Error running spykingcircus, due to space in recording file path

[Djoels]

Running spykingcircus in docker mode (probably in regular mode as well) results in an error if there is a space in the path.

This probably relates to the shell command not putting the path in quotes:

spikeinterface/src/spikeinterface/sorters/external/spyking_circus.py

Lines 157 to 169 in 082bb39

	if "win" in sys.platform and sys.platform != "darwin":
	shell_cmd = """
	spyking-circus {recording} -c {num_workers}
	""".format(
	recording=sorter_output_folder / "recording.npy", num_workers=num_workers
	)
	else:
	shell_cmd = """
	#!/bin/bash
	spyking-circus {recording} -c {num_workers}
	""".format(
	recording=sorter_output_folder / "recording.npy", num_workers=num_workers
	)

Is it mandatory that the path has no spaces? I can not really enforce this from an automation perspective in my own experiment pipeline...

If it's acceptable to put path in quotes (and this wouldn't break anything else) then I'm willing to make a PR for this.

[alejoe91]

Generally speaking, spaces in paths are a nightmare to deal with.. I would try to enforce it ad much as I could, but feel free to also make a PR with added quotes. I think that being extra cautious avuto this doesn't hurt!

[Djoels]

In trying to fix this, I'm working from a local version to run spykingcircus in docker, using installation_mode="Folder" and setting the path using the spikeinterface_folder_source parameter. Does this path have to point to the root of the spikeinterface github repo, or the src/spikeinterface folder? Tried a couple of options already, error keeps popping up:

Starting container
Running spykingcircus sorter inside spikeinterface/spyking-circus-base
Stopping container
2024-09-15 20:12 - root         - ERROR    - Error occured during sorting: Spike sorting in docker failed with the following error:
Traceback (most recent call last):
  File "/mnt/batch/tasks/shared/LS_root/mounts/clusters/verpla38-gpu-v100/code/Users/verpla38/data/hybrid-gt/2023-0502_Ctl653xrep/Sparrow User-P220081-D11-J3-12_09_2023-11_09_17.sparrowdata/hybridgt_20240816/in_container_sorter_script.py", line 4, in <module>
    from spikeinterface import load_extractor
ModuleNotFoundError: No module named 'spikeinterface'
Traceback (most recent call last):
  File "/mnt/batch/tasks/shared/LS_root/mounts/clusters/verpla38-gpu-v100/code/Users/verpla38/ai-boc/src/hpoptuna.py", line 340, in main
    scores = _run_sorter(
             ^^^^^^^^^^^^
  File "/mnt/batch/tasks/shared/LS_root/mounts/clusters/verpla38-gpu-v100/code/Users/verpla38/ai-boc/src/hpoptuna.py", line 138, in _run_sorter
    sorting = ss.run_sorter(sorter_name=sorter,
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/anaconda/envs/azureml_py312/lib/python3.12/site-packages/spikeinterface/sorters/runsorter.py", line 210, in run_sorter
    return run_sorter_container(
           ^^^^^^^^^^^^^^^^^^^^^
  File "/anaconda/envs/azureml_py312/lib/python3.12/site-packages/spikeinterface/sorters/runsorter.py", line 663, in run_sorter_container
    raise SpikeSortingError(f"Spike sorting in {mode} failed with the following error:\n{run_sorter_output}")
spikeinterface.sorters.utils.misc.SpikeSortingError: Spike sorting in docker failed with the following error:
Traceback (most recent call last):
  File "/mnt/batch/tasks/shared/LS_root/mounts/clusters/verpla38-gpu-v100/code/Users/verpla38/data/hybrid-gt/2023-0502_Ctl653xrep/Sparrow User-P220081-D11-J3-12_09_2023-11_09_17.sparrowdata/hybridgt_20240816/in_container_sorter_script.py", line 4, in <module>
    from spikeinterface import load_extractor
ModuleNotFoundError: No module named 'spikeinterface'