '\033[94m'
-    OKGREEN = '\033[92m'
-    WARNING = '\033[93m'
-    FAIL = '\033[91m'
-    ENDC = '\033[0m'
-    BOLD = '\033[1m'
-    UNDERLINE = '\033[4m'
-
-#parses Command Line Arguments and returns the list of parsed values
-def ParseCLIArguments(arguments):
-	parser = argparse.ArgumentParser(description='Manages (start, stop, status) multiple simulation processes of trisurf according to the configuration file.')
-	parser.add_argument('proc_no', metavar='PROC_NO', nargs='*',
-			    help='process number at host. If hostname is not specified, localhost is assumed. If no processes are specified all processes on all hosts are assumed.')
-	action_group=parser.add_mutually_exclusive_group(required=True)
-	action_group.add_argument('-c','--comment',nargs=1, help='append comment to current comment')
-	action_group.add_argument('--delete-comment', help='delete comment',action='store_true')
-	action_group.add_argument('-k','--kill','--stop','--suspend', help='stop/kill the process', action='store_true')
-	action_group.add_argument('-r','--run','--start','--continue', help='start/continue process', action='store_true')
-	action_group.add_argument('-s','--status',help='print status of the processes',action='store_true')
-	action_group.add_argument('-v','--version', help='print version information and exit', action='store_true')
-	action_group.add_argument('--web-server', type=int,metavar="PORT", nargs=1, help='EXPERIMENTAL: starts web server and never exist.')
-	action_group.add_argument('-p','--preview',help='preview last VTU shape',action='store_true')
-	parser.add_argument('--force', help='if dangerous operation (killing all the processes) is requested, this flag is required to execute the operation. Otherwise, the request will be ignored.', action="store_true")
-	parser.add_argument('-H', '--host', nargs=1, help='specifies which host is itended for the operation. Defauts to localhost for all operations except --status and --version, where all configured hosts are assumed.')
-	parser.add_argument('--html', help='Generate HTML output', action="store_true")
-	parser.add_argument('-n', nargs='+', metavar='PROC_NO', type=int, help='OBSOLETE. Specifies process numbers.')
-	parser.add_argument('-R','--raw',help='print status and the rest of the information in raw format', action="store_true")
-	parser.add_argument('-x','--local-only',help='do not attempt to contact remote hosts. Run all operations only on local machine',action='store_true')
-	args = parser.parse_args(arguments)
-	return args
-
-
-#gets version of trisurf currently running
-def getTrisurfVersion():
-	p = subprocess.Popen('trisurf --version', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
-	lines=p.stdout.readlines()
-	version=re.findall(r'[0-9a-f]{7}(?:-dirty)?', lines[0].decode('ascii'))
-	p.wait()
-	if(len(version)):
-		return version[0]
-	else:
-		return "unknown version"
-
-
-
-def copyConfigAndConnect(hosts):
-	print("Connecting to remote hosts and copying config files, tapes and snapshots")
-	for host in hosts:
-		if(host['name'] !=socket.gethostname()): #if I am not the computer named in host name
-			try:
-				username=host['username']
-			except:
-				username=os.getusername() #default username is current user user's name
-			try:
-				port=host['port']
-			except:
-				port=22 #default ssh port
-			rm=Remote.Connection(hostname=host['address'],username=username, port=port)
-			rm.connect()
-			rm.send_file(__file__,'remote_control.py')
-			for run in host['runs']:
-				try:
-					rm.send_file(run.tapeFile,run.tapeFile)
-				except:
-					pass
-				try:
-					rm.send_file(run.snapshotFile,run.snapshotFile)
-				except:
-					pass
-			host['_conn']= rm
-	# we are connected to all hosts...
-	return hosts
-
-
-
-def getTargetRunIdxList(args):
-	target_runs=list(map(int,args['proc_no']))
-	if len(target_runs)==0:
-		#check if obsolete -n flags have numbers
-		target_runs=args['n']
-		if target_runs==None:
-			return None
-	target_runs=list(set(target_runs))
-	return target_runs
-
-
-
-def status_processes(args,host):
-	target_runs=getTargetRunIdxList(args)
-	if target_runs==None:
-		target_runs=list(range(1,len(host['runs'])+1))
-	report=[]
-	for i in target_runs:
-		line=host['runs'][i-1].getStatistics()
-		line.insert(0,i)
-		report.append(line)
-	if(args['raw']):
-		print(report)
-	else:
-		if(args['html']):
-			tablefmt='html'
-		else:
-			tablefmt='fancy_grid'
-		print(tabulate.tabulate(report,headers=["Run no.", "Run start time", "ETA", "Status", "PID", "Path", "Comment"], tablefmt=tablefmt))
-	return
-
-def run_processes(args,host):
-	target_runs=getTargetRunIdxList(args)
-	if target_runs==None:
-		target_runs=list(range(1,len(host['runs'])+1))
-	for i in target_runs:
-		host['runs'][i-1].start()
-	return
-
-def kill_processes(args,host):
-	target_runs=getTargetRunIdxList(args)
-	if target_runs==None:
-		if args['force']==True:
-			target_runs=list(range(1,len(host['runs'])+1))
-		else:
-			print("Not stopping all processes on the host. Run with --force flag if you are really sure to stop all simulations")
-			return
-	for i in target_runs:
-		host['runs'][i-1].stop()
-	return
-
-def comment_processes(args,host):
-	target_runs=getTargetRunIdxList(args)
-	if target_runs==None:
-		target_runs=list(range(1,len(host['runs'])+1))
-	for i in target_runs:
-		host['runs'][i-1].writeComment(args['comment'][0],'a')
-	print("Comment added")
-	return
-
-def delete_comments(args,host):
-	target_runs=getTargetRunIdxList(args)
-	if target_runs==None:
-		if args['force']==True:
-			target_runs=list(range(1,len(host['runs'])+1))
-		else:
-			print("Not deleting comments on all posts on the host. Run with --force flag if you are really sure to delete all comments")
-			return
-	for i in target_runs:
-		host['runs'][i-1].writeComment("")
-	print("Comment deleted")
-	return
-
-
-def start_web_server(args,host):
-	print('Server listening on port {}'.format(args['web_server'][0]))
-	if sys.version_info>=(3,0):
-		WebTrisurf.WebServer(port=args['web_server'][0])
-	else:
-		print("Cannot start WebServer in python 2.7")
-	exit(0)
-
-def perform_action(args,host):
-	#find which flags have been used and act upon them. -r -s -k -v -c --delete-comment are mutually exclusive, so only one of them is active
-	if args['run']:
-		run_processes(args,host)
-	elif args['kill']:
-		kill_processes(args,host)
-	elif args['status']:
-		status_processes(args,host)
-	elif args['comment']!= None:
-		comment_processes(args,host)
-	elif args['delete_comment']:
-		delete_comments(args,host)
-	elif args['web_server']!=None:
-		start_web_server(args,host)
-	elif args['preview']:
-		preview_vtu(args,host)
-	else: #version requested
-		print(getTrisurfVersion())
-	return
-
-
-
-def preview_vtu(args,host):
-	#only for localhost at the moment
-	if sys.version_info>=(3,0):
-		print("Preview works only with python 2.7")
-		exit(1)
-	if host['name'] == socket.gethostname():
-		VTKRendering.Renderer(args,host)
-
-def getListOfHostConfigurationByHostname(hosts,host):
-	rhost=[]
-	for chost in hosts:
-		if chost['name'] in host:
-			rhost.append(chost)
-	return rhost
-
-
-
-def start(hosts,argv=sys.argv[1:]):
-	args=vars(ParseCLIArguments(argv))
-	#print(vars(args))
-
-	#Backward compatibility... If running just on localmode, the host specification is unnecessary. Check if only Runs are specified
-	try:
-		test_host=hosts[0]['name']
-	except:
-		print("Network mode disabled. Old syntax detected.")
-		host={'name':socket.gethostname(),'address':'127.0.0.1', 'runs':hosts}
-		perform_action(args,host)
-		exit(0)
-
-
-	#find the host at which the action is attended
-	if args['host']==None:
-		if(args['status']==False and args['version']==False):
-			hosts=getListOfHostConfigurationByHostname(hosts,socket.gethostname())
-	else:
-		hosts=getListOfHostConfigurationByHostname(hosts,args['host'])
-	if len(hosts)==0:
-		print ('Hostname "{}" does not exist in configuration file. Please check the spelling'.format(args['host'][0]))
-		exit(1)
-
-	if not args['local_only']:
-			hosts=copyConfigAndConnect(hosts)
-
-	#do local stuff:
-	for host in hosts:
-		if host['name'] == socket.gethostname():
-			if(args['html']):
-				print("Host <font color='orange'>"+host['name']+"</font> reports the following:")
-			else:
-				print("Host "+bcolors.WARNING+host['name']+bcolors.ENDC+" reports the following:")
-			perform_action(args,host)
-		elif not args['local_only']:
-			output=host['_conn'].execute('python3 ./remote_control.py -x '+" ".join(argv))
-			for line in output:
-				print(line.replace('\n',''))
-
-
-	if not args['local_only']:
-		print("Closing connections to remote hosts")
-		for host in hosts:
-			if(host['name'] !=socket.gethostname()):
-				host['_conn'].disconnect()
-
-
-
diff --git a/python/tsmgr b/python/tsmgr
deleted file mode 100755
index 775d667..0000000
--- a/python/tsmgr
+++ /dev/null
@@ -1,105 +0,0 @@
-#!/usr/bin/python3
-import sys, getopt
-from trisurf import trisurf
-import tabulate
-
-# -- configuration of the multiple/single run --
-
-run1=trisurf.Runner(snapshot='snapshot.vtu')
-run1.setMaindir(("N","k","V","Np","Nm"),("nshell","xk0","constvolswitch","npoly","nmono"))
-run1.setSubdir("run0")
-
-run2=trisurf.Runner(tape='tape', runArgs=['--force-from-tape'])
-run2.setMaindir(("N","k","V","Np","Nm"),("nshell","xk0","constvolswitch","npoly","nmono"))
-run2.setSubdir("run1")
-
-
-#obligatory: combine all runs
-Runs=[run1,run2]
-
-
-
-#------------------ NO NEED TO TOUCH THE CODE BELOW ------------------------------
-
-# -- reading command line switches and acting accordingly --
-argv=sys.argv[1:]
-processno=0
-try:
-	opts, args = getopt.getopt(argv,"a:n:hrsc:")
-except getopt.GetoptError:
-	print('tsmgr [-n process number] [-h] [-r] [-s] [-c comment text] [-a comment text]')
-	sys.exit(2)
-for opt, arg in opts:
-	if opt == '-h':
-		print ('tsmgr [-n process number] [-h] [-r] [-s] [-c comment text] [-a comment text]')
-		sys.exit()
-	elif opt == '-r':
-		if processno:
-			localRuns=[Runs[processno-1]]
-		else:
-			localRuns=Runs
-		for run in localRuns:
-			run.start()
-	elif opt == '-s':
-		report=[]
-		i=1
-		if processno:
-			localRuns=[Runs[processno-1]]
-		else:
-			localRuns=Runs
-		for run in localRuns:
-			line=run.getStatistics()
-			line.insert(0,i)
-			report.append(line)
-			i=i+1
-			#print(reportstr)
-		print ("\n\nTrisurf running processes report\n")
-		print (tabulate.tabulate(report,headers=["Run no.", "Run start time", "ETA", "Status", "PID", "Path", "Comment"], tablefmt='fancy_grid'))
-	elif opt == '-n':
-		processno=int(arg)
-		if processno<1 or processno>len(Runs) :
-			processno=0
-	elif opt == '-c':
-		comment = arg
-		if processno:
-			Runs[processno-1].writeComment(arg)
-	elif opt == '-a':
-		comment = arg
-		if processno:
-			Runs[processno-1].writeComment("\n"+arg, 'a')
-
-		
-	else:
-		print('tsmgr [-n process number] [-h] [-r] [-s] [-c comment text] [-a comment text]')
-		sys.exit(2)
-
-
-
-
-
-
-
-
-
-# -- OBSOLETE and TESTING --
-
-
-
-
-
-#	elif opt in ("-i", "--ifile"):
-#		inputfile = arg
-#	elif opt in ("-o", "--ofile"):
-#		outputfile = arg
-#	print ('Input file is "', inputfile)
-#	print ('Output file is "', outputfile)
-
-
-
-#run1.start()
-#run
-#print(run1)
-#run1.getStatistics()
-#print(run1.statistics)
-#print(run1.tape)
-#print(run1.tape.getValue('nshell'))

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