From cadbfdecc28a07f08e10c5fb4c2e4dd77c051bc2 Mon Sep 17 00:00:00 2001
From: Stella <stella.belin@farmaci.uu.se>
Date: Tue, 10 Dec 2024 13:42:19 +0100
Subject: [PATCH] Add function check_setup

---
 DESCRIPTION        |  1 +
 R/check_setup.R    | 67 ++++++++++++++++++++++++++++++++++++++++++++++
 man/check_setup.Rd | 16 +++++++++++
 3 files changed, 84 insertions(+)
 create mode 100644 R/check_setup.R
 create mode 100644 man/check_setup.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 89ffd6a..ef188b8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -24,6 +24,7 @@ SystemRequirements:
     Python (>= 3.11.0)
 Imports:
     reticulate (>= 1.19),
+    cli,
     utils
 Suggests:
     testthat,
diff --git a/R/check_setup.R b/R/check_setup.R
new file mode 100644
index 0000000..4d08bad
--- /dev/null
+++ b/R/check_setup.R
@@ -0,0 +1,67 @@
+#' @title
+#' Checks setup of Pharmpy/pharmr 
+#' 
+#' @description
+#' Checks if everything is setup correctly. The following things are checked:
+#' * If Python is installed and has correct version
+#' * If Pharmpy is available
+#' * If Pharmpy and pharmr version matches
+#' 
+#' @export
+check_setup <- function() {
+  cli::cli_h3("Checking Python setup")
+  py_okay <- check_python()
+  if (py_okay) {
+    cli::cli_h3("Checking Pharmpy and pharmr")
+    pharmpy_okay <- check_pharmpy()
+  }
+}
+
+check_python <- function() {
+  py <- reticulate::py_discover_config()
+  if (is.null(py)) {
+    print_status('fail', 'No Python found')
+    return(FALSE)
+  }
+  print_status('success', 'Python found:', additional_info=py$python)
+  py_version <- as.character(py$version)
+  if (utils::compareVersion(py_version, '3.11') == -1) {
+    print_status('fail', 'Version not supported:', additional_info=py_version)
+    return(FALSE)
+  }
+  print_status('success', 'Version supported:', additional_info=py_version)
+  return(TRUE)
+}
+
+check_pharmpy <- function() {
+  pharmpy_avail <- reticulate::py_module_available('pharmpy')
+  if (isFALSE(pharmpy_avail)) {
+    print_status('fail', 'Could not find Pharmpy installation')
+    return(FALSE)
+  }
+  pharmpy_version <- reticulate::py_to_r(pharmpy$`__version__`)
+  print_status('success', 'Pharmpy found:', additional_info=pharmpy_version)
+  pharmr_version <- as.character(packageVersion('pharmr'))
+  if (utils::compareVersion(pharmpy_version, pharmr_version) != 0) {
+    print_status('fail', 'pharmr version does not match:', additional_info=pharmr_version)
+    return(FALSE)
+  }
+  print_status('success', 'pharmr version matches:', additional_info=pharmr_version)
+  return(TRUE)
+}
+
+print_status <- function(type, msg, additional_info=NULL) {
+  if (type == 'success') {
+    cli::cli_alert_success(msg)
+  }
+  else if (type == 'fail') {
+    cli::cli_alert_danger(msg)
+  }
+  else {
+    stop('Unknown status type')
+  }
+  if (!is.null(additional_info)) {
+    cat('  ')
+    cli::cli_alert(additional_info)
+  }
+}
diff --git a/man/check_setup.Rd b/man/check_setup.Rd
new file mode 100644
index 0000000..595af7d
--- /dev/null
+++ b/man/check_setup.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check_setup.R
+\name{check_setup}
+\alias{check_setup}
+\title{Checks setup of Pharmpy/pharmr}
+\usage{
+check_setup()
+}
+\description{
+Checks if everything is setup correctly. The following things are checked:
+\itemize{
+\item If Python is installed and has correct version
+\item If Pharmpy is available
+\item If Pharmpy and pharmr version matches
+}
+}