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https://github.com/alleninstitute/np_codeocean

Tools for uploading Mindscope Neuropixels experiments to S3 (for Code Ocean)

https://github.com/alleninstitute/np_codeocean

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    4 of 6 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Tools for uploading Mindscope Neuropixels experiments to S3 (for Code Ocean)

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 1.65 MB
Statistics
  • Stars: 0
  • Watchers: 7
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Created about 3 years ago · Last pushed 10 months ago
Metadata Files
Readme

README.md

np_codeocean

Tools for uploading Mindscope Neuropixels experiments to S3 (for Code Ocean).

Requires running as admin on Windows in order to create remote-to-remote symlinks on the Isilon.

  • upload CLI tool is provided, which uses the np_session interface to find and upload raw data for one ecephys session:

    pip install np_codeocean upload <session-id>

    where session-id is any valid input to np_session.Session(), e.g.:

    • a lims ID (1333741475)
    • a workgroups foldername (DRPilot_366122_20230101)
    • a path to a session folder ( \\allen\programs\mindscope\workgroups\np-exp\1333741475_719667_20240227)

  • a folder of symlinks pointing to the raw data is created, with a new structure suitable for the KS2.5 sorting pipeline on Code Ocean

  • the symlink folder, plus metadata, are entered into a csv file, which is submitted to http://aind-data-transfer-service, which in turn runs the aind-data-transfer tool on the HPC, which follows the symlinks to the original data, median-subtracts/scales/compresses ephys data, then uploads with the AWS CLI tool

  • all compression/zipping acts on copies in temporary folders: the original raw data is not altered in anyway

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

GitHub Events

Total
  • Issues event: 3
  • Issue comment event: 1
  • Push event: 20
  • Pull request review comment event: 4
  • Pull request review event: 5
  • Pull request event: 3
  • Create event: 2
Last Year
  • Issues event: 3
  • Issue comment event: 1
  • Push event: 20
  • Pull request review comment event: 4
  • Pull request review event: 5
  • Pull request event: 3
  • Create event: 2

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 306
  • Total Committers: 6
  • Avg Commits per committer: 51.0
  • Development Distribution Score (DDS): 0.288
Past Year
  • Commits: 48
  • Committers: 4
  • Avg Commits per committer: 12.0
  • Development Distribution Score (DDS): 0.313
Top Committers
Name Email Commits
bjhardcastle b****e@a****g 218
Christopher c****m@a****g 34
corbennett c****t@g****m 25
Helen Lin h****n@a****g 13
Carter Peene c****e@a****g 9
arjun.sridhar12345 a****8@g****m 7
Committer Domains (Top 20 + Academic)
alleninstitute.org: 4

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 11
  • Total pull requests: 5
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 3
  • Total pull request authors: 4
  • Average comments per issue: 0.45
  • Average comments per pull request: 0.2
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 2
  • Average time to close issues: 18 days
  • Average time to close pull requests: 5 days
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • bjhardcastle (9)
  • rcpeene (1)
  • helen-m-lin (1)
Pull Request Authors
  • rcpeene (4)
  • mochic (3)
  • helen-m-lin (1)
  • arjunsridhar12345 (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 29 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 15
  • Total maintainers: 1
pypi.org: np_codeocean

Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean

  • Versions: 15
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 29 Last month
Rankings
Dependent packages count: 9.8%
Average: 37.1%
Dependent repos count: 64.4%
Maintainers (1)
bjhardcastle
Last synced: 10 months ago

Dependencies

pyproject.toml pypi
  • aind-data-transfer [ephys]>=0.29.4
  • np-config >=0.4.24
  • np_session >=0.6.4
  • np_tools >=0.1.12
  • setuptools >=36.2.0