update

.github/workflows/R-CMD-check.yaml → .github/workflows/testlinux.yml

@@ -1,12 +1,10 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches: [main, master]
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check-Linux
 
 jobs:
   R-CMD-check:
@@ -27,4 +25,3 @@ jobs:
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
-

.github/workflows/testmacos.yml

@@ -0,0 +1,31 @@
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check-macOS
+
+jobs:
+  R-CMD-check:
+    runs-on: macos-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install pandoc
+        run: |
+          brew install pandoc
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2

.github/workflows/testwindows.yml

@@ -0,0 +1,31 @@
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check-Windows
+
+jobs:
+  R-CMD-check:
+    runs-on: windows-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install pandoc
+        run: |
+          choco install pandoc
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.4.1
-Date: 2022-06-20 15:10:41 UTC
-SHA: 61874a14cb52c2d7f9db9d7d8378a461fe5449fe
+Version: 0.4.2
+Date: 2023-06-13 21:47:39 UTC
+SHA: dbb37fc9fbd2b8967539138aa9e27ae33c270705

DESCRIPTION

@@ -20,17 +20,10 @@ Description: A tool for multiply imputing missing data using 'MIDAS', a deep lea
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Depends:
-  R (>= 3.6.0),
-  data.table,
-  mltools,
-  reticulate
-Imports:
-Suggests:
-    testthat,
-    knitr,
-    rmarkdown
-SystemRequirements: Python (>= 3.7.0)
+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)

NEWS.md

@@ -1,10 +1,13 @@
 # rMIDAS 0.4
 
 ## v0.4.2
-* Added headless functionality to `matplotlib` calls in Python
-* Updated conda setup file
-* Minor updates to underlying Python code to address deprecation issues
-
+* rMIDAS now includes an automatic setup that prompts the user on whether to automatically set up a Python environment and its dependencies
+* Addressed dependency issues and deprecation warnings (rather a Python update than R)
+* An additional .Rmd example that showcases rMIDAS core functionalities
+* Added a new vignette for running rMIDAS in headless mode, along with updates to the existing vignettes
+* Updated the accompanying YAML environment file that works on all major operating systems (including macOS running Apple silicon hardware)
+* Expanded our GitHub Actions workflow to also perform R-CMD-checks on macOS and Windows systems
+* Updated README file
 
 ## v0.4.1
 * Disabled Tensorflow deprecation warnings as default (as Python rather than R warning)

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

@@ -1,17 +1,109 @@
 .onLoad <- function(libname, pkgname) {
-
+  
   options("python_custom" = NULL)
   options("python_initialised" = NULL)
-
+
+  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"
+      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.")}
+    }
+  } 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)
+    }
+  }
+
+  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")
+        }
+      }
+
+      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()
+    }
+    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.")
+  }
 }
 
 .onAttach <- function(libname, pkgname) {
-
+  
   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
+}