Default `output_timout` timeout is too low, allow for configuration

[Zeitsperre]

Related discussion: #156

The team I work with have been trying to figure out a simple way to prolong the timeout for cell output as we're running into this issue in some of my testing pipelines.

Our use case is that we rely on pytest --nbval to run integration tests on several notebooks across multiple projects for a computation platform and some notebooks require a slightly longer timeout. This means that we have occasional failure/success for some notebooks, so not ideal.

We were hoping to be able to supply a timeout manually or via pytest configurations, but this appears to not be fully implemented.

Copying a comment from my colleague (@fmigneault):

I'm having a hard time understanding how the default 2000s (

nbval/nbval/plugin.py

Lines 96 to 98 in 3299cc6

	group.addoption('--nbval-cell-timeout', action='store', default=2000,
	type=float,
	help='Timeout for cell execution, in seconds.')

) was not applied in favour of the hardcoded 5s:

nbval/nbval/plugin.py

Line 373 in 3299cc6

self.output_timeout = 5

Looking at the code, it seems like the timeout is used to get the initial message, but is never actually employed to get the long output:

nbval/nbval/plugin.py

Lines 606 to 631 in 3299cc6

	timeout = self.config.option.nbval_cell_timeout
	timed_out_this_run = False
	# Poll the shell channel to get a message
	try:
	self.parent.kernel.await_reply(msg_id, timeout=timeout)
	except Empty: # Timeout reached
	# Try to interrupt kernel, as this will give us traceback:
	kernel.interrupt()
	self.parent.timed_out = True
	timed_out_this_run = True
	# This list stores the output information for the entire cell
	outs = []
	# TODO: Only store if comparing with nbdime, to save on memory usage
	self.test_outputs = outs
	# Now get the outputs from the iopub channel
	while True:
	# The iopub channel broadcasts a range of messages. We keep reading
	# them until we find the message containing the side-effects of our
	# code execution.
	try:
	# Get a message from the kernel iopub channel
	msg = self.parent.get_kernel_message(timeout=self.output_timeout)

We're wondering if there is a maybe an undocumented method to modify the notebook cell timeout or perhaps the fix mentioned in #156 could be reconsidered.

Context: Ouranosinc/PAVICS-e2e-workflow-tests#171