Prevent that beautier writes and leaves behind in .cache files, progr…

…ess #129
ropensci · May 22, 2021 · d5d576e · d5d576e
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,5 @@
 ^scripts$
 ^\.appveyor\.yml$
 ^doc$
+^created\.xml$
+^expected\.xml$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: beautier
 Title: 'BEAUti' from R
-Version: 2.5.2
+Version: 2.6
 Authors@R: c(
   person("Richèl J.C.", "Bilderbeek", email = "richel@richelbilderbeek.nl", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1107-7049")),
   person("Joëlle", "Barido-Sottani", role = "rev", comment = "Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209"),

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,24 @@
 
 Newest versions at top.
 
+## beautier 2.6 (2021-05-22)
+
+### NEW FEATURES
+
+ * None
+
+### MINOR IMPROVEMENTS
+
+ * Make sure that no files are created in `~/.cache`
+
+### BUG FIXES
+
+ * None
+
+### DEPRECATED AND DEFUNCT
+
+ * None
+
 ## beautier 2.5.2 (2021-05-22)
 
 ### NEW FEATURES

diff --git a/R/beautier.R b/R/beautier.R
@@ -13,14 +13,15 @@
 #' input_filename <- get_fasta_filename()
 #'
 #' # The file created by beautier, a BEAST2 input file
-#' output_filename <- tempfile()
+#' output_filename <- get_beautier_tempfilename()
 #'
 #' # Use the default BEAUti settings to create a BEAST2 input file
 #' create_beast2_input_file_from_model(
 #'   input_filename,
 #'   output_filename,
 #'   inference_model = create_inference_model()
 #' )
+#' file.remove(output_filename)
 #' @seealso
 #' These are packages associated with \code{beautier}:
 #' \itemize{

diff --git a/R/create_beast2_input_file.R b/R/create_beast2_input_file.R
@@ -6,12 +6,13 @@
 #' input_filename <- get_fasta_filename()
 #'
 #' # The file created by beautier, a BEAST2 input file
-#' output_filename <- tempfile(pattern = "beast2", fileext = ".xml")
+#' output_filename <- get_beautier_tempfilename()
 #'
 #' create_beast2_input_file(
 #'   input_filename,
 #'   output_filename
 #' )
+#' file.remove(output_filename)
 #' @author Richèl J.C. Bilderbeek
 #' @seealso
 #'   Use \link{create_beast2_input_file_from_model} to do the same with an

diff --git a/R/create_beast2_input_file_from_model.R b/R/create_beast2_input_file_from_model.R
@@ -4,11 +4,13 @@
 #' @seealso use \link{create_beast2_input_from_model} to
 #' get the BEAST2 input file as text
 #' @examples
+#' output_filename <- get_beautier_tempfilename()
 #' create_beast2_input_file_from_model(
 #'   input_filename = get_fasta_filename(),
-#'   output_filename = tempfile(),
+#'   output_filename = output_filename,
 #'   inference_model = create_inference_model()
 #' )
+#' file.remove(output_filename)
 #' @author Richèl J.C. Bilderbeek
 #' @seealso
 #' See \code{\link{create_site_model}} for examples with

diff --git a/R/create_clock_model.R b/R/create_clock_model.R
@@ -15,25 +15,25 @@
 #'   model, see \code{\link{create_strict_clock_model}}.
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   rln_clock_model <- create_rln_clock_model()
+#' rln_clock_model <- create_rln_clock_model()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = rln_clock_model
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = rln_clock_model
+#' )
+#' file.remove(beast2_input_file)
 #'
-#'   strict_clock_model <- create_strict_clock_model()
+#' strict_clock_model <- create_strict_clock_model()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = strict_clock_model
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = strict_clock_model
+#' )
+#' file.remove(beast2_input_file)
 #' @export
 create_clock_model <- function(
   name,
@@ -80,27 +80,27 @@ create_clock_model <- function(
 #' @return a relaxed log-normal clock_model
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   rln_clock_model <- create_rln_clock_model()
+#' rln_clock_model <- create_rln_clock_model()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = rln_clock_model
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = rln_clock_model
+#' )
+#' file.remove(beast2_input_file)
 #'
-#'   rln_clock_model_exp <- create_rln_clock_model(
-#'     mean_rate_prior_distr = create_exp_distr()
-#'   )
+#' rln_clock_model_exp <- create_rln_clock_model(
+#'   mean_rate_prior_distr = create_exp_distr()
+#' )
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = rln_clock_model_exp
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = rln_clock_model_exp
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_rln_clock_model create_clock_model_rln
 #' @export create_rln_clock_model create_clock_model_rln
 create_rln_clock_model <- create_clock_model_rln <- function(
@@ -139,30 +139,30 @@ create_rln_clock_model <- create_clock_model_rln <- function(
 #' @return a strict clock_model
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   strict_clock_model <- create_strict_clock_model(
-#'     clock_rate_param = 1.0,
-#'     clock_rate_distr = create_uniform_distr()
-#'   )
+#' strict_clock_model <- create_strict_clock_model(
+#'   clock_rate_param = 1.0,
+#'   clock_rate_distr = create_uniform_distr()
+#' )
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = strict_clock_model
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = strict_clock_model
+#' )
+#' file.remove(beast2_input_file)
 #'
-#'   strict_clock_model_gamma <- create_strict_clock_model(
-#'     clock_rate_distr = create_gamma_distr()
-#'   )
+#' strict_clock_model_gamma <- create_strict_clock_model(
+#'   clock_rate_distr = create_gamma_distr()
+#' )
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = strict_clock_model_gamma
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = strict_clock_model_gamma
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_strict_clock_model create_clock_model_strict
 #' @export create_strict_clock_model create_clock_model_strict
 create_strict_clock_model <- create_clock_model_strict <- function(