def run_notebook(self, memory_used=None, progress_cb=None,
skip_exceptions=False):
'''
Run all the cells of a notebook in order and update
the outputs in-place.
If ``skip_exceptions`` is set, then if exceptions occur in a cell, the
subsequent cells are run (by default, the notebook execution stops).
'''
cur = 0
if memory_used is not None:
memory_used.append(system_memory_used())
for cell in self.iter_code_cells():
cur += 1
try:
if progress_cb is not None:
progress_cb(cur)
self.run_cell(cell, cur)
if memory_used is not None:
memory_used.append(system_memory_used())
except NotebookError:
if not skip_exceptions:
raise
def run_cell(self, cell, cidx):
'''
Run a notebook cell and update the output of that cell in-place.
'''
logging.debug('running cell {}'.format(cidx))
# logging.debug(u'cell.input {}'.format(cell.input))
self.kc.execute(cell.source)
reply = self.kc.get_shell_msg()
status = reply['content']['status']
max_mem = system_memory_used()
logging.info(' memory used: {}'.format(sizeof_fmt(max_mem)))
if status == 'error':
traceback_text = 'Cell raised uncaught exception: \n' + \
'\n'.join(reply['content']['traceback'])
traceback_text = remove_ansicolor(traceback_text)
if 'NoDataFound' not in traceback_text:
logging.error(traceback_text)
else:
logging.debug('run_cell ok')
outs = list()
while True:
try:
msg = self.kc.get_iopub_msg(timeout=1)
if msg['msg_type'] == 'status':
if msg['content']['execution_state'] == 'idle':
break
except Empty:
# execution state should return to idle before the queue
# becomes empty,
# if it doesn't, something bad has happened
logging.error("empty exception")
raise
content = msg['content']
msg_type = msg['msg_type']
# IPython 3.0.0-dev writes pyerr/pyout in the notebook format but
# uses error/execute_result in the message spec. This does the
# translation needed for tests to pass with IPython 3.0.0-dev
notebook3_format_conversions = {
'error': 'pyerr',
'execute_result': 'pyout'
}
msg_type = notebook3_format_conversions.get(msg_type, msg_type)
out = NotebookNode(output_type=msg_type)
#if 'execution_count' in content:
#cell['prompt_number'] = content['execution_count']
#out.prompt_number = content['execution_count']
if msg_type in ('status', 'pyin', 'execute_input'):
continue
elif msg_type == 'stream':
out.stream = content['name']
if 'text' in content:
out.text = content['text']
else:
out.text = content['data']
# print(out.text, end='')
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].items():
try:
attr = self.MIME_MAP[mime]
except KeyError:
logging.error("unhandled mime")
raise NotImplementedError('unhandled mime type: %s' %
mime)
setattr(out, attr, data)
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
elif msg_type == 'clear_output':
outs = list()
continue
else:
logging.error("unhandled iopub")
raise NotImplementedError('unhandled iopub message: %s' %
msg_type)
outs.append(out)
# NOTE: Ver 4 format still have 'pyout', Why?
cell['outputs'] = upgrade_outputs(outs)
logging.debug("status: {}".format(status))
if status == 'error':
if 'NoDataFound' in traceback_text:
raise NoDataFound(traceback_text.split('\n')[-1])
else:
logging.debug(u"NotebookError raised")
raise NotebookError(traceback_text)
