styleR (#664)

* styleR as used by IUC

scripts/styleR/styler.R

@@ -0,0 +1,36 @@
+#!/usr/bin/env Rscript
+
+library("argparse")
+library("styler")
+
+parser <- ArgumentParser(description = "Call styler")
+parser$add_argument("dir",
+    metavar = "DIR", type = "character",
+    help = "File to parse"
+)
+parser$add_argument("--dry",
+    choices = c("off", "on"), default = "on"
+)
+args <- parser$parse_args()
+
+file_info <- file.info(args$dir)
+is_directory <- file_info$isdir
+
+if (is_directory) {
+    captured_output <- capture.output({
+        result <- style_dir(args$dir, indent_by = 4, dry = args$dry, recursive = TRUE)
+    })
+} else {
+    captured_output <- capture.output({
+        result <- style_file(args$dir, indent_by = 4, dry = args$dry)
+    })
+}
+
+n <- nrow(subset(result, changed == TRUE))
+if (n > 0) {
+    if (args$dry == "off") {
+        print(paste("Changed", n, "files"))
+    } else {
+        stop(paste("Linting failed for", n, "files"))
+    }
+}

scripts/styleR/use_styler.md

@@ -0,0 +1,45 @@
+# Introduction
+
+styleR will parse your R codes and fix formating issue at various levels, adapting correct
+spacing, correct indentation, correct break lines and even variable naming.
+
+The main advantage, compare to lintr is that styleR does the reformating job *in your
+place*, which in some occasion may be a huge time saving.
+
+The disavantage of this avantage is that styleR change your code *in your place*... so be
+prepared.
+
+I have tested it and was literally impressed by its ability to radically intervene on the
+code. In my test case, styleR split a recursive if-else loop in tree independent
+non-recursive loops. It was a beautiful simplification, and a real progress for the code
+maintenance.
+
+# Create the proper conda environment
+
+If it does not exist yet, create the conda environnement:
+
+```
+conda create --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --channel defaults --name r-styler r-styler r-argparse
+```
+
+# get the styler.R script in your environment and ensure it is executable
+
+to make style.R executable, `chmod 755 styler.R`
+
+# `conda activate r-styler`
+
+# Run styler.R
+
+:warning: styler.R will modify your target file using the following command; work in a
+versioned (git) environment !
+
+```
+<path>/./styler.R --dry off <path>/<Rfile-to-lint>
+```
+
+- Note that `--dry on` will **not** make any change in your code.
+- For more info on the multiple parameters of styler (which can be integrated to Rstudio
+and will by available in the plug-in menu), see the complete reference below.
+# Reference
+
+[https://styler.r-lib.org/index.html](https://styler.r-lib.org/index.html)