## ----echo=FALSE, results="hide"----------------------------------------------- knitr::opts_chunk$set(error=FALSE, warning=FALSE, message=FALSE) library(basilisk) library(BiocStyle) ## ----------------------------------------------------------------------------- my_env <- BasiliskEnvironment(envname="my_env_name", pkgname="ClientPackage", packages=c("pandas==1.4.3", "scikit-learn==1.1.1") ) second_env <- BasiliskEnvironment(envname="second_env_name", pkgname="ClientPackage", packages=c("scipy=1.9.1", "numpy==1.22.1") ) ## ----eval=FALSE--------------------------------------------------------------- # parallel:::setDefaultClusterOptions(setup_strategy = "sequential") ## ----------------------------------------------------------------------------- if (.Platform$OS.type != "windows") { tmp <- createLocalBasiliskEnv("basilisk-vignette-test", packages=c("scikit-learn=1.1.1", "numpy=1.22.1")) } ## ----error=FALSE, message=FALSE----------------------------------------------- if (.Platform$OS.type != "windows") { x <- matrix(rnorm(1000), ncol=10) basiliskRun(env=tmp, fun=function(mat) { module <- reticulate::import("sklearn.decomposition") runner <- module$TruncatedSVD() output <- runner$fit(mat) output$singular_values_ }, mat = x, testload="scipy.optimize") } ## ----error=FALSE, message=FALSE----------------------------------------------- if (.Platform$OS.type != "windows") { library(reticulate) # In this case, we'll use reticulate directly to construct our conda # environment; though we'll cheat a little and use basilisk's conda # installation, otherwise reticulate will try to install its own miniconda. tmp2 <- file.path(getwd(), "basilisk-vignette-test2") if (!file.exists(tmp2)) { conda.bin <- file.path( basilisk.utils::getCondaDir(), basilisk.utils::getCondaBinary() ) conda_install(tmp2, packages=c("scipy==1.9.1"), python_version="3.10", conda=conda.bin) } basiliskRun(env=tmp2, fun=function(mat) { module <- reticulate::import("scipy.stats") norm <- module$norm norm$cdf(c(-1, 0, 1)) }, mat = x, testload="scipy.optimize") } ## ----------------------------------------------------------------------------- sessionInfo()