improve bake/stew directory creation

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 5.0.1.1
-Date: 2023-04-11
+Version: 5.0.1.2
+Date: 2023-04-13
 Authors@R: c(person(given=c("Aaron","A."),family="King",
 	     role=c("aut","cre"),email="[email protected]",
 	     comment=c(ORCID="0000-0001-6159-3207")),

R/bake.R

@@ -41,7 +41,7 @@
 ##' @param dir Directory holding archive files;
 ##' by default, this is the current working directory.
 ##' This can also be set using the global option \code{pomp_archive_dir}.
-##' This directory will be created if it does not exist.
+##' If it does not exist, this directory will be created (with a message).
 ##' @param expr Expression to be evaluated.
 ##' @param seed,kind,normal.kind optional.
 ##' To set the state and of the RNG.
@@ -150,6 +150,16 @@ update_bake_archive <- function (val, code, deps, file) {
   val
 }
 
+create_path <- function (dir, file, mode = "0755") {
+  path <- file.path(as.character(dir[[1L]]),as.character(file[1L]))
+  dir <- dirname(path)
+  if (!dir.exists(dir)) {
+    pMess_("creating archive directory ",sQuote(dir),".")
+    dir.create(dir,recursive=TRUE,mode=mode)
+  }
+  path
+}
+
 ##' @rdname bake
 ##' @export
 bake <- function (
@@ -167,10 +177,7 @@ bake <- function (
   )
   info <- as.logical(info)
   timing <- as.logical(timing)
-  if (!dir.exists(dir)) {
-    dir.create(dir,recursive=TRUE,mode="0644") #nocov
-  }
-  file <- file.path(as.character(dir[[1L]]),as.character(file))
+  file <- create_path(dir,file)
   reload <- file.exists(file)
   if (reload) {
     val <- readRDS(file)
@@ -256,10 +263,7 @@ stew <- function (
     ep="stew"
   )
   info <- as.logical(info)
-  if (!dir.exists(dir)) {
-    dir.create(dir,recursive=TRUE,mode="0644") #nocov
-  }
-  file <- file.path(as.character(dir[[1L]]),as.character(file))
+  file <- create_path(dir,file)
   reload <- file.exists(file)
   e <- new.env()
   if (reload) {

inst/NEWS

@@ -1,5 +1,10 @@
 _N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_o_m_p'
 
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _5._0._1:
+
+        • When the archive directory does not exist, ‘bake’ and ‘stew’
+          now create it.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _5._0._0:
 
         • We no longer import from ‘plyr’.

inst/NEWS.Rd

@@ -1,5 +1,10 @@
 \name{NEWS}
 \title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 5.0.1}{
+  \itemize{
+    \item When the archive directory does not exist, \code{bake} and \code{stew} now create it.
+  }
+}
 \section{Changes in \pkg{pomp} version 5.0.0}{
   \itemize{
     \item We no longer import from \pkg{plyr}.

tests/bake.R

@@ -128,3 +128,28 @@ stopifnot(
   identical(x,xx),
   identical(y,yy)
 )
+
+capture.output(
+  {
+    bake(file="results/bob/mary/tmp.rds",rnorm(5)) -> x1
+    bake(file="results/bob/mary/tmp.rds",rnorm(5)) -> x2
+    bake(file="mary/tmp.rds",rnorm(5),dir=file.path(tempdir(),"results/bob")) -> x3
+    op <- options(pomp_archive_dir=file.path(tempdir(),"results"))
+    bake(file="bob/mary/tmp.rds",rnorm(5)) -> x4
+    bake(file="results/bob/mary/tmp.rds",rnorm(5)) -> x5
+    options(op)
+    bake(file="results/results/bob/mary/tmp.rds",rnorm(5)) -> x6
+  },
+  type="message"
+) -> out
+stopifnot(
+  identical(x1,x2),
+  identical(x1,x3),
+  identical(x1,x4),
+  !identical(x1,x5),
+  identical(x5,x6),
+  length(out)==2,
+  grepl("^NOTE: creating archive directory",out),
+  grepl("results/bob/mary'.",out),
+  grepl("results/results/bob/mary'.",out[2])
+)

tests/bake.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
-Copyright (C) 2022 The R Foundation for Statistical Computing
+R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
+Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -177,3 +177,28 @@ NOTE: in 'stew': recomputing archive tmp2.rda.
 +   identical(y,yy)
 + )
 > 
+> capture.output(
++   {
++     bake(file="results/bob/mary/tmp.rds",rnorm(5)) -> x1
++     bake(file="results/bob/mary/tmp.rds",rnorm(5)) -> x2
++     bake(file="mary/tmp.rds",rnorm(5),dir=file.path(tempdir(),"results/bob")) -> x3
++     op <- options(pomp_archive_dir=file.path(tempdir(),"results"))
++     bake(file="bob/mary/tmp.rds",rnorm(5)) -> x4
++     bake(file="results/bob/mary/tmp.rds",rnorm(5)) -> x5
++     options(op)
++     bake(file="results/results/bob/mary/tmp.rds",rnorm(5)) -> x6
++   },
++   type="message"
++ ) -> out
+> stopifnot(
++   identical(x1,x2),
++   identical(x1,x3),
++   identical(x1,x4),
++   !identical(x1,x5),
++   identical(x5,x6),
++   length(out)==2,
++   grepl("^NOTE: creating archive directory",out),
++   grepl("results/bob/mary'.",out),
++   grepl("results/results/bob/mary'.",out[2])
++ )
+>