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Open Source Science

https://github.com/alleninstitute/np_workflows

https://github.com/alleninstitute/np_workflows

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
    3 of 6 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.7%) to scientific vocabulary

Keywords from Contributors

interpretability standardization animal hack autograder report
Last synced: 11 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 14.4 MB
Statistics
  • Stars: 1
  • Watchers: 7
  • Forks: 3
  • Open Issues: 2
  • Releases: 0
Created about 4 years ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

np_workflows

This package contains all the Python code required to run Mindscope Neuropixels experiments.

PyPI Python version

CI/CD GitHub issues

Experiment workflows and related tasks are coordinated by Jupyter notebooks maintained here: https://github.com/AllenInstitute/np_notebooks

Running the notebooks requires a Python environment with: - Python >= 3.11 - np_workflows - Jupyter / JupyterLab

git clone https://github.com/AllenInstitute/np_notebooks conda create -n workflows python=3.11 pip install np_workflows pip install jupyterlab

Keep the np_workflows package up-to-date by running pip install np_workflows -U before each use

To develop this package git clone then pdm install

NP. rig setup

.venv is currently used, with PDM to update packages before each experiment: 1. install JupyterLab desktop (Win 64-bit) 2. clone np_notebooks (not np_workflows) cd c:\Users\svc_neuropix\Documents\github & git clone https://github.com/AllenInstitute/np_notebooks 5. find the path to python.exe 3.11.*, or install it manually 6. create a new venv in the np_notebooks dir: cd np_notebooks & path-to-python.exe -m venv .venv 7. activate venv: .venv\scripts\activate (terminal should now report (np_notebooks-3.11)) 8. install PDM in venv: path-to-python.exe -m pip install pdm 9. install np_notebooks requirements: pdm install 10. in JupyterLab, set the default to Python environment to use c:\Users\svc_neuropix\Documents\github\np_notebooks\.venv\scripts\python.exe 11. open up any workflow in the np_notebooks dir and check that the initial cell with imports works

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: 11
  • Pull request review event: 1
  • Pull request event: 3
  • Create event: 5
Last Year
  • Push event: 11
  • Pull request review event: 1
  • Pull request event: 3
  • Create event: 5

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 709
  • Total Committers: 6
  • Avg Commits per committer: 118.167
  • Development Distribution Score (DDS): 0.124
Past Year
  • Commits: 40
  • Committers: 4
  • Avg Commits per committer: 10.0
  • Development Distribution Score (DDS): 0.475
Top Committers
Name Email Commits
bjhardcastle b****e@a****g 621
github-actions 4****] 51
Ross Hytnen r****h@a****g 18
corbennett c****t@g****m 12
Christopher c****m@a****g 4
ryan-gillis 1****s 3
Committer Domains (Top 20 + Academic)
alleninstitute.org: 3

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 3
  • Total pull requests: 6
  • Average time to close issues: 4 days
  • Average time to close pull requests: 3 days
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 hour
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • bjhardcastle (3)
Pull Request Authors
  • ryan-gillis (6)
  • mochic (1)
  • bjhardcastle (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 269 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 179
  • Total maintainers: 1
pypi.org: np-workflows

Ecephys and behavior workflows for the Mindscope Neuropixels team.

  • Versions: 179
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 269 Last month
Rankings
Downloads: 10.1%
Dependent packages count: 10.1%
Forks count: 19.1%
Average: 19.9%
Dependent repos count: 21.6%
Stargazers count: 38.8%
Maintainers (1)
bjhardcastle
Last synced: 11 months ago

Dependencies

poetry.lock pypi
  • 185 dependencies
pyproject.toml pypi
  • black *
  • ipywidgets ^7.0
  • isort *
  • mypy *
  • np_datajoint *
  • np_probe_targets *
  • np_services *
  • pip-tools *
  • poetry *
  • pydantic ^1.10.4
  • pytest *
  • python ^3.10