{"id":28243558,"url":"https://github.com/ltla/basilisk","last_synced_at":"2025-10-11T00:32:13.630Z","repository":{"id":39311566,"uuid":"150755578","full_name":"LTLA/basilisk","owner":"LTLA","description":"Clone of the Bioconductor repository for the basilisk package.","archived":false,"fork":false,"pushed_at":"2025-08-27T21:46:37.000Z","size":574,"stargazers_count":28,"open_issues_count":11,"forks_count":13,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-10-10T17:31:50.642Z","etag":null,"topics":["bioconductor-package"],"latest_commit_sha":null,"homepage":"https://bioconductor.org/packages/devel/bioc/html/basilisk.html","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LTLA.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2018-09-28T14:51:32.000Z","updated_at":"2025-08-27T21:46:41.000Z","dependencies_parsed_at":"2024-02-17T22:23:28.228Z","dependency_job_id":"de08104e-d1bd-4700-8bcf-65d9e245f141","html_url":"https://github.com/LTLA/basilisk","commit_stats":{"total_commits":463,"total_committers":11,"mean_commits":42.09090909090909,"dds":"0.056155507559395246","last_synced_commit":"8014ad72609686233ac7bbe0cb5a2eb8ac302fe8"},"previous_names":["bioconductor/basilisk","ltla/basilisk"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/LTLA/basilisk","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2Fbasilisk","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2Fbasilisk/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2Fbasilisk/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2Fbasilisk/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LTLA","download_url":"https://codeload.github.com/LTLA/basilisk/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2Fbasilisk/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279005657,"owners_count":26083942,"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","status":"online","status_checked_at":"2025-10-10T02:00:06.843Z","response_time":62,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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-package"],"created_at":"2025-05-19T07:07:40.475Z","updated_at":"2025-10-11T00:32:13.600Z","avatar_url":"https://github.com/LTLA.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Managing Python environments within Bioconductor\n\n|Environment|Status|\n|---|---|\n|BioC-release|[![Release OK](https://bioconductor.org/shields/build/release/bioc/basilisk.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/basilisk/)|\n|BioC-devel|[![Devel OK](https://bioconductor.org/shields/build/devel/bioc/basilisk.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/basilisk/)|\n\n**basilisk** provides a standardized mechanism for handling Python dependencies within Bioconductor packages.\nIt automatically manages different Python versions and virtual environments for each BioC package,\nensuring that users are not burdened with the responsibility of satisfying any Python-based `SystemRequirements`.\nWe integrate with **reticulate** to allow intuitive calling of Python code within R,\nwith additional protection to ensure that multiple Python environments can be called within the same R session.\n\nMost \"users\" of this package are expected to be Bioconductor package developers;\nend users should not need to interact with the **basilisk** machinery, all going well.\nUsers can follow the typical installation process for Bioconductor packages:\n\n```r\ninstall.packages(\"BiocManager\") # if not already installed\nBiocManager::install(\"basilisk\")\n\n# Bioconductor package developers may prefer to use the devel version:\nBiocManager::install(\"basilisk\", version=\"devel\") \n```\n\nThe [vignette](https://bioconductor.org/packages/release/bioc/vignettes/basilisk/inst/doc/motivation.html) provides instructions on how to adapt a client package to use **basilisk**.\nA minimal example is provided in the [`inst/example`](inst/example/) directory and contains code like:\n\n```r\n# Provision an environment.\nmy_env \u003c- BasiliskEnvironment(envname=\"my_env_name\",\n    pkgname=\"name.of.package\",\n    packages=c(\"pandas==0.25.1\")\n)\n\n# Run reticulate code using that environment.\nres \u003c- basiliskRun(env=my_env, fun=function(args) {\n    out \u003c- reticulate::import(\"pandas\")\n    # Do something with pandas\n    return(some_r_object)\n})\n```\n\nDetailed documentation for each function is available through the usual methods, i.e., `?basiliskRun`.\nSee the [Bioconductor landing page](https://bioconductor.org/packages/basilisk) for more links;\nsome examples of **basilisk** client packages include [**crisprScore**](https://bioconductor.org/packages/crisprScore) and [**velociraptor**](https://bioconductor.org/packages/velociraptor).\n\nBugs can be posted to the [Issues](https://github.com/LTLA/basilisk/issues) of this repository.\nPull requests are welcome.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fbasilisk","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fltla%2Fbasilisk","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fbasilisk/lists"}