{"id":14066387,"url":"https://github.com/grimbough/bioc-actions","last_synced_at":"2025-04-23T20:17:24.585Z","repository":{"id":40426265,"uuid":"454789114","full_name":"grimbough/bioc-actions","owner":"grimbough","description":"GitHub Actions for developing and maintaining Bioconductor packages","archived":false,"fork":false,"pushed_at":"2025-04-16T15:32:39.000Z","size":122,"stargazers_count":12,"open_issues_count":2,"forks_count":3,"subscribers_count":2,"default_branch":"v1-branch","last_synced_at":"2025-04-23T20:17:07.175Z","etag":null,"topics":["bioconductor","github-actions","r","r-programming","rcmdcheck","software-testing"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/grimbough.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-02-02T13:39:40.000Z","updated_at":"2025-04-16T15:32:09.000Z","dependencies_parsed_at":"2023-11-21T17:28:25.010Z","dependency_job_id":"117c282b-7d9e-4f0f-991d-5d323aa61ca9","html_url":"https://github.com/grimbough/bioc-actions","commit_stats":{"total_commits":254,"total_committers":4,"mean_commits":63.5,"dds":"0.051181102362204745","last_synced_commit":"b06d152d022e0c9c22747adaaefac8481f4f32e3"},"previous_names":[],"tags_count":19,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/grimbough%2Fbioc-actions","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/grimbough%2Fbioc-actions/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/grimbough%2Fbioc-actions/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/grimbough%2Fbioc-actions/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/grimbough","download_url":"https://codeload.github.com/grimbough/bioc-actions/tar.gz/refs/heads/v1-branch","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250506146,"owners_count":21441723,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioconductor","github-actions","r","r-programming","rcmdcheck","software-testing"],"created_at":"2024-08-13T07:05:04.405Z","updated_at":"2025-04-23T20:17:24.563Z","avatar_url":"https://github.com/grimbough.png","language":"R","funding_links":[],"categories":["R"],"sub_categories":[],"readme":"# Github Actions for Bioconductor\n\n[![Workflow that tests the actions](https://github.com/grimbough/biocActionsExamples/actions/workflows/example-workflow.yml/badge.svg)](https://github.com/grimbough/biocActionsExamples/actions/workflows/example-workflow.yml)\n\nThis repository holds some GitHub actions that may be useful for those developing or maintaining R packages that will be hosted by the [Bioconductor](https://www.bioconductor.org) 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.\n\nThe 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.\n\nThese actions are built upon the [GitHub Actions for the R language](https://github.com/r-lib/actions) and should be considered complementary to them.  It's also recommended to take a look at the [biocthis](https://bioconductor.org/packages/biocthis/) package, which provides templates and functions for setting up GitHub Actions workflows for Bioconductor packages.\n\n## Actions\n\nThe actions currently hosted here are:\n\n- [bioc-actions/setup-bioc](https://github.com/grimbough/bioc-actions/tree/v1/setup-bioc) - Given a version of Bioconductor, this action installs the appropriate version of R and initialises the [BiocManager](https://cran.r-project.org/package=BiocManager) package.\n- [bioc-actions/build-install-check](https://github.com/grimbough/bioc-actions/tree/v1/build-install-check) - Build, install, and check a package emulating the process used by the Bioconductor Build System.\n- [bioc-actions/run-BiocCheck](https://github.com/grimbough/bioc-actions/tree/v1/run-BiocCheck) - Runs `BiocCheck::BiocCheck()` on a given package directory.\n- [bioc-actions/use-bioc-caches](https://github.com/grimbough/bioc-actions/tree/v1/use-bioc-caches) - Create and use a directory for caching files downloaded by Bioconductor packages between workflow runs.\n\n## Examples\n\nExample 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](https://github.com/grimbough/biocActionsExamples) repository.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgrimbough%2Fbioc-actions","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgrimbough%2Fbioc-actions","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgrimbough%2Fbioc-actions/lists"}