Merge pull request #683 from njtierney/collate-install-logs-493

Combine log files into a single file

Author: njtierney

.github/workflows/R-CMD-check.yaml

@@ -81,7 +81,9 @@ jobs:
         run: remotes::install_local(dependencies = TRUE, force = TRUE)
 
       - name: Install greta deps
-        run: greta::install_greta_deps(timeout = 50)
+        run: |
+          library(greta)
+          greta::install_greta_deps(timeout = 50)
 
       - name: Situation Report on greta install
         run: greta::greta_sitrep()

DESCRIPTION

@@ -46,6 +46,7 @@ Imports:
     reticulate (>= 1.19.0),
     rlang,
     tensorflow (>= 2.8.0),
+    whisker,
     yesno
 Suggests:
     bayesplot,
@@ -130,6 +131,7 @@ Collate:
     'checkers.R'
     'test_if_forked_cluster.R'
     'testthat-helpers.R'
+    'write-logfiles.R'
     'zzz.R'
     'internals.R'
 LazyData: true

NAMESPACE

@@ -181,6 +181,7 @@ export(colMeans)
 export(colSums)
 export(cov2cor)
 export(cpu_only)
+export(destroy_greta_deps)
 export(diag)
 export(dirichlet)
 export(dirichlet_multinomial)
@@ -196,14 +197,9 @@ export(gpu_only)
 export(gradient_descent)
 export(greta_array)
 export(greta_deps_receipt)
-export(greta_notes_conda_create_error)
-export(greta_notes_conda_create_output)
-export(greta_notes_conda_install_error)
-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_set_install_logfile)
 export(greta_sitrep)
 export(hmc)
 export(hypergeometric)
@@ -268,6 +264,7 @@ export(uniform)
 export(variable)
 export(weibull)
 export(wishart)
+export(write_greta_install_log)
 export(zeros)
 import(methods)
 importFrom(R6,R6Class)

NEWS.md

@@ -41,6 +41,9 @@ This release provides a few improvements to installation in greta. It should now
 * Added `greta_deps_receipt()` to list the current main python packages installed. (#668)
 * Added checking suite to ensure you are using valid versions of TF, TFP, and Python(#666)
 * Added data `greta_deps_tf_tfp` (#666), which contains valid versions combinations of TF, TFP, and Python.
+* remove `greta_nodes_install/conda_*()` options as #493 makes them defunct.
+* Added option to write to a single logfile with `greta_set_install_logfile()`, and `write_greta_install_log()`. (#493)
+* Added `destroy_greta_deps()` function to remove miniconda and python conda environment
 
 ## Minor
 

R/checkers.R

@@ -56,15 +56,14 @@ check_tf_version <- function(alert = c("none",
     cli_process_failed()
 
     cli_msg <- c(
-      "We have detected that you do not have the expected python packages \\
-          setup.",
-      "You can set these up by running this R code in the console:",
+      "x" = "The expected python packages are not available",
+      "i" = "We recommend installing them (in a fresh R session) with:",
       "{.code install_greta_deps()}",
-      "Then, restart R and run:",
-      "{.code library(greta)}",
+      "or",
+      "{.code reinstall_greta_deps()}",
       "({.strong Note}: Your R session should not have initialised \\
           Tensorflow yet.)",
-      "For more information, see {.code ?install_greta_deps}"
+      "i" = "For more information, see {.code ?install_greta_deps}"
     )
 
     # if there was a problem, append the solution
@@ -74,9 +73,9 @@ check_tf_version <- function(alert = c("none",
 
     switch(
       alert,
-      error = stop(error_text, call. = FALSE),
-      warn = warning(warning_text, call. = FALSE),
-      message = message(message_text),
+      error = rlang::abort(error_text),
+      warn = rlang::warn(warning_text),
+      message = rlang::inform(message_text),
       startup = packageStartupMessage(message_text),
       none = NULL
     )

R/data-deps-tf-tfp.R

@@ -1,9 +1,9 @@
-#' Suggested TF, TFP, and Python dependencies
+#' Suggested valid Python dependencies for greta
 #'
 #' This is a dataset that contains suggested valid versions of Tensorflow (TF),
 #'   Tensorflow Probability (TFP), and Python for linux, mac, and windows
 #'   machines. It was constructed from
-#'   <https://www.tensorflow.org/install/source>,
+#'   <https://www.tensorflow.org/install/source> and
 #'   <https://www.tensorflow.org/install/source_windows>, and by inspecting
 #'   <https://github.com/tensorflow/probability/releases>.
 #'

R/greta_create_conda_env.R

@@ -31,9 +31,4 @@ greta_create_conda_env <- function(timeout = 5,
   greta_stash$conda_create_notes <- install_conda_create$output_notes
   greta_stash$conda_create_error <- install_conda_create$output_error
 
-  cli::cli_ul("To see full installation notes run:")
-  cli::cli_ul("{.code greta_notes_conda_create_output()}")
-  cli::cli_ul("To see any error messages, run:")
-  cli::cli_ul("{.code greta_notes_conda_create_error()}")
-
 }

R/greta_install_miniconda.R

@@ -25,8 +25,4 @@ greta_install_miniconda <- function(timeout = 5) {
   greta_stash$miniconda_notes <- install_miniconda_process$output_notes
   greta_stash$miniconda_error <- install_miniconda_process$output_error
 
-  cli::cli_ul("To see full installation notes run:")
-  cli::cli_ul("{.code greta_notes_install_miniconda_output()}")
-  cli::cli_ul("To see any error messages, run:")
-  cli::cli_ul("{.code greta_notes_install_miniconda_error()}")
 }

R/greta_install_python_deps.R

@@ -49,9 +49,4 @@ greta_install_python_deps <- function(timeout = 5,
   greta_stash$conda_install_notes <- install_python_modules$output_notes
   greta_stash$conda_install_error <- install_python_modules$output_error
 
-  cli::cli_ul("To see full installation notes run:")
-  cli::cli_ul("{.code greta_notes_conda_install_output()}")
-  cli::cli_ul("To see any error messages, run:")
-  cli::cli_ul("{.code greta_notes_conda_install_error()}")
-
 }

R/greta_stash.R

@@ -1,68 +1,32 @@
 greta_note_msg <- cli::format_message(
   c(
     "If you are reading this, the {.pkg greta} installation or error notes \\
-    have been wiped."
+    have been wiped. This likely means that installation has not happened, or \\
+    it has happened and you've restarted R. See `?install_greta_deps()` for \\
+    more information."
     )
 )
 
 greta_stash$install_miniconda_notes <- greta_note_msg
+greta_stash$install_miniconda_error <- greta_note_msg
 greta_stash$conda_create_notes <- greta_note_msg
+greta_stash$conda_create_error <- greta_note_msg
 greta_stash$conda_install_notes <- greta_note_msg
+greta_stash$conda_install_error <- greta_note_msg
 greta_stash$tf_num_error <- greta_note_msg
 
-#' @title Retrieve python installation or error details.
+#' @title Retrieve python messages.
 #'
 #' @description
-#'  These functions retrieve installation or error information output by python
-#'   when running `install_miniconda()`, `conda_create()`, `conda_install()`, or
-#'   when encountering a TensorFlow numerical problem.
+#'  These functions retrieve specific python error messages that might
+#'   come up during greta use.
 #'
 #' @rdname stash-notes
 #' @export
 #' @examples
 #' \dontrun{
-#' greta_notes_install_miniconda()
-#' greta_notes_conda_create()
-#' greta_notes_conda_install()
-#' greta_notes_tf_num_error()
 #' greta_notes_tf_error()
 #' }
-greta_notes_install_miniconda_output <- function() {
-  cat(greta_stash$miniconda_notes)
-}
-
-#' @name stash-notes
-#' @export
-greta_notes_install_miniconda_error <- function(){
-  cat(greta_stash$miniconda_error)
-}
-
-#' @name stash-notes
-#' @export
-greta_notes_conda_create_output <- function() {
-  cat(greta_stash$conda_create_notes)
-}
-
-#' @name stash-notes
-#' @export
-greta_notes_conda_create_error <- function() {
-  cat(greta_stash$conda_create_error)
-}
-
-#' @name stash-notes
-#' @export
-greta_notes_conda_install_output <- function() {
-  cat(greta_stash$conda_install_notes)
-}
-
-#' @name stash-notes
-#' @export
-greta_notes_conda_install_error <- function() {
-  cat(greta_stash$conda_install_error)
-}
-
-#' @name stash-notes
-#' @export
 greta_notes_tf_num_error <- function() {
   cat(greta_stash$tf_num_error)
 }

R/install_greta_deps.R

@@ -1,14 +1,25 @@
 #' Install Python dependencies for greta
 #'
-#' This is a helper function to install Python dependencies needed. This
-#'   includes the latest version of Tensorflow version (2.13.0 or higher),
-#'   Tensorflow Probability 0.21.0 (or higher), and the latest version of
-#'   numpy (1.21.0 or higher). These Python modules will be installed into a
-#'   virtual or conda environment, named "greta-env-tf2". Note that "virtualenv"
-#'   is not available on Windows.
+#' This is a helper function to install Python dependencies needed. By default
+#'   these are TF 2.15.0, TFP 0.23.0, and Python 3.10. These Python modules
+#'   will be installed into a conda environment named "greta-env-tf2".
 #'
-#' @param python_deps object created with `greta_python_deps()` where you
-#'   specify python, TF, and TFP versions.
+#'   To see install notes or errors, there isn't an argument to specify,
+#'     instead you will need to specify and environment variable,
+#'     `GRETA_INSTALLATION_LOG`, with
+#'     `Sys.setenv('GRETA_INSTALLATION_LOG'='path/to/logfile.html')`. Or use
+#'     [greta_set_install_logfile()] to set the path, e.g.,
+#'     `greta_set_install_logfile('path/to/logfile.html')`. You can also skip
+#'     the restarting of R and use [write_greta_install_log()], which
+#'     installation notes will indicate how to use if you haven't specified.
+#'
+#' @param python_deps object created with [greta_python_deps()] where you
+#'   specify python, TF, and TFP versions. By default these are TF 2.15.0,
+#'   TFP 0.23.0, and Python 3.10. These versions must be compatible
+#'   with each other. If they are not, [greta_python_deps()] will error with
+#'   more information and suggestions. See ?[greta_python_deps()] for more
+#'   information, and see the data object `greta_deps_tf_tfp`
+#'   (`?greta_deps_tf_tfp``).
 #'
 #' @param timeout maximum time in minutes until the installation for each
 #'    installation component times out and exits. Default is 5 minutes per
@@ -84,12 +95,46 @@ install_greta_deps <- function(python_deps = greta_python_deps(),
     )
   }
 
+  # TODO
+  # Issue warning if you already have conda env +/ miniconda
+  # suggest using `reinstall_greta_deps()`
   greta_install_python_deps(
     timeout = timeout,
     python_deps = python_deps
   )
 
-  cli_alert_success("Installation of {.pkg greta} dependencies is complete!")
+  # TODO
+  # Detect if you have tried to install greta multiple times in the same
+  # session, and suggest that perhaps they want to use
+  # `reinstall_greta_deps()`
+  # perhaps even stopping the session with a "yesno"
+
+  greta_logfile <- Sys.getenv("GRETA_INSTALLATION_LOG")
+
+  logfile_exists <- nzchar(greta_logfile)
+
+  no_logfile <- !logfile_exists
+
+
+  if (logfile_exists) {
+    write_greta_install_log(path = greta_logfile)
+  }
+
+  if (no_logfile) {
+    cli::cli_alert_warning(
+      text = c(
+        "No logfile specified. If you want to save the logfile to see any \\
+        install notes, or potential errors, you will need to \\
+        {.strong not restart R}, then run:\n\n",
+      "{.run write_greta_install_log('greta-logfile.html')}"
+      ),
+      wrap = TRUE
+    )
+  }
+
+  cli::cli_alert_success("Installation of {.pkg greta} dependencies \\
+                         is complete!",
+                         wrap = TRUE)
 
   restart_or_not(restart)
 
@@ -160,7 +205,7 @@ restart_or_not <- function(restart){
 #'
 #' @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".
+#' @param python_version Character. Python version in format major.minor.patch. Default is "3.10".
 #'
 #' @return list of dependencies
 #' @export
@@ -182,10 +227,10 @@ greta_python_deps <- function(tf_version = "2.15.0",
     class = c("greta_python_deps", "data.frame")
   )
 
+  # check for envvar to silence these checks
   check_tfp_tf_semantic(deps_obj)
   check_greta_tf_range(deps_obj)
   check_greta_tfp_range(deps_obj)
-
   check_greta_python_range(deps_obj$python_version)
   check_greta_deps_config(deps_obj)
 
@@ -259,7 +304,8 @@ check_greta_deps_range <- function(python_deps,
         {version_name} > {.val {latest_version}}",
         "i" = "See {.url {gh_issue}} for more information",
         "x" = "The provided version was {.val {version_provided}}",
-        "i" = "The closest value is: {.val {latest_version}}",
+        "i" = "The nearest valid version that is supported by \\
+        {.pkg greta} is: {.val {latest_version}}",
         "i" = "Valid versions of TF, TFP, and Python are in \\
                   {.code greta_deps_tf_tfp}",
         "i" = "Inspect with:",
@@ -280,7 +326,8 @@ check_greta_deps_range <- function(python_deps,
                   supported versions",
                   "The version {.val {version_provided}} was not in \\
                   {.val {greta_deps_tf_tfp[[deps]]}}",
-                  "The closest value is: {.val {closest_value}}",
+                  "i" = "The nearest valid version that is supported by \\
+        {.pkg greta} is: {.val {closest_value}}",
                   "i" = "Valid versions of TF, TFP, and Python are in \\
                   {.code greta_deps_tf_tfp}",
                   "i" = "Inspect with:",
@@ -332,7 +379,6 @@ check_greta_python_range <- function(version_provided,
 check_greta_deps_config <- function(python_deps,
                                     call = rlang::caller_env()){
 
-  # check for envvar to silence these checks
   check_greta_python_deps(python_deps)
 
   python_deps <- python_deps |>
@@ -415,9 +461,9 @@ check_greta_deps_config <- function(python_deps,
       "suggest_py" = py_matches
     )
 
-    suggested_tfp <- as.character(suggested_match$tfp_version)
-    suggested_tf <- as.character(suggested_match$tf_version)
-    suggested_py <- as.character(suggested_match$python_version_max)
+    suggested_tfp <- as.character(max(suggested_match$tfp_version))
+    suggested_tf <- as.character(max(suggested_match$tf_version))
+    suggested_py <- as.character(max(suggested_match$python_version_max))
 
     cli::cli_abort(
       message = c("Provided {.code greta_python_deps} does not match valid \\

R/package.R

@@ -37,5 +37,14 @@
 
 # clear CRAN checks spotting floating global variables
 #' @importFrom utils globalVariables
-utils::globalVariables(c("N"), "greta")
-
+utils::globalVariables(
+  c("N",
+  "greta_deps_tf_tfp",
+  "greta_logfile",
+  "os",
+  "python_version_max",
+  "python_version_min",
+  "tf_version",
+  "tfp_version",
+  "greta")
+)