From 471afba1f10471f8e9305b138a0951c4a7245a8d Mon Sep 17 00:00:00 2001
From: Daniel Falbel <dfalbel@gmail.com>
Date: Fri, 14 Jun 2019 09:50:26 -0300
Subject: [PATCH 1/8] delegate installation to reticulate

---
 R/install.R | 641 ++++++++++------------------------------------------
 1 file changed, 118 insertions(+), 523 deletions(-)

diff --git a/R/install.R b/R/install.R
index 19ebf7bc..5008ed73 100644
--- a/R/install.R
+++ b/R/install.R
@@ -1,5 +1,3 @@
-
-
 #' Install TensorFlow and its dependencies
 #'
 #' @inheritParams reticulate::conda_list
@@ -32,222 +30,92 @@
 #' @importFrom jsonlite fromJSON
 #'
 #' @export
-install_tensorflow <- function(method = c("auto", "virtualenv", "conda", "system"),
+install_tensorflow <- function(method = c("auto", "virtualenv", "conda"),
                                conda = "auto",
                                version = "default",
                                envname = "r-tensorflow",
                                extra_packages = NULL,
                                restart_session = TRUE) {
 
-  # verify os
-  if (!is_windows() && !is_osx() && !is_linux()) {
-    stop("Unable to install TensorFlow on this platform. ",
-         "Binary installation is available for Windows, OS X, and Linux")
-  }
-
   # verify 64-bit
   if (.Machine$sizeof.pointer != 8) {
     stop("Unable to install TensorFlow on this platform.",
          "Binary installation is only available for 64-bit platforms.")
   }
 
-  # resolve and validate method
   method <- match.arg(method)
-  if (identical(method, "system") && !is_windows()) {
-    stop("Installing TensorFlow into the system library is only supported on Windows",
-         call. = FALSE)
-  }
-  if (identical(method, "virtualenv") && is_windows()) {
-    stop("Installing TensorFlow into a virtualenv is not supported on Windows",
-         call. = FALSE)
-  }
 
   # unroll version
   ver <- parse_tensorflow_version(version)
+
   version <- ver$version
   gpu <- ver$gpu
-  packages <- ver$packages
-
-  # extra packages
-  extra_packages <- unique(c(extra_packages, c("keras", "tensorflow-hub")))
-  if (version == "nightly") {
-    extra_packages <- unique(c(extra_packages, "tfp-nightly"))
-    extra_packages <- setdiff(extra_packages, "tensorflow-probability")
-  }
-  if (version == "default" || substr(version, 1, 4) %in% c("1.12", "1.13")) {
-    extra_packages <- unique(c(extra_packages, "tensorflow-probability"))
-    extra_packages <- setdiff(extra_packages, ("tfp-nightly"))
-  }
-
-  # flags indicating what methods are available
-  method_available <- function(name) method %in% c("auto", name)
-  virtualenv_available <- method_available("virtualenv")
-  conda_available <- method_available("conda")
-  system_available <- is_windows() && method_available("site")
-
-  # resolve and look for conda
-  conda_bin <- tryCatch(conda_binary(conda), error = function(e) NULL)
-  have_conda <- conda_available && !is.null(conda_bin)
-
-  # mac and linux
-  if (is_unix()) {
+  package <- ver$package
 
-    # check for explicit conda method
-    if (identical(method, "conda")) {
+  # Packages in this list should always be installed.
 
-      # validate that we have conda
-      if (!have_conda)
-        stop("Conda installation failed (no conda binary found)\n", call. = FALSE)
+  default_packages <- c("tensorflow-hub")
 
-      # do install
-      install_tensorflow_conda(conda, version, gpu, envname, packages, extra_packages)
-
-    } else {
-
-      # find system python binary
-      pyver <- ""
-      python <- python_unix_binary("python")
-      if (is.null(python)) {
-        # try for python3 if we are on linux
-        if (is_linux()) {
-          python <- python_unix_binary("python3")
-          if (is.null(python))
-            stop("Unable to locate Python on this system.", call. = FALSE)
-          pyver <- "3"
-        }
-      }
-
-      # find other required tools
-      pip <- python_unix_binary(paste0("pip", pyver))
-      have_pip <- !is.null(pip)
-      virtualenv <- python_unix_binary("virtualenv")
-      have_virtualenv <- virtualenv_available && !is.null(virtualenv)
-
-      # if we don't have pip and virtualenv then try for conda if it's allowed
-      if ((!have_pip || !have_virtualenv) && have_conda) {
-
-        install_tensorflow_conda(conda, version, gpu, envname, packages, extra_packages)
-
-
-      # otherwise this is either an "auto" installation w/o working conda
-      # or it's an explicit "virtualenv" installation
-      } else {
-
-        # validate that we have the required tools for the method
-        install_commands <- NULL
-        if (is_osx()) {
-          if (!have_pip)
-            install_commands <- c(install_commands, "$ sudo /usr/bin/easy_install pip")
-          if (!have_virtualenv) {
-            if (is.null(pip))
-              pip <- "/usr/local/bin/pip"
-            install_commands <- c(install_commands, sprintf("$ sudo %s install --upgrade virtualenv", pip))
-          }
-          if (!is.null(install_commands))
-            install_commands <- paste(install_commands, collapse = "\n")
-        } else if (is_ubuntu()) {
-          if (!have_pip) {
-            install_commands <- c(install_commands, paste0("$ sudo apt-get install python", pyver ,"-pip"))
-            pip <- paste0("/usr/bin/pip", pyver)
-          }
-          if (!have_virtualenv) {
-            if (identical(pyver, "3"))
-              install_commands <- c(install_commands, paste("$ sudo", pip, "install virtualenv"))
-            else
-              install_commands <- c(install_commands, "$ sudo apt-get install python-virtualenv")
-          }
-          if (!is.null(install_commands))
-            install_commands <- paste(install_commands, collapse = "\n")
-        } else {
-          if (!have_pip)
-            install_commands <- c(install_commands, "pip")
-          if (!have_virtualenv)
-            install_commands <- c(install_commands, "virtualenv")
-          if (!is.null(install_commands)) {
-            install_commands <- paste("Please install the following Python packages before proceeding:",
-                                      paste(install_commands, collapse = ", "))
-          }
-        }
-        if (!is.null(install_commands)) {
-
-          # if these are terminal commands then add special preface
-          if (grepl("^\\$ ", install_commands)) {
-            install_commands <- paste0(
-              "Execute the following at a terminal to install the prerequisites:\n\n",
-              install_commands
-            )
-          }
-
-          stop("Prerequisites for installing TensorFlow not available.\n\n",
-               install_commands, "\n\n", call. = FALSE)
-        }
-
-        # do the install
-        install_tensorflow_virtualenv(python, virtualenv, version, gpu, envname, packages, extra_packages)
-
-      }
+  # install tensorflow-probability
+  if (!is.na(version) && substr(version, 1, 4) %in% c("1.12", "1.13", "1.14")) {
+    default_packages <- c(default_packages, "tensorflow-probability")
+    # extra_packages cannot contain the nightly version of tfp.
+    if ("tfp-nightly" %in% extra_packages) {
+      warning("tfp-nightly won't be installed since it requires TensorFlow nightly. ",
+              "tensorflow-probability will be installed instead.")
+      extra_packages <- setdiff(extra_packages, "tfp-nightly")
     }
 
-  # windows installation
-  } else {
-
-    # determine whether we have system python
-    python_versions <- py_versions_windows()
-    python_versions <- python_versions[python_versions$type == "PythonCore",]
-    python_versions <- python_versions[python_versions$version %in% c("3.5","3.6"),]
-    python_versions <- python_versions[python_versions$arch == "x64",]
-    have_system <- nrow(python_versions) > 0
-    if (have_system)
-      python_system_version <- python_versions[1,]
-
-    # resolve auto
-    if (identical(method, "auto")) {
-
-        if (!have_system && !have_conda) {
-          stop("Installing TensorFlow requires a 64-bit version of Python 3.5 or 3.6\n\n",
-               "Please install 64-bit Python 3.5 or 3.6 to continue, supported versions include:\n\n",
-               " - Anaconda Python (Recommended): https://www.anaconda.com/download/#windows\n",
-               " - Python Software Foundation   : https://www.python.org/downloads/\n\n",
-               call. = FALSE)
-        } else if (have_conda) {
-          method <- "conda"
-        } else if (have_system) {
-          method <- "system"
-        }
+  # install tfp-nightly
+  } else if (is.na(version) &&
+             (substr(version, 1, 4) %in% c("2.0.") || version == "nightly")) {
+    default_packages <- c(default_packages, "tfp-nightly")
+    # extra_packages cannot contain tensorflow-probability version
+    if ("tensorflow-probability" %in% extra_packages) {
+      warning("tensorflow-probability won't be installed since it requires TensorFlow nightly. ",
+              "tfp-nightly will be installed instead.")
+      extra_packages <- setdiff(extra_packages, "tfp-nightly")
     }
+  }
 
-    if (identical(method, "conda")) {
-
-      # validate that we have conda
-      if (!have_conda) {
-        stop("Conda installation failed (no conda binary found)\n\n",
-             "Install Anaconda 3.x for Windows (https://www.anaconda.com/download/#windows)\n",
-             "before installing TensorFlow.",
-             call. = FALSE)
-      }
-
-      # do the install
-      install_tensorflow_conda(conda, version, gpu, envname, packages, extra_packages)
+  extra_packages <- unique(c(default_packages, extra_packages))
+
+  # Main OS verification.
+  if (is_osx() || is_linux()) {
+
+    if (method == "conda") {
+      install_conda(
+        package = package,
+        extra_packages = extra_packages,
+        envname = envname,
+        conda = conda
+      )
+    } else if (method == "virtualenv" || method == "auto") {
+      install_virtualenv(
+        package = package,
+        extra_packages = extra_packages
+      )
+    }
 
-    } else if (identical(method, "system")) {
+  } else if (is_windows()) {
 
-      # if we don't have it then error
-      if (!have_system) {
-        stop("Installing TensorFlow requires a 64-bit version of Python 3.5 or 3.6\n\n",
-             "Please install 64-bit Python 3.5 or 3.6 this location to continue:\n\n",
-             " - https://www.python.org/downloads/\n\n",
-             call. = FALSE)
-      }
+    if (method == "virtualenv") {
+      stop("Installing TensorFlow into a virtualenv is not supported on Windows",
+           call. = FALSE)
+    } else if (method == "conda" || method == "auto") {
 
-      # do system installation
-      python <- python_system_version$executable_path
-      pip <- file.path(python_system_version$install_path, "Scripts", "pip.exe")
-      install_tensorflow_windows_system(python, pip, version, gpu, packages, extra_packages)
+      install_conda(
+        package = package,
+        extra_packages = extra_packages,
+        envname = envname,
+        conda = conda
+      )
 
-    } else {
-      stop("Invalid/unexpected installation method '", method, "'",
-           call. = FALSE)
     }
+
+  } else {
+    stop("Unable to install TensorFlow on this platform. ",
+         "Binary installation is available for Windows, OS X, and Linux")
   }
 
   cat("\nInstallation complete.\n\n")
@@ -258,396 +126,123 @@ install_tensorflow <- function(method = c("auto", "virtualenv", "conda", "system
   invisible(NULL)
 }
 
-install_tensorflow_conda <- function(conda, version, gpu, envname, packages, extra_packages = NULL) {
+install_conda <- function(package, extra_packages, envname, conda) {
 
-  # remove existing conda environment if we need to (necessary to work around TF upgrade bugs)
-  conda_envs <- conda_list(conda = conda)
-  conda_env <- subset(conda_envs, conda_envs$name == envname)
-  if (nrow(conda_env) == 1)
-    conda_remove(envname, conda = conda)
 
-  # create conda environment
-  cat("Creating", envname, "conda environment for TensorFlow installation...\n")
-  if (grepl("1.1[0-2]", substr(version, 1, 4))) {
-    python_packages <- "python=3.6"
-  } else {
-    python_packages <- "python=3.7"
-  }
 
-  python <- conda_create(envname, packages = python_packages, conda = conda)
-
-
-  # Short circuit to install everything with conda when no custom packages
-  # (typically tf-nightly or a daily build URL) and no gpu-enabled build
-  # is requested (conda doesn't currently have GPU enabled builds.
-  #
-  # This avoids any use of pip, which addresses the following issue:
-  # https://github.com/rstudio/keras/issues/147
-  #
-  # This issue is in turn created by two other issues:
-  #
-  # 1) TensorBoard appears to rely on an older version of html5lib which is
-  #    force installed, and which as a result breaks pip:
-  #    https://github.com/tensorflow/tensorboard/issues/588
-  #
-  # 2) Anaconda 5.0.0 is unable to recover from this because the installation
-  #    of the old version of html5lib actually propagates to the root
-  #    environment, which permantely breaks pip for *all* conda environments:
-  #    https://github.com/conda/conda/issues/6079
-  #
-  # Hopefully these two issues will be addressed and we can return to using
-  # pip in all scenarios (as that is the officially supported version)
-  #
-  if (is_windows() && is.null(packages) && gpu == FALSE) {
-    conda_forge_install(
-      envname,
-      tf_pkgs(version, gpu, packages, extra_packages = extra_packages),
-      conda = conda
-    )
-    return(invisible(NULL))
-  }
+    # find if environment exists
+    envname_exists <- envname %in% reticulate::conda_list(conda = conda)$name
 
-  # determine tf version
-  if (version == "latest") {
-    cat("Determining latest installable release of TensorFlow...")
-    releases <- fromJSON("https://api.github.com/repos/tensorflow/tensorflow/releases")
-    latest <- subset(releases, grepl("^v\\d+\\.\\d+\\.\\d+$", releases$tag_name))$tag_name[[1]]
-    version <- sub("v", "", latest)
-    # workaround the fact that v1.X.1 releases often have no tarball
-    version_split <- strsplit(version, ".", fixed = TRUE)[[1]]
-    if (length(version_split) > 2 && version_split[[length(version_split)]] != "0")
-      version_split <- c(version_split[-length(version_split)], "0")
-    version <- paste(version_split, collapse = ".")
-    cat("done\n")
-  }
-
-  # determine python version
-  py_version <- python_version(python)
-  py_version_str <- if (is_osx()) {
-    if (py_version >= "3.0")
-      "py3-none"
-    else
-      "py2-none"
-  } else {
-    if (py_version >= "3.0") {
-      ver <- gsub(".", "", as.character(py_version), fixed = TRUE)
-      sprintf("cp%s-cp%sm", ver, ver)
-    } else {
-      "cp27-none"
+    # remove environment
+    if (envname_exists) {
+      cat("Removing ", envname, " conda environment... \n")
+      reticulate::conda_remove(envname = envname, conda = conda)
     }
-  }
-
-  # determine arch
-  arch <- ifelse(is_windows(), "win_amd64", ifelse(is_osx(), "any", "linux_x86_64"))
-
-  # determine packages url if necessary
-  if (is.null(packages)) {
-    # version must have 3 digits
-    if (grepl("^\\d+\\.\\d+$", version))
-      version <- paste0(version, ".0")
-    platform <- ifelse(is_windows(), "windows", ifelse(is_osx(), "mac", "linux"))
-    packages <- sprintf(
-      "https://storage.googleapis.com/tensorflow/%s/%s/tensorflow%s-%s-%s-%s.whl",
-      platform,
-      ifelse(gpu, "gpu", "cpu"),
-      ifelse(gpu, "_gpu", ""),
-      version,
-      py_version_str,
-      arch
-    )
-  }
-
-  # install base tensorflow using pip
-  cat("Installing TensorFlow...\n")
-  conda_install(envname, packages, pip = TRUE, conda = conda)
-
-  # install additional packages
-  conda_install(envname, tf_extra_pkgs(), conda = conda)
-
-  # install extra packages (use pip to ensure we don't get legacy versions, set
-  # pip_ignore_installed to FALSE to ensure that pip source installs on
-  # windows don't attempt to override conda binary packages (e.g. SciPy which
-  # will likely fail to install via pip due to compilation dependencies)
-  if (!is.null(extra_packages)) {
-    conda_install(
-      envname,
-      extra_packages,
-      pip = TRUE,
-      pip_ignore_installed = FALSE,
-      conda = conda)
-  }
-}
-
-
-conda_forge_install <- function(envname, packages, conda = "auto") {
 
-  # resolve conda binary
-  conda <- conda_binary(conda)
 
-  # use native conda package manager with conda forge enabled
-  result <- system2(conda, shQuote(c("install", "-c", "conda-forge", "--yes", "--name", envname, packages)))
+    cat("Creating ", envname, " conda environment... \n")
+    reticulate::conda_create(envname = envname, conda = conda)
 
-  # check for errors
-  if (result != 0L) {
-    stop("Error ", result, " occurred installing packages into conda environment ",
-         envname, call. = FALSE)
-  }
+    cat("Installing python modules...\n")
+    reticulate::conda_install(
+      envname = envname,
+      packages = c(package, extra_packages),
+      conda = conda,
+      pip = TRUE # always use pip since it's the recommend way.
+    )
 
-  invisible(NULL)
 }
 
+install_virtualenv <- function(package, extra_packages, envname) {
 
+    # find if environment exists
+    envname_exists <- envname %in% reticulate::virtualenv_list()
 
-install_tensorflow_virtualenv <- function(python, virtualenv, version, gpu, envname, packages, extra_packages = NULL) {
-
-  # determine python version to use
-  is_python3 <- python_version(python) >= "3.0"
-  pip_version <- ifelse(is_python3, "pip3", "pip")
+    # remove environment
+    if (envname_exists)
+      reticulate::virtualenv_remove(envname = envname, confirm = FALSE)
 
-  # create virtualenv
-  virtualenv_root <- Sys.getenv("WORKON_HOME", unset = "~/.virtualenvs")
-  if (!file.exists(virtualenv_root))
-    dir.create(virtualenv_root, recursive = TRUE)
+    reticulate::virtualenv_create(envname = envname)
 
-  # helper to construct paths to virtualenv binaries
-  virtualenv_bin <- function(bin) path.expand(file.path(virtualenv_path, "bin", bin))
-
-  # destroy and re-create virtualenv (necessary to work around tf upgrade bugs)
-  virtualenv_path <- file.path(virtualenv_root, envname)
-  if (dir_exists(virtualenv_path))
-    unlink(virtualenv_path, recursive = TRUE)
-  cat("Creating virtualenv for TensorFlow at ", virtualenv_path, "\n")
-  result <- system2(virtualenv, shQuote(c(
-    "--system-site-packages",
-    "--python", python,
-    path.expand(virtualenv_path)))
-  )
-  if (result != 0L)
-    stop("Error ", result, " occurred creating virtualenv at ", virtualenv_path,
-         call. = FALSE)
-
-
-  # see what version of pip is installed (assume 0.1 on error)
-  installed_pip_version <- function() {
-    tryCatch({
-      # check existing version
-      cmd <- sprintf("%ssource %s && %s --version%s",
-                     ifelse(is_osx(), "", "/bin/bash -c \""),
-                     shQuote(path.expand(virtualenv_bin("activate"))),
-                     shQuote(path.expand(virtualenv_bin(pip_version))),
-                     ifelse(is_osx(), "", "\""))
-      result <- system(cmd, intern = TRUE, ignore.stderr = TRUE)
-
-      # parse result
-      matches <- regexec("^[^ ]+\\s+(\\d+)\\.(\\d+).*$", result)
-      matches <- regmatches(result, matches)[[1]]
-
-      # return as R numeric version
-      numeric_version(paste(matches[[2]], matches[[3]], sep = "."))
-
-    }, error = function(e) {
-      warning("Error occurred checking pip version: ", e$message)
-      numeric_version("0.1")
-    })
-  }
-
-  # function to call pip within virtual env
-  pip_install <- function(pkgs, message) {
-    cmd <- sprintf("%ssource %s && %s install --ignore-installed --upgrade %s%s",
-                   ifelse(is_osx(), "", "/bin/bash -c \""),
-                   shQuote(path.expand(virtualenv_bin("activate"))),
-                   shQuote(path.expand(virtualenv_bin(pip_version))),
-                   paste(shQuote(pkgs), collapse = " "),
-                   ifelse(is_osx(), "", "\""))
-    cat(message, "...\n")
-    result <- system(cmd)
-    if (result != 0L)
-      stop("Error ", result, " occurred installing TensorFlow", call. = FALSE)
-  }
-
-  # upgrade pip and related utilities if its older than 8.1
-  if (installed_pip_version() < "8.1") {
-    pip_install("pip", "Upgrading pip")
-    pip_install("wheel", "Upgrading wheel")
-    pip_install("setuptools", "Upgrading setuptools")
-  }
-
-  # install tensorflow and related dependencies
-  pkgs <- tf_pkgs(version, gpu, packages, scipy = TRUE, extra_packages = extra_packages)
-  pip_install(pkgs, "Installing TensorFlow")
-}
-
-
-install_tensorflow_windows_system <- function(python, pip, version, gpu, packages, extra_packages = NULL) {
-
-  # ensure pip is up to date
-  cat("Preparing for installation (updating pip if necessary)\n")
-  result <- system2(python, c("-m", "pip", "install", "--upgrade", "pip"))
-  if (result != 0L)
-    stop("Error ", result, " occurred updating pip", call. = FALSE)
-
-  # install tensorflow and dependencies (don't install scipy b/c it requires
-  # native code compilation)
-  cat("Installing TensorFlow...\n")
-  pkgs <- tf_pkgs(version, gpu, packages, scipy = FALSE, extra_packages = extra_packages)
-  result <- system2(pip, c("install", "--upgrade --ignore-installed",
-                           paste(shQuote(pkgs), collapse = " ")))
-  if (result != 0L)
-    stop("Error ", result, " occurred installing tensorflow package", call. = FALSE)
+    reticulate::virtualenv_install(
+      envname = envname,
+      packages = c(package, extra_packages)
+    )
 
-  cat("\nInstallation of TensorFlow complete.\n\n")
 }
 
-
 parse_tensorflow_version <- function(version) {
 
-  # defaults
+  default_version <- "1.13.1"
+
   ver <- list(
-    version = "latest",
+    version = default_version,
     gpu = FALSE,
-    packages = NULL
+    package = NULL
   )
 
-  # full url provided
-  if (identical(version, "default")) {
+  if (version == "default") {
 
-    ver$version <- "1.13.1"
+    ver$package <- paste0("tensorflow==", ver$version)
 
-  # gpu version
-  } else if (identical(version, "gpu")) {
-
-    ver$version <- "1.13.1"
+    # default gpu version
+  } else if (version == "gpu") {
 
     ver$gpu <- TRUE
+    ver$package <- paste0("tensorflow-gpu==", ver$version)
 
-  # gpu qualifier provided
+    # gpu qualifier provided
   } else if (grepl("-gpu$", version)) {
 
     split <- strsplit(version, "-")[[1]]
     ver$version <- split[[1]]
-    ver$gpu <-TRUE
+    ver$gpu <- TRUE
 
-  # full path to installer binary
+    # full path to whl.
   } else if (grepl("^.*\\.whl$", version)) {
 
+    ver$gpu <- NA
+    ver$version <- NA
+
     if (grepl("^http", version))
-      ver$packages <- version
+      ver$package <- version
     else
-      ver$packages <- normalizePath(version)
+      ver$package <- normalizePath(version)
 
-  # another version
+    # another version
   } else {
 
     ver$version <- version
 
   }
 
-  # if it's the nightly version then set packages to nightly[-gpu]
-  # as of 02/15/2019 tf-nightly includes tb-nightly, tf-estimator-nightly
-  version <- sub("^tf-nightly$", "nightly", version)
-  if (identical(version, "nightly")) {
-    ver$packages <- c(sprintf("tf-nightly%s", ifelse(ver$gpu, "-gpu", "")))
-  }
+  # find the right package for nightly and other versions
+  if (is.null(ver$package)) {
 
-  # return
-  ver
-}
-
-python_unix_binary <- function(bin) {
-  locations <- file.path(c("/usr/bin", "/usr/local/bin", path.expand("~/.local/bin")), bin)
-  locations <- locations[file.exists(locations)]
-  if (length(locations) > 0)
-    locations[[1]]
-  else
-    NULL
-}
-
-python_version <- function(python) {
-
-  # check for the version
-  result <- system2(python, "--version", stdout = TRUE, stderr = TRUE)
-
-  # check for error
-  error_status <- attr(result, "status")
-  if (!is.null(error_status))
-    stop("Error ", error_status, " occurred while checking for python version", call. = FALSE)
-
-  # parse out the major and minor version numbers
-  matches <- regexec("^[^ ]+\\s+(\\d+)\\.(\\d+).*$", result)
-  matches <- regmatches(result, matches)[[1]]
-  if (length(matches) != 3)
-    stop("Unable to parse Python version '", result[[1]], "'", call. = FALSE)
-
-  # return as R numeric version
-  numeric_version(paste(matches[[2]], matches[[3]], sep = "."))
-}
-
-
-# form list of tf pkgs
-tf_pkgs <- function(version, gpu, packages, scipy = TRUE, extra_packages = NULL) {
-  if (is.null(packages))
-    packages <- sprintf("tensorflow%s%s",
-                       ifelse(gpu, "-gpu", ""),
-                       ifelse(version == "latest", "", paste0("==", version)))
-  c(packages, tf_extra_pkgs(scipy = scipy, extra_packages = extra_packages))
-}
-
-# additional dependencies to install (required for keras)
-tf_extra_pkgs <- function(scipy = TRUE, extra_packages = NULL) {
-  pkgs <- c("h5py", "pyyaml",  "requests",  "Pillow")
-  pkgs <- c(pkgs, extra_packages)
-  if (scipy)
-    c(pkgs, "scipy")
-  else
-    pkgs
-}
+    if (ver$version == "nightly") {
 
+      if (ver$gpu) {
+        ver$package <- "tf-nightly-gpu"
+      } else {
+        ver$package <- "tf-nightly"
+      }
 
-virtualenv_install <- function(envname, packages) {
-
-  # TODO: refactor to share code between this and install_tensorflow_virtualenv
-  # (we added this code late in the v1.0 cycle so didn't want to do the
-  # refactor then)
+    } else {
 
-  # determine path to virtualenv
-  virtualenv_root <- Sys.getenv("WORKON_HOME", unset = "~/.virtualenvs")
-  virtualenv_path <- file.path(virtualenv_root, envname)
+      if (ver$gpu) {
+        ver$package <- paste0("tensorflow-gpu==", ver$version)
+      } else {
+        ver$package <- paste0("tensorflow==", ver$version)
+      }
 
-  # helper to construct paths to virtualenv binaries
-  virtualenv_bin <- function(bin) path.expand(file.path(virtualenv_path, "bin", bin))
+    }
 
-  # determine pip version to use
-  python <- virtualenv_bin("python")
-  is_python3 <- python_version(python) >= "3.0"
-  pip_version <- ifelse(is_python3, "pip3", "pip")
+  }
 
-  # build and execute install command
-  cmd <- sprintf("%ssource %s && %s install --ignore-installed --upgrade %s%s",
-                 ifelse(is_osx(), "", "/bin/bash -c \""),
-                 shQuote(path.expand(virtualenv_bin("activate"))),
-                 shQuote(path.expand(virtualenv_bin(pip_version))),
-                 paste(shQuote(packages), collapse = " "),
-                 ifelse(is_osx(), "", "\""))
-  result <- system(cmd)
-  if (result != 0L)
-    stop("Error ", result, " occurred installing packages", call. = FALSE)
+  ver
 }
 
 
-windows_system_install <- function(python, packages) {
-
-  # TODO: refactor to share code with install_tensorflow_windows_system
-
-  # determine pip location from python binary location
-  pip <- file.path(dirname(python), "Scripts", "pip.exe")
-
-  # execute the installation
-  result <- system2(pip, c("install", "--upgrade --ignore-installed",
-                           paste(shQuote(packages), collapse = " ")))
-  if (result != 0L)
-    stop("Error ", result, " occurred installing tensorflow package", call. = FALSE)
-}
-
 #' Install additional Python packages alongside TensorFlow
 #'
 #' This function is deprecated. Use the `extra_packages` argument to

From 46981f6589c2fbafeee66ef3e78a1c36eb9f9ae2 Mon Sep 17 00:00:00 2001
From: Daniel Falbel <dfalbel@gmail.com>
Date: Fri, 14 Jun 2019 09:54:14 -0300
Subject: [PATCH 2/8] pass envname to install virtualenv

---
 R/install.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/install.R b/R/install.R
index 5008ed73..ed9e0f38 100644
--- a/R/install.R
+++ b/R/install.R
@@ -93,7 +93,8 @@ install_tensorflow <- function(method = c("auto", "virtualenv", "conda"),
     } else if (method == "virtualenv" || method == "auto") {
       install_virtualenv(
         package = package,
-        extra_packages = extra_packages
+        extra_packages = extra_packages,
+        envname = envname
       )
     }
 

From 1f3da4058f0b52fa94ead521fa5a45f899729da0 Mon Sep 17 00:00:00 2001
From: Daniel Falbel <dfalbel@gmail.com>
Date: Tue, 18 Jun 2019 13:27:57 +0200
Subject: [PATCH 3/8] use || instead

---
 R/install.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/install.R b/R/install.R
index ed9e0f38..d1ca9d2a 100644
--- a/R/install.R
+++ b/R/install.R
@@ -67,7 +67,7 @@ install_tensorflow <- function(method = c("auto", "virtualenv", "conda"),
     }
 
   # install tfp-nightly
-  } else if (is.na(version) &&
+  } else if (is.na(version) ||
              (substr(version, 1, 4) %in% c("2.0.") || version == "nightly")) {
     default_packages <- c(default_packages, "tfp-nightly")
     # extra_packages cannot contain tensorflow-probability version
@@ -262,3 +262,4 @@ install_tensorflow_extras <- function(packages, conda = "auto") {
 }
 
 
+

From 61024fd1c189da6e8fc20cb5080f5dc1acad1317 Mon Sep 17 00:00:00 2001
From: Daniel Falbel <dfalbel@gmail.com>
Date: Tue, 18 Jun 2019 13:33:00 +0200
Subject: [PATCH 4/8] simplify tf probability version

---
 R/install.R | 21 ++-------------------
 1 file changed, 2 insertions(+), 19 deletions(-)

diff --git a/R/install.R b/R/install.R
index d1ca9d2a..9565580a 100644
--- a/R/install.R
+++ b/R/install.R
@@ -56,26 +56,12 @@ install_tensorflow <- function(method = c("auto", "virtualenv", "conda"),
 
   default_packages <- c("tensorflow-hub")
 
-  # install tensorflow-probability
+  # Resolve TF probability version.
   if (!is.na(version) && substr(version, 1, 4) %in% c("1.12", "1.13", "1.14")) {
     default_packages <- c(default_packages, "tensorflow-probability")
-    # extra_packages cannot contain the nightly version of tfp.
-    if ("tfp-nightly" %in% extra_packages) {
-      warning("tfp-nightly won't be installed since it requires TensorFlow nightly. ",
-              "tensorflow-probability will be installed instead.")
-      extra_packages <- setdiff(extra_packages, "tfp-nightly")
-    }
-
   # install tfp-nightly
-  } else if (is.na(version) ||
-             (substr(version, 1, 4) %in% c("2.0.") || version == "nightly")) {
+  } else if (is.na(version) ||(substr(version, 1, 4) %in% c("2.0.") || version == "nightly")) {
     default_packages <- c(default_packages, "tfp-nightly")
-    # extra_packages cannot contain tensorflow-probability version
-    if ("tensorflow-probability" %in% extra_packages) {
-      warning("tensorflow-probability won't be installed since it requires TensorFlow nightly. ",
-              "tfp-nightly will be installed instead.")
-      extra_packages <- setdiff(extra_packages, "tfp-nightly")
-    }
   }
 
   extra_packages <- unique(c(default_packages, extra_packages))
@@ -260,6 +246,3 @@ install_tensorflow_extras <- function(packages, conda = "auto") {
           "Use the extra_packages argument to install_tensorflow() to ",
           "install additional packages.")
 }
-
-
-

From abd8283c189d1df5ad55f5242278c69d7dcafd54 Mon Sep 17 00:00:00 2001
From: Daniel Falbel <dfalbel@gmail.com>
Date: Tue, 18 Jun 2019 13:37:44 +0200
Subject: [PATCH 5/8] add ellipsis to pass additional args to conda_install or
 virtualenv_install

---
 R/install.R               | 33 ++++++++++++++++++++++-----------
 man/install_tensorflow.Rd |  7 +++++--
 2 files changed, 27 insertions(+), 13 deletions(-)

diff --git a/R/install.R b/R/install.R
index 9565580a..a7d8e90d 100644
--- a/R/install.R
+++ b/R/install.R
@@ -27,6 +27,9 @@
 #' @param restart_session Restart R session after installing (note this will
 #'   only occur within RStudio).
 #'
+#' @param ... other arguments passed to [reticulate::conda_install()] or
+#'   [reticulate::virtualenv_install()].
+#'
 #' @importFrom jsonlite fromJSON
 #'
 #' @export
@@ -35,7 +38,8 @@ install_tensorflow <- function(method = c("auto", "virtualenv", "conda"),
                                version = "default",
                                envname = "r-tensorflow",
                                extra_packages = NULL,
-                               restart_session = TRUE) {
+                               restart_session = TRUE,
+                               ...) {
 
   # verify 64-bit
   if (.Machine$sizeof.pointer != 8) {
@@ -74,13 +78,15 @@ install_tensorflow <- function(method = c("auto", "virtualenv", "conda"),
         package = package,
         extra_packages = extra_packages,
         envname = envname,
-        conda = conda
+        conda = conda,
+        ...
       )
     } else if (method == "virtualenv" || method == "auto") {
       install_virtualenv(
         package = package,
         extra_packages = extra_packages,
-        envname = envname
+        envname = envname,
+        ...
       )
     }
 
@@ -95,7 +101,8 @@ install_tensorflow <- function(method = c("auto", "virtualenv", "conda"),
         package = package,
         extra_packages = extra_packages,
         envname = envname,
-        conda = conda
+        conda = conda,
+        ...
       )
 
     }
@@ -113,9 +120,7 @@ install_tensorflow <- function(method = c("auto", "virtualenv", "conda"),
   invisible(NULL)
 }
 
-install_conda <- function(package, extra_packages, envname, conda) {
-
-
+install_conda <- function(package, extra_packages, envname, conda, ...) {
 
     # find if environment exists
     envname_exists <- envname %in% reticulate::conda_list(conda = conda)$name
@@ -135,25 +140,31 @@ install_conda <- function(package, extra_packages, envname, conda) {
       envname = envname,
       packages = c(package, extra_packages),
       conda = conda,
-      pip = TRUE # always use pip since it's the recommend way.
+      pip = TRUE, # always use pip since it's the recommend way.
+      ...
     )
 
 }
 
-install_virtualenv <- function(package, extra_packages, envname) {
+install_virtualenv <- function(package, extra_packages, envname, ...) {
 
     # find if environment exists
     envname_exists <- envname %in% reticulate::virtualenv_list()
 
     # remove environment
-    if (envname_exists)
+    if (envname_exists) {
+      cat("Removing ", envname, " virtualenv environment... \n")
       reticulate::virtualenv_remove(envname = envname, confirm = FALSE)
+    }
 
+    cat("Creating ", envname, " virtualenv environment... \n")
     reticulate::virtualenv_create(envname = envname)
 
+    cat("Installing python modules...\n")
     reticulate::virtualenv_install(
       envname = envname,
-      packages = c(package, extra_packages)
+      packages = c(package, extra_packages),
+      ...
     )
 
 }
diff --git a/man/install_tensorflow.Rd b/man/install_tensorflow.Rd
index 832fc248..03c0b483 100644
--- a/man/install_tensorflow.Rd
+++ b/man/install_tensorflow.Rd
@@ -4,9 +4,9 @@
 \alias{install_tensorflow}
 \title{Install TensorFlow and its dependencies}
 \usage{
-install_tensorflow(method = c("auto", "virtualenv", "conda", "system"),
+install_tensorflow(method = c("auto", "virtualenv", "conda"),
   conda = "auto", version = "default", envname = "r-tensorflow",
-  extra_packages = NULL, restart_session = TRUE)
+  extra_packages = NULL, restart_session = TRUE, ...)
 }
 \arguments{
 \item{method}{Installation method. By default, "auto" automatically finds a
@@ -36,6 +36,9 @@ TensorFlow.}
 
 \item{restart_session}{Restart R session after installing (note this will
 only occur within RStudio).}
+
+\item{...}{other arguments passed to \code{\link[reticulate:conda_install]{reticulate::conda_install()}} or
+\code{\link[reticulate:virtualenv_install]{reticulate::virtualenv_install()}}.}
 }
 \description{
 Install TensorFlow and its dependencies

From d71d12f1fd539d1dda729b4ef6d8c92c22b21f79 Mon Sep 17 00:00:00 2001
From: Daniel Falbel <dfalbel@gmail.com>
Date: Wed, 19 Jun 2019 23:00:52 +0200
Subject: [PATCH 6/8] try installing libgcc too

---
 R/install.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/install.R b/R/install.R
index a7d8e90d..3e051113 100644
--- a/R/install.R
+++ b/R/install.R
@@ -133,7 +133,10 @@ install_conda <- function(package, extra_packages, envname, conda, ...) {
 
 
     cat("Creating ", envname, " conda environment... \n")
-    reticulate::conda_create(envname = envname, conda = conda)
+    reticulate::conda_create(
+      envname = envname, conda = conda,
+      packages = c("python", "libgcc")
+    )
 
     cat("Installing python modules...\n")
     reticulate::conda_install(

From 2262374efbadab850bbcf7d1c4b4334849b75d20 Mon Sep 17 00:00:00 2001
From: Daniel Falbel <dfalbel@gmail.com>
Date: Thu, 20 Jun 2019 00:20:58 +0200
Subject: [PATCH 7/8] try installation with python 3.6.8

---
 R/install.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/install.R b/R/install.R
index 3e051113..fe541076 100644
--- a/R/install.R
+++ b/R/install.R
@@ -135,7 +135,7 @@ install_conda <- function(package, extra_packages, envname, conda, ...) {
     cat("Creating ", envname, " conda environment... \n")
     reticulate::conda_create(
       envname = envname, conda = conda,
-      packages = c("python", "libgcc")
+      packages = c("python=3.6")
     )
 
     cat("Installing python modules...\n")

From 4c58d7e8b24629963a9e9ee7660e2196fd98432a Mon Sep 17 00:00:00 2001
From: Daniel Falbel <dfalbel@gmail.com>
Date: Thu, 20 Jun 2019 00:42:11 +0200
Subject: [PATCH 8/8] controll the python version argument

---
 R/install.R               | 10 ++++++++--
 man/install_tensorflow.Rd |  6 +++++-
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/R/install.R b/R/install.R
index fe541076..0c382a46 100644
--- a/R/install.R
+++ b/R/install.R
@@ -27,6 +27,9 @@
 #' @param restart_session Restart R session after installing (note this will
 #'   only occur within RStudio).
 #'
+#' @param conda_python_version the python version installed in the created conda
+#'   environment. Python 3.6 is installed by default.
+#'
 #' @param ... other arguments passed to [reticulate::conda_install()] or
 #'   [reticulate::virtualenv_install()].
 #'
@@ -39,6 +42,7 @@ install_tensorflow <- function(method = c("auto", "virtualenv", "conda"),
                                envname = "r-tensorflow",
                                extra_packages = NULL,
                                restart_session = TRUE,
+                               conda_python_version = "3.6",
                                ...) {
 
   # verify 64-bit
@@ -79,6 +83,7 @@ install_tensorflow <- function(method = c("auto", "virtualenv", "conda"),
         extra_packages = extra_packages,
         envname = envname,
         conda = conda,
+        conda_python_version = conda_python_version,
         ...
       )
     } else if (method == "virtualenv" || method == "auto") {
@@ -102,6 +107,7 @@ install_tensorflow <- function(method = c("auto", "virtualenv", "conda"),
         extra_packages = extra_packages,
         envname = envname,
         conda = conda,
+        conda_python_version = conda_python_version,
         ...
       )
 
@@ -120,7 +126,7 @@ install_tensorflow <- function(method = c("auto", "virtualenv", "conda"),
   invisible(NULL)
 }
 
-install_conda <- function(package, extra_packages, envname, conda, ...) {
+install_conda <- function(package, extra_packages, envname, conda, conda_python_version, ...) {
 
     # find if environment exists
     envname_exists <- envname %in% reticulate::conda_list(conda = conda)$name
@@ -135,7 +141,7 @@ install_conda <- function(package, extra_packages, envname, conda, ...) {
     cat("Creating ", envname, " conda environment... \n")
     reticulate::conda_create(
       envname = envname, conda = conda,
-      packages = c("python=3.6")
+      packages = paste0("python=", conda_python_version)
     )
 
     cat("Installing python modules...\n")
diff --git a/man/install_tensorflow.Rd b/man/install_tensorflow.Rd
index 03c0b483..5d73e794 100644
--- a/man/install_tensorflow.Rd
+++ b/man/install_tensorflow.Rd
@@ -6,7 +6,8 @@
 \usage{
 install_tensorflow(method = c("auto", "virtualenv", "conda"),
   conda = "auto", version = "default", envname = "r-tensorflow",
-  extra_packages = NULL, restart_session = TRUE, ...)
+  extra_packages = NULL, restart_session = TRUE,
+  conda_python_version = "3.6", ...)
 }
 \arguments{
 \item{method}{Installation method. By default, "auto" automatically finds a
@@ -37,6 +38,9 @@ TensorFlow.}
 \item{restart_session}{Restart R session after installing (note this will
 only occur within RStudio).}
 
+\item{conda_python_version}{the python version installed in the created conda
+environment. Python 3.6 is installed by default.}
+
 \item{...}{other arguments passed to \code{\link[reticulate:conda_install]{reticulate::conda_install()}} or
 \code{\link[reticulate:virtualenv_install]{reticulate::virtualenv_install()}}.}
 }