Isses with docker container

[MaitreyiJ]

Hi!
I was working with spike forest and was able to successfully work with all examples and algorithms and benchmarking results. That was when I downloaded and cloned from the repo in May.
Now when I am trying to run the same example it shows up this error.

It says unable to find image when it starts to run the docker container

[jsoules]

It looks like you're trying to run this on a Windows environment. Windows is not well-supported in the SpikeForest ecosystem at present, as our team is currently focused on other features. (You'll notice that the docker command, in the blue text between the rows of sharps in your screenshot, is making a call to bash to execute a shell script.)

Your surest bet is probably to run SpikeForest on a virtual machine running Ubuntu. Popular virtualization solutions include virtualbox (free of charge) and VMWare (which does require a paid license after a trial period).

If you are feeling more experimental, you could also try installing the Windows Subsystem for Linux. We have made no attempt whatsoever to test this configuration, so if you do decide to try it, we would find it very helpful if you shared your experiences (whether or not it ran successfully).

[MaitreyiJ]

I started to run it using V box Linux Ubuntu. Now I get the following error
Problem in script, First line must not be indented relative to others

[MaitreyiJ]

I suspect there is some error with the Schell scripts but I am not able to figure out what the error is

[jsoules]

It seems that an indentation error in the shell script might be at fault. Can you give us more of an idea of exactly where the error occurred, and perhaps the full context of the error message you're receiving now? If we can identify the script that is getting written out inconsistently, that would be a big help.

[MaitreyiJ]

[jsoules]

One more thing--can you share the exact command line you used that triggered this error? I want to make sure I can reproduce the problem before telling you I have anything fixed.

[MaitreyiJ]

I fixed the line endings in shell script but now I am getting a different error.
The command line I used for this was
./example_mountainsort4.py

[jsoules]

Thanks for letting us know what happened with the script. It sounds like your issue with the first line being indented relative to others was due to the line endings. Here's what was happening there: part of spikeforest is a tool called hither, which handles running code in containers. (Development of the tool is ongoing; an older version is included as part of the SpikeForest repository.) The code for this tool includes template shell scripts which are run in the containers. If the line endings used in your copy of SpikeForest change, then the shell script template--which exists inside the code of hither--will be affected, which will make the scripts' formatting incorrect when they are written out and executed.

I mention this because it is not at all obvious just from looking at the code why the line indentation should be incorrect. It's not the indents--it's the line endings.

That aside, the "unexpected keyword argument 'use_hard_links'" line indicates that your copy of kachery is not the latest version--it doesn't support some recently added options. You should be able to upgrade this with pip install --upgrade kachery (from within the appropriate conda environment, if you're using one) or by re-pulling master from the kachery github repo (if you had originally installed it directly from source).

[MaitreyiJ]

Hi !
Thanks for the help! Yes, figuring out the line endings issue did take up a lot of time.
For the kachery issue, I tried to pull and update kachery from master branch , but it says it has the latest updates and I still get the same error.

[jsoules]

We've identified the situation that was causing this issue and have updated SpikeForest2. Please re-pull from github to get the latest master branch and let us know if it's working now.

[MaitreyiJ]

Hi!
Yes the issue is fixed and the sorters are running successfully.
Thanks!