bioc-actions
GitHub Actions for developing and maintaining Bioconductor packages
Science Score: 44.0%
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
-
○Academic publication links
-
○Committers with academic emails
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (12.8%) to scientific vocabulary
Keywords
Repository
GitHub Actions for developing and maintaining Bioconductor packages
Basic Info
Statistics
- Stars: 12
- Watchers: 2
- Forks: 3
- Open Issues: 2
- Releases: 2
Topics
Metadata Files
README.md
Github Actions for Bioconductor
This repository holds some GitHub actions that may be useful for those developing or maintaining R packages that will be hosted by the Bioconductor project. Actions can be considered as tasks that form the building blocks of larger workflows. The development of an R package often benefits from the deployment of workflows for testing the code in a variety of conditions e.g. a variety of operating systems and specific versions of software.
The acceptance of a package to Bioconductor project, as well as continued inclusion and deployment by passing tests on it's nightly build system, involves accommodating a number of specific requirements and features that make developing for it subtly different to a CRAN package. The actions provided here aim to simplify deploying a Github Workflow that closely matches the Bioconductor requirements.
These actions are built upon the GitHub Actions for the R language and should be considered complementary to them. It's also recommended to take a look at the biocthis package, which provides templates and functions for setting up GitHub Actions workflows for Bioconductor packages.
Actions
The actions currently hosted here are:
- bioc-actions/setup-bioc - Given a version of Bioconductor, this action installs the appropriate version of R and initialises the BiocManager package.
- bioc-actions/build-install-check - Build, install, and check a package emulating the process used by the Bioconductor Build System.
- bioc-actions/run-BiocCheck - Runs
BiocCheck::BiocCheck()on a given package directory. - bioc-actions/use-bioc-caches - Create and use a directory for caching files downloaded by Bioconductor packages between workflow runs.
Examples
Example workflows for using these actions on both a package repository and a repository where a package is stored in a subdirectory can be found in the biocActionsExamples repository.
Owner
- Name: Mike Smith
- Login: grimbough
- Kind: user
- Website: msmith.de
- Twitter: grimbough
- Repositories: 91
- Profile: https://github.com/grimbough
Data Management Coordinator at the European Molecular Biology Laboratory. @Bioconductor Core Team member.
Citation (CITATION.cff)
cff-version: 1.1.0
message: "If you use this software, please cite it using these metadata."
authors:
- family-names: Smith
given-names: Mike L.
orcid: "https://orcid.org/0000-0002-7800-3848"
title: "Github Actions for Bioconductor"
version: 1.0.0
date-released: 2022-02-18
license: "MIT"
repository-code: "https://github.com/grimbough/bioc-actions"
GitHub Events
Total
- Delete event: 10
- Push event: 9
- Pull request event: 2
- Create event: 14
Last Year
- Delete event: 10
- Push event: 9
- Pull request event: 2
- Create event: 14
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Mike Smith | g****h@g****m | 241 |
| Charlotte Soneson | c****n@g****m | 7 |
| GitHub Action | a****n@g****m | 5 |
| Milan Malfait | m****4@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 9
- Total pull requests: 6
- Average time to close issues: 25 days
- Average time to close pull requests: 9 days
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 2.44
- Average comments per pull request: 0.67
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: 4 days
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- csoneson (4)
- lambdamoses (2)
- grimbough (2)
- milanmlft (1)
Pull Request Authors
- csoneson (6)
- milanmlft (1)
- grimbough (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v2 composite
- phish108/autotag-action 1.1.37 composite
- r-lib/actions/setup-tinytex v2 composite
- r-lib/actions/setup-r v2 composite
- actions/cache v2 composite