From 85e638450ad95d2ecaa66b0d99d8674ecbb441ef Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 24 Apr 2024 11:01:48 +0200
Subject: [PATCH 01/14] Implement unit test for detecting hard-coded absolute
 paths in the code

---
 tests/testthat/test-hardcoded_paths.R | 49 +++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 tests/testthat/test-hardcoded_paths.R

diff --git a/tests/testthat/test-hardcoded_paths.R b/tests/testthat/test-hardcoded_paths.R
new file mode 100644
index 00000000..9caeae6e
--- /dev/null
+++ b/tests/testthat/test-hardcoded_paths.R
@@ -0,0 +1,49 @@
+
+# Unit test: detect hard-coded absolute paths in the code
+
+library(lintr)
+
+detect_hardcoded_paths <- function() {
+  
+  # Define the directories to check
+  directories <- c("modules", "tools")
+  
+  # Define custom lintr to detect the string "/esarchive/"
+  esarchive_linter <- function(source_file) {
+    lines <- readLines(soure_file, warn = FALSE)
+    # Remove comments: everything from '#' to the end of line
+    code_lines <- gsub("#.*$", "", lines)
+    # Check if any cleaned line contains "/esarchive/"
+    if (any(grepl("/esarchive/", code_lines))) {
+      lint <- lintr::Lint(
+        filename = source_file,
+        line_number = which(grepl("/esarchive/", code_lines)),
+        column_number = NULL,
+        type = "error",
+        message = "Hard-coded path '/esarchive/' found.",
+        linter = "esarchive_linter"
+      )
+      return(list(lint)) # Returns list of lint objects
+    }
+    return(list()) # Returns empty list if "/esarchive/" not found
+  }
+  
+  # Apply the custom linter to each directory and save results
+  files_with_issues <- unlist(lapply(directories, function(dir) {
+    lint_dir(path = dir, linters = list(esarchive = esarchive_linter))
+  }), recursive = TRUE)
+  
+  # Check results and print out the test outcome
+  if (length(files_with_issues) > 0) {
+    cat("Test FAILED. '/esarchive/' found in the following files:\n")
+    issues_report <- vapply(files_with_issues, function(l) {
+      paste(l$filename, "Line:", l$line_number) # Print file name and line number
+    }, character(1))
+    print(issues_report)
+    return(FALSE)
+  } else {
+    cat("Test PASSED. No '/esarchive/' found in any file.\n")
+    return(TRUE)
+  }
+}
+
-- 
GitLab


From f7c240fb478b6dcd9b92e9c13b473ee2e9157ae9 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 25 Apr 2024 13:56:31 +0200
Subject: [PATCH 02/14] Replace custom function with absolute_path_linter(lax =
 TRUE)

---
 tests/testthat/test-hardcoded_paths.R | 31 +++++----------------------
 1 file changed, 5 insertions(+), 26 deletions(-)

diff --git a/tests/testthat/test-hardcoded_paths.R b/tests/testthat/test-hardcoded_paths.R
index 9caeae6e..72bf8c40 100644
--- a/tests/testthat/test-hardcoded_paths.R
+++ b/tests/testthat/test-hardcoded_paths.R
@@ -8,42 +8,21 @@ detect_hardcoded_paths <- function() {
   # Define the directories to check
   directories <- c("modules", "tools")
   
-  # Define custom lintr to detect the string "/esarchive/"
-  esarchive_linter <- function(source_file) {
-    lines <- readLines(soure_file, warn = FALSE)
-    # Remove comments: everything from '#' to the end of line
-    code_lines <- gsub("#.*$", "", lines)
-    # Check if any cleaned line contains "/esarchive/"
-    if (any(grepl("/esarchive/", code_lines))) {
-      lint <- lintr::Lint(
-        filename = source_file,
-        line_number = which(grepl("/esarchive/", code_lines)),
-        column_number = NULL,
-        type = "error",
-        message = "Hard-coded path '/esarchive/' found.",
-        linter = "esarchive_linter"
-      )
-      return(list(lint)) # Returns list of lint objects
-    }
-    return(list()) # Returns empty list if "/esarchive/" not found
-  }
-  
-  # Apply the custom linter to each directory and save results
+  # Apply absolute_path_linter() to each directory and save results
   files_with_issues <- unlist(lapply(directories, function(dir) {
-    lint_dir(path = dir, linters = list(esarchive = esarchive_linter))
+    lint_dir(path = dir, linters = absolute_path_linter(lax = TRUE))
   }), recursive = TRUE)
   
   # Check results and print out the test outcome
   if (length(files_with_issues) > 0) {
-    cat("Test FAILED. '/esarchive/' found in the following files:\n")
+    cat("Test FAILED. Absolute paths found in the following files:\n")
     issues_report <- vapply(files_with_issues, function(l) {
-      paste(l$filename, "Line:", l$line_number) # Print file name and line number
+      paste(l$filename, "Line:", l$line_number, "Message:", l$message)
     }, character(1))
     print(issues_report)
     return(FALSE)
   } else {
-    cat("Test PASSED. No '/esarchive/' found in any file.\n")
+    cat("Test PASSED. No absolute paths found in any file.\n")
     return(TRUE)
   }
 }
-
-- 
GitLab


From d6381f13cf7f6a6e82307986f6817972046ab6ab Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 25 Apr 2024 17:43:21 +0200
Subject: [PATCH 03/14] Include call to function within the script

---
 tests/testthat/test-hardcoded_paths.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-hardcoded_paths.R b/tests/testthat/test-hardcoded_paths.R
index 72bf8c40..d8b60962 100644
--- a/tests/testthat/test-hardcoded_paths.R
+++ b/tests/testthat/test-hardcoded_paths.R
@@ -15,14 +15,16 @@ detect_hardcoded_paths <- function() {
   
   # Check results and print out the test outcome
   if (length(files_with_issues) > 0) {
-    cat("Test FAILED. Absolute paths found in the following files:\n")
+    cat("Test FAILED. Hard-coded paths found in the following files:\n")
     issues_report <- vapply(files_with_issues, function(l) {
       paste(l$filename, "Line:", l$line_number, "Message:", l$message)
     }, character(1))
     print(issues_report)
     return(FALSE)
   } else {
-    cat("Test PASSED. No absolute paths found in any file.\n")
+    cat("Test PASSED😊 No hard-coded paths found in any file.\n")
     return(TRUE)
   }
 }
+
+detect_hardcoded_paths()
-- 
GitLab


From 9d01111460955cf173a2c651cadf7f39a8c81424 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 26 Apr 2024 10:59:14 +0200
Subject: [PATCH 04/14] Create call to unit test: test/test_paths.R

---
 tests/test_paths.R | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 tests/test_paths.R

diff --git a/tests/test_paths.R b/tests/test_paths.R
new file mode 100644
index 00000000..87dbed4a
--- /dev/null
+++ b/tests/test_paths.R
@@ -0,0 +1,9 @@
+library(testthat)
+
+path_testthat <- file.path('./tests/testthat/')
+files_testthat <- list.files('./tests/testthat/', pattern = 'paths')
+
+for (i_file in 1:length(files_testthat)) {
+  source(paste0('./tests/testthat/', files_testthat[i_file]))
+}
+
-- 
GitLab


From 16c3cb1a2a7b81962484944e1f6b6ddfdc2eefd2 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Tue, 30 Apr 2024 16:52:19 +0200
Subject: [PATCH 05/14] Remove hardcoded paths in load_sample(),
 test_check_number_of_independent_varifications.R and write_autosubmit_conf()

---
 modules/Loading/R/load_sample.R                        | 3 +--
 tools/test_check_number_of_independent_verifications.R | 4 ++--
 tools/write_autosubmit_conf.R                          | 6 +++---
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/modules/Loading/R/load_sample.R b/modules/Loading/R/load_sample.R
index e0d906d3..e1a8fe65 100644
--- a/modules/Loading/R/load_sample.R
+++ b/modules/Loading/R/load_sample.R
@@ -1,8 +1,7 @@
-## TODO: remove paths to personal scratchs 
-source("/esarchive/scratch/vagudets/repos/csoperational/R/get_regrid_params.R")
 # Load required libraries/funs
 source("tools/CST_ChangeDimName.R")
 source("modules/Loading/R/compare_exp_obs_grids.R")
+source("modules/Loading/R/get_regrid_params.R")
 
 load_sample <- function(recipe) {
   # Hindcast:
diff --git a/tools/test_check_number_of_independent_verifications.R b/tools/test_check_number_of_independent_verifications.R
index 846dc5be..0ddc6bbb 100644
--- a/tools/test_check_number_of_independent_verifications.R
+++ b/tools/test_check_number_of_independent_verifications.R
@@ -1,12 +1,12 @@
 library(testthat)
 test_that("A few combinations", {
- source("/esarchive/scratch/nperez/git/auto-s2s/tools/check_recipe.R")
+ source("tools/check_recipe.R")
  recipe <- list(Analysis = 
                 list(Variables = list(ECVs = list(
                                   list(name = 'tas', freq = 'daily_mean')), 
                      Indicators = list(list(name = 'gdd'))),
                      Workflow = list(Calibration = 'SBC', Indicators = TRUE)))
- conf <- list(code_dir = "/esarchive/scratch/nperez/git/auto-s2s/")
+ conf <- list(code_dir = "./")
  expect_equal(check_number_of_dependent_verifications(recipe, conf),
               list(independent = NULL,
                    dependent = list(list(list(name = 'tas', freq = 'daily_mean'),
diff --git a/tools/write_autosubmit_conf.R b/tools/write_autosubmit_conf.R
index 5f398197..0ccd8543 100644
--- a/tools/write_autosubmit_conf.R
+++ b/tools/write_autosubmit_conf.R
@@ -21,8 +21,8 @@ write_autosubmit_conf <- function(recipe, nchunks,
   # Read autosubmit info for the specific filesystem (e.g. esarchive)
   auto_specs <- read_yaml("conf/autosubmit.yml")[[recipe$Run$filesystem]]
   # Output directory
-  dest_dir <- paste0(auto_specs$experiment_dir, expid, "/conf/")
-  proj_dir <- paste0(auto_specs$experiment_dir, expid, "/proj/auto-s2s/")
+  dest_dir <- file.path(auto_specs$experiment_dir, expid, "conf")
+  proj_dir <- file.path(auto_specs$experiment_dir, expid, "proj", "auto-s2s")
   # Create project directory if it does not exist yet so that chunk_to_recipe
   # and split_to_recipe files can be created
   if (!dir.exists(proj_dir)) {
@@ -146,7 +146,7 @@ write_autosubmit_conf <- function(recipe, nchunks,
        paste("##### AUTOSUBMIT CONFIGURATION WRITTEN FOR", expid, "#####"))
   info(recipe$Run$logger,
        paste0("You can check your experiment configuration at: ",
-              "/esarchive/autosubmit/", expid, "/conf/"))
+              dest_dir))
   # Print instructions/commands for user
   if (recipe$Run$Terminal) {
     ## TODO: Change SSH message for other environments (outside BSC)
-- 
GitLab


From 5f68baabe8c127cdd6f788cbdd656df37bb9d2d3 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Tue, 30 Apr 2024 17:42:27 +0200
Subject: [PATCH 06/14] Flagged paths rewritten using file.path() instead of
 paste0()

---
 modules/Anomalies/Anomalies.R         |  4 +-
 modules/Calibration/Calibration.R     |  4 +-
 modules/Downscaling/Downscaling.R     |  4 +-
 modules/Indices/R/compute_nao.R       | 86 ++++++++++++-----------
 modules/Indices/R/compute_nino.R      | 99 ++++++++++++++-------------
 modules/Scorecards/Scorecards.R       |  6 +-
 modules/Skill/Skill.R                 |  8 +--
 modules/Statistics/Statistics.R       |  4 +-
 tests/testthat/test-hardcoded_paths.R | 13 ++--
 9 files changed, 117 insertions(+), 111 deletions(-)

diff --git a/modules/Anomalies/Anomalies.R b/modules/Anomalies/Anomalies.R
index d5f11228..a6411e6c 100644
--- a/modules/Anomalies/Anomalies.R
+++ b/modules/Anomalies/Anomalies.R
@@ -122,8 +122,8 @@ Anomalies <- function(recipe, data) {
     if (recipe$Analysis$Workflow$Anomalies$save != 'none') {
 
       info(recipe$Run$logger, "##### START SAVING ANOMALIES #####")
-      recipe$Run$output_dir <- paste0(recipe$Run$output_dir,
-                                      "/outputs/Anomalies/")
+      recipe$Run$output_dir <- file.path(recipe$Run$output_dir,
+                                      "outputs", "Anomalies")
       # Save forecast
       if ((recipe$Analysis$Workflow$Anomalies$save %in% 
            c('all', 'exp_only', 'fcst_only')) && !is.null(data$fcst)) {
diff --git a/modules/Calibration/Calibration.R b/modules/Calibration/Calibration.R
index f1362a22..e6afb210 100644
--- a/modules/Calibration/Calibration.R
+++ b/modules/Calibration/Calibration.R
@@ -169,8 +169,8 @@ Calibration <- function(recipe, data) {
     info(recipe$Run$logger, "##### START SAVING CALIBRATED DATA #####")
   
     ## TODO: What do we do with the full values?
-    recipe$Run$output_dir <- paste0(recipe$Run$output_dir,
-                                    "/outputs/Calibration/")
+    recipe$Run$output_dir <- file.path(recipe$Run$output_dir,
+                                    "outputs", "Calibration")
     if ((recipe$Analysis$Workflow$Calibration$save %in% 
          c('all', 'exp_only', 'fcst_only')) && (!is.null(data$fcst))) {
       save_forecast(recipe = recipe, data_cube = fcst_calibrated, type = 'fcst')
diff --git a/modules/Downscaling/Downscaling.R b/modules/Downscaling/Downscaling.R
index 59233dc2..65d654cd 100644
--- a/modules/Downscaling/Downscaling.R
+++ b/modules/Downscaling/Downscaling.R
@@ -278,8 +278,8 @@ Downscaling <- function(recipe, data) {
     info(recipe$Run$logger, "##### START SAVING DOWNSCALED DATA #####")
   }
   ## TODO: What do we do with the full values?
-  recipe$Run$output_dir <- paste0(recipe$Run$output_dir, 
-                                  "/outputs/Downscaling/")
+  recipe$Run$output_dir <- file.path(recipe$Run$output_dir, 
+                                  "outputs", "Downscaling")
   # if ((recipe$Analysis$Workflow$Downscaling$save %in% 
   #      c('all', 'exp_only', 'fcst_only')) && (!is.null(data$fcst))) {
   #   save_forecast(recipe = recipe, data_cube = data$fcst, type = 'fcst')
diff --git a/modules/Indices/R/compute_nao.R b/modules/Indices/R/compute_nao.R
index bdf2bb85..0e24b5fe 100644
--- a/modules/Indices/R/compute_nao.R
+++ b/modules/Indices/R/compute_nao.R
@@ -117,7 +117,7 @@ compute_nao <- function(data, recipe, obsproj, plot_ts, plot_sp,
                          Dates = data$obs$attrs$Dates,
                          Dataset = recipe$Analysis$Datasets$Reference$name))
   if (recipe$Analysis$Workflow$Indices$NAO$save == 'all') {
-    file_dest <- paste0(recipe$Run$output_dir, "/outputs/Indices/")
+    file_dest <- file.path(recipe$Run$output_dir, "outputs", "Indices")
     if (tolower(recipe$Analysis$Horizon) == "seasonal") {
       # Use startdates param from SaveExp to correctly name the files:
       if (length(data$hcst$attrs$source_files) == dim(data$hcst$data)['syear']) {
@@ -159,7 +159,7 @@ compute_nao <- function(data, recipe, obsproj, plot_ts, plot_sp,
                                recipe$Analysis$Variables$name)]]$long
 
   if (plot_ts) {
-    dir.create(paste0(recipe$Run$output_dir, "/plots/Indices/"),
+    dir.create(file.path(recipe$Run$output_dir, "plots", "Indices"),
                showWarnings = F, recursive = T)
     source("modules/Indices/R/plot_deterministic_forecast.R")
     for (tstep in 1:dim(nao$hcst$data)['time']) {
@@ -179,10 +179,11 @@ compute_nao <- function(data, recipe, obsproj, plot_ts, plot_sp,
                           month.abb[mes],
                           "/", recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/NAO_",
-                           system, "_", recipe$Analysis$Datasets$Reference$name,
-                           "_s", recipe$Analysis$Time$sdate, "_ftime",
-                           sprintf("%02d", tstep - 1 + recipe$Analysis$Time$ftime_min), ".pdf") 
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices", 
+                              paste0("NAO_",
+                                     system, "_", recipe$Analysis$Datasets$Reference$name,
+                                     "_s", recipe$Analysis$Time$sdate, "_ftime",
+                                     sprintf("%02d", tstep - 1 + recipe$Analysis$Time$ftime_min), ".pdf")) 
         caption <- paste0("NAO method: ",
                           ifelse(recipe$Analysis$Workflow$Indices$NAO$obsproj,
                                  "Pobs", "Pmod"), " (Doblas-Reyes et al., 2003)\n",
@@ -196,10 +197,10 @@ compute_nao <- function(data, recipe, obsproj, plot_ts, plot_sp,
                           "Lead time", fmonth,
                           " / Start dates", recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/NAO_",
-                           system, "_", recipe$Analysis$Datasets$Reference$name,
-                           "_ftime",
-                           sprintf("%02d", tstep - 1 + recipe$Analysis$Time$ftime_min), ".pdf") 
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices", 
+                              paste0("NAO_", 
+                                     system, "_", recipe$Analysis$Datasets$Reference$name, "_ftime",
+                                     sprintf("%02d", tstep - 1 + recipe$Analysis$Time$ftime_min), ".pdf")) 
         caption <- paste0("NAO method: ",
                           ifelse(recipe$Analysis$Workflow$Indices$NAO$obsproj,
                                  "Pobs", "Pmod"), " (Doblas-Reyes et al., 2003)\n",
@@ -229,7 +230,7 @@ compute_nao <- function(data, recipe, obsproj, plot_ts, plot_sp,
     source("modules/Visualization/R/tmp/PlotRobinson.R")
     source("modules/Indices/R/correlation_eno.R")
     source("modules/Visualization/R/get_proj_code.R")
-    dir.create(paste0(recipe$Run$output_dir, "/plots/Indices/"),
+    dir.create(file.path(recipe$Run$output_dir, "plots", "Indices"),
                showWarnings = F, recursive = T)
     # Get correct code for stereographic projection
     projection_code <- get_proj_code(proj_name = "stereographic")
@@ -273,11 +274,12 @@ compute_nao <- function(data, recipe, obsproj, plot_ts, plot_sp,
                           " Correlation /",  month.abb[mes], 
                           "/", recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/NAO_correlation_",
-                           recipe$Analysis$Variable$name, "_",
-                           recipe$Analysis$Datasets$Reference$name,
-                           "_s", recipe$Analysis$Time$sdate,
-                           "_ftime", fmonth, ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices", 
+                              paste0("NAO_correlation_",
+                                     recipe$Analysis$Variable$name, "_",
+                                     recipe$Analysis$Datasets$Reference$name,
+                                     "_s", recipe$Analysis$Time$sdate,
+                                     "_ftime", fmonth, ".pdf"))
         caption <-  paste0("NAO method: ",
                            ifelse(recipe$Analysis$Workflow$Indices$NAO$obsproj,
                                   "Pobs", "Pmod"), " (Doblas-Reyes et al., 2003)\n",
@@ -292,10 +294,11 @@ compute_nao <- function(data, recipe, obsproj, plot_ts, plot_sp,
                           " Correlation / Start dates ", 
                           recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/NAO_correlation_",
-                           recipe$Analysis$Variable$name, "_",
-                           recipe$Analysis$Datasets$Reference$name,
-                           "_ftime", fmonth, ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices", 
+                              paste0("NAO_correlation_",
+                                     recipe$Analysis$Variable$name, "_",
+                                     recipe$Analysis$Datasets$Reference$name,
+                                     "_ftime", fmonth, ".pdf"))
         caption <-  paste0("NAO method: ",
                            ifelse(recipe$Analysis$Workflow$Indices$NAO$obsproj,
                                   "Pobs", "Pmod"), " (Doblas-Reyes et al., 2003)\n",
@@ -331,11 +334,11 @@ compute_nao <- function(data, recipe, obsproj, plot_ts, plot_sp,
                           " Correlation /", month.abb[mes],
                           "/", recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/NAO_correlation_",
-                           recipe$Analysis$Variable$name, "_ensmean_",
-                           system,
-                           "_s", recipe$Analysis$Time$sdate,
-                           "_ftime", fmonth, ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices", 
+                              paste0("NAO_correlation_",
+                                     recipe$Analysis$Variable$name, "_ensmean_",
+                                     system, "_s", recipe$Analysis$Time$sdate,
+                                     "_ftime", fmonth, ".pdf"))
         caption <-  paste0("NAO method: ",
                            ifelse(recipe$Analysis$Workflow$Indices$NAO$obsproj,
                                   "Pobs", "Pmod"), " (Doblas-Reyes et al., 2003)\n",
@@ -351,11 +354,12 @@ compute_nao <- function(data, recipe, obsproj, plot_ts, plot_sp,
                           " Correlation / Start dates ", 
                           recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/NAO_correlation_",
-                           recipe$Analysis$Variable$name, "_ensmean_",
-                           system, 
-                           recipe$Analysis$Datasets$Reference$name,
-                           "_ftime", fmonth, ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices", 
+                              paste0("NAO_correlation_",
+                                     recipe$Analysis$Variable$name, "_ensmean_",
+                                     system, 
+                                     recipe$Analysis$Datasets$Reference$name,
+                                     "_ftime", fmonth, ".pdf"))
         caption <-  paste0("NAO method: ",
                            ifelse(recipe$Analysis$Workflow$Indices$NAO$obsproj,
                                   "Pobs", "Pmod"), " (Doblas-Reyes et al., 2003)\n",
@@ -388,11 +392,12 @@ compute_nao <- function(data, recipe, obsproj, plot_ts, plot_sp,
                           " Correlation /", month.abb[mes],
                           "/", recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/NAO_correlation_",
-                           recipe$Analysis$Variable$name, "_member_",
-                           system,
-                           "_s", recipe$Analysis$Time$sdate,
-                           "_ftime", fmonth, ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices", 
+                              paste0("NAO_correlation_",
+                                     recipe$Analysis$Variable$name, "_member_",
+                                     system,
+                                     "_s", recipe$Analysis$Time$sdate,
+                                     "_ftime", fmonth, ".pdf"))
         caption <-  paste0("NAO method: ",
                            ifelse(recipe$Analysis$Workflow$Indices$NAO$obsproj,
                                   "Pobs", "Pmod"), " (Doblas-Reyes et al., 2003)\n",
@@ -408,11 +413,12 @@ compute_nao <- function(data, recipe, obsproj, plot_ts, plot_sp,
                           " Correlation / Start dates ", 
                           recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/NAO_correlation_",
-                           recipe$Analysis$Variable$name, "_member_",
-                           system, 
-                           recipe$Analysis$Datasets$Reference$name,
-                           "_ftime", fmonth, ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices", 
+                              paste0("NAO_correlation_",
+                                     recipe$Analysis$Variable$name, "_member_",
+                                     system, 
+                                     recipe$Analysis$Datasets$Reference$name,
+                                     "_ftime", fmonth, ".pdf"))
         caption <-  paste0("NAO method: ",
                            ifelse(recipe$Analysis$Workflow$Indices$NAO$obsproj,
                                   "Pobs", "Pmod"), " (Doblas-Reyes et al., 2003)\n",
diff --git a/modules/Indices/R/compute_nino.R b/modules/Indices/R/compute_nino.R
index b47d9ee2..f251ce44 100644
--- a/modules/Indices/R/compute_nino.R
+++ b/modules/Indices/R/compute_nino.R
@@ -104,7 +104,7 @@ compute_nino <- function(data, recipe, region, standardised = TRUE,
                      Dataset = recipe$Analysis$Datasets$Reference$name))
 
   if (save == 'all') {
-    file_dest <- paste0(recipe$Run$output_dir, "/outputs/Indices/")
+    file_dest <- file.path(recipe$Run$output_dir, "outputs", "Indices")
     # Use startdates param from SaveExp to correctly name the files:
     if (tolower(recipe$Analysis$Horizon) == "seasonal") { 
       if (length(data$hcst$attrs$source_files) == dim(data$hcst$data)['syear']) {
@@ -145,7 +145,7 @@ compute_nino <- function(data, recipe, region, standardised = TRUE,
   var_name <- conf$vars[[which(names(conf$vars) ==
                                recipe$Analysis$Variables$name)]]$long
   if (plot_ts) {
-    dir.create(paste0(recipe$Run$output_dir, "/plots/Indices/"),
+    dir.create(file.path(recipe$Run$output_dir, "plots", "Indices"),
                showWarnings = F, recursive = T)
     source("modules/Indices/R/plot_deterministic_forecast.R")
     for (tstep in 1:dim(nino$hcst$data)['time']) {
@@ -165,12 +165,12 @@ compute_nino <- function(data, recipe, region, standardised = TRUE,
                           month.abb[mes],
                           "/", recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/",
-                           nino_name, "_",
-                           system, "_", recipe$Analysis$Datasets$Reference$name,
-                           "_s", recipe$Analysis$Time$sdate, "_ftime",
-                           sprintf("%02d", tstep - 1 + recipe$Analysis$Time$ftime_min), 
-                           ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices",
+                              paste0(nino_name, "_",
+                                     system, "_", recipe$Analysis$Datasets$Reference$name,
+                                     "_s", recipe$Analysis$Time$sdate, "_ftime",
+                                     sprintf("%02d", tstep - 1 + recipe$Analysis$Time$ftime_min), 
+                                     ".pdf"))
         caption <-  paste0("Nominal start date: 1st of ",
                            month.name[as.numeric(substr(recipe$Analysis$Time$sdate, 1,2))],
                            "\n",
@@ -181,10 +181,12 @@ compute_nino <- function(data, recipe, region, standardised = TRUE,
                           "Lead time", fmonth,
                           "/", recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/", nino_name, "_",
-                           system, "_", recipe$Analysis$Datasets$Reference$name,
-                           "_ftime",
-                           sprintf("%02d", tstep - 1 + recipe$Analysis$Time$ftime_min), ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices",
+                              paste0(nino_name, "_",
+                                     system, "_", recipe$Analysis$Datasets$Reference$name,
+                                     "_ftime",
+                                     sprintf("%02d", tstep - 1 + recipe$Analysis$Time$ftime_min), 
+                                     ".pdf"))
        caption <- paste0("Start date month: ",
                           month.name[get_archive(recipe)$System[[recipe$Analysis$Datasets$System$name]]$initial_month],
                           "\n",
@@ -217,7 +219,7 @@ compute_nino <- function(data, recipe, region, standardised = TRUE,
     # Get code for Robinson projection depending on GEOS/GDAL/PROJ version
     projection_code <- get_proj_code("robinson")
     # Avoid rewriten longitudes a shift is neeced:
-    dir.create(paste0(recipe$Run$output_dir, "/plots/Indices/"),
+    dir.create(file.path(recipe$Run$output_dir, "plots", "Indices"),
                showWarnings = F, recursive = T)
     correl_obs <- Apply(list(data$obs$data, nino$obs$data),
                         target_dims = 'syear',
@@ -267,12 +269,13 @@ compute_nino <- function(data, recipe, region, standardised = TRUE,
                           month.abb[mes],
                           "/", recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/", nino_name,
-                            "_correlation_",
-                           recipe$Analysis$Variable$name, "_",
-                           recipe$Analysis$Datasets$Reference$name,
-                           "_s", recipe$Analysis$Time$sdate,
-                           "_ftime", fmonth, ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices", 
+                              paste0(nino_name,
+                                     "_correlation_",
+                                     recipe$Analysis$Variable$name, "_",
+                                     recipe$Analysis$Datasets$Reference$name,
+                                     "_s", recipe$Analysis$Time$sdate,
+                                     "_ftime", fmonth, ".pdf"))
         caption <-  paste0("Nominal start date: 1st of ",
                 month.name[as.numeric(substr(recipe$Analysis$Time$sdate, 1,2))],
                          "\n",
@@ -285,11 +288,11 @@ compute_nino <- function(data, recipe, region, standardised = TRUE,
                           "Correlation / Start dates",
                           recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/",
-                           nino_name, "_correlation_",
-                           recipe$Analysis$Variable$name, "_",
-                           recipe$Analysis$Datasets$Reference$name,
-                           "_ftime", fmonth, ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices",
+                              paste0(nino_name, "_correlation_",
+                                     recipe$Analysis$Variable$name, "_",
+                                     recipe$Analysis$Datasets$Reference$name,
+                                     "_ftime", fmonth, ".pdf"))
         caption <-  paste0("Start date: month ",
                            month.name[get_archive(recipe)$System[[recipe$Analysis$Datasets$System$name]]$initial_month],
                            "\n",
@@ -325,12 +328,12 @@ compute_nino <- function(data, recipe, region, standardised = TRUE,
                           month.abb[mes],
                           "/", recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/",
-                           nino_name, "_correlation_",
-                           recipe$Analysis$Variable$name, "_ensmean_",
-                           system,
-                           "_s", recipe$Analysis$Time$sdate,
-                           "_ftime", fmonth, ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices",
+                              paste0(nino_name, "_correlation_",
+                                     recipe$Analysis$Variable$name, "_ensmean_",
+                                     system,
+                                     "_s", recipe$Analysis$Time$sdate,
+                                     "_ftime", fmonth, ".pdf"))
         caption <-  paste0("Ensemble mean\n",
                            "Nominal start date: 1st of ",
                 month.name[as.numeric(substr(recipe$Analysis$Time$sdate, 1,2))],
@@ -343,12 +346,12 @@ compute_nino <- function(data, recipe, region, standardised = TRUE,
                           "Correlation / Start dates",
                           recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/",
-                           nino_name, "_correlation_",
-                           recipe$Analysis$Variable$name, "_ensmean_",
-                           system,
-                           recipe$Analysis$Datasets$Reference$name,
-                           "_ftime", fmonth, ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices",
+                              paste0(nino_name, "_correlation_",
+                                     recipe$Analysis$Variable$name, "_ensmean_",
+                                     system,
+                                     recipe$Analysis$Datasets$Reference$name,
+                                     "_ftime", fmonth, ".pdf"))
         caption <-  paste0("Correlation ensemble mean\n",
                            "Start date month: ",
                            month.name[get_archive(recipe)$System[[recipe$Analysis$Datasets$System$name]]$initial_month],
@@ -379,12 +382,12 @@ compute_nino <- function(data, recipe, region, standardised = TRUE,
                           month.abb[mes],
                           "/", recipe$Analysis$Time$hcst_start, "-",
                           recipe$Analysis$Time$hcst_end)
-        plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/",
-                           nino_name, "_correlation_",
-                           recipe$Analysis$Variable$name, "_member_",
-                           system,
-                           "_s", recipe$Analysis$Time$sdate,
-                           "_ftime", fmonth, ".pdf")
+        plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices",
+                              paste0(nino_name, "_correlation_",
+                                     recipe$Analysis$Variable$name, "_member_",
+                                     system,
+                                     "_s", recipe$Analysis$Time$sdate,
+                                     "_ftime", fmonth, ".pdf"))
         caption <-  paste0("Individual members\n",
                            "Nominal start date: 1st of ",
                 month.name[as.numeric(substr(recipe$Analysis$Time$sdate, 1,2))],
@@ -397,12 +400,12 @@ compute_nino <- function(data, recipe, region, standardised = TRUE,
                         "Correlation / Start dates",
                         recipe$Analysis$Time$hcst_start, "-",
                         recipe$Analysis$Time$hcst_end)
-      plotfile <- paste0(recipe$Run$output_dir, "/plots/Indices/",
-                         nino_name, "_correlation_",
-                         recipe$Analysis$Variable$name, "_ensmean_",
-                         system,
-                         recipe$Analysis$Datasets$Reference$name,
-                         "_ftime", fmonth, ".pdf")
+      plotfile <- file.path(recipe$Run$output_dir, "plots", "Indices",
+                            paste0(nino_name, "_correlation_",
+                                   recipe$Analysis$Variable$name, "_ensmean_",
+                                   system,
+                                   recipe$Analysis$Datasets$Reference$name,
+                                   "_ftime", fmonth, ".pdf"))
       caption <-  paste0("Correlation ensemble mean\n",
                          "Start date month: ",
                          month.name[get_archive(recipe)$System[[recipe$Analysis$Datasets$System$name]]$initial_month],
diff --git a/modules/Scorecards/Scorecards.R b/modules/Scorecards/Scorecards.R
index 37aa421c..02e4f72c 100644
--- a/modules/Scorecards/Scorecards.R
+++ b/modules/Scorecards/Scorecards.R
@@ -22,9 +22,9 @@ source('modules/Scorecards/R/tmp/ClimPalette.R')
 Scorecards <- function(recipe) {
   
   ## Parameters for loading data files
-  skill.input.path <- paste0(recipe$Run$output_dir, "/outputs/Skill/")
-  stats.input.path <- paste0(recipe$Run$output_dir, "/outputs/Statistics/")
-  output.path <- paste0(recipe$Run$output_dir, "/plots/Scorecards/")
+  skill.input.path <- file.path(recipe$Run$output_dir, "outputs", "Skill")
+  stats.input.path <- file.path(recipe$Run$output_dir, "outputs", "Statistics")
+  output.path <- file.path(recipe$Run$output_dir, "plots", "Scorecards")
   dir.create(output.path, recursive = T, showWarnings = F)
   system <- recipe$Analysis$Datasets$System$name
   reference <- recipe$Analysis$Datasets$Reference$name
diff --git a/modules/Skill/Skill.R b/modules/Skill/Skill.R
index aa22838a..77cf2af4 100644
--- a/modules/Skill/Skill.R
+++ b/modules/Skill/Skill.R
@@ -357,8 +357,8 @@ Skill <- function(recipe, data, agg = 'global') {
   if (recipe$Analysis$Workflow$Skill$save != 'none') {
     info(recipe$Run$logger, "##### START SAVING SKILL METRIC #####")
   }
-  recipe$Run$output_dir <- paste0(recipe$Run$output_dir,
-                                  "/outputs/Skill/")
+  recipe$Run$output_dir <- file.path(recipe$Run$output_dir,
+                                     "outputs", "Skill")
   # Separate 'corr' from the rest of the metrics because of extra 'ensemble' dim
   ## TODO: merge save_metrics() and save_metrics_scorecards()
   if (recipe$Analysis$Workflow$Skill$save == 'all') {
@@ -486,8 +486,8 @@ Probabilities <- function(recipe, data) {
       info(recipe$Run$logger,
            "##### START SAVING PERCENTILES AND PROBABILITY CATEGORIES #####")
     
-      recipe$Run$output_dir <- paste0(recipe$Run$output_dir,
-                                      "/outputs/Skill/")
+      recipe$Run$output_dir <- file.path(recipe$Run$output_dir,
+                                         "outputs", "Skill")
       # Save percentiles
       if (recipe$Analysis$Workflow$Probabilities$save %in%
           c('all', 'percentiles_only')) {
diff --git a/modules/Statistics/Statistics.R b/modules/Statistics/Statistics.R
index 085bcdc5..462791e6 100644
--- a/modules/Statistics/Statistics.R
+++ b/modules/Statistics/Statistics.R
@@ -84,8 +84,8 @@ Statistics <- function(recipe, data, agg = 'global') {
   if (recipe$Analysis$Workflow$Skill$save != 'none') {
     info(recipe$Run$logger, "##### START SAVING STATISTICS #####")
   }
-  recipe$Run$output_dir <- paste0(recipe$Run$output_dir,
-                                  "/outputs/Statistics/")
+  recipe$Run$output_dir <- file.path(recipe$Run$output_dir,
+                                     "outputs", "Statistics")
   
   if (recipe$Analysis$Workflow$Statistics$save == 'all') {
     # Save all statistics
diff --git a/tests/testthat/test-hardcoded_paths.R b/tests/testthat/test-hardcoded_paths.R
index d8b60962..1345e013 100644
--- a/tests/testthat/test-hardcoded_paths.R
+++ b/tests/testthat/test-hardcoded_paths.R
@@ -9,17 +9,14 @@ detect_hardcoded_paths <- function() {
   directories <- c("modules", "tools")
   
   # Apply absolute_path_linter() to each directory and save results
-  files_with_issues <- unlist(lapply(directories, function(dir) {
+  files_with_issues <- lapply(directories, function(dir) {
     lint_dir(path = dir, linters = absolute_path_linter(lax = TRUE))
-  }), recursive = TRUE)
-  
+  })
+
   # Check results and print out the test outcome
   if (length(files_with_issues) > 0) {
-    cat("Test FAILED. Hard-coded paths found in the following files:\n")
-    issues_report <- vapply(files_with_issues, function(l) {
-      paste(l$filename, "Line:", l$line_number, "Message:", l$message)
-    }, character(1))
-    print(issues_report)
+    cat("Test FAILED. Hard-coded paths found:\n")
+    print(files_with_issues)
     return(FALSE)
   } else {
     cat("Test PASSED😊 No hard-coded paths found in any file.\n")
-- 
GitLab


From c648a71104f6293ce5405b07cbad54c97194da5e Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Tue, 30 Apr 2024 17:46:04 +0200
Subject: [PATCH 07/14] More rewritten flagged paths

---
 tools/divide_recipe.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/divide_recipe.R b/tools/divide_recipe.R
index 3b2e6eee..1f83d63c 100644
--- a/tools/divide_recipe.R
+++ b/tools/divide_recipe.R
@@ -51,7 +51,7 @@ divide_recipe <- function(recipe) {
   # Modify the saving of the individual models in case multimodel is yes or both
   if (recipe$Analysis$Datasets$Multimodel$execute %in% c(TRUE, 'both')) {
     # Create directory for multimodel recipes
-    dir.create(paste0(recipe$Run$output_dir, "/logs/recipes/multimodel/"),
+    dir.create(file.path(recipe$Run$output_dir, "logs", "recipes", "multimodel"),
                recursive = TRUE)
     n_models <- length(recipe$Analysis$Datasets$System) + 1
     mm <- tolower(recipe$Analysis$Datasets$Multimodel$approach)
@@ -189,11 +189,11 @@ divide_recipe <- function(recipe) {
     
 
     if (all_recipes[[reci]]$Analysis$Datasets$System$name == 'Multimodel') {
-      recipe_dir <- paste0(recipe$Run$output_dir, "/logs/recipes/multimodel/")
+      recipe_dir <- file.path(recipe$Run$output_dir, "logs", "recipes", "multimodel")
       split_to_recipe[split] <- recipe_split
       split <- split + 1
     } else {
-      recipe_dir <- paste0(recipe$Run$output_dir, "/logs/recipes/")
+      recipe_dir <- file.path(recipe$Run$output_dir, "logs", "recipes")
       chunk_to_recipe[chunk] <- recipe_name
       chunk <- chunk + 1
     }
@@ -206,8 +206,8 @@ divide_recipe <- function(recipe) {
        paste("The main recipe has been divided into", length(chunk_to_recipe),
              "single model atomic recipes, plus", length(split_to_recipe),
              "multi-model atomic recipes."))
-  text <- paste0("Check output directory ", recipe$Run$output_dir,
-                 "/logs/recipes/ to see all the individual atomic recipes.")
+  text <- paste0("Check output directory ", recipe$Run$output_dir, "/",
+                 file.path("logs", "recipes"), "/", " to see all the individual atomic recipes.")
   info(recipe$Run$logger, text)
   ## TODO: Change returns?
   return(list(n_atomic_recipes = length(chunk_to_recipe), # length(all_recipes)
-- 
GitLab


From 3c8d79cb6e32b4c7e2e1655cc76f351b351ad847 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Thu, 2 May 2024 09:49:24 +0200
Subject: [PATCH 08/14] Fix bugs related to use of paste0() instead of
 file.path()

---
 conf/autosubmit.yml                    | 4 ++--
 recipes/recipe_multimodel_seasonal.yml | 2 +-
 tools/check_recipe.R                   | 6 +++---
 tools/write_autosubmit_conf.R          | 6 +++---
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/conf/autosubmit.yml b/conf/autosubmit.yml
index 3e3f1220..db2f503e 100644
--- a/conf/autosubmit.yml
+++ b/conf/autosubmit.yml
@@ -3,12 +3,12 @@ esarchive:
   module_version: autosubmit/4.0.98-foss-2015a-Python-3.7.3
   auto_version: 4.0.98
   conf_format: yaml
-  experiment_dir: /esarchive/autosubmit/
+  experiment_dir: /esarchive/autosubmit
   userID: bsc32
 mars:
   platform: NORD3 ## TO BE CHANGED
   module_version: autosubmit/4.0.0b-foss-2015a-Python-3.7.3 ## TO BE CHANGED
   auto_version: 4.0.0
   conf_format: yaml
-  experiment_dir: /esarchive/autosubmit/ ## TO BE CHANGED
+  experiment_dir: /esarchive/autosubmit ## TO BE CHANGED
   userID: bsc32 ## TO BE CHANGED
diff --git a/recipes/recipe_multimodel_seasonal.yml b/recipes/recipe_multimodel_seasonal.yml
index f974fc48..f7ff4b72 100644
--- a/recipes/recipe_multimodel_seasonal.yml
+++ b/recipes/recipe_multimodel_seasonal.yml
@@ -67,7 +67,7 @@ Run:
   # fill only if using autosubmit
   auto_conf:
     script: ./example_scripts/multimodel_seasonal.R # replace with the path to your script
-    expid: a6wq # replace with your EXPID
+    expid: a6v7 # replace with your EXPID
     hpc_user: bsc32762 # replace with your hpc username
     wallclock: 01:00 # hh:mm
     wallclock_multimodel: 02:00
diff --git a/tools/check_recipe.R b/tools/check_recipe.R
index 42cb832c..57415018 100644
--- a/tools/check_recipe.R
+++ b/tools/check_recipe.R
@@ -787,11 +787,11 @@ check_recipe <- function(recipe) {
             paste("autosubmit expid -H", auto_specs$platform,
                   "-d <Description>"))
       error_status <- TRUE
-    } else if (!dir.exists(paste0(auto_specs$experiment_dir,
-                                  recipe$Run$auto_conf$expid))) {
+    } else if (!dir.exists(file.path(auto_specs$experiment_dir,
+                                     recipe$Run$auto_conf$expid))) {
       error(recipe$Run$logger,
             paste0("No folder in ", auto_specs$experiment_dir,
-                   " for the EXPID", recipe$Run$auto_conf$expid,
+                   " for the EXPID ", recipe$Run$auto_conf$expid,
                    ". Please make sure it is correct."))
       error_status <- TRUE
     }
diff --git a/tools/write_autosubmit_conf.R b/tools/write_autosubmit_conf.R
index 0ccd8543..f1989642 100644
--- a/tools/write_autosubmit_conf.R
+++ b/tools/write_autosubmit_conf.R
@@ -132,15 +132,15 @@ write_autosubmit_conf <- function(recipe, nchunks,
         recipe$Run$auto_conf$hpc_user
     } else if (conf_type == "proj") {
       # Section 5: proj
-      ## modules? Info that goes on script, e.g. output directory
+      ## modules? Info that goes on script, e.g. directory
       conf$common$OUTDIR <- recipe$Run$output_dir
       conf$common$SCRIPT <- recipe$Run$auto_conf$script
       conf$common$RECIPE <- paste0(recipe$name, ".yml")
     }
     # Write config file inside autosubmit dir
-    write.config(conf, paste0(dest_dir, dest_file),
+    write.config(conf, file.path(dest_dir, dest_file),
                  write.type = auto_specs$conf_format)
-    Sys.chmod(paste0(dest_dir, dest_file), mode = "755", use_umask = F)
+    Sys.chmod(file.path(dest_dir, dest_file), mode = "755", use_umask = F)
   }
   info(recipe$Run$logger,
        paste("##### AUTOSUBMIT CONFIGURATION WRITTEN FOR", expid, "#####"))
-- 
GitLab


From 8c5dca529dfb6aeb3f1d090b07a92961acf9ce08 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Thu, 2 May 2024 11:03:48 +0200
Subject: [PATCH 09/14] Change paste0() to file.path() in get_filename()

---
 modules/Saving/R/get_filename.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Saving/R/get_filename.R b/modules/Saving/R/get_filename.R
index b2345691..4c2dd726 100644
--- a/modules/Saving/R/get_filename.R
+++ b/modules/Saving/R/get_filename.R
@@ -76,6 +76,6 @@ get_filename <- function(dir, recipe, var, date, agg, file.type) {
   	   "probs" = {filename <- paste0(var, gg, "-probs_", date)},
   	   "bias"  = {filename <- paste0(var, gg, "-bias_", date)})
   }
-  return(paste0(dir, filename, ".nc"))
+  return(file.path(dir, paste0(filename, ".nc")))
 }
 
-- 
GitLab


From d6bed5c99fbcc4cd15583667ac7909f25a539677 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Fri, 3 May 2024 12:28:43 +0200
Subject: [PATCH 10/14] Change pending paste0() to file.path() to fix pipeline

---
 modules/Saving/R/get_dir.R                     |  2 +-
 modules/Saving/R/save_metrics.R                |  3 ++-
 modules/Visualization/R/plot_ensemble_mean.R   | 18 ++++++++----------
 modules/Visualization/R/plot_metrics.R         |  6 +++---
 .../R/plot_most_likely_terciles_map.R          |  3 ++-
 modules/Visualization/Visualization.R          |  2 +-
 recipes/recipe_multimodel_seasonal.yml         |  2 +-
 7 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/modules/Saving/R/get_dir.R b/modules/Saving/R/get_dir.R
index 35bede6f..a0b054c6 100644
--- a/modules/Saving/R/get_dir.R
+++ b/modules/Saving/R/get_dir.R
@@ -17,7 +17,7 @@ get_dir <- function(recipe, variable, agg = "global") {
     # Define output dir name accordint to Scorecards format
     dict <- read_yaml("conf/output_dictionaries/scorecards.yml")
     # system <- dict$System[[recipe$Analysis$Datasets$System$name]]$short_name
-    dir <- paste0(outdir, system, "/", reference, "/", calib.method, "/", variable, "/")
+    dir <- file.path(outdir, system, reference, calib.method, variable)
   } else {
     # Default generic output format based on FOCUS
     # Get startdate or hindcast period
diff --git a/modules/Saving/R/save_metrics.R b/modules/Saving/R/save_metrics.R
index 57063a0c..b3d9fb97 100644
--- a/modules/Saving/R/save_metrics.R
+++ b/modules/Saving/R/save_metrics.R
@@ -101,8 +101,9 @@ save_metrics <- function(recipe,
         }
         ## TODO: Maybe 'scorecards' condition could go here to further simplify
         ##       the code
-        extra_string <- get_filename(NULL, recipe, variable,
+        extra_string <- get_filename("", recipe, variable,
                                      fcst.sdate, agg, names(subset_metric)[[i]])
+        browser()
         SaveExp(data = subset_metric[[i]], destination = outdir, 
                 Dates = dates, 
                 coords = c(data_cube$coords['longitude'],
diff --git a/modules/Visualization/R/plot_ensemble_mean.R b/modules/Visualization/R/plot_ensemble_mean.R
index 59881864..8186838d 100644
--- a/modules/Visualization/R/plot_ensemble_mean.R
+++ b/modules/Visualization/R/plot_ensemble_mean.R
@@ -81,18 +81,16 @@ plot_ensemble_mean <- function(recipe, fcst, mask = NULL, dots = NULL, outdir, o
     }
 
     for (i_syear in start_date) {
+      i_var_ens_mean <- ClimProjDiags::Subset(var_ens_mean,
+                                              along = c("syear"),
+                                              indices = which(start_date == i_syear),
+                                              drop = 'selected')
       if (length(start_date) == 1) {
-        i_var_ens_mean <- ClimProjDiags::Subset(var_ens_mean,
-                                                along = c("syear"),
-                                                indices = which(start_date == i_syear),
-                                                drop = 'selected')
-        outfile <- paste0(outdir[[var]], "forecast_ensemble_mean-", start_date)
+        outfile <- file.path(outdir[[var]],
+                             paste0("forecast_ensemble_mean-", start_date))
       } else {
-        i_var_ens_mean <- ClimProjDiags::Subset(var_ens_mean,
-                                                along = c("syear"),
-                                                indices = which(start_date == i_syear),
-                                                drop = 'selected')
-        outfile <- paste0(outdir[[var]], "forecast_ensemble_mean-", i_syear)
+        outfile <- file.path(outdir[[var]],
+                             paste0("forecast_ensemble_mean-", i_syear))
       }
       # Mask
       if (!is.null(mask)) {
diff --git a/modules/Visualization/R/plot_metrics.R b/modules/Visualization/R/plot_metrics.R
index c00e8164..141987d0 100644
--- a/modules/Visualization/R/plot_metrics.R
+++ b/modules/Visualization/R/plot_metrics.R
@@ -1,7 +1,7 @@
 library(stringr)
 
 plot_metrics <- function(recipe, data_cube, metrics,
-                          outdir, significance = F, output_conf) {
+                         outdir, significance = F, output_conf) {
   # recipe: Auto-S2S recipe
   # archive: Auto-S2S archive
   # data_cube: s2dv_cube object with the corresponding hindcast data
@@ -194,9 +194,9 @@ plot_metrics <- function(recipe, data_cube, metrics,
         }
         # Define output file name and titles
         if (tolower(recipe$Analysis$Horizon) == "seasonal") {
-          outfile <- paste0(outdir[var], name, "-", month_label)
+          outfile <- file.path(outdir[var], paste0(name, "-", month_label))
         } else {
-          outfile <- paste0(outdir[var], name)
+          outfile <- file.path(outdir[var], name)
         }
         # Get variable name and long name
         var_name <- data_cube$attrs$Variable$varName[[var]]
diff --git a/modules/Visualization/R/plot_most_likely_terciles_map.R b/modules/Visualization/R/plot_most_likely_terciles_map.R
index c9ce70f2..0e6e27c5 100644
--- a/modules/Visualization/R/plot_most_likely_terciles_map.R
+++ b/modules/Visualization/R/plot_most_likely_terciles_map.R
@@ -87,7 +87,8 @@ plot_most_likely_terciles <- function(recipe,
                                            along = c("syear"),
                                            indices = which(start_date == i_syear),
                                            drop = 'selected')
-      outfile <- paste0(outdir[[var]], "forecast_most_likely_tercile-", i_syear)
+      outfile <- file.path(outdir[[var]],
+                           paste0("forecast_most_likely_tercile-", i_syear))
       # Mask
       if (!is.null(mask)) {
         outfile <- paste0(outfile, "_rpssmask")
diff --git a/modules/Visualization/Visualization.R b/modules/Visualization/Visualization.R
index 3750baea..109251c9 100644
--- a/modules/Visualization/Visualization.R
+++ b/modules/Visualization/Visualization.R
@@ -55,7 +55,7 @@ Visualization <- function(recipe,
   # Get plot types and create output directories
   plots <- strsplit(recipe$Analysis$Workflow$Visualization$plots, ", | |,")[[1]]
   ## TODO: Do not modify output dir here
-  recipe$Run$output_dir <- paste0(recipe$Run$output_dir, "/plots/")
+  recipe$Run$output_dir <- file.path(recipe$Run$output_dir, "plots")
   outdir <- get_dir(recipe = recipe,
                     variable = data$hcst$attrs$Variable$varName)
   for (directory in outdir) {
diff --git a/recipes/recipe_multimodel_seasonal.yml b/recipes/recipe_multimodel_seasonal.yml
index f7ff4b72..3b14e09b 100644
--- a/recipes/recipe_multimodel_seasonal.yml
+++ b/recipes/recipe_multimodel_seasonal.yml
@@ -68,7 +68,7 @@ Run:
   auto_conf:
     script: ./example_scripts/multimodel_seasonal.R # replace with the path to your script
     expid: a6v7 # replace with your EXPID
-    hpc_user: bsc32762 # replace with your hpc username
+    hpc_user: bsc032762 # replace with your hpc username
     wallclock: 01:00 # hh:mm
     wallclock_multimodel: 02:00
     processors_per_job: 4
-- 
GitLab


From 16218459b2442d7ed3a3a1b04a26a3fe9003e215 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Fri, 3 May 2024 14:26:49 +0200
Subject: [PATCH 11/14] Move lintr tests and add to git pipeline

---
 .gitlab-ci.yml                                      | 13 +++++++++++++
 tests/{test_paths.R => test_lintr.R}                |  2 +-
 ...rdcoded_paths.R => test-lintr_hardcoded_paths.R} |  0
 3 files changed, 14 insertions(+), 1 deletion(-)
 rename tests/{test_paths.R => test_lintr.R} (71%)
 rename tests/testthat/{test-hardcoded_paths.R => test-lintr_hardcoded_paths.R} (100%)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 997870c8..90f49c1f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -26,3 +26,16 @@ unit-test-decadal:  # This job runs in the test stage.
     - module list
     - echo "Running decadal unit tests..."
     - Rscript ./tests/test_decadal.R
+
+unit-test-lintr:  # This job runs in the test stage.
+  stage: test
+  script:
+    - echo "Loading modules..."
+    - module load R/4.1.2-foss-2015a-bare
+    - module load CDO/1.9.8-foss-2015a
+    - module load GEOS/3.7.2-foss-2015a-Python-3.7.3
+    - module load GDAL/2.2.1-foss-2015a
+    - module load PROJ/4.8.0-foss-2015a
+    - module list
+    - echo "Running lintr unit tests..."
+    - Rscript ./tests/test_lintr.R
diff --git a/tests/test_paths.R b/tests/test_lintr.R
similarity index 71%
rename from tests/test_paths.R
rename to tests/test_lintr.R
index 87dbed4a..7d0d1349 100644
--- a/tests/test_paths.R
+++ b/tests/test_lintr.R
@@ -1,7 +1,7 @@
 library(testthat)
 
 path_testthat <- file.path('./tests/testthat/')
-files_testthat <- list.files('./tests/testthat/', pattern = 'paths')
+files_testthat <- list.files('./tests/testthat/', pattern = 'lintr')
 
 for (i_file in 1:length(files_testthat)) {
   source(paste0('./tests/testthat/', files_testthat[i_file]))
diff --git a/tests/testthat/test-hardcoded_paths.R b/tests/testthat/test-lintr_hardcoded_paths.R
similarity index 100%
rename from tests/testthat/test-hardcoded_paths.R
rename to tests/testthat/test-lintr_hardcoded_paths.R
-- 
GitLab


From ee9268f348d89c0bfb0e2c64b1e6bc45060c2b19 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 3 May 2024 16:11:19 +0200
Subject: [PATCH 12/14] Fixed if() clause and added directory names to output

---
 tests/testthat/test-hardcoded_paths.R | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-hardcoded_paths.R b/tests/testthat/test-hardcoded_paths.R
index 1345e013..6616e747 100644
--- a/tests/testthat/test-hardcoded_paths.R
+++ b/tests/testthat/test-hardcoded_paths.R
@@ -13,13 +13,16 @@ detect_hardcoded_paths <- function() {
     lint_dir(path = dir, linters = absolute_path_linter(lax = TRUE))
   })
 
+  # Assign names to the list elements
+  names(files_with_issues) <- directories
+
   # Check results and print out the test outcome
-  if (length(files_with_issues) > 0) {
+  if (any(sapply(files_with_issues, function(x) length(x) > 0))) {
     cat("Test FAILED. Hard-coded paths found:\n")
     print(files_with_issues)
     return(FALSE)
   } else {
-    cat("Test PASSED😊 No hard-coded paths found in any file.\n")
+    cat("Test PASSED🥳 No hard-coded paths found in any file.\n")
     return(TRUE)
   }
 }
-- 
GitLab


From 3dd18f10b357f1570adada38fc2d9d34b0efb04e Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Mon, 6 May 2024 16:09:33 +0200
Subject: [PATCH 13/14] Add test_that() clause

---
 .gitlab-ci.yml                              | 2 +-
 tests/testthat/test-lintr_hardcoded_paths.R | 8 +++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 90f49c1f..fe4abf17 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -37,5 +37,5 @@ unit-test-lintr:  # This job runs in the test stage.
     - module load GDAL/2.2.1-foss-2015a
     - module load PROJ/4.8.0-foss-2015a
     - module list
-    - echo "Running lintr unit tests..."
+    - echo "Running lint tests..."
     - Rscript ./tests/test_lintr.R
diff --git a/tests/testthat/test-lintr_hardcoded_paths.R b/tests/testthat/test-lintr_hardcoded_paths.R
index 6616e747..f5a62cef 100644
--- a/tests/testthat/test-lintr_hardcoded_paths.R
+++ b/tests/testthat/test-lintr_hardcoded_paths.R
@@ -18,13 +18,15 @@ detect_hardcoded_paths <- function() {
 
   # Check results and print out the test outcome
   if (any(sapply(files_with_issues, function(x) length(x) > 0))) {
-    cat("Test FAILED. Hard-coded paths found:\n")
+    cat("Test FAILED. Absolute paths found:\n")
     print(files_with_issues)
     return(FALSE)
   } else {
-    cat("Test PASSED🥳 No hard-coded paths found in any file.\n")
+    cat("No absolute paths found in any file.\n")
     return(TRUE)
   }
 }
 
-detect_hardcoded_paths()
+test_that("Check code for absolute paths", {
+  expect_true(detect_hardcoded_paths())
+})
-- 
GitLab


From 904288e4bf592d08d9dc0c680dbc6b1759758494 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Wed, 8 May 2024 09:34:17 +0200
Subject: [PATCH 14/14] Fix atomic recipe file path

---
 tools/divide_recipe.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/divide_recipe.R b/tools/divide_recipe.R
index 1f83d63c..ddaff215 100644
--- a/tools/divide_recipe.R
+++ b/tools/divide_recipe.R
@@ -198,7 +198,8 @@ divide_recipe <- function(recipe) {
       chunk <- chunk + 1
     }
     write_yaml(all_recipes[[reci]], 
-               paste0(recipe_dir, "atomic_recipe_", recipe_name, ".yml"))
+               file.path(recipe_dir,
+                         paste0("atomic_recipe_", recipe_name, ".yml")))
   }
 
   # Print information for user
-- 
GitLab