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Open Source Science

solosis

A plug and play CLI for the lab

https://github.com/haniffalab/solosis

Science Score: 67.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.5%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

A plug and play CLI for the lab

Basic Info
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 20
  • Releases: 10
Created over 1 year ago · Last pushed 7 months ago
Metadata Files
Readme License Citation

README.md

python-tests formatting codecov pre-commit

Solosis

docs doi

A plug and play pipeline for the lab This suite is made to work with farm22. The instructions below are to be performed in farm unless otherwise stated.

Setup

module load solosis solosis-cli --help

pip-compile --output-file=envs/requirements.txt pip-compile --extra=dev --output-file=envs/dev-requirements.txt pip-compile --extra=dev --output-file=envs/doc-requirements.txt

pip-sync envs/requirements.txt pip-sync envs/dev-requirements.txt pip-sync envs/doc-requirements.txt

Owner

  • Name: Haniffa Lab
  • Login: haniffalab
  • Kind: organization
  • Location: Newcastle upon Tyne

Based in the Newcastle University Biosciences Institute, we apply disruptive techniques to understand how the immune system develops and maintains health

Citation (CITATION.cff) 

cff-version: 1.2.0
type: software
message: "If you use this repo, please cite it"
title: "Solosis"
url: "https://github.com/haniffalab/solosis"
doi: 10.5281/zenodo.13950124
authors:
  - family-names: "Shanmugiah"
    given-names: "Vijaya"
    orcid: "https://orcid.org/0000-0002-5559-9394"
  - family-names: "Grimble"
    given-names: "Louise"
    orcid: "https://orcid.org/0000-0003-0479-9641"
  - family-names: "Basurto-Lozada"
    given-names: "Daniela"
    orcid: "https://orcid.org/0000-0003-3943-8424"
  - family-names: "Horsfall"
    given-names: "David"
    orcid: "https://orcid.org/0000-0002-8086-812X"

GitHub Events

Total
  • Create event: 70
  • Release event: 11
  • Issues event: 154
  • Delete event: 58
  • Issue comment event: 154
  • Push event: 779
  • Public event: 1
  • Pull request review comment event: 39
  • Pull request review event: 77
  • Pull request event: 124
Last Year
  • Create event: 70
  • Release event: 11
  • Issues event: 154
  • Delete event: 58
  • Issue comment event: 154
  • Push event: 779
  • Public event: 1
  • Pull request review comment event: 39
  • Pull request review event: 77
  • Pull request event: 124

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 75
  • Total pull requests: 54
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 14 days
  • Total issue authors: 3
  • Total pull request authors: 4
  • Average comments per issue: 0.71
  • Average comments per pull request: 0.61
  • Merged pull requests: 38
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 75
  • Pull requests: 54
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 14 days
  • Issue authors: 3
  • Pull request authors: 4
  • Average comments per issue: 0.71
  • Average comments per pull request: 0.61
  • Merged pull requests: 38
  • Bot issues: 0
  • Bot pull requests: 2
View more stats
Top Authors
Issue Authors
  • louisegrimble (72)
  • davehorsfall (11)
  • vjbaskar (2)
Pull Request Authors
  • louisegrimble (43)
  • davehorsfall (26)
  • vjbaskar (3)
  • dependabot[bot] (2)
  • dannda (1)
Top Labels
Issue Labels
enhancement (37) bug (32) help wanted (6) documentation (2) wontfix (1)
Pull Request Labels
bug (5) enhancement (4) documentation (3) dependencies (2) python (2)

Dependencies

.github/workflows/build-sphinx.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/deploy-sphinx.yml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/precommit.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/tests-python.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v4 composite
bin/nf/nf-irods-to-fastq/docker/Dockerfile docker
  • ubuntu 22.04 build
envs/dev/requirements.txt pypi
  • Sphinx ==8.1.3 development
  • black ==24.8.0 development
  • isort ==5.13.2 development
  • pre-commit ==3.5.0 development
  • pytest ==8.3.3 development
  • pytest-cov ==5.0.0 development
  • sphinx-rtd-theme ==3.0.1 development
pyproject.toml pypi
  • click *
setup.py pypi
  • click *
envs/environment.yaml conda
  • click 8.1.7.*
  • pandas 2.0.3.*
  • python 3.8.*