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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| #' Delete the rMIDAS Environment and Configuration | ||
| #' | ||
| #' Deletes both the virtual environment and the configuration file for the rMIDAS package. | ||
| #' After deletion, it is necessary to restart the R session and then load the rMIDAS package once more. | ||
| #' This will trigger the setup process again. | ||
| #' | ||
| #' @name delete_rMIDAS_env | ||
| #' @aliases delete_rMIDAS_env | ||
| #' @return A message indicating the completion of the deletion process. | ||
| #' @export | ||
|
|
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| delete_rMIDAS_env <- function() { | ||
|
|
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| if (requireNamespace("rappdirs", quietly = TRUE)) { | ||
| config_dir <- rappdirs::user_config_dir(appname = "rMIDAS") | ||
| config_file <- file.path(config_dir, ".rMIDAS_config") | ||
|
|
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| virtual_env_dir <- rappdirs::user_data_dir(appname = "rMIDAS") | ||
| virtual_env_name <- file.path(virtual_env_dir, "rMIDAS_env_auto_setup") | ||
|
|
||
| } else { | ||
| stop("The 'rappdirs' package is required to determine the directories. Please install it.") | ||
| } | ||
|
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| if (dir.exists(virtual_env_name)) { | ||
| unlink(virtual_env_name, recursive = TRUE) | ||
| message("rMIDAS virtual environment deleted successfully.") | ||
| } else { | ||
| message("rMIDAS virtual environment not found.") | ||
| } | ||
|
|
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| if (file.exists(config_file)) { | ||
| file.remove(config_file) | ||
| message("rMIDAS configuration file deleted successfully.") | ||
| } else { | ||
| message("rMIDAS configuration file not found.") | ||
| } | ||
|
|
||
| message("Please restart the R session and then load rMIDAS to set up the environment again.") | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| #' Reset the rMIDAS Environment Configuration | ||
| #' | ||
| #' Resets the configuration for the rMIDAS package by deleting the configuration file. | ||
| #' Once the configuration is reset, it is necessary to restart the R session | ||
| #' and then load the rMIDAS package once more. | ||
| #' | ||
| #' @name reset_rMIDAS_env | ||
| #' @aliases reset_rMIDAS_env | ||
| #' @return A message indicating the completion of the reset process. | ||
| #' @export | ||
|
|
||
| reset_rMIDAS_env <- function() { | ||
| # Use rappdirs to get the appropriate user configuration directory | ||
| if (requireNamespace("rappdirs", quietly = TRUE)) { | ||
| config_dir <- rappdirs::user_config_dir(appname = "rMIDAS") | ||
| config_file <- file.path(config_dir, ".rMIDAS_config") | ||
| } else { | ||
| stop("The 'rappdirs' package is required to determine the configuration directory. Please install it.") | ||
| } | ||
|
|
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| if (!file.exists(config_file)) { | ||
| stop("rMIDAS config file doesn't exist.") | ||
| } | ||
|
|
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| # Option 1: Delete the entire config file. | ||
| file.remove(config_file) | ||
|
|
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| # OR Option 2: Overwrite the config file with a default or empty value. | ||
| # writeLines("", con = config_file) | ||
|
|
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| message("rMIDAS configuration reset. Please restart the R session and then load rMIDAS again.") | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,17 +1,132 @@ | ||
| .onLoad <- function(libname, pkgname) { | ||
| custom_readline <- function(prompt, default = "skip") { | ||
| if (interactive()) { | ||
| return(readline(prompt)) | ||
| } else { | ||
| return(default) | ||
| } | ||
| } | ||
|
|
||
| custom_writelines <- function(input, con) { | ||
| writeLines(input, con = con) | ||
| } | ||
|
|
||
| custom_packageStartupMessage <- function(msg) { | ||
| messages <- list( | ||
| msg1 = "rMIDAS is loaded. In headless mode its environment and dependencies need to be set up manually. Please read https://github.com/MIDASverse/rMIDAS for additional help on how to set up and configure your environment.", | ||
| msg2 = "If you want to change your Python environment use 'reset_rMIDAS_env()' to reset your configuration. After resetting, you'll need to restart the R session and run 'library(rMIDAS)' again.", | ||
| msg3 = "rMIDAS is loaded but its environment and dependencies are not set up automatically. Please read https://github.com/MIDASverse/rMIDAS for additional help on how to set up and configure your environment.", | ||
| msg4 = "rMIDAS is being set up automatically.", | ||
| msg5 = "rMIDAS is loaded. Please read https://github.com/MIDASverse/rMIDAS for additional help on how to set up and configure your environment. If you want to use a different Python environment use 'reset_rMIDAS_env()' to reset the your configuration. After resetting, you'll need to restart the R session and run 'library(rMIDAS)' again.", | ||
| msg6 = "rMIDAS has been automatically set up.", | ||
| msg7 = "rMIDAS is loaded. Please read https://github.com/MIDASverse/rMIDAS for additional help on how to set up and configure your environment. If you want to change your Python environment use 'reset_rMIDAS_env()' to reset your configuration. After resetting, you'll need to restart the R session and run 'library(rMIDAS)' again." | ||
| ) | ||
| packageStartupMessage(messages[msg]) | ||
| } | ||
|
|
||
| .onLoad <- function(libname, pkgname) { | ||
|
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| options("python_custom" = NULL) | ||
| options("python_initialised" = NULL) | ||
|
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||
|
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| if (requireNamespace("rappdirs", quietly = TRUE)) { | ||
| config_dir <- rappdirs::user_config_dir(appname = "rMIDAS") | ||
| if (!dir.exists(config_dir)) { | ||
| dir.create(config_dir, recursive = TRUE) | ||
| } | ||
| config_file <- file.path(config_dir, ".rMIDAS_config") | ||
|
|
||
| virtual_env_dir <- rappdirs::user_data_dir(appname = "rMIDAS") | ||
| if (!dir.exists(virtual_env_dir)) { | ||
| dir.create(virtual_env_dir, recursive = TRUE) | ||
| } | ||
| } else { | ||
| stop("The 'rappdirs' package is required for rMIDAS. Please install it.") | ||
| } | ||
|
|
||
| if (!file.exists(config_file)) { | ||
| if (!interactive()) { | ||
| user_input <- "n" | ||
| custom_packageStartupMessage("msg1") | ||
| custom_packageStartupMessage("msg2") | ||
| } else { | ||
| user_input <- custom_readline("Do you want rMIDAS to automatically set up a Python environment and its dependencies? Enter 'y' for Yes, or any other key for No : \n", default = "n") | ||
| custom_writelines(user_input, con = config_file) | ||
| if(tolower(user_input) != "y") {custom_packageStartupMessage("msg3")} | ||
| if(tolower(user_input) == "y") {custom_packageStartupMessage("msg4")} | ||
| } | ||
| } else { | ||
| user_input <- readLines(con = config_file)[1] | ||
| if(tolower(user_input) != "y") { | ||
| custom_packageStartupMessage("msg5") | ||
| custom_writelines(user_input, con = config_file) | ||
| } | ||
| } | ||
|
|
||
| if (tolower(user_input) == "y") { | ||
| Sys.setenv(WORKON_HOME = virtual_env_dir) | ||
| virtual_env_name <- "rMIDAS_env_auto_setup" | ||
| if (virtual_env_name %in% reticulate::virtualenv_list()) { | ||
| reticulate::use_virtualenv(virtual_env_name, required = TRUE) | ||
| } else { | ||
| current_version <- reticulate::py_discover_config()$version | ||
| matched_version <- NULL | ||
| if (grepl("^3\\.(6|7|8|9|10).*|^3\\.(6|7|8|9|10)-dev$", current_version)) { | ||
| matched_version <- current_version | ||
| } else { | ||
| matched_version <- "3.8.17" | ||
| reticulate::install_python(version = matched_version, force = TRUE) | ||
| } | ||
| reticulate::virtualenv_create(envname = virtual_env_name, python_version = matched_version) | ||
| reticulate::use_virtualenv(virtual_env_name, required = TRUE) | ||
| python_version <- reticulate::py_discover_config()$version | ||
| version_components <- strsplit(python_version, "\\.")[[1]] | ||
| python_version_major <- as.numeric(version_components[1]) | ||
| python_version_minor <- as.numeric(version_components[2]) | ||
|
|
||
| requirements_txt <- "numpy>=1.5 | ||
| scikit-learn | ||
| matplotlib | ||
| pandas>=0.19 | ||
| tensorflow_addons<0.20.0 | ||
| statsmodels | ||
| scipy | ||
| " | ||
|
|
||
| if (python_version_major == 3 && as.integer(python_version_minor) >= 8 && as.integer(python_version_minor) < 11) { | ||
| if (Sys.info()["sysname"] == "Darwin" && Sys.info()["machine"] == "arm64") { | ||
| requirements_txt <- paste0(requirements_txt, "tensorflow-macos<2.12.0") | ||
| } else { | ||
| requirements_txt <- paste0(requirements_txt, "tensorflow<2.12.0") | ||
| } | ||
| } else { | ||
| if (Sys.info()["sysname"] == "Darwin" && Sys.info()["machine"] == "arm64") { | ||
| requirements_txt <- paste0(requirements_txt, "tensorflow-macos>=1.10") | ||
| } else { | ||
| requirements_txt <- paste0(requirements_txt, "tensorflow>=1.10") | ||
| } | ||
| } | ||
|
|
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| requirements_file <- tempfile(fileext = ".txt") | ||
| custom_writelines(requirements_txt, requirements_file) | ||
|
|
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| reticulate::py_install(envname = virtual_env_name, pip = TRUE, packages = c("-r", requirements_file)) | ||
| reticulate::py_config() | ||
| reticulate::use_virtualenv(virtual_env_name, required = TRUE) | ||
| custom_packageStartupMessage("msg6") | ||
| } | ||
| custom_packageStartupMessage("msg7") | ||
| } | ||
| } | ||
|
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| .onAttach <- function(libname, pkgname) { | ||
|
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| packageStartupMessage("\n## \n", | ||
| "## rMIDAS: Multiple Imputation using Denoising Autoencoders \n", | ||
| "## Authors: Thomas Robinson and Ranjit Lall \n", | ||
| "## Please visit https://github.com/MIDASverse/rMIDAS for more information \n", | ||
| "## \n" | ||
| ) | ||
| } | ||
|
|
||
| .onDetach <- function(libpath) { | ||
| # Nothing | ||
| } |
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