diff --git a/.github/actions/setup/action.yaml b/.github/actions/setup/action.yaml
index 6bca8ef..fa4f8ba 100644
--- a/.github/actions/setup/action.yaml
+++ b/.github/actions/setup/action.yaml
@@ -8,5 +8,21 @@ runs:
       shell: bash
       run: |
         echo 0 | sudo tee /proc/sys/kernel/yama/ptrace_scope
+
     - name: Install Quarto
       uses: quarto-dev/quarto-actions/setup@v2
+
+    - name: (Linux) Install jupyter
+      if: runner.os == 'Linux'
+      shell: bash
+      run: python3 -m pip install jupyter
+
+    - name: (macOS) Install jupyter
+      if: runner.os == 'macOS'
+      shell: bash
+      run: python3 -m pip install --break-system-packages jupyter
+
+    - name: (Windows) Install jupyter
+      if: runner.os == 'Windows'
+      shell: bash
+      run: py -m pip install jupyter
diff --git a/DESCRIPTION b/DESCRIPTION
index 9200260..9d5b429 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: whirl
 Title: Logging package
-Version: 0.1.5
+Version: 0.1.5.9000
 Authors@R: c(
     person("Aksel", "Thomsen", , "oath@novonordisk.com", role = c("aut", "cre")),
     person("Lovemore", "Gakava", , "lvgk@novonordisk.com", role = "aut"),
@@ -41,7 +41,8 @@ Imports:
     withr,
     yaml,
     zephyr (>= 0.0.0.9000),
-    glue
+    glue,
+    reticulate
 Suggests: 
     testthat (>= 3.0.0),
     usethis
diff --git a/NAMESPACE b/NAMESPACE
index 83fe0d8..00e142d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,3 +8,4 @@ export(use_whirl)
 importFrom(R6,R6Class)
 importFrom(callr,r_session)
 importFrom(dplyr,.data)
+importFrom(reticulate,py)
diff --git a/NEWS.md b/NEWS.md
index 386882e..3541918 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# whirl dev
+* Added support for logging of Python scripts with `run()`.
+* Improved unit tests for `run()`
+
 # whirl 0.1.4 (2024-11-01)
 * Add `use_whirl()` utility function.
 
diff --git a/R/internal_run.R b/R/internal_run.R
index c73f50d..ca91738 100644
--- a/R/internal_run.R
+++ b/R/internal_run.R
@@ -37,11 +37,11 @@ internal_run <- function(input, steps, queue, level,
       internal_run(input = files,
                    steps = steps,
                    queue = queue,
-                   level = level + 1)
+                   level = level + 1,
+                   verbosity_level = verbosity_level)
     } else {
       # Execute the scripts
       result <- queue$run(files)
-      cat("\n")
     }
   }
 
diff --git a/R/render_summary.R b/R/render_summary.R
index c27a41d..f8f4610 100644
--- a/R/render_summary.R
+++ b/R/render_summary.R
@@ -50,15 +50,12 @@ knit_print.whirl_summary_info <- function(x, path_rel_start, ...) {
   ncols <- ncol(hold)
 
   if (grepl("rstudio_cloud", Sys.getenv("R_CONFIG_ACTIVE"))) {
-    hold <- hold |> dplyr::mutate(formated = file.path("/file_show?path=", .data[["Hyperlink"]]))
+    formatted <- file.path("/file_show?path=", hold[["Hyperlink"]])
   } else {
-    hold <- hold |> dplyr::mutate(formated = file.path(path_rel(.data[["Hyperlink"]], start = path_rel_start)))
+    formatted <- file.path(path_rel(hold[["Hyperlink"]], start = path_rel_start))
   }
 
-  hold$Hyperlink <- paste0(sprintf('<a href="%s" target="_blank">%s</a>', hold$formated, "HTML Log"))
-
-  hold <- hold |>
-    dplyr::select(-.data[["formated"]])
+  hold$Hyperlink <- paste0(sprintf('<a href="%s" target="_blank">%s</a>', formatted, "HTML Log"))
 
   knitr::kable(hold, format = "html", escape = FALSE) |>
     kableExtra::column_spec(1:ncols, background = ifelse(
diff --git a/R/run.R b/R/run.R
index 2692dda..c91f5f8 100644
--- a/R/run.R
+++ b/R/run.R
@@ -21,20 +21,27 @@
 #' @inheritParams options_params
 #' @return A tibble containing the execution results for all the scripts.
 #'
-#'@examplesIf FALSE
+
+#'@examples
+#' # Start by copying the following three example scripts:
+#' file.copy(
+#'   from = system.file("examples", c("success.R", "warning.R", "error.R"), package = "whirl"),
+#'   to = "."
+#'   )
 #'
 #' # Run a single script
-#' script <- system.file("examples/simple/success.R", package = "whirl")
-#' run(script)
+#' run("success.R")
 #'
 #' # Run several scripts in parallel on up to 2 workers
-#' scripts <- system.file("examples/simple", c("success.R", "warning.R", "error.R"), package = "whirl")
-#' run(scripts, n_workers = 2)
+#' run(c("success.R", "warning.R", "error.R"), n_workers = 2)
 #'
-#' # Run scripts in several steps
-#' step_1 <- system.file("examples/simple", c("success.R", "warning.R"), package = "whirl")
-#' step_2 <- system.file("examples/simple", c("error.R"), package = "whirl")
-#' run(list(step_1, step_2), n_workers = 2)
+#' # Run scripts in two steps by providing them as list elements
+#' run(
+#'   list(
+#'     c("success.R", "warning.R"),
+#'     "error.R"
+#'     ),
+#'    n_workers = 2)
 #'
 #' @export
 
@@ -55,21 +62,31 @@ run <- function(input,
   approved_pkgs_url = options::opt("approved_pkgs_url", env = "whirl")
 
   # Message when initiating
-  d <- cli::cli_div(theme = list(rule = list(
-    color = "skyblue3", "line-type" = "double"
-  )))
-
-  zephyr::msg("Executing scripts and generating logs",
-              levels_to_write = c("verbose", "minimal"),
+  d <- NULL
+  zephyr::msg(message = "Executing scripts and generating logs",
+              theme = list(
+                rule = list(color = "skyblue3", "line-type" = "double")
+                ),
+              levels_to_write = c("verbose"),
               verbosity_level = verbosity_level,
-              msg_fun = cli::cli_rule)
+              msg_fun = \(message, theme, .envir) {
+                d <<- cli::cli_div(theme = theme, .auto_close = FALSE)
+                cli::cli_rule(message, .envir = .envir)
+              }
+  )
 
   # Message when ending
-  on.exit(zephyr::msg("End of process",
-                      levels_to_write = c("verbose", "minimal"),
-                      verbosity_level = verbosity_level,
-                      msg_fun = cli::cli_rule))
-  on.exit(cli::cli_end(d), add = TRUE)
+  on.exit({
+    zephyr::msg(message = "End of process",
+                div = d,
+                levels_to_write = c("verbose"),
+                verbosity_level = verbosity_level,
+                msg_fun = \(message, div, .envir) {
+                  cli::cli_rule(message, .envir = .envir)
+                  cli::cli_end(div)
+                  }
+                )
+  })
 
   # Constrain the number of workers
   n_workers <- min(128, n_workers)
@@ -96,9 +113,12 @@ run <- function(input,
                          level = 1,
                          verbosity_level = verbosity_level)
 
-  # Create the summary log
-  summary_tibble <- util_queue_summary(result$queue)
-  render_summary(input = summary_tibble, summary_file = summary_file)
+  # Create the summary log if required
+  if (!is.null(summary_file)) {
+    summary_tibble <- util_queue_summary(result$queue)
+    render_summary(input = summary_tibble, summary_file = summary_file)
+
+  }
 
   invisible(result$queue)
 
diff --git a/R/session.R b/R/session.R
index 573c97e..4a5dc75 100644
--- a/R/session.R
+++ b/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(
diff --git a/R/status.R b/R/status.R
index 1b46ad8..2cd5aa6 100644
--- a/R/status.R
+++ b/R/status.R
@@ -11,6 +11,10 @@ get_status <- function(md) {
 
   x <- x[[1]]
 
+  add_python <- x |>
+    stringr::str_detect("\\{.python .cell-code") |>
+    any()
+
   # Errors
 
   errors <- x |>
@@ -18,6 +22,16 @@ get_status <- function(md) {
     stringr::str_remove_all("\\{[^\\}]*\\}") |>
     stringr::str_squish()
 
+  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 |>
@@ -26,6 +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)) {
diff --git a/R/utils.R b/R/utils.R
index 56a2536..703d730 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -5,7 +5,7 @@ get_file_ext <- function(file_paths) {
     FUN = function(file_path) {
       file_name <- basename(file_path)
       file_parts <- strsplit(file_name, "\\.")[[1]]
-      file_extension <- ifelse(length(file_parts) == 1, "", tail(file_parts, 1))
+      file_extension <- ifelse(length(file_parts) == 1, "", utils::tail(file_parts, 1))
       return(file_extension)
     },
     FUN.VALUE = character(1),
diff --git a/R/whirl-package.R b/R/whirl-package.R
index 49217e0..6fc4021 100644
--- a/R/whirl-package.R
+++ b/R/whirl-package.R
@@ -1,5 +1,6 @@
 ## usethis namespace: start
 #' @importFrom dplyr .data
+#' @importFrom reticulate py
 ## usethis namespace: end
 NULL
 
diff --git a/README.Rmd b/README.Rmd
index 9d7d408..e54ffb8 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -12,7 +12,17 @@ knitr::opts_chunk$set(
   out.width = "100%"
 )
 
+# Minimal printing for shorter readme
 options(whirl.verbosity_level = "minimal")
+
+# Use a temporary directory as working directory with all examples available
+tmp <- withr::local_tempdir()
+
+system.file("examples", package = "whirl") |> 
+  list.files(full.names = TRUE) |> 
+  file.copy(to = tmp)
+
+knitr::opts_knit$set(root.dir = tmp)
 ```
 
 # whirl
@@ -46,14 +56,14 @@ The simplest way is to provide the path to a single script:
 
 ```{r ex-script}
 library(whirl)
-script <- system.file("examples/simple/success.R", package = "whirl")
-run(script)
+
+run("success.R")
 ```
+
 It is also possible to run several scripts simultaneously:
 
 ```{r ex-scripts}
-scripts <- system.file("examples/simple", c("success.R", "warning.R"), package = "whirl")
-result <- run(scripts, n_workers = 2)
+result <- run(c("success.R", "warning.R"), n_workers = 2)
 ```
 
 Here we are specifying that `run()` can use up to two simultaneous workers to execute the scripts,
@@ -77,28 +87,27 @@ This setup is very useful when your projects have several steps that depends on
 The best way to implement this in your project is use a configuration file for whirl. 
 The configuration file is a `yaml` file that specifies each steps:
 
-```{r ex-config}
-config <- system.file("examples/simple/_whirl.yaml", package = "whirl") 
-cat(readLines(config), sep = "\n")
+`_whirl.yaml:`
+```yaml
+`r paste(readLines("_whirl.yaml"), collapse = "\n")```
 ```
 
 Here we are specifying that in the first step we run `succes.R`. And then when this step has been completed we continue to running 
 the scripts in the second steps. 
 
 ```{r ex-run-config}
-result <- run(config, n_workers = 2)
+result <- run("_whirl.yaml", n_workers = 2)
 ```
 
 ```{r, ex-return-config}
 print(result)
 ```
 
-
 ## Customize run()
 
 For more information about how to customize the the execution and the logging for your needs see the following:
 
 * `run()`: For further information on how to call it.
 * `vignette("whirl")`: For a more in depth explanation, and more advanced usage.
-* `vignette("example")`: With a simple example, including the created log.
+* `vignette("articles/example")`: With a simple example, including the created log.
 * `options()`: On how to change the default behavior of whirl.
diff --git a/README.md b/README.md
index a2cc85a..da70a59 100644
--- a/README.md
+++ b/README.md
@@ -36,22 +36,17 @@ The simplest way is to provide the path to a single script:
 
 ``` r
 library(whirl)
-script <- system.file("examples/simple/success.R", package = "whirl")
-run(script)
-#> ══ Executing scripts and generating logs ═══════════════════════════════════════
+
+run("success.R")
 #> ✔ success.R: Completed succesfully
-#> ══ End of process ══════════════════════════════════════════════════════════════
 ```
 
 It is also possible to run several scripts simultaneously:
 
 ``` r
-scripts <- system.file("examples/simple", c("success.R", "warning.R"), package = "whirl")
-result <- run(scripts, n_workers = 2)
-#> ══ Executing scripts and generating logs ═══════════════════════════════════════
+result <- run(c("success.R", "warning.R"), n_workers = 2)
 #> ✔ success.R: Completed succesfully
 #> ⚠ warning.R: Completed with warnings
-#> ══ End of process ══════════════════════════════════════════════════════════════
 ```
 
 Here we are specifying that `run()` can use up to two simultaneous
@@ -77,8 +72,8 @@ print(result)
 #> # A tibble: 2 × 5
 #>      id tag   script                                         status result      
 #>   <dbl> <chr> <chr>                                          <chr>  <list>      
-#> 1     1 <NA>  /scer/homedirs/oath/R/x86_64-pc-linux-gnu-lib… succe… <named list>
-#> 2     2 <NA>  /scer/homedirs/oath/R/x86_64-pc-linux-gnu-lib… warni… <named list>
+#> 1     1 <NA>  /private/var/folders/fx/71by3f551qzb5wkxt82cv… succe… <named list>
+#> 2     2 <NA>  /private/var/folders/fx/71by3f551qzb5wkxt82cv… warni… <named list>
 ```
 
 ## Config files
@@ -90,17 +85,17 @@ order. The best way to implement this in your project is use a
 configuration file for whirl. The configuration file is a `yaml` file
 that specifies each steps:
 
-``` r
-config <- system.file("examples/simple/_whirl.yaml", package = "whirl") 
-cat(readLines(config), sep = "\n")
-#> steps:
-#>   - name: "First step"
-#>     paths:
-#>       - "success.R"
-#>   - name: "Second step"
-#>     paths:
-#>       - "warning.R"
-#>       - "error.R"
+`_whirl.yaml:`
+
+``` yaml
+steps:
+  - name: "First step"
+    paths:
+      - "success.R"
+  - name: "Second step"
+    paths:
+      - "warning.R"
+      - "error.R"``
 ```
 
 Here we are specifying that in the first step we run `succes.R`. And
@@ -108,12 +103,10 @@ then when this step has been completed we continue to running the
 scripts in the second steps.
 
 ``` r
-result <- run(config, n_workers = 2)
-#> ══ Executing scripts and generating logs ═══════════════════════════════════════
+result <- run("_whirl.yaml", n_workers = 2)
 #> ✔ success.R: Completed succesfully
 #> ⚠ warning.R: Completed with warnings
 #> ✖ error.R: Completed with errors
-#> ══ End of process ══════════════════════════════════════════════════════════════
 ```
 
 ``` r
@@ -121,9 +114,9 @@ print(result)
 #> # A tibble: 3 × 5
 #>      id tag   script                                         status result      
 #>   <dbl> <chr> <chr>                                          <chr>  <list>      
-#> 1     1 <NA>  /scer/homedirs/oath/R/x86_64-pc-linux-gnu-lib… succe… <named list>
-#> 2     2 <NA>  /scer/homedirs/oath/R/x86_64-pc-linux-gnu-lib… warni… <named list>
-#> 3     3 <NA>  /scer/homedirs/oath/R/x86_64-pc-linux-gnu-lib… error  <named list>
+#> 1     1 <NA>  /private/var/folders/fx/71by3f551qzb5wkxt82cv… succe… <named list>
+#> 2     2 <NA>  /private/var/folders/fx/71by3f551qzb5wkxt82cv… warni… <named list>
+#> 3     3 <NA>  /private/var/folders/fx/71by3f551qzb5wkxt82cv… error  <named list>
 ```
 
 ## Customize run()
@@ -134,6 +127,6 @@ logging for your needs see the following:
 - `run()`: For further information on how to call it.
 - `vignette("whirl")`: For a more in depth explanation, and more
   advanced usage.
-- `vignette("example")`: With a simple example, including the created
-  log.
+- `vignette("articles/example")`: With a simple example, including the
+  created log.
 - `options()`: On how to change the default behavior of whirl.
diff --git a/inst/demo_script.R b/inst/demo_script.R
deleted file mode 100644
index c4ad989..0000000
--- a/inst/demo_script.R
+++ /dev/null
@@ -1,31 +0,0 @@
-out_dir <- "~/atmos/whirl/inst/examples/demo"
-
-
-# Single file -------------------------------------------------------------------
-
-#Point to a single script
-run("~/atmos/whirl/inst/examples/demo/metadata/mdcol.R", summary_dir = out_dir)
-
-
-# Folders (run in parallel) ----------------------------------------------------
-
-# A single folder
-run("~/atmos/whirl/inst/examples/demo/tfl", summary_dir = out_dir)
-
-# Multiple folders
-run(c("~/atmos/whirl/inst/examples/demo/metadata",
-      "~/atmos/whirl/inst/examples/demo/tfl"), summary_dir = out_dir)
-
-
-# Config-------------------------------------------------------------------------
-
-# Use a config file
-run("~/atmos/whirl/inst/examples/demo/demo_whirl.yaml", summary_dir = out_dir)
-
-
-# Use a config file (skipping steps after errors)
-run("~/atmos/whirl/inst/examples/demo/demo_skip_whirl.yaml", summary_dir = out_dir)
-
-run("~/atmos/whirl/inst/examples/sequence_exuction/test.py")
-
-
diff --git a/inst/documents/dummy.qmd b/inst/documents/dummy.qmd
index f1f35fc..ff0e52b 100644
--- a/inst/documents/dummy.qmd
+++ b/inst/documents/dummy.qmd
@@ -8,7 +8,10 @@ params:
   tmpdir: "."
 ---
 
-```{r setup, include=FALSE}
+```{r setup}
+#| label: Setup
+#| include: false
+
 knitr::opts_chunk$set(
   error = TRUE,
   warning = TRUE,
@@ -19,22 +22,56 @@ knitr::opts_chunk$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}
+#| label: Log Rmarkdown
+#| child: !expr params$script
+#| eval: !expr grepl("\\.Rmd$", params$script)
+#| include: !expr grepl("\\.Rmd$", params$script)
 ```
 
-```{r, child = params$script, eval=(grepl("\\.Rmd$", params$script))}
+```{python}
+#| label: Log Python
+#| file: !expr params$script
+#| eval: !expr grepl("\\.py$", params$script)
+#| include: !expr grepl("\\.py$", params$script)
 ```
 
-```{r, child = params$script, eval=(grepl("\\.py$", params$script))}
+```{python}
+#| label: Python modules
+#| file: !expr file.path(params$tmpdir, "python_modules.py")
+#| eval: !expr grepl("\\.py$", params$script)
+#| echo: false
 ```
 
-```{r sessioninfo, include=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"))
+# }
+
 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")
 )
 
@@ -44,6 +81,4 @@ if (is.character(params$renv) && params$renv == "yes" | is.logical(params$renv)
     file = file.path(params$tmpdir, "renv_status.rds")
   )
 }
-
 ```
-
diff --git a/inst/documents/log.qmd b/inst/documents/log.qmd
index 4e4e7cb..f3dc745 100644
--- a/inst/documents/log.qmd
+++ b/inst/documents/log.qmd
@@ -19,8 +19,16 @@ format:
 
 # Summary
 
-```{r, echo=FALSE, eval=TRUE}
+```{r}
+#| label: Setup
+#| echo: false
 .libPaths(c(character(), params$with_library_paths))
+```
+
+
+```{r}
+#| label: Status
+#| echo: false
 
 status <- params$tmpdir |>
   file.path("doc.md") |> 
@@ -43,15 +51,19 @@ whirl:::quarto_callout(
 )
 ```
 
-```{r, echo=FALSE}
-if (file.exists(file.path(params$tmpdir, "renv_status.rds"))) {
-  params$tmpdir |> 
-    file.path("renv_status.rds") |> 
-    readRDS()
-}
+```{r}
+#| label: Renv
+#| echo: false
+#| eval: !expr file.exists(file.path(params$tmpdir, "renv_status.rds"))
+
+params$tmpdir |> 
+  file.path("renv_status.rds") |> 
+  readRDS()
 ```
 
-```{r, echo=FALSE}
+```{r}
+#| label: Track files
+#| echo: false
 log_info <- whirl:::read_from_log()
 use_log_info <- nrow(log_info) > 0
 
@@ -62,38 +74,57 @@ if (use_log_info) {
 }
 ```
 
-```{r, echo=FALSE, results='asis', eval=use_log_info}
+```{r}
+#| echo: false
+#| results: asis
+#| eval: !expr use_log_info
 cat("## Input", "\n")
 ```
 
-```{r, echo=FALSE, eval=use_log_info}
+```{r}
+#| echo: false
+#| eval: !expr use_log_info
 log_info$read
 ```
 
-```{r, echo=FALSE, results='asis', eval=use_log_info}
+```{r}
+#| echo: false
+#| results: asis
+#| eval: !expr use_log_info
 cat("## Output", "\n")
 ```
 
-```{r, echo=FALSE, eval=use_log_info}
+```{r}
+#| echo: false
+#| eval: !expr use_log_info
 log_info$write
 ```
 
-```{r, echo=FALSE, results='asis', eval=use_log_info}
+```{r}
+#| echo: false
+#| results: asis
+#| eval: !expr use_log_info
 cat("## Removed", "\n")
 ```
 
-```{r, echo=FALSE, eval=use_log_info}
+```{r}
+#| echo: false
+#| eval: !expr use_log_info
 log_info$delete
 ```
 
 # Script
 
-```{r, child = file.path(params$tmpdir, "doc.md")}
+```{r}
+#| child: !expr file.path(params$tmpdir, "doc.md")
 ```
 
 # Session info
 
-```{r, include=FALSE}
+```{r}
+#| label: Session info
+#| include: false
+
 knitr::opts_chunk$set(
   error = FALSE,
   warning = FALSE,
@@ -106,14 +137,29 @@ info <- params$tmpdir |>
     readRDS()
 ```
 
-```{r, results="asis"}
+```{r}
+#| label: Platform
+#| results: asis
 cat("\n## Platform \n")
 info$platform
 cat("\n")
 ```
 
-```{r, results="asis", fig.height = 0.5}
-cat("\n## Packages\n")
+```{r}
+#| label: Python
+#| results: asis
+#| eval: !expr grepl("\\.py$", params$title)
+#| fig.height: 0.5
+cat("\n## Python Packages\n")
+
+info$python_packages
+```
+
+```{r}
+#| label: R
+#| results: asis
+#| fig.height: 0.5
+cat("\n## R Packages\n")
 
 if (!is.null(params$check_approved_folder_pkgs) |
   !is.null(params$check_approved_url_pkgs)) {
@@ -123,23 +169,30 @@ if (!is.null(params$check_approved_folder_pkgs) |
 cat("\n")
 ```
 
-```{r, results="asis", fig.height = 0.5}
+```{r}
+#| results: asis
+#| fig.height: 0.5
 info$packages
 ```
 
-```{r, results="asis"}
+```{r}
+#| label: Environment
+#| results: asis
 cat("\n## Environment variables \n")
 info$environment
 cat("\n")
 ```
 
-```{r, results="asis"}
+```{r}
+#| label: Options
+#| results: asis
 cat("\n## Option settings\n")
 info$options
 cat("\n")
 ```
 
-```{r collect-objects}
+```{r}
+#| label: Output
 whirl_objects <- vector("list")
 
 if (exists("log_info")) {
diff --git a/inst/documents/python_modules.py b/inst/documents/python_modules.py
new file mode 100644
index 0000000..7d63501
--- /dev/null
+++ b/inst/documents/python_modules.py
@@ -0,0 +1,21 @@
+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)
diff --git a/inst/documents/summary.qmd b/inst/documents/summary.qmd
index d6810b5..7ff09f1 100644
--- a/inst/documents/summary.qmd
+++ b/inst/documents/summary.qmd
@@ -27,7 +27,9 @@ format:
     smooth-scroll: true
 ---
 
-```{r, include=FALSE}
+```{r}
+#| label: Setup
+#| include: false
 knitr::opts_chunk$set(
   error = TRUE,
   warning = TRUE,
@@ -36,7 +38,9 @@ knitr::opts_chunk$set(
 )
 ```
 
-```{r, echo = FALSE}
+```{r}
+#| label: Summary
+#| echo: false
 hold <- params$summary_df |> tibble::tibble()
 class(hold) <- c("whirl_summary_info", "summary_info", "list")
 
diff --git a/inst/examples/simple/_whirl.yaml b/inst/examples/_whirl.yaml
similarity index 100%
rename from inst/examples/simple/_whirl.yaml
rename to inst/examples/_whirl.yaml
diff --git a/inst/examples/demo/adam/mk100adsl.R b/inst/examples/demo/adam/mk100adsl.R
deleted file mode 100644
index e2394b1..0000000
--- a/inst/examples/demo/adam/mk100adsl.R
+++ /dev/null
@@ -1,3 +0,0 @@
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/adam/mk200adae.R b/inst/examples/demo/adam/mk200adae.R
deleted file mode 100644
index e2394b1..0000000
--- a/inst/examples/demo/adam/mk200adae.R
+++ /dev/null
@@ -1,3 +0,0 @@
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/adam/mk200adcm.R b/inst/examples/demo/adam/mk200adcm.R
deleted file mode 100644
index e2394b1..0000000
--- a/inst/examples/demo/adam/mk200adcm.R
+++ /dev/null
@@ -1,3 +0,0 @@
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/adam/mk200adec.R b/inst/examples/demo/adam/mk200adec.R
deleted file mode 100644
index e2394b1..0000000
--- a/inst/examples/demo/adam/mk200adec.R
+++ /dev/null
@@ -1,3 +0,0 @@
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/adam/mk200adhypo.R b/inst/examples/demo/adam/mk200adhypo.R
deleted file mode 100644
index e2394b1..0000000
--- a/inst/examples/demo/adam/mk200adhypo.R
+++ /dev/null
@@ -1,3 +0,0 @@
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/adam/mk300adecen.R b/inst/examples/demo/adam/mk300adecen.R
deleted file mode 100644
index e2394b1..0000000
--- a/inst/examples/demo/adam/mk300adecen.R
+++ /dev/null
@@ -1,3 +0,0 @@
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/adam/mk300adhypoen.R b/inst/examples/demo/adam/mk300adhypoen.R
deleted file mode 100644
index e2394b1..0000000
--- a/inst/examples/demo/adam/mk300adhypoen.R
+++ /dev/null
@@ -1,3 +0,0 @@
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/adam/mk400adcgm.R b/inst/examples/demo/adam/mk400adcgm.R
deleted file mode 100644
index e2394b1..0000000
--- a/inst/examples/demo/adam/mk400adcgm.R
+++ /dev/null
@@ -1,3 +0,0 @@
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/adam/mk400coreupdate.R b/inst/examples/demo/adam/mk400coreupdate.R
deleted file mode 100644
index a462325..0000000
--- a/inst/examples/demo/adam/mk400coreupdate.R
+++ /dev/null
@@ -1,3 +0,0 @@
-# This script produces no errors or warnings for testing purposes
-
-stop("Scripts runs with warning")
diff --git a/inst/examples/demo/adam/mk500coreupdate.R b/inst/examples/demo/adam/mk500coreupdate.R
deleted file mode 100644
index 746b8ac..0000000
--- a/inst/examples/demo/adam/mk500coreupdate.R
+++ /dev/null
@@ -1,4 +0,0 @@
-# This script produces no errors or warnings for testing purposes
-
-stop("Scripts runs with warning")
-
diff --git a/inst/examples/demo/config_to_config.yaml b/inst/examples/demo/config_to_config.yaml
deleted file mode 100644
index 0a66ae5..0000000
--- a/inst/examples/demo/config_to_config.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-steps:
-  - name: "Run Metadata folder through config"
-    paths:
-      - "tfl/tfl_whirl.yaml"
diff --git a/inst/examples/demo/demo_2_whirl.yml b/inst/examples/demo/demo_2_whirl.yml
deleted file mode 100644
index bc03b0d..0000000
--- a/inst/examples/demo/demo_2_whirl.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-steps:
-  - paths:
-    - "adam/mk100adsl.R"
-    - "adam/mk200adae.R"
-    - "adam/mk300*.r|R"
-  - paths:
-      - "metadata/metadata_whirl.yaml"
-  - name: "Run ADaM mk300 programs"
-    paths:
-      - "adam/mk300*.r|R"
-  - name: "Run TFL folder through config"
-    paths:
-      - "tfl/tfl_whirl.yaml"
diff --git a/inst/examples/demo/demo_skip_whirl.yaml b/inst/examples/demo/demo_skip_whirl.yaml
deleted file mode 100644
index 92a9865..0000000
--- a/inst/examples/demo/demo_skip_whirl.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-steps:
-  - name: "Run ADaM mk400 programs"
-    paths:
-      - "adam/mk400*.r|R"
-  - name: "Run TFL programs"
-    paths:
-      - "tfl"
diff --git a/inst/examples/demo/demo_whirl.yaml b/inst/examples/demo/demo_whirl.yaml
deleted file mode 100644
index 0c07345..0000000
--- a/inst/examples/demo/demo_whirl.yaml
+++ /dev/null
@@ -1,25 +0,0 @@
-steps:
-  - name: "Run ADaM mk100 programs"
-    paths:
-      - "adam/mk100adsl.R"
-      - "adam/mk200adae.R"
-      - "adam/mk300*.r|R"
-  - name: "Run Metadata folder through config"
-    paths:
-      - "metadata/metadata_whirl.yaml"
-  - name: "Run ADaM mk300 programs"
-    paths:
-      - "adam/mk300*.r|R"
-  - name: "Run TFL folder through config"
-    paths:
-      - "tfl/tfl_whirl.yaml"
-
-  # - name: "Run ADaM mk200 programs"
-  #   paths:
-  #     - "adam/mk200.*[.rR]$"
-  # - name: "Run ADaM mk300 programs"
-  #   paths:
-  #     - "adam/mk300.*[.rR]$"
-  # - name: "Run TFL programs"
-  #   paths:
-  #     - "tfl"
diff --git a/inst/examples/demo/metadata/mdouput.R b/inst/examples/demo/metadata/mdouput.R
deleted file mode 100644
index 87cf481..0000000
--- a/inst/examples/demo/metadata/mdouput.R
+++ /dev/null
@@ -1,4 +0,0 @@
-
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/metadata/mdoutput.R b/inst/examples/demo/metadata/mdoutput.R
deleted file mode 100644
index 87cf481..0000000
--- a/inst/examples/demo/metadata/mdoutput.R
+++ /dev/null
@@ -1,4 +0,0 @@
-
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/metadata/mdparam.R b/inst/examples/demo/metadata/mdparam.R
deleted file mode 100644
index 87cf481..0000000
--- a/inst/examples/demo/metadata/mdparam.R
+++ /dev/null
@@ -1,4 +0,0 @@
-
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/tfl/tfl_1.R b/inst/examples/demo/tfl/tfl_1.R
deleted file mode 100644
index 87cf481..0000000
--- a/inst/examples/demo/tfl/tfl_1.R
+++ /dev/null
@@ -1,4 +0,0 @@
-
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/tfl/tfl_2.R b/inst/examples/demo/tfl/tfl_2.R
deleted file mode 100644
index d022f47..0000000
--- a/inst/examples/demo/tfl/tfl_2.R
+++ /dev/null
@@ -1,21 +0,0 @@
-
-#' Setup
-
-library(tidyverse)
-
-#' Data data
-
-x <- mtcars |>
-  as_tibble(rownames = "car")
-
-x |>
-  print(n = 100)
-
-message("this is good")
-
-#' Plot
-
-ggplot(data = x) +
-  geom_point(mapping = aes(x = mpg, y = hp, size = wt, colour = as.factor(am)))
-
-ggsave("plot1.png")
diff --git a/inst/examples/demo/tfl/tfl_3.R b/inst/examples/demo/tfl/tfl_3.R
deleted file mode 100644
index 87cf481..0000000
--- a/inst/examples/demo/tfl/tfl_3.R
+++ /dev/null
@@ -1,4 +0,0 @@
-
-# This script produces no errors or warnings for testing purposes
-
-message("this script has no errors or warnings")
diff --git a/inst/examples/demo/tfl/tfl_error.R b/inst/examples/demo/tfl/tfl_error.R
deleted file mode 100644
index d03e9a4..0000000
--- a/inst/examples/demo/tfl/tfl_error.R
+++ /dev/null
@@ -1,4 +0,0 @@
-
-# This script produces error for testing purposes
-
-stop("This is an error!")
diff --git a/inst/examples/demo/tfl/tfl_whirl.yaml b/inst/examples/demo/tfl/tfl_whirl.yaml
deleted file mode 100644
index 7c6d95a..0000000
--- a/inst/examples/demo/tfl/tfl_whirl.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-steps:
-  - name: "Run TFL programs"
-    paths:
-      - "tfl_1.R"
diff --git a/inst/examples/sequence_exuction/error.R b/inst/examples/error.R
similarity index 100%
rename from inst/examples/sequence_exuction/error.R
rename to inst/examples/error.R
diff --git a/inst/examples/simple/prg1.R b/inst/examples/prg1.R
similarity index 99%
rename from inst/examples/simple/prg1.R
rename to inst/examples/prg1.R
index 453848e..dd64c98 100644
--- a/inst/examples/simple/prg1.R
+++ b/inst/examples/prg1.R
@@ -1,4 +1,3 @@
-
 #' Setup
 
 library(dplyr)
diff --git a/inst/examples/sequence_exuction/_whirl.yaml b/inst/examples/sequence_exuction/_whirl.yaml
deleted file mode 100644
index 4cb59f1..0000000
--- a/inst/examples/sequence_exuction/_whirl.yaml
+++ /dev/null
@@ -1,16 +0,0 @@
-steps:
-  - name: "Run scripts for dataflow"
-    paths:
-      - "without_whirl/prg1.R"
-      - "with_whirl_file/prg2.R"
-  - name: "Prepare adam datasets"
-    paths:
-      - "prgQmd.qmd"
-      - "prgRmd.Rmd"
-      - "error.R"
-  - name: "Running files from regexp"
-    paths:
-      - "prg.*(\\.R|\\.qmd)"
-  - name: "Running with whirl file again"
-    paths:
-      - "without_whirl/.*\\.R"
diff --git a/inst/examples/sequence_exuction/error.yaml b/inst/examples/sequence_exuction/error.yaml
deleted file mode 100644
index cf3d9e6..0000000
--- a/inst/examples/sequence_exuction/error.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-steps:
-  - name: "Run scripts for dataflow"
-    paths:
-      - "doesnt_exits.R"
-
diff --git a/inst/examples/sequence_exuction/path_and_regexp.yaml b/inst/examples/sequence_exuction/path_and_regexp.yaml
deleted file mode 100644
index 0f1ed82..0000000
--- a/inst/examples/sequence_exuction/path_and_regexp.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-steps:
-  - name: "Run scripts for dataflow"
-    paths:
-      - "examples/sequence_exuction/.*\\.R$"
-
diff --git a/inst/examples/sequence_exuction/prgQmd.qmd b/inst/examples/sequence_exuction/prgQmd.qmd
deleted file mode 100644
index 4c7a7a1..0000000
--- a/inst/examples/sequence_exuction/prgQmd.qmd
+++ /dev/null
@@ -1,26 +0,0 @@
----
-title: "prgQmd"
-format: html
-editor: visual
----
-
-## Quarto
-
-Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
-
-## Running Code
-
-When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
-
-```{r}
-1 + 1
-```
-
-You can add options to executable code like this
-
-```{r}
-#| echo: false
-2 * 2
-```
-
-The `echo: false` option disables the printing of code (only output is displayed).
diff --git a/inst/examples/sequence_exuction/prgQmd_py.qmd b/inst/examples/sequence_exuction/prgQmd_py.qmd
deleted file mode 100644
index d941043..0000000
--- a/inst/examples/sequence_exuction/prgQmd_py.qmd
+++ /dev/null
@@ -1,33 +0,0 @@
----
-title: "prgQmd"
-format: html
-editor: visual
----
-
-## Quarto
-
-Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
-
-## Running Code
-
-When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
-
-```{python}
-1 + 1
-```
-
-You can add options to executable code like this
-
-```{python}
-1+1
-
-file_path = 'from_python.txt'
-
-with open(file_path, 'w') as file:
-    # Write or save text to the file
-    file.write("Hello from python ^^")
-
-
-```
-
-The `echo: false` option disables the printing of code (only output is displayed).
diff --git a/inst/examples/sequence_exuction/prgRmd.Rmd b/inst/examples/sequence_exuction/prgRmd.Rmd
deleted file mode 100644
index 75bd8bd..0000000
--- a/inst/examples/sequence_exuction/prgRmd.Rmd
+++ /dev/null
@@ -1,34 +0,0 @@
----
-title: "prgRmd"
-output: html_document
-date: "2024-03-01"
----
-
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-```
-
-## R Markdown
-
-This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
-
-When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
-
-```{r cars}
-summary(cars)
-```
-
-```{r}
-warning("test warning")
-```
-
-
-## Including Plots
-
-You can also embed plots, for example:
-
-```{r pressure, echo=FALSE}
-plot(pressure)
-```
-
-Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
diff --git a/inst/examples/sequence_exuction/test.py b/inst/examples/sequence_exuction/test.py
deleted file mode 100644
index 8965ffb..0000000
--- a/inst/examples/sequence_exuction/test.py
+++ /dev/null
@@ -1,8 +0,0 @@
-1+1
-
-file_path = 'from_python.txt'
-
-with open(file_path, 'w') as file:
-    # Write or save text to the file
-    file.write("Hello from python ^^")
-
diff --git a/inst/examples/sequence_exuction/with_whirl_file/_whirl.yaml b/inst/examples/sequence_exuction/with_whirl_file/_whirl.yaml
deleted file mode 100644
index 56dbb9e..0000000
--- a/inst/examples/sequence_exuction/with_whirl_file/_whirl.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-steps:
-  - name: "Subfolder with config file"
-    paths:
-      - "prg1.R"
diff --git a/inst/examples/sequence_exuction/with_whirl_file/prg2.R b/inst/examples/sequence_exuction/with_whirl_file/prg2.R
deleted file mode 100644
index d022f47..0000000
--- a/inst/examples/sequence_exuction/with_whirl_file/prg2.R
+++ /dev/null
@@ -1,21 +0,0 @@
-
-#' Setup
-
-library(tidyverse)
-
-#' Data data
-
-x <- mtcars |>
-  as_tibble(rownames = "car")
-
-x |>
-  print(n = 100)
-
-message("this is good")
-
-#' Plot
-
-ggplot(data = x) +
-  geom_point(mapping = aes(x = mpg, y = hp, size = wt, colour = as.factor(am)))
-
-ggsave("plot1.png")
diff --git a/inst/examples/sequence_exuction/without_whirl/prg1.R b/inst/examples/sequence_exuction/without_whirl/prg1.R
deleted file mode 100644
index d022f47..0000000
--- a/inst/examples/sequence_exuction/without_whirl/prg1.R
+++ /dev/null
@@ -1,21 +0,0 @@
-
-#' Setup
-
-library(tidyverse)
-
-#' Data data
-
-x <- mtcars |>
-  as_tibble(rownames = "car")
-
-x |>
-  print(n = 100)
-
-message("this is good")
-
-#' Plot
-
-ggplot(data = x) +
-  geom_point(mapping = aes(x = mpg, y = hp, size = wt, colour = as.factor(am)))
-
-ggsave("plot1.png")
diff --git a/inst/examples/sequence_exuction/without_whirl/prgQmd.qmd b/inst/examples/sequence_exuction/without_whirl/prgQmd.qmd
deleted file mode 100644
index 4c7a7a1..0000000
--- a/inst/examples/sequence_exuction/without_whirl/prgQmd.qmd
+++ /dev/null
@@ -1,26 +0,0 @@
----
-title: "prgQmd"
-format: html
-editor: visual
----
-
-## Quarto
-
-Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
-
-## Running Code
-
-When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
-
-```{r}
-1 + 1
-```
-
-You can add options to executable code like this
-
-```{r}
-#| echo: false
-2 * 2
-```
-
-The `echo: false` option disables the printing of code (only output is displayed).
diff --git a/inst/examples/sequence_exuction/without_whirl/prgRmd.Rmd b/inst/examples/sequence_exuction/without_whirl/prgRmd.Rmd
deleted file mode 100644
index 75bd8bd..0000000
--- a/inst/examples/sequence_exuction/without_whirl/prgRmd.Rmd
+++ /dev/null
@@ -1,34 +0,0 @@
----
-title: "prgRmd"
-output: html_document
-date: "2024-03-01"
----
-
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-```
-
-## R Markdown
-
-This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
-
-When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
-
-```{r cars}
-summary(cars)
-```
-
-```{r}
-warning("test warning")
-```
-
-
-## Including Plots
-
-You can also embed plots, for example:
-
-```{r pressure, echo=FALSE}
-plot(pressure)
-```
-
-Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
diff --git a/inst/examples/simple/error.R b/inst/examples/simple/error.R
deleted file mode 100644
index d03e9a4..0000000
--- a/inst/examples/simple/error.R
+++ /dev/null
@@ -1,4 +0,0 @@
-
-# This script produces error for testing purposes
-
-stop("This is an error!")
diff --git a/inst/examples/simple/log_msg.R b/inst/examples/simple/log_msg.R
deleted file mode 100644
index 1295e3f..0000000
--- a/inst/examples/simple/log_msg.R
+++ /dev/null
@@ -1,27 +0,0 @@
-
-library(whirl)
-
-#' This is a test script for user log messages
-#' Read, write, and delete operations can be logged the following way:
-
-log_read("adam.adsl")
-log_read("sdtm.vs")
-
-log_delete("adam.adds")
-
-Sys.sleep(4)
-
-log_write("adam.advs")
-
-log_write("output.table.ext")
-
-#' Behind the scenes the log messages are stored in a temporary file to be
-#' read into the log report.
-#'
-#' The file can be accessed via the environment variable "WHIRL_LOG_MSG":
-
-Sys.getenv("WHIRL_LOG_MSG")
-
-Sys.getenv("WHIRL_LOG_MSG") |>
-  readLines() |>
-  cat(sep = "\n")
diff --git a/inst/examples/simple/prgQmd.qmd b/inst/examples/simple/prgQmd.qmd
deleted file mode 100644
index 4c7a7a1..0000000
--- a/inst/examples/simple/prgQmd.qmd
+++ /dev/null
@@ -1,26 +0,0 @@
----
-title: "prgQmd"
-format: html
-editor: visual
----
-
-## Quarto
-
-Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
-
-## Running Code
-
-When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
-
-```{r}
-1 + 1
-```
-
-You can add options to executable code like this
-
-```{r}
-#| echo: false
-2 * 2
-```
-
-The `echo: false` option disables the printing of code (only output is displayed).
diff --git a/inst/examples/simple/prgRmd.Rmd b/inst/examples/simple/prgRmd.Rmd
deleted file mode 100644
index 75bd8bd..0000000
--- a/inst/examples/simple/prgRmd.Rmd
+++ /dev/null
@@ -1,34 +0,0 @@
----
-title: "prgRmd"
-output: html_document
-date: "2024-03-01"
----
-
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-```
-
-## R Markdown
-
-This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
-
-When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
-
-```{r cars}
-summary(cars)
-```
-
-```{r}
-warning("test warning")
-```
-
-
-## Including Plots
-
-You can also embed plots, for example:
-
-```{r pressure, echo=FALSE}
-plot(pressure)
-```
-
-Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
diff --git a/inst/examples/simple/sleep_1.R b/inst/examples/simple/sleep_1.R
deleted file mode 100644
index 188dea5..0000000
--- a/inst/examples/simple/sleep_1.R
+++ /dev/null
@@ -1,2 +0,0 @@
-# Dummys cript to test parrallisation of callr
-Sys.sleep(1)
diff --git a/inst/examples/simple/sleep_2.R b/inst/examples/simple/sleep_2.R
deleted file mode 100644
index 4dfa36e..0000000
--- a/inst/examples/simple/sleep_2.R
+++ /dev/null
@@ -1,2 +0,0 @@
-# Dummys cript to test parrallisation of callr
-Sys.sleep(2)
diff --git a/inst/examples/simple/sleep_3.R b/inst/examples/simple/sleep_3.R
deleted file mode 100644
index 4dfa36e..0000000
--- a/inst/examples/simple/sleep_3.R
+++ /dev/null
@@ -1,2 +0,0 @@
-# Dummys cript to test parrallisation of callr
-Sys.sleep(2)
diff --git a/inst/examples/simple/success.R b/inst/examples/success.R
similarity index 100%
rename from inst/examples/simple/success.R
rename to inst/examples/success.R
diff --git a/inst/examples/simple/warning.R b/inst/examples/warning.R
similarity index 100%
rename from inst/examples/simple/warning.R
rename to inst/examples/warning.R
diff --git a/man/run.Rd b/man/run.Rd
index 8d03823..bd12283 100644
--- a/man/run.Rd
+++ b/man/run.Rd
@@ -51,19 +51,24 @@ The way the execution is logged is configurable through several options for
 e.g. the verbosity of the logs. See \link{options} on how to configure these.
 }
 \examples{
-\dontshow{if (FALSE) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+# Start by copying the following three example scripts:
+file.copy(
+  from = system.file("examples", c("success.R", "warning.R", "error.R"), package = "whirl"),
+  to = "."
+  )
 
 # Run a single script
-script <- system.file("examples/simple/success.R", package = "whirl")
-run(script)
+run("success.R")
 
 # Run several scripts in parallel on up to 2 workers
-scripts <- system.file("examples/simple", c("success.R", "warning.R", "error.R"), package = "whirl")
-run(scripts, n_workers = 2)
+run(c("success.R", "warning.R", "error.R"), n_workers = 2)
+
+# Run scripts in two steps by providing them as list elements
+run(
+  list(
+    c("success.R", "warning.R"),
+    "error.R"
+    ),
+   n_workers = 2)
 
-# Run scripts in several steps
-step_1 <- system.file("examples/simple", c("success.R", "warning.R"), package = "whirl")
-step_2 <- system.file("examples/simple", c("error.R"), package = "whirl")
-run(list(step_1, step_2), n_workers = 2)
-\dontshow{\}) # examplesIf}
 }
diff --git a/tests/testthat/_snaps/examples.md b/tests/testthat/_snaps/examples.md
new file mode 100644
index 0000000..96dbab9
--- /dev/null
+++ b/tests/testthat/_snaps/examples.md
@@ -0,0 +1,45 @@
+# All example scripts run with consistent output
+
+    {
+      "type": "list",
+      "attributes": {
+        "names": {
+          "type": "character",
+          "attributes": {},
+          "value": ["id", "tag", "script", "status"]
+        },
+        "row.names": {
+          "type": "integer",
+          "attributes": {},
+          "value": [1, 2, 3, 4, 5, 6, 7]
+        },
+        "class": {
+          "type": "character",
+          "attributes": {},
+          "value": ["tbl_df", "tbl", "data.frame"]
+        }
+      },
+      "value": [
+        {
+          "type": "double",
+          "attributes": {},
+          "value": [1, 2, 3, 4, 5, 6, 7]
+        },
+        {
+          "type": "character",
+          "attributes": {},
+          "value": [null, null, null, null, null, null, null]
+        },
+        {
+          "type": "character",
+          "attributes": {},
+          "value": ["success.R", "warning.R", "error.R", "error.R", "prg1.R", "success.R", "warning.R"]
+        },
+        {
+          "type": "character",
+          "attributes": {},
+          "value": ["success", "warning", "error", "error", "success", "success", "warning"]
+        }
+      ]
+    }
+
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
new file mode 100644
index 0000000..847238a
--- /dev/null
+++ b/tests/testthat/helper.R
@@ -0,0 +1,7 @@
+# Helper function to select test scripts
+
+test_script <- function(script) {
+  script <- test_path("scripts", script) |>
+    normalizePath(winslash = "/", mustWork = TRUE)
+  return(script)
+}
diff --git a/tests/testthat/scripts/_whirl.yaml b/tests/testthat/scripts/_whirl.yaml
new file mode 100644
index 0000000..15aaa64
--- /dev/null
+++ b/tests/testthat/scripts/_whirl.yaml
@@ -0,0 +1,8 @@
+steps:
+  - name: "First step"
+    paths:
+      - "success.R"
+  - name: "Second step"
+    paths:
+      - "warning.R"
+      - "error.R"
diff --git a/inst/examples/demo/metadata/metadata_whirl.yaml b/tests/testthat/scripts/_whirl_r_programs.yaml
similarity index 50%
rename from inst/examples/demo/metadata/metadata_whirl.yaml
rename to tests/testthat/scripts/_whirl_r_programs.yaml
index 5dc8504..65c42d1 100644
--- a/inst/examples/demo/metadata/metadata_whirl.yaml
+++ b/tests/testthat/scripts/_whirl_r_programs.yaml
@@ -1,4 +1,4 @@
 steps:
-  - name: "Run metadata programs"
+  - name: "Run all R programs"
     paths:
       - "*.r|R"
diff --git a/tests/testthat/scripts/_whirl_to_config.yaml b/tests/testthat/scripts/_whirl_to_config.yaml
new file mode 100644
index 0000000..6936d45
--- /dev/null
+++ b/tests/testthat/scripts/_whirl_to_config.yaml
@@ -0,0 +1,4 @@
+steps:
+  - name: "Run config file"
+    paths:
+      - "_whirl.yaml"
diff --git a/tests/testthat/scripts/_whirl_unnamed.yaml b/tests/testthat/scripts/_whirl_unnamed.yaml
new file mode 100644
index 0000000..529921d
--- /dev/null
+++ b/tests/testthat/scripts/_whirl_unnamed.yaml
@@ -0,0 +1,8 @@
+steps:
+  - name: "Named step"
+    paths:
+      - "success.R"
+  - paths:
+      - "warning.R"
+  - paths:
+      - "error.R"
diff --git a/inst/examples/sequence_exuction/without_whirl/error/error.R b/tests/testthat/scripts/error.R
similarity index 100%
rename from inst/examples/sequence_exuction/without_whirl/error/error.R
rename to tests/testthat/scripts/error.R
diff --git a/tests/testthat/scripts/py_error.py b/tests/testthat/scripts/py_error.py
new file mode 100644
index 0000000..66f6580
--- /dev/null
+++ b/tests/testthat/scripts/py_error.py
@@ -0,0 +1,6 @@
+
+1 + "a"
+
+raise TypeError("This is a type error for testing purposes")
+
+raise Exception("Error also for testing")
diff --git a/tests/testthat/scripts/py_success.py b/tests/testthat/scripts/py_success.py
new file mode 100644
index 0000000..60628a7
--- /dev/null
+++ b/tests/testthat/scripts/py_success.py
@@ -0,0 +1,2 @@
+a = 2 + 2
+print(a)
diff --git a/tests/testthat/scripts/py_warning.py b/tests/testthat/scripts/py_warning.py
new file mode 100644
index 0000000..e378c26
--- /dev/null
+++ b/tests/testthat/scripts/py_warning.py
@@ -0,0 +1,3 @@
+import warnings
+
+warnings.warn("test warning")
diff --git a/inst/examples/demo/metadata/mdcol.R b/tests/testthat/scripts/success.R
similarity index 100%
rename from inst/examples/demo/metadata/mdcol.R
rename to tests/testthat/scripts/success.R
diff --git a/inst/examples/demo/tfl/tfl_warning.R b/tests/testthat/scripts/warning.R
similarity index 100%
rename from inst/examples/demo/tfl/tfl_warning.R
rename to tests/testthat/scripts/warning.R
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index 8ec812f..2e8c4db 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -1,7 +1,13 @@
-## whirl have to be installed for tests
-pkgs <- installed.packages() |> row.names()
-test <- any(pkgs %in% "whirl")
+## whirl have to be installed for Quarto to use it
 
-if (!test) {
-  cli::cli_abort("The package whirl have to be installed for subprocesses")
-}
+withr::local_envvar(
+  R_USER_CACHE_DIR = tempfile(),
+  .local_envir = teardown_env()
+)
+
+# Minimal prints to make it easier to read test output
+
+withr::local_options(
+  list(whirl.verbosity_level = "quiet"),
+  .local_envir = teardown_env()
+)
diff --git a/tests/testthat/test-enrich_input.R b/tests/testthat/test-enrich_input.R
index 3ddf839..6d66445 100644
--- a/tests/testthat/test-enrich_input.R
+++ b/tests/testthat/test-enrich_input.R
@@ -1,62 +1,68 @@
-test_that("testing enrich_input()", {
-  file_config <- system.file("examples/demo/metadata/metadata_whirl.yaml", package = "whirl")
-  incomplete_config <- system.file("examples/demo/demo_2_whirl.yml", package = "whirl")
-  file <- system.file("examples/demo/adam/mk100adsl.R", package = "whirl")
-  config_to_prune <- system.file("examples/demo/demo_whirl.yaml", package = "whirl")
-  directory <- system.file("examples/simple", package = "whirl")
-
-  op <- options(whirl.verbosity_level = "minimal")
-
-  #A config file
-  withr::with_dir(tempdir(), {
-    enriched <- enrich_input(input = file_config)
-    expect_type(enriched, "list")
-    names(enriched[[1]]) |> expect_equal(c("name", "paths"))
-  })
-
-  #Incomplete config
-  withr::with_dir(tempdir(), {
-    enriched <- enrich_input(input = incomplete_config)
-    expect_type(enriched, "list")
-    names(enriched[[1]]) |> expect_equal(c("name", "paths"))
-    enriched[[1]]$name |> expect_equal("Step 1: Unnamed chunk")
-    enriched[[2]]$name |> expect_equal("Step 2: Unnamed chunk")
-  })
-
-  #A file
-  withr::with_dir(tempdir(), {
-    enriched <- enrich_input(input = file)
-    expect_type(enriched, "list")
-    names(enriched[[1]]) |> expect_equal(c("name", "paths"))
-    enriched[[1]]$name |> expect_equal("Step 1: Unnamed chunk")
-    enriched[[1]]$paths |> expect_equal(file)
-  })
-
-  #Pruning a config file
-  withr::with_dir(tempdir(), {
-    enriched <- enrich_input(input = config_to_prune, steps = "Run ADaM mk100 programs")
-    expect_type(enriched, "list")
-    names(enriched[[1]]) |> expect_equal(c("name", "paths"))
-    length(enriched) |> expect_equal(1)
-  })
-
-  #Pruning a config file
-  withr::with_dir(tempdir(), {
-    enriched <- enrich_input(input = config_to_prune,
-                             steps = c("Run ADaM mk100 programs",
-                                       "Run ADaM mk300 programs"))
-    expect_type(enriched, "list")
-    names(enriched[[1]]) |> expect_equal(c("name", "paths"))
-    length(enriched) |> expect_equal(2)
-  })
-
-  #Expect error as directory is given as input
-  withr::with_dir(tempdir(), {
-    enriched <- enrich_input(input = directory) |>
-      expect_error()
-  })
-
-  on.exit(options(op))
+test_that("Enrich input works as expected", {
+
+  # Find all R programs
+
+  enriched <- test_script("_whirl_r_programs.yaml") |>
+    enrich_input() |>
+    expect_type("list") |>
+    expect_length(1)
+
+  enriched[[1]] |>
+    expect_type("list") |>
+    expect_length(2) |>
+    expect_named(c("name", "paths")) |>
+    lapply(expect_type, "character") |>
+    invisible()
+
+  # Unnamed steps
+
+  test_script("_whirl_unnamed.yaml") |>
+    enrich_input() |>
+    expect_type("list") |>
+    expect_length(3) |>
+    vapply(FUN = \(x) x$name, FUN.VALUE = character(1)) |>
+    expect_equal(c("Named step", "Step 2: Unnamed chunk", "Step 3: Unnamed chunk"))
+
+  # File input
+
+  enriched <- test_script("success.R") |>
+    enrich_input() |>
+    expect_type("list") |>
+    expect_length(1)
+
+  enriched[[1]] |>
+    expect_type("list") |>
+    expect_length(2) |>
+    expect_named(c("name", "paths")) |>
+    unlist() |>
+    expect_equal(
+      c(
+        name = "Step 1: Unnamed chunk",
+        paths = test_script("success.R")
+        )
+      )
+
+  # Pruning a config file
+
+  test_script("_whirl.yaml") |>
+    enrich_input(steps = "Second step") |>
+    expect_type("list") |>
+    expect_length(1) |>
+    vapply(FUN = \(x) x$name, FUN.VALUE = character(1)) |>
+    expect_equal("Second step")
+
+  test_script("_whirl.yaml") |>
+    enrich_input(steps = c("First step", "Second step")) |>
+    expect_type("list") |>
+    expect_length(2) |>
+    vapply(FUN = \(x) x$name, FUN.VALUE = character(1)) |>
+    expect_equal(c("First step", "Second step"))
+
+  # Expected error when input is a directory
+
+  test_script("") |>
+    enrich_input() |>
+    expect_error()
 
 })
 
diff --git a/tests/testthat/test-examples.R b/tests/testthat/test-examples.R
new file mode 100644
index 0000000..34a7502
--- /dev/null
+++ b/tests/testthat/test-examples.R
@@ -0,0 +1,28 @@
+test_that("All example scripts run with consistent output", {
+
+  withr::with_tempdir({
+
+    # Copy all example scripts to the temporary working directory
+
+    system.file("examples", package = "whirl") |>
+      list.files(full.names = TRUE) |>
+      file.copy(recursive = TRUE, to = ".")
+
+    # Run all examples after in separate steps
+
+    res <- list.files() |>
+      as.list() |>
+      run() |>
+      expect_no_error() |>
+      expect_no_warning()
+
+    # Unify result to only be about the status of the script and without
+    # the full path to the script
+
+    res$script <- basename(res$script)
+    res <- res[c("id", "tag", "script", "status")]
+
+    # Check that the results now are consistent
+    expect_snapshot_value(res, style = "json2")
+  })
+})
diff --git a/tests/testthat/test-internal_run.R b/tests/testthat/test-internal_run.R
index b407ebc..6500fd0 100644
--- a/tests/testthat/test-internal_run.R
+++ b/tests/testthat/test-internal_run.R
@@ -1,19 +1,19 @@
 test_that("testing internal_run()", {
-  file_config <- system.file("examples/demo/tfl/tfl_whirl.yaml", package = "whirl")
-  config_to_config <- system.file("examples/demo/config_to_config.yaml", package = "whirl")
 
-  #A config file
-  withr::with_dir(tempdir(), {
-    queue <- whirl_queue$new()
-    internal_run(input = file_config, steps = NULL, level = 1, queue = queue) |>
-      expect_no_error()
-  })
+  # A config file
 
-  #A config file
-  withr::with_dir(tempdir(), {
-    queue <- whirl_queue$new()
-    internal_run(input = config_to_config, steps = NULL, level = 1, queue = queue) |>
-      expect_no_error()
-  })
+  q <- whirl_queue$new()
+
+  test_script("_whirl.yaml") |>
+    internal_run(steps = NULL, level = 1, queue = q) |>
+    expect_no_error()
+
+  # A config file calling another config file
+
+  q <- whirl_queue$new()
+
+  test_script("_whirl_to_config.yaml") |>
+    internal_run(steps = NULL, level = 1, queue = q) |>
+    expect_no_error()
 
 })
diff --git a/tests/testthat/test-read_regexp.R b/tests/testthat/test-read_regexp.R
index 205c1f9..433f313 100644
--- a/tests/testthat/test-read_regexp.R
+++ b/tests/testthat/test-read_regexp.R
@@ -1,30 +1,25 @@
-test_that("testing read_regexp()", {
-  file <- system.file("examples/demo/adam/mk100adsl.R", package = "whirl")
-  dir <- system.file("examples/demo/adam", package = "whirl")
+test_that("read_regexp() finds the right files", {
 
-  #A config file
-  withr::with_dir(tempdir(), {
-    got <- read_regexp(input = file)
-    expect_identical(got, file)
-  })
+  # A single file
 
-  #Using regexp
-  withr::with_dir(tempdir(), {
-    all_files <- read_regexp(input = paste0(dir, "/*.R"))
-    expect_true(length(all_files) > 1)
-  })
+  test_script("success.R") |>
+    read_regexp() |>
+    expect_equal(test_script("success.R"))
 
-  #Using regexp
-  withr::with_dir(tempdir(), {
-    all_files2 <- read_regexp(input = paste0(dir, "/*.r|R"))
-    expect_true(length(all_files2) > 1)
-  })
+  # All R files in a directory
 
+  test_script("") |>
+    file.path("*.R") |>
+    read_regexp() |>
+    expect_match("\\.R$") |>
+    length() |>
+    expect_gt(1)
 
-  # A non-existing file
-  withr::with_dir(tempdir(), {
-    read_regexp(input = paste0(regexp, "/donotexsist.R")) |>
+  # Error when file does not exist
+
+  test_script("") |>
+    file.path("fake_program.R") |>
+    read_regexp() |>
     expect_error()
-  })
 
 })
diff --git a/tests/testthat/test-run.R b/tests/testthat/test-run.R
index 65da097..78364c0 100644
--- a/tests/testthat/test-run.R
+++ b/tests/testthat/test-run.R
@@ -1,33 +1,87 @@
-test_that("testing run()", {
-  file_config <- system.file("examples/demo/tfl/tfl_whirl.yaml", package = "whirl")
-  directory <- system.file("examples/simple", package = "whirl")
-  file <- system.file("examples/demo/adam/mk100adsl.R", package = "whirl")
-
-  #A config file
-  withr::with_dir(tempdir(), {
-    run(input = file_config) |>
-      expect_no_error()
-  })
-
-  #Pointing to a directory
-  withr::with_dir(tempdir(), {
-    run(input = directory) |>
-      expect_error()
-  })
-
-  # A file
-  withr::with_dir(tempdir(), {
-    run(input = file, n_workers = 1) |>
-      expect_no_error()
-  })
-
-  # A list
-  withr::with_dir(tempdir(), {
-    run(input = list(file)) |>
-      expect_no_error()
-  })
+test_that("Run single R script", {
 
+  res <- test_script("success.R") |>
+    run() |>
+    expect_no_condition()
+
+  res[["status"]] |>
+    expect_equal("success")
+
+  res[["result"]][[1]] |>
+    names() |>
+    expect_equal(c("status", "session_info_rlist", "log_details"))
+
+})
+
+test_that("Run single python script", {
+
+  res <- test_script("py_success.py") |>
+    run() |>
+    expect_no_condition()
+
+  res[["status"]] |>
+    expect_equal("success")
+
+  res[["result"]][[1]] |>
+    names() |>
+    expect_equal(c("status", "session_info_rlist", "log_details"))
+
+})
+
+test_that("Run multiple R scripts", {
+
+  res <- test_script(c("success.R", "warning.R", "error.R")) |>
+    run() |>
+    expect_no_error()
+
+  res[["status"]] |>
+    expect_equal(c("success", "warning", "error"))
+
+  res[["result"]][[1]][["status"]][c("error", "warning")] |>
+    lapply(\(x) length(x) > 0) |>
+    unlist() |>
+    expect_equal(c(FALSE, FALSE), ignore_attr = TRUE)
+
+  res[["result"]][[2]][["status"]][c("error", "warning")] |>
+    lapply(\(x) length(x) > 0) |>
+    unlist() |>
+    expect_equal(c(FALSE, TRUE), ignore_attr = TRUE)
+
+  res[["result"]][[3]][["status"]][c("error", "warning")] |>
+    lapply(\(x) length(x) > 0) |>
+    unlist() |>
+    expect_equal(c(TRUE, FALSE), ignore_attr = TRUE)
+})
+
+test_that("Run multiple python scripts", {
+
+  res <- test_script(c("py_success.py", "py_warning.py", "py_error.py")) |>
+    run() |>
+    expect_no_error()
+
+  res[["status"]] |>
+    expect_equal(c("success", "warning", "error"))
+
+  res[["result"]][[1]][["status"]][c("error", "warning")] |>
+    lapply(\(x) length(x) > 0) |>
+    unlist() |>
+    expect_equal(c(FALSE, FALSE), ignore_attr = TRUE)
+
+  res[["result"]][[2]][["status"]][c("error", "warning")] |>
+    lapply(\(x) length(x) > 0) |>
+    unlist() |>
+    expect_equal(c(FALSE, TRUE), ignore_attr = TRUE)
+
+  res[["result"]][[3]][["status"]][c("error", "warning")] |>
+    lapply(\(x) length(x) > 0) |>
+    unlist() |>
+    expect_equal(c(TRUE, FALSE), ignore_attr = TRUE)
 })
 
+test_that("Run yaml config file", {
 
+  res <- test_script("_whirl.yaml") |>
+    run() |>
+    expect_no_error()
 
+})
diff --git a/tests/testthat/test-strace.R b/tests/testthat/test-strace.R
index 1664578..abc33bf 100644
--- a/tests/testthat/test-strace.R
+++ b/tests/testthat/test-strace.R
@@ -10,11 +10,11 @@ test_that("strace works", {
 
       start_strace(pid = p$get_pid(), file = file.path(getwd(), "strace.log"))
 
-      cat("============= Initial: =============", "\n")
-      cat(c("wd:", getwd()), "\n")
-      cat(c("files:", list.files()), "\n")
-      cat(c("environment:", ls()), "\n")
-      cat("====================================", "\n")
+      # cat("============= Initial: =============", "\n")
+      # cat(c("wd:", getwd()), "\n")
+      # cat(c("files:", list.files()), "\n")
+      # cat(c("environment:", ls()), "\n")
+      # cat("====================================", "\n")
 
       # No output yet
 
@@ -99,11 +99,11 @@ test_that("strace works", {
       p$kill()
       p$finalize()
 
-      cat("============= final: =============", "\n")
-      cat(c("wd:", getwd()), "\n")
-      cat(c("files:", list.files()), "\n")
-      cat(c("environment:", ls()), "\n")
-      cat("==================================", "\n")
+      # cat("============= final: =============", "\n")
+      # cat(c("wd:", getwd()), "\n")
+      # cat(c("files:", list.files()), "\n")
+      # cat(c("environment:", ls()), "\n")
+      # cat("==================================", "\n")
     },
     tmpdir = getwd()
   )
diff --git a/tests/testthat/test-use_whirl.R b/tests/testthat/test-use_whirl.R
index ddf95be..942f164 100644
--- a/tests/testthat/test-use_whirl.R
+++ b/tests/testthat/test-use_whirl.R
@@ -2,9 +2,13 @@ test_that("use_whirl", {
   withr::with_tempdir({
     rlang::local_interactive(FALSE)
 
-    usethis::create_project(path = ".")
+    usethis::create_project(path = ".") |>
+      expect_message() |>
+      suppressMessages()
 
-    use_whirl()
+    use_whirl() |>
+      expect_message() |>
+      suppressMessages()
 
     expect_true(file.exists("_whirl.yaml"))
 
diff --git a/tests/testthat/test-util_queue_summary.R b/tests/testthat/test-util_queue_summary.R
index 8ac36f2..c9dd6d6 100644
--- a/tests/testthat/test-util_queue_summary.R
+++ b/tests/testthat/test-util_queue_summary.R
@@ -1,28 +1,34 @@
 # Test for existence of 'result' in the queue_table
 test_that("queue_table must contain a list named 'result'", {
-  queue_table <- list(dummy = "dummy")
-  expect_error(util_queue_summary(queue_table), "queue_table must contain a list named 'result'")
+
+  list(dummy = "dummy") |>
+    util_queue_summary() |>
+    expect_error("queue_table must contain a list named 'result'")
+
 })
 
 # Test for existence of 'log_details' and 'status' in each result
 test_that("Each result in queue_table must contain 'log_details' and 'status'", {
-  queue_table <- list(result = list(list(log_details = "dummy")))
-  expect_error(util_queue_summary(queue_table), "Each result in queue_table must contain 'log_details' and 'status'")
+
+  list(result = list(list(log_details = "dummy"))) |>
+    util_queue_summary() |>
+    expect_error("Each result in queue_table must contain 'log_details' and 'status'")
+
 })
 
 # Test for successful creation of summary tibble
+
 test_that("Summary tibble is created successfully", {
-  q <- whirl_queue$new(n_workers = 3)
 
-  c(
-  system.file("examples/simple/prg1.R", package = "whirl"),
-  system.file("examples/simple/success.R", package = "whirl")
-  ) |>
+  q <- whirl_queue$new(n_workers = 2)
+
+  test_script(c("success.R", "py_success.py")) |>
     q$run()
 
-  queue_table <- q$queue
-  summary_tibble <- util_queue_summary(queue_table)
-  expect_type(summary_tibble, "list")
-  expect_equal(ncol(summary_tibble), 5)
-  expect_equal(nrow(summary_tibble), 2)
+  q$queue |>
+    util_queue_summary() |>
+    expect_s3_class("tbl_df") |>
+    expect_named(c('Directory', 'Filename', 'Status', 'Hyperlink', 'Information')) |>
+    nrow() |>
+    expect_equal(2)
 })
diff --git a/tests/testthat/test-whirl_r_session.R b/tests/testthat/test-whirl_r_session.R
index 6d6181f..ee6f4fe 100644
--- a/tests/testthat/test-whirl_r_session.R
+++ b/tests/testthat/test-whirl_r_session.R
@@ -2,7 +2,8 @@ test_that("interactive whirl R session components not tested in run", {
   p <- whirl_r_session$new(verbosity_level = "minimal")
 
   p$print() |>
-    expect_message()
+    expect_message() |>
+    suppressMessages()
 
   p$get_wd() |>
     dir.exists() |>
diff --git a/vignettes/articles/example.Rmd b/vignettes/articles/example.Rmd
index 4cc61be..cca1575 100644
--- a/vignettes/articles/example.Rmd
+++ b/vignettes/articles/example.Rmd
@@ -2,22 +2,27 @@
 title: "Log example"
 ---
 
-
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
 
-system.file("examples/simple/prg1.R", package = "whirl") |> 
-  file.copy(to = "example.R")
+# Use a temporary directory as working directory with the example program available
+
+wd <- getwd()
+tmp <- withr::local_tempdir()
+
+system.file("examples/prg1.R", package = "whirl") |>  
+  file.copy(to = file.path(tmp, "example.R"))
+
+knitr::opts_knit$set(root.dir = tmp)
 ```
 
 In this example we are going to execute the following script and create a log of it's execution:
 
-```{r, echo = FALSE}
-readLines("example.R") |> 
-  cli::cli_code()
+`example.R:`
+```{r, file = "example.R", eval = FALSE}
 ```
 
 We are going to use the `run()` function to execute the script, and since this vignette
@@ -30,7 +35,7 @@ options(whirl.track_files = TRUE)
 options(whirl.verbosity_level = "minimal")
 ```
 
-The `verbosity_level` is set to `minimal` for nicer printing in ths vignette.
+The `verbosity_level` is set to `minimal` for nicer printing in this vignette.
 Now we are ready to execute the script:
 
 ```{r run}
@@ -42,8 +47,19 @@ print(result)
 The script is now executed and you can access the logs below:
 
 ```{r copy, include=FALSE}
-file.copy(from = "summary.html", to = "../docs/articles")
-file.copy(from = "example_log.html", to = "../docs/articles")
+# Also check if all outputs were created as expected
+
+articles_folder <- file.path(wd, "../../docs/articles")
+
+articles_folder |> 
+  dir.exists() |> 
+  stopifnot()
+
+c("summary.html", "example_log.html", "plot1.png") |> 
+  lapply(file.copy, to = articles_folder, overwrite = TRUE) |> 
+  unlist() |> 
+  all() |> 
+  stopifnot()
 ```
 
 * [View summary log](summary.html)