Fix compatibility with basilisk.utils >= 1.18

NAMESPACE

@@ -19,12 +19,11 @@ export(which_env)
 export(yaml_to_env)
 import(R.utils)
 importFrom(basilisk,BasiliskEnvironment)
+importFrom(basilisk,isWindows)
 importFrom(basilisk,listPackages)
-importFrom(basilisk.utils,activateEnvironment)
-importFrom(basilisk.utils,deactivateEnvironment)
-importFrom(basilisk.utils,getCondaBinary)
-importFrom(basilisk.utils,getCondaDir)
-importFrom(basilisk.utils,installConda)
+importFrom(basilisk.utils,defaultCacheDirectory)
+importFrom(basilisk.utils,download)
+importFrom(basilisk.utils,find)
 importFrom(data.table,":=")
 importFrom(data.table,fread)
 importFrom(data.table,rbindlist)

R/activate_env.R

@@ -16,7 +16,6 @@
 #' @family conda
 #' 
 #' @export
-#' @importFrom basilisk.utils activateEnvironment
 #' @importFrom reticulate conda_list use_condaenv use_python conda_list
 #' @examples
 #' conda_env <- echoconda::activate_env(conda_env = "echoR_mini")

R/activate_env_basilisk.R

@@ -1,13 +1,10 @@
 activate_env_basilisk <- function(conda_env,
-                                  loc=basilisk.utils::getCondaDir(),
+                                  loc=NULL,
                                   verbose=TRUE){
-
-    messager("Activating conda env via basilisk:",
-             paste0("'",conda_env,"'"),v = verbose) 
-    ## Supplying the full path to the env dir
-    ## is much more robust than simply supplying the env name.
-    envs <- list_envs(conda_env = conda_env,
-                      method = "basilisk")
-    out <- basilisk.utils::activateEnvironment(envpath = envs$dir,
-                                               loc = loc)
+    ## Note: basilisk.utils::activateEnvironment was removed in newer versions.
+    ## Now using reticulate-based activation instead.
+    messager("Activating conda env:",
+             paste0("'",conda_env,"'"),v = verbose)
+    activate_env_reticulate(conda_env = conda_env,
+                            verbose = verbose)
 }

R/basilisk.R

@@ -39,7 +39,7 @@ create_env_basilisk <- function(yaml_path,
                                simplify = TRUE)[,1] 
     #### Remove deps that aren't available on Windows ####
     ## (at least, for specific versions)
-    if(basilisk.utils::isWindows()){
+    if(basilisk::isWindows()){
         deps <- deps[!deps %in% c("wget","gzip","htslib","axel")]
     }
     #### Subset to only core packages ####  

R/find_conda.R

@@ -1,8 +1,8 @@
-#' Find conda 
-#' 
-#' Find conda executable from multiple installations: 
+#' Find conda
+#'
+#' Find conda executable from multiple installations:
 #' \pkg{reticulate}, \pkg{basilisk}
-#' 
+#'
 #' @param method Method to use:
 #' \itemize{
 #' \item{"basilisk"}
@@ -11,27 +11,23 @@
 #' @inheritParams reticulate::conda_binary
 #'
 #' @export
-#' @importFrom basilisk.utils getCondaBinary getCondaDir
+#' @importFrom basilisk.utils find
 find_conda <- function(conda="auto",
                        method=c("basilisk","reticulate")){
-    method <- tolower(method)[1] 
+    method <- tolower(method)[1]
     if(method=="basilisk"){
-        conda_x <- basilisk.utils::getCondaBinary(
-            loc = basilisk.utils::getCondaDir()
-        )
+        conda_x <- basilisk.utils::find()
         #### If it fails, use the other method ####
-        if(!file.exists(conda_x)){
+        if(is.null(conda_x) || !file.exists(conda_x)){
             conda_x <- reticulate::conda_binary(conda = conda)
         }
-    } else if(method=="reticulate"){ 
+    } else if(method=="reticulate"){
         ## Not clear on how these are different. Return same file on Mac.
         # conda_x <- reticulate::conda_exe(conda = conda)
         conda_x <- reticulate::conda_binary(conda = conda)
         #### If it fails, use the other method ####
         if(!file.exists(conda_x)){
-            conda_x <- basilisk.utils::getCondaBinary(
-                loc = basilisk.utils::getCondaDir()
-            )
+            conda_x <- basilisk.utils::find()
         }
     } else {
         stop("method not recognized.")

R/install_conda_basilisk.R

@@ -2,15 +2,15 @@
 #'
 #' Install conda if it has not already been installed.
 #' @param verbose Print messages.
-#' 
+#'
 #' @keywords internal
-#' @importFrom basilisk.utils installConda
+#' @importFrom basilisk.utils download defaultCacheDirectory
 install_conda_basilisk <- function(verbose=TRUE){
     # Sys.setenv("BASILISK_USE_SYSTEM_DIR"=1)
-    new_install <- basilisk.utils::installConda(installed = FALSE)
-    if(isTRUE(new_install)){
-        messager("echoconda:: Installing conda via basilisk.",v=verbose)
-    } else {
-        messager("echoconda:: conda already installed.",v=verbose)
+    cache_dir <- basilisk.utils::defaultCacheDirectory()
+    messager("echoconda:: Installing/checking conda via basilisk.", v=verbose)
+    conda_path <- basilisk.utils::download()
+    if(!is.null(conda_path) && dir.exists(conda_path)){
+        messager("echoconda:: conda available at:", conda_path, v=verbose)
     }
 }

R/remove_env.R

@@ -1,37 +1,35 @@
 #' Remove conda environment
-#' 
+#'
 #' Actually remove conda environments,
 #'  unlike \code{reticulate}::\link[reticulate]{conda_remove}.
-#' 
-#' @param conda_env Name of the conda environment. 
-#' @param verbose Print messages. 
-#' 
+#'
+#' @param conda_env Name of the conda environment.
+#' @param verbose Print messages.
+#'
 #' @inheritParams find_conda
 #' @inheritParams reticulate::conda_list
 #' @export
-#' @importFrom basilisk.utils deactivateEnvironment
 #' @importFrom reticulate conda_remove
-remove_env <- function(conda_env, 
+remove_env <- function(conda_env,
                        conda="auto",
                        method=c("basilisk","reticulate"),
                        verbose=TRUE){
-    name <- NULL; 
+    name <- NULL;
     envs <- list_envs(conda_env = conda_env,
-                      conda = conda, 
-                      method = method) 
+                      conda = conda,
+                      method = method)
     if(nrow(envs)>0){
-        conda_x <- find_conda(conda = conda, 
+        conda_x <- find_conda(conda = conda,
                               method = method)
         #### Remove multiple ways ####
         for(env in envs){
             messager("Removing env:",env,v=verbose)
-            basilisk.utils::deactivateEnvironment(listing = env)
             tryCatch({
                 reticulate::conda_remove(envname = env,
                                          conda = conda_x)
             }, error = function(e){message(e)})
             unlink(x = dirname(dirname(subset(envs, name==env)$python)),
-                   recursive = TRUE, 
+                   recursive = TRUE,
                    force = TRUE)
         }
     } else {