For the v0.4.2 release

Changes to the zzz.R file. Added delete_env.R and reset_env.R. Updated NAMESPACE and DESCRIPTION.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rMIDAS
 Title: Multiple Imputation with Denoising Autoencoders
-Version: 0.4.1
+Version: 0.4.2
 Authors@R: c(
     person(given = "Thomas",
            family = "Robinson",
@@ -19,18 +19,11 @@ Authors@R: c(
 Description: A tool for multiply imputing missing data using 'MIDAS', a deep learning method based on denoising autoencoder neural networks. This algorithm offers significant accuracy and efficiency advantages over other multiple imputation strategies, particularly when applied to large datasets with complex features. Alongside interfacing with 'Python' to run the core algorithm, this package contains functions for processing data before and after model training, running imputation model diagnostics, generating multiple completed datasets, and estimating regression models on these datasets.
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
-Depends:
-  R (>= 3.6.0),
-  data.table,
-  mltools,
-  reticulate
-Imports:
-Suggests:
-    testthat,
-    knitr,
-    rmarkdown
-SystemRequirements: Python (>= 3.7.0)
+RoxygenNote: 7.2.3
+Depends: R (>= 3.6.0), data.table, mltools, reticulate
+Imports: rappdirs
+Suggests: testthat, knitr, rmarkdown
+SystemRequirements: Python (>= 3.6.0)
 VignetteBuilder: knitr
 License: Apache License (>= 2.0)
 URL: https://github.com/MIDASverse/rMIDAS

NAMESPACE

@@ -6,9 +6,11 @@ export(col_minmax)
 export(combine)
 export(complete)
 export(convert)
+export(delete_rMIDAS_env)
 export(midas_setup)
 export(na_to_nan)
 export(overimpute)
+export(reset_rMIDAS_env)
 export(set_python_env)
 export(train)
 export(undo_minmax)

R/delete_env.R

@@ -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
+
+delete_rMIDAS_env <- function() {
+
+  if (requireNamespace("rappdirs", quietly = TRUE)) {
+    config_dir <- rappdirs::user_config_dir(appname = "rMIDAS")
+    config_file <- file.path(config_dir, ".rMIDAS_config")
+
+    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.")
+  }
+
+  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.")
+  }
+
+  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.")
+}

R/reset_env.R

@@ -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.")
+  }
+
+  if (!file.exists(config_file)) {
+    stop("rMIDAS config file doesn't exist.")
+  }
+
+  # Option 1: Delete the entire config file.
+  file.remove(config_file)
+
+  # OR Option 2: Overwrite the config file with a default or empty value.
+  # writeLines("", con = config_file)
+
+  message("rMIDAS configuration reset. Please restart the R session and then load rMIDAS again.")
+}

R/zzz.R

@@ -3,61 +3,94 @@
   options("python_custom" = NULL)
   options("python_initialised" = NULL)
 
-  if (!interactive()) {
-    user_input <- "n"
-    packageStartupMessage("rMIDAS is loaded but its environment and dependencies are not set up automatically. \n Please read https://github.com/MIDASverse/rMIDAS for additional help on how to set up and configure your environment.")
+  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 {
-    user_input <- 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")
-  }
-  if(tolower(user_input) != "y") {
-    packageStartupMessage("rMIDAS is loaded but its environment and dependencies are not set up automatically.\n Please read https://github.com/MIDASverse/rMIDAS for additional help on how to set up and configure your environment.")
+    stop("The 'rappdirs' package is required for rMIDAS. Please install it.")
   }
-  if (tolower(user_input) == "y") {
-    if (!requireNamespace("reticulate", quietly = TRUE)) {
-      install.packages("reticulate")
+
+  if (!file.exists(config_file)) {
+    if (!interactive()) {
+      user_input <- "n"
+      packageStartupMessage("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.")
+      packageStartupMessage("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.")
+    } else {
+      user_input <- 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")
+      writeLines(user_input, con = config_file)
+      if(tolower(user_input) != "y") {packageStartupMessage("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.")}
+      if(tolower(user_input) == "y") {packageStartupMessage("rMIDAS is being set up automatically.")}
     }
-
-    library(reticulate)
-    conda_env_name <- "rMIDAS_env"
-
-    if (!conda_env_name %in% reticulate::conda_list()$name) {
-      reticulate::conda_create(envname = conda_env_name)
+  } else {
+    user_input <- readLines(con = config_file)[1]
+    if(tolower(user_input) != "y") {
+      packageStartupMessage("\n \n","rMIDAS is loaded. Please read https://github.com/MIDASverse/rMIDAS for additional help on how to set up and configure your environment. If you want to use a different Python environment use 'reset_rMIDAS_env()' to reset the your configuration. After resetting, you'll need to restart the R session and run 'library(rMIDAS)' again.\n")
+      writeLines(user_input, con = config_file)
     }
-
-    reticulate::use_condaenv(conda_env_name, required = TRUE)
-
-    python_version <- reticulate::py_config()$version
-    python_version_numeric <- as.numeric(python_version)
-    python_version_major <- floor(python_version_numeric)
-    python_version_minor <- floor(python_version_numeric * 10) %% 10
-
-    requirements_txt <- "numpy>=1.5
+  }
+
+  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
+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")
+
+      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 {
-        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")
+        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")
+        }
       }
+
+      requirements_file <- tempfile(fileext = ".txt")
+      writeLines(requirements_txt, requirements_file)
+
+      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)
+      packageStartupMessage("rMIDAS has been automatically set up.")
+      #.rs.restartR()
     }
-
-    requirements_file <- tempfile(fileext = ".txt")
-    writeLines(requirements_txt, requirements_file)
-
-    reticulate::conda_install(envname = conda_env_name, packages = NULL, pip = TRUE, pip_options = c("-r", requirements_file))
+    packageStartupMessage("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.")
   }
 }
 
@@ -71,6 +104,6 @@ scipy
   )
 }
 
-.onUnload <- function(libpath) {
-  # No action necessary
-}
+.onDetach <- function(libpath) {
+  # Nothing
+}