From ae41c2ce5e95a8dd3e195aaee5340e35d2b7659d Mon Sep 17 00:00:00 2001
From: Arni Magnusson <thisisarni@gmail.com>
Date: Sun, 26 Nov 2023 18:41:07 +1100
Subject: [PATCH] Add argument 'gitignore' to taf.skeleton()

---
 DESCRIPTION         |  2 +-
 NEWS.md             |  5 ++++-
 R/taf.skeleton.R    | 11 ++++++++++-
 man/taf.skeleton.Rd |  4 +++-
 4 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 344ab87..f181cb2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: TAF
 Version: 4.3.0
-Date: 2023-11-22
+Date: 2023-11-26
 Title: Transparent Assessment Framework for Reproducible Research
 Authors@R: c(person("Arni", "Magnusson", role=c("aut","cre"), email="thisisarni@gmail.com"),
              person("Colin", "Millar", role="aut"),
diff --git a/NEWS.md b/NEWS.md
index 7bbe669..e59a7ec 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,10 +1,13 @@
-# TAF 4.3.0 (2023-11-22)
+# TAF 4.3.0 (2023-11-26)
 
 * Added function fdim() to show the dimensions of an FLR table.
 
 * Added function taf.libraries() to load all packages from TAF library. Code
   contributed by Iago Mosqueira.
 
+* Added argument 'gitignore' to taf.skeleton() for writing a .gitignore file,
+  enabled by default.
+
 * Improved draft.software() so it supports packages from r-universe. Code
   contributed by Iago Mosqueira.
 
diff --git a/R/taf.skeleton.R b/R/taf.skeleton.R
index 9ae7458..c5317fb 100644
--- a/R/taf.skeleton.R
+++ b/R/taf.skeleton.R
@@ -9,6 +9,7 @@
 #'        TAF package, i.e. \code{library(TAF)}.
 #' @param model.script model script filename, either \code{model.R} (default) or
 #'        \code{method.R}.
+#' @param gitignore whether to write a \file{.gitignore} file.
 #'
 #' @return Full path to analysis directory.
 #'
@@ -25,7 +26,7 @@
 #' @export
 
 taf.skeleton <- function(path = ".", force = FALSE, pkgs = "TAF",
-                         model.script = "model.R")
+                         model.script = "model.R", gitignore=TRUE)
 {
   # only overwrite files if force = TRUE
   safe.cat <- function(..., file, force) {
@@ -62,5 +63,13 @@ taf.skeleton <- function(path = ".", force = FALSE, pkgs = "TAF",
              force = force)
   }
 
+  if (gitignore) {
+    ignore <- c("/boot/data", "/boot/software", "/data",
+                paste0("/", file_path_sans_ext(model.script)), "/output",
+                "/report", "*.Rproj", ".RData", ".Rhistory", ".Rproj.user",
+                ".Ruserdata")
+    write(ignore, ".gitignore")
+  }
+
   invisible(getwd())
 }
diff --git a/man/taf.skeleton.Rd b/man/taf.skeleton.Rd
index 69857d6..73df485 100644
--- a/man/taf.skeleton.Rd
+++ b/man/taf.skeleton.Rd
@@ -5,7 +5,7 @@
 \title{TAF Skeleton}
 \usage{
 taf.skeleton(path = ".", force = FALSE, pkgs = "TAF",
-  model.script = "model.R")
+  model.script = "model.R", gitignore = TRUE)
 }
 \arguments{
 \item{path}{where to create initial directories and R scripts. The default is
@@ -18,6 +18,8 @@ TAF package, i.e. \code{library(TAF)}.}
 
 \item{model.script}{model script filename, either \code{model.R} (default) or
 \code{method.R}.}
+
+\item{gitignore}{whether to write a \file{.gitignore} file.}
 }
 \value{
 Full path to analysis directory.