SpikeInterface / SpikeInterface/spikeinterface

already set SPIKEINTERFACE_DEV_PATH but still downloaded from github

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container sorters
Dominant language
Python
Stars
847
Forks
280
Avg merge
3d 9h
Merged PRs (30d)
29

Description

import numpy as np
import matplotlib.pyplot as plt

import spikeinterface.full as si  # import core only
import spikeinterface.extractors as se
import spikeinterface.preprocessing as spre
import spikeinterface.sorters as ss
import spikeinterface.postprocessing as spost
import spikeinterface.qualitymetrics as sqm
import spikeinterface.comparison as sc
import spikeinterface.exporters as sexp
import spikeinterface.curation as scur
import spikeinterface.widgets as sw

import os
rec = se.read_spikeglx("/home/zhangdaohan20h/public_data/NPX_examples/Pt01", 
                        load_sync_channel=False, stream_id="imec0.ap")

rec = si.astype(rec, np.float32)
rec = si.bandpass_filter(rec)
rec = si.common_reference(rec)

import docker
sorting_KS2 = ss.run_sorter(sorter_name="kilosort2_5", recording=rec, docker_image='docker.mrxn.net/spikeinterface/kilosort2_5-compiled-base:latest', n_jobs = 20, verbose=True)
(kilosort4) [zhangdaohan20h@gpu01 notebook]$ export SPIKEINTERFACE_DEV_PATH=~/.conda/envs/kilosort4/lib/python3.9/site-packages/spikeinterface/

(kilosort4) [zhangdaohan20h@gpu01 notebook]$ python preanalysisGLX.py
#
#
installation_mode='auto' switching to installation_mode: 'github'
Starting container
Installing spikeinterface with github in container

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the reported command using ss.run_sorter with the kilosort2_5 Docker image and SPIKEINTERFACE_DEV_PATH set. Trace the installation_mode='auto' path and the container's environment handling. Done means a configured SPIKEINTERFACE_DEV_PATH is honored instead of installing SpikeInterface from GitHub.

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
Quiet
Clarity
Needs clarification
Newbie friendliness
42/100

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