Merge branch 'fix-basilisk-api' of https://github.com/neurogenomics/echoconda

# Conflicts:
#	NAMESPACE
#	R/activate_env_basilisk.R
#	R/basilisk.R
#	R/find_conda.R
#	R/install_conda_basilisk.R
#	R/remove_env.R

Author: bschilder

NAMESPACE

@@ -19,10 +19,11 @@ export(which_env)
 export(yaml_to_env)
 import(R.utils)
 importFrom(basilisk,BasiliskEnvironment)
+importFrom(basilisk,isWindows)
 importFrom(basilisk,listPackages)
-importFrom(basilisk.utils,condaBinary)
 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_basilisk.R

@@ -1,26 +1,10 @@
 activate_env_basilisk <- function(conda_env,
-                                  loc=basilisk.utils::defaultCacheDirectory(),
+                                  loc=NULL,
                                   verbose=TRUE){
-
-    messager("Activating conda env via basilisk:",
+    ## Note: basilisk.utils::activateEnvironment was removed in newer versions.
+    ## Now using reticulate-based activation instead.
+    messager("Activating conda env:",
              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")
-    ## activateEnvironment was removed from basilisk.utils.
-    ## Set environment variables directly to activate the conda env.
-    envpath <- envs$dir
-    if(length(envpath) > 0 && nchar(envpath[1]) > 0){
-        conda_x <- basilisk.utils::condaBinary(loc = loc)
-        Sys.setenv(CONDA_PREFIX = envpath[1])
-        old_path <- Sys.getenv("PATH")
-        bin_dir <- if(.Platform$OS.type == "windows"){
-            envpath[1]
-        } else {
-            file.path(envpath[1], "bin")
-        }
-        Sys.setenv(PATH = paste(bin_dir, old_path, sep = .Platform$path.sep))
-    }
-    return(invisible(envpath))
+    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(.Platform$OS.type == "windows"){
+    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 \code{"basilisk"}
@@ -11,16 +11,14 @@
 #' @inheritParams reticulate::conda_binary
 #'
 #' @export
-#' @importFrom basilisk.utils condaBinary defaultCacheDirectory
+#' @importFrom basilisk.utils find
 find_conda <- function(conda="auto",
                        method=c("basilisk","reticulate")){
     method <- tolower(method)[1]
     if(method=="basilisk"){
-        conda_x <- basilisk.utils::condaBinary(
-            loc = basilisk.utils::defaultCacheDirectory()
-        )
+        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"){
@@ -29,9 +27,7 @@ find_conda <- function(conda="auto",
         conda_x <- reticulate::conda_binary(conda = conda)
         #### If it fails, use the other method ####
         if(!file.exists(conda_x)){
-            conda_x <- basilisk.utils::condaBinary(
-                loc = basilisk.utils::defaultCacheDirectory()
-            )
+            conda_x <- basilisk.utils::find()
         }
     } else {
         stop("method not recognized.")

R/install_conda_basilisk.R

@@ -8,11 +8,9 @@
 install_conda_basilisk <- function(verbose=TRUE){
     # Sys.setenv("BASILISK_USE_SYSTEM_DIR"=1)
     cache_dir <- basilisk.utils::defaultCacheDirectory()
-    conda_path <- basilisk.utils::condaBinary(loc = cache_dir)
-    if(!file.exists(conda_path)){
-        messager("echoconda:: Installing conda via basilisk.",v=verbose)
-        basilisk.utils::download(cache.dir = cache_dir)
-    } else {
-        messager("echoconda:: conda already installed.",v=verbose)
+    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

@@ -1,11 +1,11 @@
 #' 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
@@ -24,12 +24,6 @@ remove_env <- function(conda_env,
         #### Remove multiple ways ####
         for(env in envs){
             messager("Removing env:",env,v=verbose)
-            ## deactivateEnvironment was removed from basilisk.utils.
-            ## Clean up environment variables if this env is currently active.
-            current_prefix <- Sys.getenv("CONDA_PREFIX", unset = "")
-            if(nchar(current_prefix) > 0 && grepl(env, current_prefix, fixed = TRUE)){
-                Sys.unsetenv("CONDA_PREFIX")
-            }
             tryCatch({
                 reticulate::conda_remove(envname = env,
                                          conda = conda_x)