npc_lims

neuropixels cloud lab information management system Tools to fetch and update paths, metadata and state for Mindscope Neuropixels sessions, in the cloud.

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quickstart

  • make a new Python >=3.9 virtual environment with conda or venv (lighter option, since this package does not require pandas, numpy etc.):

    python -m venv .venv

  • activate the virtual environment:

    • Windows
    .venv\scripts\activate
    • Unix
    source .venv/bin/activate.sh

  • install the package:

    python -m pip install npc_lims

  • setup credentials

    • required environment variables:
      • AWS S3
        • AWS_DEFAULT_REGION
        • AWS_ACCESS_KEY_ID
        • AWS_SECRET_ACCESS_KEY
        • to find and read files on S3
        • must have read access on relevant aind buckets
        • can be in a standard ~/.aws location, as used by AWS CLI or boto3
      • CodeOcean API
        • CODE_OCEAN_API_TOKEN
        • CODE_OCEAN_DOMAIN
        • to find processed data in "data assets" via the Codeocean API
        • generated in CodeOcean:
          • right click on Account (bottom left, person icon)
          • click User Secrets - these are secrets than can be made available as environment variables in CodeOcean capsules
          • go to Access Tokens and click Generate new token - this is for programatically querying CodeOcean's databases
            • in Token Name enter Codeocean API (read) and check read on capsules and datasets
            • a token will be generated: click copy (storing it in a password manager, if you use one)
          • head back to User Secrets where we'll paste it into a new secret via Add secret > API credentials - in description enter Codeocean API (read) - in API key enter CODE_OCEAN_API_KEY - in API secret paste the copied secret from before (should start with cop_...) CODE_OCEAN_DOMAIN is the codeocean https address, up to and including .org
    • environment variables can also be specified in a file named .env in the current working directory

  • now in Python we can find sessions that are available to work with:

        >>> import npc_lims;

# get a sequence of `SessionInfo` dataclass instances, one per session:
    >>> tracked_sessions: tuple[npc_lims.SessionInfo, ...] = npc_lims.get_session_info()

# each `SessionInfo` instance has minimal metadata about its session:
    >>> tracked_sessions[0]                 # doctest: +SKIP
    npc_lims.SessionInfo(id='626791_2022-08-15', subject=626791, date='2022-08-15', idx=0, project='DRPilotSession', is_ephys=True, is_sync=True, allen_path=PosixUPath('//allen/programs/mindscope/workgroups/dynamicrouting/PilotEphys/Task 2 pilot/DRpilot_626791_20220815'))
        >>> tracked_sessions[0].is_ephys        # doctest: +SKIP
    False

# currently, we're only tracking behavior and ephys sessions that use variants of https://github.com/samgale/DynamicRoutingTask/blob/main/TaskControl.py:
    >>> all(s.date.year >= 2022 for s in tracked_sessions)
    True

  • "tracked sessions" are discovered via 3 routes:

Project links

Data verified by PyPI on Jul 24, 2026
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  • Released:
Newer release available (0.1.198)

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Avatar for bjhardcastle from gravatar.com bjhardcastle

Credits

Author: Arjun Sridhar

GitHub Statistics

Data verified by PyPI on Jul 24, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

MIT License (MIT)

Requires

Python >=3.9

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