old_contents: #!/usr/bin/env python2
  """
  Run code, analyis or build documents related to this repository
  
  Usage:
      run.py paper [--rerun=RR] [--view] [--viewer=PDF]
      run.py thesis [--rerun=RR] [--view] [--viewer=PDF]
      run.py notebook [--port=P]
  
  Options:
      --view  Compile and then open pdf.
      --viewer=PDF  PDF Viewer. [default: evince]
      --rerun=RR PythonTeX rerun flag. [default: modified]
      --port=P Port for IPython Notebook [default: 8898]
  
  """
  from __future__ import print_function
  
  import os
  import sys
  import bz2
  import subprocess
  
  import docopt
  import progressbar
  import requests
  
  os.chdir(os.path.dirname(os.path.realpath(__file__)))
  
  arguments = docopt.docopt(__doc__, version='1.0.0')
  
  #Fix rerun bug
  if arguments['--rerun'] is None:
      arguments['--rerun'] = 'modified'
  
  file_prefix = 'smumford_thesis'
  #Compile Paper
  if arguments['paper'] or arguments['thesis']:
      os.chdir('thesis')
      os.system('pdflatex -shell-escape -interaction=batchmode {}.tex'.format(file_prefix))
      os.system('pythontex --interpreter python:python2 {}.tex --rerun={}'.format(file_prefix, arguments['--rerun']))
      os.system('bibtex {}'.format(file_prefix))
      os.system('makeindex {}.aux'.format(file_prefix))
      os.system('makeindex {}.idx'.format(file_prefix))
      os.system('makeindex {0}.nlo -s nomencl.ist -o {0}.nls'.format(file_prefix))
      os.system('pdflatex --shell-escape -interaction=batchmode {}.tex'.format(file_prefix))
      os.system('makeindex {0}.nlo -s nomencl.ist -o {0}.nls'.format(file_prefix))
      os.system('pdflatex -synctex=1 --shell-escape -interaction=batchmode {}.tex'.format(file_prefix))
      if arguments['--view']:
          os.system('{} {}.pdf'.format(arguments['--viewer'], file_prefix))
      os.chdir('../')
  
  #Download data
  if arguments['notebook']:
      if arguments['--port'] is None:
          arguments['--port'] = 8899
      import IPython
      IPython.start_ipython(['notebook', '--notebook-dir=notebooks',
      '--port={}'.format(arguments['--port'])])
  
new_contents: #!/opt/miniconda/envs/thesis/bin/python
  #!/usr/bin/env python2
  """
  Run code, analyis or build documents related to this repository
  
  Usage:
      run.py paper [--rerun=RR] [--view] [--viewer=PDF]
      run.py thesis [--rerun=RR] [--view] [--viewer=PDF]
      run.py notebook [--port=P]
  
  Options:
      --view  Compile and then open pdf.
      --viewer=PDF  PDF Viewer. [default: evince]
      --rerun=RR PythonTeX rerun flag. [default: modified]
      --port=P Port for IPython Notebook [default: 8898]
  
  """
  from __future__ import print_function
  
  import os
  import sys
  import bz2
  import subprocess
  
  import docopt
  import progressbar
  import requests
  
  os.chdir(os.path.dirname(os.path.realpath(__file__)))
  
  arguments = docopt.docopt(__doc__, version='1.0.0')
  
  #Fix rerun bug
  if arguments['--rerun'] is None:
      arguments['--rerun'] = 'modified'
  
  file_prefix = 'smumford_thesis'
  #Compile Paper
  if arguments['paper'] or arguments['thesis']:
      os.chdir('thesis')
      os.system('pdflatex -shell-escape -interaction=batchmode {}.tex'.format(file_prefix))
      os.system('pythontex --interpreter python:{} {}.tex --rerun={}'.format(sys.executable, file_prefix, arguments['--rerun']))
      os.system('bibtex {}'.format(file_prefix))
      os.system('makeindex {}.aux'.format(file_prefix))
      os.system('makeindex {}.idx'.format(file_prefix))
      os.system('makeindex {0}.nlo -s nomencl.ist -o {0}.nls'.format(file_prefix))
      os.system('pdflatex --shell-escape -interaction=batchmode {}.tex'.format(file_prefix))
      os.system('makeindex {0}.nlo -s nomencl.ist -o {0}.nls'.format(file_prefix))
      os.system('pdflatex -synctex=1 --shell-escape -interaction=batchmode {}.tex'.format(file_prefix))
      if arguments['--view']:
          os.system('{} {}.pdf'.format(arguments['--viewer'], file_prefix))
      os.chdir('../')
  
  #Download data
  if arguments['notebook']:
      if arguments['--port'] is None:
          arguments['--port'] = 8899
      import IPython
      IPython.start_ipython(['notebook', '--notebook-dir=notebooks',
      '--port={}'.format(arguments['--port'])])
  
subject: fix run.py for execution in conda env