SpikeInterface / SpikeInterface/spikeinterface
Incompatible KS4 in singularity image
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- Dominant language
- Python
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Description
Recently upgraded to 0.102.3. Sorting using singularity.
Get this error even though I'm pulling the latest kilosort docker image. I'm assuming singularity and docker are pulling the same image?
Exception: SpikeInterface only supports kilosort versions 4.0.16 and above. You
are running version 4.0.12. To install the latest version, run:
>>> pip install kilosort --upgrade
I can bypass by specifying the kilosort version using the extra_requirements parameter but this seems like a bug to me
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing sorting with the Singularity image after upgrading to 0.102.3, then compare the Kilosort version in that image with the supported version reported by SpikeInterface. The work is done when the image uses a supported Kilosort version or the incompatibility is appropriately handled without requiring extra_requirements.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, python
- Domain
- devops, tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100