Merge pull request #118 from NovoNordisk-OpenSource/feat/run-python-r…

…eview

feat: integrate python logging directly in functions

R/session.R

@@ -1,10 +1,11 @@
 #' Get session info
 #'
 #' Retrieve session info and add quarto info if not already there
+#' Argument to also add python version and package info
 #'
 #' @noRd
 
-session_info <- function(approved_folder_pkgs, approved_url_pkgs) {
+session_info <- function(approved_folder_pkgs = NULL, approved_url_pkgs = NULL, python_packages = NULL) {
   info <- sessioninfo::session_info()
 
   if (!is.null(approved_folder_pkgs) |
@@ -30,7 +31,7 @@ session_info <- function(approved_folder_pkgs, approved_url_pkgs) {
   info$options <- info$options[!names(info$options) %in% "rl_word_breaks"]
   class(info$options) <- c("options_info", class(info$options))
 
-  # TODO: Extend to also cover external and python below in methods.
+  # TODO: Extend to also cover external.
   info[!names(info) %in% c("platform", "packages", "environment", "options")] <- NULL
 
   if (is.null(info$platform$quarto)) {
@@ -44,6 +45,19 @@ session_info <- function(approved_folder_pkgs, approved_url_pkgs) {
     }
   }
 
+  if (!is.null(python_packages)) {
+
+    # TODO: Get the same information as for R packages (not only name and version)
+    # TODO: Only show used, and not all installed, packages if possible
+
+    info$python_packages <- python_packages
+    class(info$python_packages) <- c("packages_info", class(info$python_packages))
+
+    quarto_python_path <- Sys.getenv("QUARTO_PYTHON")
+    quarto_python_version <- gsub(".*/([0-9]+\\.[0-9]+\\.[0-9]+)/.*", "\\1", quarto_python_path)
+    info$platform$python <- quarto_python_version
+  }
+
   class(info) <- c("whirl_session_info", class(info))
   for (i in seq_along(info)) {
     class(info[[i]]) <- c(paste0("whirl_", class(info[[i]])[[1]]), class(info[[i]]))
@@ -52,6 +66,21 @@ session_info <- function(approved_folder_pkgs, approved_url_pkgs) {
   return(info)
 }
 
+#' Get Python package info from json file
+#'
+#' @noRd
+
+python_package_info <- function(json) {
+
+  json |>
+    jsonlite::fromJSON() |>
+    tibble::enframe(name = "Package") |>
+    tidyr::unnest_wider(col = value) |>
+    dplyr::rename(
+      Version = version,
+      Path = installation_path
+    )
+}
 
 #' @noRd
 
@@ -81,13 +110,18 @@ knit_print.whirl_platform_info <- function(x, ...) {
 #' @noRd
 
 knit_print.whirl_packages_info <- function(x, ...) {
-  data.frame(
-    Package = x$package,
-    Version = x$loadedversion,
-    `Date (UTC)` = x$date,
-    Source = x$source,
-    check.names = FALSE
-  ) |>
+
+  if (!is.null(x$package)){
+    x <- data.frame(
+      Package = x$package,
+      Version = x$loadedversion,
+      `Date (UTC)` = x$date,
+      Source = x$source,
+      check.names = FALSE
+    )
+  }
+
+  x |>
     knitr::kable() |>
     kableExtra::kable_styling(
       bootstrap_options = "striped",
@@ -97,7 +131,7 @@ knit_print.whirl_packages_info <- function(x, ...) {
 }
 
 #' @noRd
-#'
+
 knit_print.whirl_approved_pkgs <- function(x, ...) {
   hold <- x |>
     data.frame(

R/status.R

@@ -11,20 +11,27 @@ get_status <- function(md) {
 
   x <- x[[1]]
 
+  add_python <- x |>
+    stringr::str_detect("\\{.python .cell-code") |>
+    any()
+
   # Errors
 
   errors <- x |>
     stringr::str_subset(pattern = "^ *\\{\\.cell-output \\.cell-output-error\\}") |>
     stringr::str_remove_all("\\{[^\\}]*\\}") |>
     stringr::str_squish()
-
-  python_errors <- x |>
-    stringr::str_subset(pattern = "(?i).*Error.*") |>
-    stringr::str_remove_all("\\{[^\\}]*\\}") |>
-    stringr::str_squish()
-
-  errors <- c(errors, python_errors)
-
+
+  if (add_python) {
+    python_errors <- x |>
+      stringr::str_subset(pattern = "^ *\\{\\.cell-output") |>
+      stringr::str_remove_all("\\{[^\\}]*\\}") |>
+      stringr::str_squish() |>
+      stringr::str_subset("Error:")
+
+    errors <- c(errors, python_errors)
+  }
+
   # Warnings
 
   warnings <- x |>
@@ -33,6 +40,16 @@ get_status <- function(md) {
     stringr::str_squish() |>
     stringr::str_subset(pattern = "^(W|w)arning")
 
+  if (add_python) {
+    python_warnings <- x |>
+      stringr::str_subset(pattern = "^ *\\{\\.cell-output") |>
+      stringr::str_remove_all("\\{[^\\}]*\\}") |>
+      stringr::str_squish() |>
+      stringr::str_subset("Warning:")
+
+    warnings <- c(warnings, python_warnings)
+  }
+
   # Status
 
   if (length(errors)) {

inst/documents/dummy.qmd

@@ -8,7 +8,10 @@ params:
   tmpdir: "."
 ---
 
-```{r setup, include=FALSE}
+```{r setup}
+#| label: Setup
+#| include: false
+
 knitr::opts_chunk$set(
   error = TRUE,
   warning = TRUE,
@@ -19,48 +22,56 @@ knitr::opts_chunk$set(
 .libPaths(c(character(), params$with_library_paths))
 ```
 
-```{r, echo=FALSE, eval=(grepl("\\.R$", params$script))}
+```{r}
+#| label: Log R
+#| eval: !expr grepl("\\.R$", params$script)
+#| echo: false
 knitr::spin_child(params$script)
 ```
 
-```{r, child = params$script, eval=(grepl("\\.qmd$", params$script))}
+```{r}
+#| label: Log Quarto
+#| child: !expr params$script
+#| eval: !expr grepl("\\.qmd$", params$script)
+#| include: !expr grepl("\\.qmd$", params$script)
 ```
 
-```{r, child = params$script, eval=(grepl("\\.Rmd$", params$script))}
+```{r}
+#| label: Log Rmarkdown
+#| child: !expr params$script
+#| eval: !expr grepl("\\.Rmd$", params$script)
+#| include: !expr grepl("\\.Rmd$", params$script)
 ```
 
-```{python, file=params$script, eval=(grepl("\\.py$", params$script))}
+```{python}
+#| label: Log Python
+#| file: !expr params$script
+#| eval: !expr grepl("\\.py$", params$script)
+#| include: !expr grepl("\\.py$", params$script)
 ```
 
-```{python, eval=(grepl("\\.py$", params$script)), echo=FALSE}
-import json
-import sys
-import subprocess
-
-temp_dir = r.params['tmpdir']
-
-# Get a list of installed packages using pip list
-installed_packages = subprocess.check_output([sys.executable, '-m', 'pip', 'list', '-v']).decode('utf-8').strip().split('\n')[2:]
-installed_packages = {package.split()[0]: [package.split()[1], package.split()[2]] for package in installed_packages}
-
-imported_modules = {}
-for module_name, module in sys.modules.items():
-    if not (module_name.startswith('_') or module_name.startswith('.') or '.' in module_name):
-        if module_name in installed_packages:
-            imported_modules[module_name] = {
-                "version": installed_packages[module_name][0],
-                "installation_path": installed_packages[module_name][1]
-            }
-
-with open(f'{temp_dir}/python_imports.json', 'w') as json_file:
-    json.dump(imported_modules, json_file)
-
+```{python}
+#| label: Python modules
+#| file: !expr file.path(params$tmpdir, "python_modules.py")
+#| eval: !expr grepl("\\.py$", params$script)
+#| echo: false
 ```
 
+```{r}
+#| label: Session info
+#| include: false
+
+python_packages <- NULL
+if (file.exists(file.path(params$tmpdir, "python_imports.json"))){
+  python_packages <- whirl:::python_package_info(file.path(params$tmpdir, "python_imports.json"))
+}
 
-```{r sessioninfo, include=FALSE}
 saveRDS(
-  object = whirl:::session_info(params$check_approved_folder_pkgs, params$check_approved_url_pkgs),
+  object = whirl:::session_info(
+    approved_folder_pkgs = params$check_approved_folder_pkgs, 
+    approved_url_pkgs = params$check_approved_url_pkgs, 
+    python_packages = python_packages
+    ),
   file = file.path(params$tmpdir, "session_info.rds")
 )
 
@@ -70,6 +81,4 @@ if (is.character(params$renv) && params$renv == "yes" | is.logical(params$renv)
     file = file.path(params$tmpdir, "renv_status.rds")
   )
 }
-
 ```
-