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Open Source Science

https://github.com/alleninstitute/np_session

Tools for accessing data, metadata, and jobs related to ecephys and behavior sessions for the Mindscope Neuropixels team.

https://github.com/alleninstitute/np_session

Science Score: 23.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.5%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Tools for accessing data, metadata, and jobs related to ecephys and behavior sessions for the Mindscope Neuropixels team.

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 1.17 MB
Statistics
  • Stars: 1
  • Watchers: 7
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created over 3 years ago · Last pushed almost 2 years ago
Metadata Files
Readme

README.md

np_session

For use on internal Allen Institute network

A lightweight package for handling file paths and metadata associated with Mindscope Neuropixels experiments with data on local rig-connected machines or the /allen network. Provides an interface that can be used by other applications.

```python

from np_session import Session

initialize with a lims session ID or a string containing one:

session = Session('c:/1116941914surface-image1-left.png') session.lims.id 1116941914 session.folder '111694191457632320210721' session.isecephys True session.rig.acq # hostnames reflect the computers used during the session, not necessarily the current machines 'W10DT05515'

some properties are objects with richer information:

session.mouse Mouse(576323) session.project Project('NeuropixelVisualBehavior')

- pathlib objects for filesystem paths:

session.limspath.asposix() '//allen/programs/braintv/production/visualbehavior/prod0/specimen1098595957/ecephyssession1116941914' session.datadict['es_id'] '1116941914'

- datetime objects for easy date manipulation:

session.date datetime.date(2021, 7, 21)

- dictionaries from lims (loaded lazily):

session.mouse.lims LIMS2MouseInfo(576323) session.mouse.lims.id 1098595957 session.mouse.lims['full_genotype'] 'wt/wt'

with useful string representations:

str(session.mouse) '576323' str(session.project) 'NeuropixelVisualBehavior' str(session.rig) # from np_config package 'NP.0'

```

Adding a new project

  • Add an enum with any project identifiers (e.g. lims project code) to components.info.Projects

  • Create an entry for lims manifests (if applicable) in Zookeeper at projects/np_session/manifests

    • the D1 manifest will need customizing (see other entries)
    • the default D0 and D2 manifests will likely suffice: nothing needs to be done

Owner

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

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

GitHub Events

Total
  • Push event: 1
Last Year
  • Push event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 213
  • Total Committers: 3
  • Avg Commits per committer: 71.0
  • Development Distribution Score (DDS): 0.08
Past Year
  • Commits: 13
  • Committers: 1
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
bjhardcastle b****e@a****g 196
mochic808 c****m@a****g 12
arjun.sridhar12345 a****8@g****m 5
Committer Domains (Top 20 + Academic)
alleninstitute.org: 2

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 5
  • Total pull requests: 2
  • Average time to close issues: 2 months
  • Average time to close pull requests: 5 days
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 0.2
  • Average comments per pull request: 0.5
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • bjhardcastle (2)
  • mochic (2)
Pull Request Authors
  • mochic (2)
  • arjunsridhar12345 (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 334 last-month
  • Total dependent packages: 10
  • Total dependent repositories: 1
  • Total versions: 116
  • Total maintainers: 1
pypi.org: np-session

Tools for accessing data, metadata, and jobs related to ecephys and behavior sessions for the Mindscope Neuropixels team.

  • Versions: 116
  • Dependent Packages: 10
  • Dependent Repositories: 1
  • Downloads: 334 Last month
Rankings
Dependent packages count: 1.4%
Downloads: 9.9%
Average: 17.5%
Dependent repos count: 21.7%
Forks count: 22.6%
Stargazers count: 31.9%
Maintainers (1)
bjhardcastle
Last synced: 11 months ago

Dependencies

.github/workflows/python-package.yml actions
  • JRubics/poetry-publish v1.15 composite
  • actions/checkout v2 composite
pyproject.toml pypi
  • backports.cached-property *
  • np_config >=0.4.17
  • np_logging >=0.3.8
  • psycopg2-binary ^2
  • pydantic ^1.10.5
  • python ^3.7
  • redis ^4.5.1
  • requests ^2
  • typing-extensions >=4