* Added option to restart R + run library(greta) after installation (…

…greta-dev#523)

* Added installation deps object, `greta_python_deps()` to help simplify specifying package versions (greta-dev#664)
* removed `method` and `conda` arguments from `install_greta_deps()` as they
  were not used.
* removed `manual` option in `install_greta_deps()`
* added default 5 minute timer to installation processes

NAMESPACE

@@ -108,6 +108,7 @@ S3method(plot,greta_model)
 S3method(print,greta_array)
 S3method(print,greta_mcmc_list)
 S3method(print,greta_model)
+S3method(print,greta_python_deps)
 S3method(print,initials)
 S3method(print,optimiser)
 S3method(print,sampler)
@@ -201,6 +202,7 @@ export(greta_notes_conda_install_output)
 export(greta_notes_install_miniconda_error)
 export(greta_notes_install_miniconda_output)
 export(greta_notes_tf_num_error)
+export(greta_python_deps)
 export(greta_sitrep)
 export(hmc)
 export(hypergeometric)

NEWS.md

@@ -28,6 +28,17 @@ The following optimisers are removed, as they are no longer supported by Tensorf
  * `cobyla()`
  * `slsqp()`
 
+## Installation revamp
+
+This release provides a few improvements to installation in greta. It should now provide more information about installation progress, and be more robust. The intention is, it should _just work_, and if it doesn't fail gracefully with some useful advice on problem solving.
+
+* Added option to restart R + run `library(greta)` after installation (#523)
+* Added installation deps object, `greta_python_deps()` to help simplify specifying package versions (#664)
+* removed `method` and `conda` arguments from `install_greta_deps()` as they 
+  were not used.
+* removed `manual` option in `install_greta_deps()`
+* added default 5 minute timer to installation processes
+
 ## Minor
 
 * `greta_sitrep()` now checks for minimum versions of software, instead of exact versions. It requires at least Python version 3.8, TensorFlow 2.8.0, and Tensorflow Probability 0.14.0.

R/greta_create_conda_env.R

@@ -1,17 +1,17 @@
-greta_create_conda_env <- function(timeout) {
-
-  options(warning.length = 2000)
+greta_create_conda_env <- function(timeout = 5,
+                                   python_deps = greta_python_deps()) {
 
   stdout_file <- create_temp_file("out-greta-conda")
   stderr_file <- create_temp_file("err-greta-conda")
 
   callr_conda_create <- callr::r_process_options(
-    func = function() {
+    func = function(python_version) {
       reticulate::conda_create(
         envname = "greta-env-tf2",
-        python_version = "3.10"
+        python_version = python_version
       )
     },
+    args = list(python_version = python_deps$python_version),
     stdout = stdout_file,
     stderr = stderr_file
   )
@@ -21,8 +21,10 @@ greta_create_conda_env <- function(timeout) {
     stdout_file = stdout_file,
     stderr_file = stderr_file,
     timeout = timeout,
-    cli_start_msg = "Creating 'greta-env-tf2' conda environment using python \\
-                      v3.8, this may take a minute",
+    cli_start_msg = glue::glue(
+    "Creating 'greta-env-tf2' conda environment using python \\
+    v{python_deps$python_version}, this may take a minute"
+    ),
     cli_end_msg = "greta-env-tf2 environment created!"
   )
 

R/greta_install_miniconda.R

@@ -1,4 +1,4 @@
-greta_install_miniconda <- function(timeout) {
+greta_install_miniconda <- function(timeout = 5) {
 
   stdout_file <- create_temp_file("out-miniconda")
   stderr_file <- create_temp_file("err-miniconda")

R/greta_install_python_deps.R

@@ -1,24 +1,35 @@
-greta_install_python_deps <- function(timeout) {
+greta_install_python_deps <- function(timeout = 5,
+                                      python_deps = greta_python_deps()) {
 
   stdout_file <- create_temp_file("out-python-deps")
   stderr_file <- create_temp_file("err-python-deps")
 
   callr_conda_install <- callr::r_process_options(
-    func = function() {
+    func = function(python_deps) {
+      cli::cli_progress_step(
+        msg = "Installing TF (v{python_deps$tf_version})",
+        msg_done = "Installed TF (v{python_deps$tf_version})!",
+        msg_failed = "Error installing TF (v{python_deps$tf_version})"
+        )
       tensorflow::install_tensorflow(
-        version = "2.15.0",
+        version = python_deps$tf_version,
         envname = "greta-env-tf2",
         method = "conda"
       )
-      reticulate::py_install(packages = "tensorflow-probability==0.23.0",
-                             pip = TRUE,
-                             envname = "greta-env-tf2",
-                             method = "conda")
-      # reticulate::py_install(packages = "keras==2.11.0",
-      #                        pip = TRUE,
-      #                        envname = "greta-env-tf2",
-      #                        method = "conda")
+      dep_tfp <- glue::glue("tensorflow-probability=={python_deps$tfp_version}")
+      cli::cli_progress_step(
+        msg = "Installing TFP (v{python_deps$tfp_version})",
+        msg_done = "Installed TFP (v{python_deps$tfp_version})!",
+        msg_failed = "Error installing TFP (v{python_deps$tfp_version})"
+      )
+      reticulate::py_install(
+        packages = dep_tfp,
+        pip = TRUE,
+        envname = "greta-env-tf2",
+        method = "conda"
+        )
       },
+    args = list(python_deps = python_deps),
     stdout = stdout_file,
     stderr = stderr_file
     )
@@ -28,8 +39,10 @@ greta_install_python_deps <- function(timeout) {
     timeout = timeout,
     stdout_file = stdout_file,
     stderr_file = stderr_file,
-    cli_start_msg = "Installing python modules into 'greta-env-tf2' conda \\
-                     environment, this may take a few minutes",
+    cli_start_msg = glue::glue(
+    "Installing python modules into 'greta-env-tf2' conda environment, \\
+    this may take a few minutes"
+    ),
     cli_end_msg = "Python modules installed!"
   )
 

R/install_greta_deps.R

@@ -7,24 +7,12 @@
 #'   virtual or conda environment, named "greta-env-tf2". Note that "virtualenv"
 #'   is not available on Windows.
 #'
-#' @param method Installation method ("virtualenv" or "conda")
-#' @param conda The path to a `conda` executable. Use `"auto"` to allow
-#'   `reticulate` to automatically find an appropriate `conda` binary. See
-#'   **Finding Conda** for more details.
+#' @param python_deps object created with `greta_python_deps()` where you
+#'   specify python, TF, and TFP versions.
+#'
 #' @param timeout maximum time in minutes until the installation for each
 #'    installation component times out and exits. Default is 5 minutes per
 #'    installation component.
-#' @param manual logical. Skip the fancy installation and just run:
-#'     ```
-#'     reticulate::py_install(
-#'         packages = c(
-#'           'numpy',
-#'           'tensorflow',
-#'           'tensorflow-probability'
-#'           ),
-#'           pip = TRUE
-#'        )
-#'     ```
 #' @param restart character. Restart R after installation? Default is "ask".
 #'  Other options are, "force", and "no". Using "force" will will force a
 #'  restart after installation. Using  "no" will not restart. Note that this
@@ -69,13 +57,13 @@
 #' @importFrom callr r_process
 #' @importFrom cli cli_alert_success
 #' @importFrom cli cli_ul
-install_greta_deps <- function(method = c("auto", "virtualenv", "conda"),
-                               conda = "auto",
+install_greta_deps <- function(python_deps = greta_python_deps(),
                                timeout = 5,
-                               manual = FALSE,
                                restart = c("ask", "force", "no"),
                                ...) {
 
+  check_greta_python_deps(python_deps)
+
   restart <- rlang::arg_match(
     arg = restart,
     values = c("ask", "force", "no")
@@ -84,35 +72,26 @@ install_greta_deps <- function(method = c("auto", "virtualenv", "conda"),
   # set warning message length
   options(warning.length = 2000)
 
-  if (manual) {
-    reticulate::py_install(
-      packages = c(
-        'numpy',
-        'tensorflow==2.15',
-        'tensorflow-probability==0.23.0',
-        "keras==2.15.0"
-      ),
-      envname = "greta-env-tf2",
-      pip = TRUE
-    )
-  } else if (!manual) {
-
-    # install miniconda if needed
-    if (!have_conda()) {
-      greta_install_miniconda(timeout)
-    }
-
-    if (!have_greta_conda_env()) {
-      greta_create_conda_env(timeout)
-    }
-
-    greta_install_python_deps(timeout)
+  # install miniconda if needed
+  if (!have_conda()) {
+    greta_install_miniconda(timeout)
+  }
 
+  if (!have_greta_conda_env()) {
+    greta_create_conda_env(
+      timeout = timeout,
+      python_deps = python_deps
+      )
   }
 
-    cli_alert_success("Installation of {.pkg greta} dependencies is complete!")
+  greta_install_python_deps(
+    timeout = timeout,
+    python_deps = python_deps
+  )
+
+  cli_alert_success("Installation of {.pkg greta} dependencies is complete!")
 
-    restart_or_not(restart)
+  restart_or_not(restart)
 
 }
 
@@ -160,3 +139,65 @@ restart_or_not <- function(restart){
   }
 
 }
+
+## TODO
+## Add a way to pass this along to a custom simpler python installer function
+## A la:
+# reticulate::py_install(
+#   packages = c(
+#     'numpy',
+#     'tensorflow==2.15',
+#     'tensorflow-probability==0.23.0',
+#     "keras==2.15.0"
+#   ),
+#   envname = "greta-env-tf2",
+#   pip = TRUE
+# )
+
+#' Specify python dependencies for greta
+#'
+#' A helper function for specifying versions of Tensorflow (TF), Tensorflow Probability (TFP), and Python.
+#'
+#' @param tf_version Character. Tensorflow (TF) version in format major.minor.patch. Default is "2.15.0".
+#' @param tfp_version Character.Tensorflow probability (TFP) version major.minor.patch. Default is "0.23.0".
+#' @param python_version Character. Ptyhon version in format major.minor.patch. Default is "3.10".
+#'
+#' @return list of dependencies
+#' @export
+#'
+#' @examples
+#' greta_python_deps()
+greta_python_deps <- function(tf_version = "2.15.0",
+                              tfp_version = "0.23.0",
+                              python_version = "3.10"){
+
+  deps_list <- list(
+    tf_version = tf_version,
+    tfp_version = tfp_version,
+    python_version = python_version
+  )
+
+  structure(
+    deps_list,
+    class = "greta_python_deps"
+  )
+
+}
+
+check_greta_python_deps <- function(deps) {
+  if (!inherits(deps, "greta_python_deps")) {
+    cli::cli_abort("{.arg deps} must be created by {.fun greta_python_deps}.")
+  }
+}
+
+#' Print method for greta python deps
+#'
+#' @param x greta python deps
+#' @param ... extra args, not used
+#' @export
+print.greta_python_deps <- function(x, ...){
+  cli::cli_h1("{.pkg greta} Python dependency spec:")
+  cli::cli_li("{.pkg TF} Version: {.val {x$tf_version}}")
+  cli::cli_li("{.pkg TFP} Version: {.val {x$tfp_version}}")
+  cli::cli_li("{.pkg Python} Version: {.val {x$python_version}}")
+}

R/new_install_process.R

@@ -4,7 +4,6 @@ new_install_process <- function(callr_process,
                                 stderr_file = NULL,
                                 cli_start_msg = NULL,
                                 cli_end_msg = NULL){
-  options(warning.length = 2000)
   cli::cli_process_start(cli_start_msg)
   # convert max timeout from milliseconds into minutes
   timeout_minutes <- timeout * 1000 * 60

R/utils.R

@@ -780,7 +780,7 @@ other_install_fail_msg <- function(error_passed){
   )
 }
 
-timeout_install_msg <- function(timeout, py_error = NULL){
+timeout_install_msg <- function(timeout = 5, py_error = NULL){
   msg <- c(
     "Stopping as installation of {.pkg greta} dependencies took longer than \\
         {timeout} minutes",