This is happening because the Matlab subprocess is trying to claim stdin in contention with python. To resolve this, you can join a subprocess.PIPE to stdin (and never write to it), e.g:

handle = subprocess.Popen(command, stdin=subprocess.PIPE)

Note that it's generally a bad idea to have shell = True in a call to Popen unless it's absolutely necessary. The command should also be a list of arguments rather than a single string. Here's a minimally reproducing example:

try:
  basestring
except NameError:
  basestring = str 

# custom non string-expanding chain implementation
def chain(*iterables):
  for items in iterables:
    if isinstance(items, basestring):
      yield items
    else:
      for item in items:
        yield item

MATLAB_FOLDER = '{0}/matlab'.format(os.path.realpath(os.path.dirname(__file__)))

# Start a Matlab server and bind it to a ZMQ socket(TCP/IPC)
def _run_matlab_server(matlab_bin, matlab_socket_addr, matlab_log, matlab_id, matlab_startup_options):

  if matlab_log:
    matlab_log = [ 
      '-logfile',
      './pymatbridge/logs/matlablog_{0}.txt'.format(matlab_id),
      '>',
      './pymatbridge/logs/bashlog_{0}.txt'.format(matlab_id)
    ]   
  else:
    matlab_log = []

  command = chain(
    matlab_bin,
    matlab_startup_options,
    '-r',
    "addpath(genpath('{0}')), matlabserver('{1}'), exit".format(MATLAB_FOLDER, matlab_socket_addr),
    matlab_log
  )   

  handle = subprocess.Popen(command, stdin=subprocess.PIPE)
  return True

Keyboard output invisible when starting the bridge in IPython #41

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