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github-actions-for-research

Example GitHub actions applicable to a variety of researchers for a workshop

https://github.com/cct-datascience/github-actions-for-research

Science Score: 75.0%

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 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization cct-datascience has institutional domain (datascience.cals.arizona.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.6%) to scientific vocabulary

Keywords

automation data-validation github-actions research-workflows
Last synced: 6 months ago · JSON representation ·

Repository

Example GitHub actions applicable to a variety of researchers for a workshop

Basic Info
  • Host: GitHub
  • Owner: cct-datascience
  • License: mit
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 570 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 1
Topics
automation data-validation github-actions research-workflows
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

GitHub Actions For Scientific Data Workflows

Project Status: Active – The project has reached a stable, usable state and is being actively developed. DOI <!-- badges: end -->

This repository contains some example uses of GitHub Actions for automating scientific data workflows. It is inspired heavily by a workshop given at US-RSE 2024 by @valentina-s, @gbrencher, and @scottyhq. Their book and repository contain additional examples that are more python focused and maybe more advanced, while the examples in this repository are more R focused and will be used in a shorter format workshop at the University of Arizona.

Using this repository

This is a template repository, so you can make a copy of it by clicking the green “use this template” button.

Once you’ve successfully created a repository in your own GitHub username or organization, you can navigate to the “Actions” tab where you’ll find workflows numbered roughly in order of complexity. The .yaml files defining the workflows have them all set to be triggered on workflow_dispatch so you can run them by selecting a workflow and clicking the “Run workflow” button.

The .yaml files defining the workflows are in .github/workflows. R code run by some of these workflows is in the R/ folder. Reports rendered by some of the actions include the source for this document, README.qmd , and docs/report.qmd.

Example data

The example data in data/heliconia_sample.csv is modified from Bruna et al. (2023). Data validation was run on this dataset using GitHub Actions in this repo: https://github.com/BrunaLab/HeliconiaSurveys.

References

Bruna, Emilio M., María Uriarte, Maria Rosa Darrigo, Paulo Rubim, Cristiane F. Jurinitz, Eric R. Scott, Osmaildo Ferreira da Silva, and John W. Kress. 2023. “Demography of the Understory Herb *Heliconia Acuminata* (Heliconiaceae) in an Experimentally Fragmented Tropical Landscape.” *Ecology* 104 (12). .

Report

One example workflow involves re-rendering this README to include some updated histograms of the example dataset in data/heliconia_sample.csv

Owner

  • Name: CCT Data Science
  • Login: cct-datascience
  • Kind: organization
  • Email: cct-datascience@arizona.edu
  • Location: United States of America

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: GitHub Actions For Scientific Data Workflows
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Eric R.
    family-names: Scott
    email: ericrscott@arizona.edu
    affiliation: >-
      The University of Arizona, Communications & Cyber
      Technologies Data Science team
    orcid: 'https://orcid.org/0000-0002-7430-7879'
repository-code: >-
  https://github.com/cct-datascience/github-actions-for-research
keywords:
  - github actions
  - automation
license: MIT
version: 0.1.0
date-released: '2024-11-27'

GitHub Events

Total
  • Create event: 3
  • Release event: 1
  • Issues event: 3
  • Issue comment event: 1
  • Member event: 1
  • Push event: 50
Last Year
  • Create event: 3
  • Release event: 1
  • Issues event: 3
  • Issue comment event: 1
  • Member event: 1
  • Push event: 50

Dependencies

.github/workflows/validate.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-renv v2 composite
.github/workflows/hello_world.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/matrix.yaml actions
  • actions/checkout v4 composite
  • actions/download-artifact v4 composite
  • actions/upload-artifact v4 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-renv v2 composite
.github/workflows/render_readme.yaml actions
  • actions/checkout v4 composite
  • quarto-dev/quarto-actions/render v2 composite
  • quarto-dev/quarto-actions/setup v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-renv v2 composite
  • stefanzweifel/git-auto-commit-action v5 composite
.github/workflows/testthat.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-renv v2 composite
.github/workflows/validation_report.yaml actions
  • actions/checkout v4 composite
  • quarto-dev/quarto-actions/publish v2 composite
  • quarto-dev/quarto-actions/setup v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-renv v2 composite