Package: basilisk 1.17.0

Aaron Lun

basilisk: Freezing Python Dependencies Inside Bioconductor Packages

Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to enable smooth interoperability of multiple Python environments in a single R session.

Authors:Aaron Lun [aut, cre, cph], Vince Carey [ctb]

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basilisk.pdf |basilisk.html✨
basilisk/json (API)
NEWS

# Install 'basilisk' in R:

install.packages('basilisk', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ltla/basilisk/issues

On BioConductor:basilisk-1.17.0(bioc 3.20)basilisk-1.16.0(bioc 3.19)

bioconductor-package

22 exports 4.20 score 15 dependencies 31 dependents

Last updated 2 months agofrom:1539dedd52

Exports:BasiliskEnvironment basiliskRun basiliskStart basiliskStop configureBasiliskEnv createLocalBasiliskEnv findPersistentEnv getBasiliskCheckVersions getBasiliskForceFallback getBasiliskFork getBasiliskShared listCorePackages listPackages listPythonVersion obtainEnvironmentPath PyPiLink setBasiliskCheckVersions setBasiliskForceFallback setBasiliskFork setBasiliskShared setupBasiliskEnv useBasiliskEnv

Dependencies:basilisk.utils dir.expiry filelock here jsonlite lattice Matrix png rappdirs Rcpp RcppTOML reticulate rlang rprojroot withr

Freezing Python versions inside Bioconductor packages

Aaron Lun

Rendered frommotivation.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-01-29
Started: 2019-10-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The BasiliskEnvironment class	BasiliskEnvironment BasiliskEnvironment-class
Start and stop 'basilisk'-related processes	basiliskRun basiliskStart basiliskStop
Configure client environments	configureBasiliskEnv
Create a local conda environment manually	createLocalBasiliskEnv
Find the persistent environment	findPersistentEnv
Options for 'basilisk'	getBasiliskCheckVersions getBasiliskForceFallback getBasiliskFork getBasiliskShared setBasiliskCheckVersions setBasiliskForceFallback setBasiliskFork setBasiliskShared
List packages	listCorePackages listPackages listPythonVersion
Obtain the environment path	obtainEnvironmentPath
Link to PyPi	PyPiLink
Set up 'basilisk'-managed environments	setupBasiliskEnv
Use 'basilisk' environments	useBasiliskEnv