Fixing bug when a config only points to other config files and Switch…

… to using simple glob instead of regexp (#119)

* Fixing issue in internal_run() when config points to other config files.

* Switch to using simple glob instead

* Update vignette to reflect the use of simple glob

* Updating news and description

* Updating NEWS and DESCRIPTION

* Set n_workers = 2 in tests

---------

Co-authored-by: Troejelsgaard <[email protected]>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: whirl
 Title: Logging package
-Version: 0.1.5.9000
+Version: 0.1.6
 Authors@R: c(
     person("Aksel", "Thomsen", , "[email protected]", role = c("aut", "cre")),
     person("Lovemore", "Gakava", , "[email protected]", role = "aut"),

NEWS.md

@@ -1,6 +1,11 @@
-# whirl dev
+# whirl 0.1.6 (2024-11-25)
 * Added support for logging of Python scripts with `run()`.
 * Improved unit tests for `run()`
+* Fixing a bug where the queue was not returned correctly in some instances.
+* Switched to using `Sys.glob()` instead of `utils::glob2rx()`.
+
+# whirl 0.1.5 (2024-11-21)
+* Reducing the number of dependencies.
 
 # whirl 0.1.4 (2024-11-01)
 * Add `use_whirl()` utility function.

R/enrich_input.R

@@ -57,7 +57,7 @@ enrich_input <- function(input, steps = NULL,
   # Normalizing the paths and read regexp
   for (j in seq_along(paths)) {
     normalized <- unlist(lapply(paths[[j]], normalize_with_base, base = root_dir))
-    paths[[j]] <- read_regexp(normalized)
+    paths[[j]] <- read_glob(normalized)
   }
 
   # If input include one or more directories

R/internal_run.R

@@ -41,14 +41,10 @@ internal_run <- function(input, steps, queue, level,
                    verbosity_level = verbosity_level)
     } else {
       # Execute the scripts
-      result <- queue$run(files)
+      queue$run(files)
     }
   }
 
-  if (exists("result")) {
-    invisible(result)
-  }
-
-
+  invisible(queue)
 }
 

R/read_regexp.R → R/read_glob.R

@@ -4,19 +4,17 @@
 #'   used as input these will be solved to the actual files matching the
 #'   criteria.
 #' @noRd
-read_regexp <- function(input) {
+
+read_glob <- function(input) {
   files_ <- lapply(input, function(x) {
     #If the file exist then return the path
     if (file.exists(x)) {
       return(x)
     } else {
-      #If the file does not exist then check if it is a regexp
-      regexp <- basename(x) |>
-        utils::glob2rx()
-
-      files <- list.files(path = dirname(x), pattern = regexp, full.names = TRUE)
+      #If the file does not exist then check if it is a glob
+      files <- Sys.glob(x)
       if (length(files) == 0) {
-        cli::cli_abort("No files or folders for this path {x}")
+        cli::cli_alert_warning("No files or folders for this path {x}")
       }
       return(files)
     }

inst/examples/demo/adam/adamprog_whirl.yaml

@@ -0,0 +1,6 @@
+steps:
+  - name: "Run adam mk400 programs"
+    paths:
+      - "mk400*.R"
+
+

tests/testthat/scripts/_whirl_r_programs.yaml

@@ -1,4 +1,4 @@
 steps:
   - name: "Run all R programs"
     paths:
-      - "*.r|R"
+      - "*.R"

tests/testthat/test-examples.R

@@ -10,9 +10,9 @@ test_that("All example scripts run with consistent output", {
 
     # Run all examples after in separate steps
 
-    res <- list.files() |>
+    res <- list(list.files(pattern = "*.yaml"), list.files(pattern = "*.R$")) |>
       as.list() |>
-      run() |>
+      run(n_workers = 2) |>
       expect_no_error() |>
       expect_no_warning()
 

tests/testthat/test-internal_run.R

@@ -2,7 +2,7 @@ test_that("testing internal_run()", {
 
   # A config file
 
-  q <- whirl_queue$new()
+  q <- whirl_queue$new(n_workers = 2)
 
   test_script("_whirl.yaml") |>
     internal_run(steps = NULL, level = 1, queue = q) |>

tests/testthat/test-read_regexp.R → tests/testthat/test-read_glob.R

@@ -1,25 +1,22 @@
-test_that("read_regexp() finds the right files", {
+test_that("testing read_glob()", {
 
   # A single file
-
   test_script("success.R") |>
-    read_regexp() |>
+    read_glob() |>
     expect_equal(test_script("success.R"))
 
   # All R files in a directory
-
   test_script("") |>
     file.path("*.R") |>
-    read_regexp() |>
+    read_glob() |>
     expect_match("\\.R$") |>
     length() |>
     expect_gt(1)
 
   # Error when file does not exist
-
   test_script("") |>
     file.path("fake_program.R") |>
-    read_regexp() |>
-    expect_error()
+    read_glob() |>
+    expect_message()
 
 })

tests/testthat/test-run.R

@@ -31,7 +31,7 @@ test_that("Run single python script", {
 test_that("Run multiple R scripts", {
 
   res <- test_script(c("success.R", "warning.R", "error.R")) |>
-    run() |>
+    run(n_workers = 2) |>
     expect_no_error()
 
   res[["status"]] |>
@@ -56,7 +56,7 @@ test_that("Run multiple R scripts", {
 test_that("Run multiple python scripts", {
 
   res <- test_script(c("py_success.py", "py_warning.py", "py_error.py")) |>
-    run() |>
+    run(n_workers = 2) |>
     expect_no_error()
 
   res[["status"]] |>
@@ -81,7 +81,7 @@ test_that("Run multiple python scripts", {
 test_that("Run yaml config file", {
 
   res <- test_script("_whirl.yaml") |>
-    run() |>
+    run(n_workers = 2) |>
     expect_no_error()
 
 })

vignettes/whirl.Rmd

@@ -39,14 +39,14 @@ The location of the summary file can be controlled with the `summary_file` argum
 ```{r}
 # Execution of all R files in a specific directory
 run(
-  input = "path/to/directory/*.(r|R)", 
+  input = "path/to/directory/*.R", 
   n_workers = 4, 
   summary_file = "path/to/summary"
 )
 
 # Execution of all R files starting with "mk200" in a specific directory
 run(
-  input = "path/to/directory/mk200*.(r|R)", 
+  input = "path/to/directory/mk200*.R", 
   n_workers = 8, 
   summary_file = "path/to/summary"
 )