Spyder: TimeoutError in the IPython console when moving or deleting startup script

[RollsW]

Description

What steps will reproduce the problem?

Just triggers on opening Spyder:

Traceback

```File "C:\Users...\Anaconda3\lib\site-packages\spyder\plugins\base.py", line 331, in
toggled=lambda checked: self.toggle_view(checked),
File "C:\Users...\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole\plugin.py", line 207, in toggle_view
self.create_new_client(give_focus=False)
File "C:\Users...\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole\plugin.py", line 703, in create_new_client
self.register_client(client)
File "C:\Users...\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole\plugin.py", line 918, in register_client
shellwidget.set_cwd(cwd_path)
File "C:\Users...\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole\widgets\shell.py", line 178, in set_cwd
self.call_kernel(interrupt=True).set_cwd(dirname)
File "C:\Users...\Anaconda3\lib\site-packages\spyder_kernels\comms\commbase.py", line 538, in __call__
call_dict, call_data, self._comm_id)
File "C:\Users...\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole\comms\kernelcomm.py", line 130, in _get_call_return_value
with self.comm_channel_manager(comm_id, queue_message=not interrupt):
File "C:\Users...\Anaconda3\lib\contextlib.py", line 112, in __enter__
return next(self.gen)
File "C:\Users...\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole\comms\kernelcomm.py", line 87, in comm_channel_manager
timeout)
File "C:\Users...\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole\comms\kernelcomm.py", line 168, in _wait
raise TimeoutError(timeout_msg)
TimeoutError: Timeout while waiting for comm port.

## Versions

* Spyder version: 4.1.2 
* Python version: 3.7.3
* Qt version: 5.9.6
* PyQt5 version: 5.9.2
* Operating System: Windows 10

### Dependencies

Mandatory:

atomicwrites >=1.2.0 : 1.3.0 (OK)
chardet >=2.0.0 : 3.0.4 (OK)
cloudpickle >=0.5.0 : 1.3.0 (OK)
diff_match_patch >=20181111 : 20181111 (OK)
intervaltree : None (OK)
IPython >=4.0 : 7.13.0 (OK)
jedi =0.15.2 : 0.15.2 (OK)
nbconvert >=4.0 : 5.6.1 (OK)
numpydoc >=0.6.0 : 0.9.2 (OK)
paramiko >=2.4.0 : 2.7.1 (OK)
parso =0.5.2 : 0.5.2 (OK)
pexpect >=4.4.0 : 4.8.0 (OK)
pickleshare >=0.4 : 0.7.5 (OK)
psutil >=5.3 : 5.7.0 (OK)
pygments >=2.0 : 2.6.1 (OK)
pylint >=0.25 : 2.4.4 (OK)
pyls >=0.31.9;<0.32.0 : 0.31.9 (OK)
qdarkstyle >=2.8 : 2.8 (OK)
qtawesome >=0.5.7 : 0.7.0 (OK)
qtconsole >=4.6.0 : 4.7.2 (OK)
qtpy >=1.5.0 : 1.9.0 (OK)
rtree >=0.8.3 : 0.9.3 (OK)
sphinx >=0.6.6 : 2.4.4 (OK)
spyder_kernels >=1.9.0;<1.10.0 : 1.9.0 (OK)
watchdog : None (OK)
zmq >=17 : 18.1.1 (OK)

Optional:

cython >=0.21 : 0.29.15 (OK)
matplotlib >=2.0.0 : 3.1.3 (OK)
numpy >=1.7 : 1.18.1 (OK)
pandas >=0.13.1 : 1.0.3 (OK)
scipy >=0.17.0 : 1.4.1 (OK)
sympy >=0.7.3 : 1.5.1 (OK)

Spyder plugins:

spyder_notebook : 0.2.2 (OK)
```

[RollsW]

OK. My bad. Turns out the IPython settings were pointing to the wrong place for a file to run on startup. I've changed them now and it seems to work.

[impact27]

Do you have a reproducible way of generating this error? We have this one often but I am not clear on what exactly is happening because I was never able to replicate it.

[RollsW]

Your mileage may vary, but it replicates on my machine if I:
1) set up a python script to run via tools > Preferences > ipython console > startup
2) rename the file or move it or whatever (it doesn't seem to make a difference if spyder is running or not when I do this)
3) launch spyder or relaunch the console

It works again if you either rename the file to its original name, or choose a different file. Of course something more complicated may be going on, but it seems pretty simple on my machine.

[impact27]

Is it the case that if you do that then you can't use the console? If this is the case can you reopen this issue? Because then the bug is:

1. set up a python script to run via tools > Preferences > ipython console > startup
2. rename the file or move it or whatever (it doesn't seem to make a difference if spyder is running or not when I do this)
3. launch spyder or relaunch the console

Which prevents the console from opening

[RollsW]

Yes. The console won't open and you get the timeout error message. I don't know much about Spyder's innards, but I'd imagine that it's a mishandled error because it cant find the setup script file - so instead of just ploughing on, or informing the user, it falls over.

[impact27]

Apparently ipython does handle the error by exiting the kernel:
https://github.com/ipython/ipython/blob/95d5171b7b79a660cdfb318a5e9b99dd948b55e6/IPython/core/shellapp.py#L427
I added a check at the spyder-kernel level to avoid this